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Kapfhammer" Date: Thu, 20 Aug 2026 12:55:18 -0400 Subject: [PATCH 02/50] chore: Update the .github/workflows/build.yml file to use uv instead of poetry. --- .github/workflows/build.yml | 21 ++++++++------------- 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index f454f37..7c108ef 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -57,34 +57,29 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - # Install pip - - name: Install Pip + # Install uv + - name: Install uv if: always() - run: | - python -m pip install --upgrade pip - # Install poetry - - name: Install Poetry - if: always() - uses: abatilo/actions-poetry@v2.0.0 + uses: astral-sh/setup-uv@v5 with: - poetry-version: 1.4.0 + enable-cache: true # Install dependencies - name: Install dependencies if: always() run: | - poetry install + uv sync --group dev # Run the linters - name: Run Linters if: always() run: | - poetry run task lint + uv run task lint # Run the program - name: Run program if: always() run: | - poetry run cellveyor --spreadsheet-directory $PWD/spreadsheets/ --spreadsheet-file $PWD/spreadsheets/fake_spreadsheet.xlsx/ --sheet-name Main --key-attribute "Student GitHub" --key-value "gkapfham" --column-regexp '^(Summary Grade|Final Grade) .*$' --feedback-regexp "Summary Grade 1 - Feedback" --feedback-file $PWD/spreadsheets/feedback.yml/ + uv run cellveyor --spreadsheet-directory $PWD/spreadsheets/ --spreadsheet-file $PWD/spreadsheets/fake_spreadsheet.xlsx/ --sheet-name Main --key-attribute "Student GitHub" --key-value "gkapfham" --column-regexp '^(Summary Grade|Final Grade) .*$' --feedback-regexp "Summary Grade 1 - Feedback" --feedback-file $PWD/spreadsheets/feedback.yml/ # Run the tests - name: Run Tests if: always() run: | - poetry run task test + uv run task test From 5d6563cd51cc42c573c70386cf6fe71a5dc90e55 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Thu, 20 Aug 2026 12:59:49 -0400 Subject: [PATCH 03/50] docs: Update the README.md file to reflect the use of uv instead of poetry. --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 843404d..c873cc4 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ ## Example Command ``` -poetry run cellveyor --spreadsheet-directory \ +uv run cellveyor --spreadsheet-directory \ /home/gkapfham/working/data/gradebook/2023 --spreadsheet-file CMPSC-203-Fall-2023-Gradebook.xlsx \ --sheet-name Main \ @@ -68,4 +68,4 @@ Follow these steps to install the Cellveyor program: 1. Copy the ssh key of the repo 2. ```Git clone``` the repository onto your personal computer - ```git clone (ssh key)``` -3. Type ```poetry run cellveyor --help``` to learn how to use the tool +3. Type ```uv run cellveyor --help``` to learn how to use the tool From 4dfabcda5b6aa29f94cf7cf2db536563e6628564 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Thu, 20 Aug 2026 13:02:11 -0400 Subject: [PATCH 04/50] chore: Update the pyproject.toml file to reflect the migration to uv and away from poetry. --- pyproject.toml | 91 ++++++++++++++++++++++++++++---------------------- 1 file changed, 51 insertions(+), 40 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 6c2f779..13dc06c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,37 +1,46 @@ -[tool.poetry] +[project] name = "cellveyor" version = "0.1.0" description = "" -authors = ["Gregory M. Kapfhammer "] readme = "README.md" +requires-python = ">=3.11,<3.14" +authors = [{name = "Gregory M. Kapfhammer", email = "gkapfham@allegheny.edu"}] +dependencies = [ + "rich>=13.4.2,<14.0.0", + "pandas>=2.1.1,<3.0.0", + "openpyxl>=3.1.2,<4.0.0", + "requests>=2.31.0,<3.0.0", + "pygithub>=2.1.1,<3.0.0", + "pyyaml>=6.0.1,<7.0.0", + "typer>=0.20.0,<1.0.0", +] -[tool.poetry.dependencies] -python = ">=3.11,<3.14" -rich = "^13.4.2" -pandas = "^2.1.1" -openpyxl = "^3.1.2" -requests = "^2.31.0" -pygithub = "^2.1.1" -pyyaml = "^6.0.1" -typer = "^0.20.0" - -[tool.poetry.scripts] +[project.scripts] cellveyor = "cellveyor.main:cli" -[tool.poetry.group.dev.dependencies] -pytest = "^7.4.0" -taskipy = "^1.11.0" -mypy = "^1.4.1" -isort = "^5.12.0" -hypothesis = {extras = ["cli"], version = "^6.81.1"} -pytest-clarity = "^1.0.1" -pytest-randomly = "^3.13.0" -pytest-pretty = "^1.2.0" -pytest-xdist = "^3.3.1" -types-pyyaml = "^6.0.12.12" -pandas-stubs = "^2.1.1.230928" -ruff = "0.1.15" -symbex = "^1.4" +[dependency-groups] +dev = [ + "pytest>=7.4.0,<8.0.0", + "taskipy>=1.11.0,<2.0.0", + "mypy>=1.4.1,<2.0.0", + "isort>=5.12.0,<6.0.0", + "hypothesis[cli]>=6.81.1,<7.0.0", + "pytest-clarity>=1.0.1,<2.0.0", + "pytest-randomly>=3.13.0,<4.0.0", + "pytest-pretty>=1.2.0,<2.0.0", + "pytest-xdist>=3.3.1,<4.0.0", + "types-pyyaml>=6.0.12.12,<7.0.0", + "pandas-stubs>=2.1.1.230928,<3.0.0", + "ruff==0.1.15", + "symbex>=1.4,<2.0.0", +] + +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[tool.hatch.build.targets.wheel] +packages = ["cellveyor"] [tool.pytest.ini_options] filterwarnings = [ @@ -41,17 +50,17 @@ filterwarnings = [ [tool.ruff] line-length = 79 ignore = [ - "E501", # do not check line length + "E501", ] select = [ - "E", # pycodestyle errors - "I", # isort - "F", # Pyflakes - "PL", # pylint - "Q", # flake8-quotes - "RUF", # ruff-specific - "W", # pycodestyle warnings - "T201" # flake8-print + "E", + "I", + "F", + "PL", + "Q", + "RUF", + "W", + "T201" ] [tool.isort] @@ -81,7 +90,7 @@ lint = "task format && task check && task mypy && task symbex" check = { cmd = "{check-command}", help = "Run the ruff linting checks", use_vars = true } format = { cmd = "{format-command}", help = "Run the ruff formatter on source code", use_vars = true } format-fix = { cmd = "{fixformat-command}", help = "Run the ruff formatter to fix source code", use_vars = true} -mypy = { cmd = "poetry run mypy cellveyor", help = "Run the mypy type checker for potential type errors" } +mypy = { cmd = "uv run mypy cellveyor", help = "Run the mypy type checker for potential type errors" } symbex = "task symbex-typed && task symbex-documented" symbex-typed = { cmd = "{symbex-typed-command}", help = "Run symbex for fully typed functions", use_vars = true } symbex-documented = { cmd = "{symbex-documented-command}", help = "Run symbex for documentation", use_vars = true } @@ -92,6 +101,8 @@ test-silent = { cmd = "pytest -x --show-capture=no -n auto", help = "Run the pyt test-silent-not-randomly = { cmd = "pytest -x --show-capture=no -p no:randomly", help = "Run the pytest test suite without showing output and order randomization" } test-silent-not-xdist = { cmd = "pytest -x --show-capture=no -p no:xdist", help = "Run the pytest test suite without showing output and test distribution" } -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +[tool.mypy] +python_version = "3.13" +warn_return_any = true +warn_unused_configs = true +ignore_missing_imports = true From ab0a651e4a6acdb049270c235e41b83f1edafefd Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Thu, 20 Aug 2026 13:03:21 -0400 Subject: [PATCH 05/50] refactor: Remove the poetry.lock file and then update multiple files to make command-line argument parsing more defensive. --- cellveyor/data.py | 14 +- cellveyor/filesystem.py | 36 +- cellveyor/main.py | 141 +++- cellveyor/report.py | 44 +- cellveyor/transfer.py | 73 +- poetry.lock | 1545 --------------------------------------- 6 files changed, 251 insertions(+), 1602 deletions(-) delete mode 100644 poetry.lock diff --git a/cellveyor/data.py b/cellveyor/data.py index adfd3a3..3f65cb5 100644 --- a/cellveyor/data.py +++ b/cellveyor/data.py @@ -26,10 +26,20 @@ def key_attribute_column_filter( key_attribute_value: str = "", ) -> Tuple[pandas.DataFrame, pandas.DataFrame]: """Extract a region of a dataframe defined by a key attribute and columns that match a regular expression.""" + # validate that the key attribute column exists + if key_attribute_name not in sheet_dataframe.columns: + available = ", ".join(map(str, sheet_dataframe.columns.tolist())) + raise ValueError( + f"Key attribute '{key_attribute_name}' not found. Available columns: {available}" + ) # use the provided regular expression to extract from the data frame # only those columns that have a name that matches the regular expression - # selected_columns = sheet_dataframe.filter(regex=column_regexp).dropna() - selected_columns = sheet_dataframe.filter(regex=column_regexp) + try: + selected_columns = sheet_dataframe.filter(regex=column_regexp) + except Exception as exc: + raise ValueError( + f"Invalid column regular expression '{column_regexp}': {exc}" + ) from exc # extract the attribute that has the key name and also select all of # those columns that matched the regular expression result_df = sheet_dataframe[ diff --git a/cellveyor/filesystem.py b/cellveyor/filesystem.py index c5cdb90..4017191 100644 --- a/cellveyor/filesystem.py +++ b/cellveyor/filesystem.py @@ -46,23 +46,39 @@ def confirm_valid_file_in_directory( return False -def read_feedback_files(feedback_files_list: List[Path]) -> Dict[str, str]: +def read_feedback_files( + feedback_files_list: List[Path] | None, +) -> Dict[str, str]: """Read all of the feedback files and return them in a combined dictionary.""" + # handle the case where no feedback files were provided + if feedback_files_list is None: + return {} feedback_dict_list: List[Dict[str, str]] = [] # iterate through all of the provided feedback files for feedback_file_path in feedback_files_list: # confirm that the file is valid; if it is valid # then its contents will be read and converted to a dictionary if confirm_valid_file(feedback_file_path): - # read the contents of the file, which are a string - # that contains within it the contents of the YAML file - feedback_file_contents = feedback_file_path.read_text() - # convert the string that encodes a YAML file to a dictionary - feedback_file_contents_dict = yaml.safe_load( - feedback_file_contents - ) - # add the dictionary to the overall list of feedback dictionaries - feedback_dict_list.append(feedback_file_contents_dict) + try: + # read the contents of the file, which are a string + # that contains within it the contents of the YAML file + feedback_file_contents = feedback_file_path.read_text() + # convert the string that encodes a YAML file to a dictionary + feedback_file_contents_dict = yaml.safe_load( + feedback_file_contents + ) + # yaml.safe_load can return None for empty files; skip those + if feedback_file_contents_dict is None: + continue + # ensure the loaded content is a dict before adding + if not isinstance(feedback_file_contents_dict, dict): + continue + # add the dictionary to the overall list of feedback dictionaries + feedback_dict_list.append(feedback_file_contents_dict) + except (OSError, yaml.YAMLError): + # silently skip unreadable or malformed feedback files; + # caller can warn if desired + continue # create an empty dictionary and then use it to store the # unified contents of all of the other dictionaries coming from # the previously input YAML files that contains the feedback pairs diff --git a/cellveyor/main.py b/cellveyor/main.py index f8b2d42..5c5ffb8 100644 --- a/cellveyor/main.py +++ b/cellveyor/main.py @@ -37,7 +37,7 @@ def display_reports(reports_dict: Dict[str, str]) -> None: @cli.command() -def transport( # noqa: PLR0913 +def transport( # noqa: PLR0912, PLR0913, PLR0915 spreadsheet_directory: Path = typer.Option( ..., "--spreadsheet-directory", @@ -115,13 +115,30 @@ def transport( # noqa: PLR0913 spreadsheet_file, spreadsheet_directory ): console.print( - ":person_shrugging: Unable to access file and/or directory" + "[red]:person_shrugging: Unable to access file and/or directory[/red]" ) + # provide more specific diagnostics + if not filesystem.confirm_valid_directory(spreadsheet_directory): + console.print( + f"[red] Directory not found: {spreadsheet_directory}[/red]" + ) + else: + console.print( + f"[red] File not found in directory: {spreadsheet_directory / spreadsheet_file}[/red]" + ) + raise typer.Exit(code=1) # access all of the sheets inside of the valid spreadsheet file fully_qualified_spreadsheet_file = spreadsheet_directory / spreadsheet_file console.print( f":delivery_truck: Accessing: {fully_qualified_spreadsheet_file}" ) + # warn about any feedback files that do not exist + if feedback_file is not None: + for fb_path in feedback_file: + if not filesystem.confirm_valid_file(fb_path): + console.print( + f"[yellow]:warning: Feedback file not found, skipping: {fb_path}[/yellow]" + ) # access all of the feedback files and combine them into a single # dictionary organized in the following fashion: # --> key: label like "header" or "footer" or a label @@ -134,35 +151,117 @@ def transport( # noqa: PLR0913 # note that each sheet in the spreadsheet can be accessed by: # --> name of the sheet: str # --> dataframe of the sheet: pandas dataframe - sheet_dataframe_dict = data.access_dataframes( - fully_qualified_spreadsheet_file - ) + try: + sheet_dataframe_dict = data.access_dataframes( + fully_qualified_spreadsheet_file + ) + except FileNotFoundError: + console.print( + f"[red]:person_shrugging: Spreadsheet file not found: {fully_qualified_spreadsheet_file}[/red]" + ) + raise typer.Exit(code=1) + except Exception as exc: + console.print( + f"[red]:person_shrugging: Failed to read spreadsheet: {exc}[/red]" + ) + raise typer.Exit(code=1) + # validate that the requested sheet exists + if sheet_name not in sheet_dataframe_dict: + available_sheets = ", ".join(sheet_dataframe_dict.keys()) + console.print( + f"[red]:person_shrugging: Sheet '{sheet_name}' not found[/red]" + ) + console.print(f"[red] Available sheets: {available_sheets}[/red]") + raise typer.Exit(code=1) # console.print(sheet_dataframe_dict.keys()) # access the requested sheet within the spreadsheet sheet_dataframe = sheet_dataframe_dict[sheet_name] # access the data for: # --> the key attribute # --> the column(s) that match the regular expression - selected_columns, result_df = data.key_attribute_column_filter( - sheet_dataframe, key_attribute, column_regexp, key_value - ) + try: + selected_columns, result_df = data.key_attribute_column_filter( + sheet_dataframe, key_attribute, column_regexp, key_value + ) + except ValueError as exc: + console.print(f"[red]:person_shrugging: {exc}[/red]") + # also show available columns for key attribute errors + if "Key attribute" in str(exc): + available_cols = ", ".join( + map(str, sheet_dataframe.columns.tolist()) + ) + console.print( + "[red] Hint: check --key-attribute and --column-regexp[/red]" + ) + raise typer.Exit(code=1) + except Exception as exc: + console.print( + f"[red]:person_shrugging: Failed to filter columns: {exc}[/red]" + ) + raise typer.Exit(code=1) + # warn if column regexp matched no columns + if selected_columns.empty or len(selected_columns.columns) == 0: + console.print( + f"[yellow]:warning: No columns matched --column-regexp '{column_regexp}'[/yellow]" + ) + available_cols = ", ".join(map(str, sheet_dataframe.columns.tolist())) + console.print( + f"[yellow] Available columns: {available_cols}[/yellow]" + ) + # warn if result has no rows + if result_df.empty: + console.print( + "[yellow]:warning: No rows found after filtering — check --key-attribute and --column-regexp[/yellow]" + ) # create a unique message for each row in the dataframe - per_key_report = report.create_per_key_report( - key_attribute, - result_df, - selected_columns, - feedback_regexp, - combined_feedback_dict, - ) + try: + per_key_report = report.create_per_key_report( + key_attribute, + result_df, + selected_columns, + feedback_regexp, + combined_feedback_dict, + ) + except Exception as exc: + console.print( + f"[red]:person_shrugging: Failed to create reports: {exc}[/red]" + ) + raise typer.Exit(code=1) + if not per_key_report: + console.print( + "[yellow]:warning: No reports generated (no matching rows)[/yellow]" + ) # display the generated reports display_reports(per_key_report) # if the --transfer flag was enabled then this means # that the generated reports should be uploaded to GitHub # as a comment inside of the standard pull request if transfer_report: - transfer.transfer_reports_to_github( - github_token, - github_organization, - github_repository_prefix, - per_key_report, - ) + # validate required GitHub arguments before attempting transfer + missing_github_args = [] + if not github_token: + missing_github_args.append("--github-token") + if not github_organization: + missing_github_args.append("--github-organization") + if not github_repository_prefix: + missing_github_args.append("--github-repository-prefix") + if missing_github_args: + console.print( + f"[red]:person_shrugging: Missing required GitHub arguments for --transfer-report: {', '.join(missing_github_args)}[/red]" + ) + console.print( + "[red] Hint: provide all GitHub options or omit --transfer-report[/red]" + ) + raise typer.Exit(code=1) + try: + transfer.transfer_reports_to_github( + github_token, + github_organization, + github_repository_prefix, + per_key_report, + ) + except Exception as exc: + console.print( + f"[red]:person_shrugging: GitHub transfer failed: {exc}[/red]" + ) + raise typer.Exit(code=1) diff --git a/cellveyor/report.py b/cellveyor/report.py index 4773eb6..a99a6df 100644 --- a/cellveyor/report.py +++ b/cellveyor/report.py @@ -34,6 +34,9 @@ def add_feedback_if_exists( if feedback_key in feedback_dict: # extract the specific feedback from the dictionary feedback = feedback_dict[feedback_key] + # handle non-string feedback values (e.g., list/dict from YAML) gracefully + if not isinstance(feedback, str): + feedback = str(feedback) # if the function was not asked to create a list, then # add the feedback and then a newline, a space, and then # the message; since lists do not need newlines after them, @@ -43,7 +46,8 @@ def add_feedback_if_exists( # if the feedback should appear in a list, then make sure # that it is prefaced with a dash and then a space else: - final_report = final_report + f"{DASH}{SPACE}{feedback}" + # ensure each list entry ends with a newline + final_report = final_report + f"{DASH}{SPACE}{feedback}{NEWLINE}" # return the potentially improved feedback report return final_report @@ -111,19 +115,35 @@ def create_per_key_report( + f"{DASH}{SPACE}**{column_name}**:{SPACE}{column_value}{NEWLINE}" ) # extract the specific row of feedback from the selected feedback columns - feedback_comma_list = str(selected_feedback_columns.iloc[index, 0]) # type: ignore - # create a, potentially empty, list of feedback - feedback_list = create_feedback_list(feedback_comma_list) + # handle case where feedback_regexp matches no columns or index out of range + if ( + selected_feedback_columns.empty + or selected_feedback_columns.shape[1] == 0 + ): + feedback_list: List[str] = [] + else: + try: + feedback_comma_list = str( + selected_feedback_columns.iloc[index, 0] # type: ignore + ) + except (IndexError, KeyError): + feedback_comma_list = "" + # create a, potentially empty, list of feedback + feedback_list = create_feedback_list(feedback_comma_list) # if there is feedback, then add each of the feedback points # in a list and then add the content that belongs in the footer - if feedback_list: + # only show feedback section if at least one key exists in the dict + effective_feedback_keys = [ + k for k in feedback_list if k in feedback_dict + ] + if effective_feedback_keys: current_report = ( current_report + f"{NEWLINE}{NEWLINE}**{FEEDBACK_LABEL}**{NEWLINE}{NEWLINE}" ) # make an entry for each of the types of feedback, ensuring that # each feedback is an entry inside of a list - for feedback_key in feedback_list: + for feedback_key in effective_feedback_keys: # only add feedback in a list-based fashion when there is # a feedback value for the key inside of the feedback dictionary current_report = add_feedback_if_exists( @@ -131,10 +151,14 @@ def create_per_key_report( ) # add the footer to the feedback report, making sure to add newlines that # will provide adequate separation from the potential feedback list - current_report = ( - current_report - + f"{NEWLINE}{NEWLINE}{feedback_dict[FOOTER]}{NEWLINE}" - ) + footer_content = feedback_dict.get(FOOTER, "") + # handle case where footer value is not a string (e.g., list from YAML) + if isinstance(footer_content, list): + footer_content = str(footer_content) + if footer_content: + current_report = ( + current_report + f"{NEWLINE}{NEWLINE}{footer_content}{NEWLINE}" + ) # now that creation of the current_report is finished, store it # inside of the dictionary of the markdown_reports and move to the next one markdown_reports[key_attribute_value] = current_report diff --git a/cellveyor/transfer.py b/cellveyor/transfer.py index b77808e..d71f4c9 100644 --- a/cellveyor/transfer.py +++ b/cellveyor/transfer.py @@ -3,6 +3,7 @@ from typing import Dict from github import Auth, Github, GithubException +from rich.console import Console from rich.progress import ( BarColumn, MofNCompleteColumn, @@ -69,6 +70,26 @@ def transfer_reports_to_github( github_reports_dict: Dict[str, str], ) -> None: """Transfer all reports to GitHub.""" + console = Console() + # validate required GitHub arguments + if not github_token: + console.print( + "[red]:person_shrugging: GitHub token is missing (--github-token)[/red]" + ) + return + if not github_organization: + console.print( + "[red]:person_shrugging: GitHub organization is missing (--github-organization)[/red]" + ) + return + if not github_repository_prefix: + console.print( + "[red]:person_shrugging: GitHub repository prefix is missing (--github-repository-prefix)[/red]" + ) + return + if not github_reports_dict: + console.print("[yellow]:warning: No reports to transfer[/yellow]") + return # extract the keys for the different repositories on # GitHub that will receive a report during this transfer github_report_keys = github_reports_dict.keys() @@ -127,25 +148,49 @@ def transfer_reports_to_github( f"{INDENT}[red]{DETAILS}[/red]{SPACE}{github_exception}" ) continue + except Exception as exc: + # catch broader errors like auth failures, network errors, bad repo names + progress.console.print( + f"{XMARK}{SPACE}[red]{current_github_repository}" + ) + progress.console.print( + f"{INDENT}[red]{DETAILS}[/red]{SPACE}{exc}" + ) + continue def transfer_report_to_github( github_token: str, repository: str, report: str ) -> None: """Transfer a report to a pull request in a GitHub repository.""" + # validate inputs before attempting GitHub API calls + if not github_token or not isinstance(github_token, str): + raise ValueError("GitHub token is missing or invalid") + if not repository or not isinstance(repository, str): + raise ValueError("GitHub repository name is missing or invalid") + if FORWARD_SLASH not in repository or DASH not in repository: + # basic sanity check; let PyGithub raise more detailed errors + pass # authorize the conveyor app to access GitHub through # the use of the provided personal access token - authorization = Auth.Token(github_token) - github = Github(auth=authorization) - # use the fully qualified name of the GitHub repository to - # create a connection to it - github_repository = github.get_repo(repository) - # access the default pull request according to the - # convention established by GitHub Classroom - pull_request = github_repository.get_pull(PULL_REQUEST_ID) - # create an issue comment in this specific pull request; - # note that this is a stand-alone comment for a pull request - # and not specifically connected to the review of the pull - # request itself; this is the reason why it is actually - # using the issue GitHub API to create the comment - pull_request.create_issue_comment(report) + try: + authorization = Auth.Token(github_token) + github = Github(auth=authorization) + # use the fully qualified name of the GitHub repository to + # create a connection to it + github_repository = github.get_repo(repository) + # access the default pull request according to the + # convention established by GitHub Classroom + pull_request = github_repository.get_pull(PULL_REQUEST_ID) + # create an issue comment in this specific pull request; + # note that this is a stand-alone comment for a pull request + # and not specifically connected to the review of the pull + # request itself; this is the reason why it is actually + # using the issue GitHub API to create the comment + pull_request.create_issue_comment(report) + except (GithubException, ValueError): + # re-raise known GitHub/auth errors for caller to handle + raise + except Exception as exc: + # wrap unexpected errors as GithubException-like for uniform handling + raise GithubException(500, str(exc), None) from exc diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 9a0ca04..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1545 +0,0 @@ -# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. - 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Kapfhammer" Date: Thu, 20 Aug 2026 13:23:02 -0400 Subject: [PATCH 06/50] refactor: Update the formatting of the error and feedback blocks produced by cellveyor/data.py and cellveyor/main.py and cellveyor/transfer.py so that they are more easily read in the terminal window. --- cellveyor/data.py | 5 +- cellveyor/main.py | 121 +++++++++++++++++++++++++++++++----------- cellveyor/transfer.py | 19 +++++-- 3 files changed, 107 insertions(+), 38 deletions(-) diff --git a/cellveyor/data.py b/cellveyor/data.py index 3f65cb5..1ffe719 100644 --- a/cellveyor/data.py +++ b/cellveyor/data.py @@ -28,10 +28,7 @@ def key_attribute_column_filter( """Extract a region of a dataframe defined by a key attribute and columns that match a regular expression.""" # validate that the key attribute column exists if key_attribute_name not in sheet_dataframe.columns: - available = ", ".join(map(str, sheet_dataframe.columns.tolist())) - raise ValueError( - f"Key attribute '{key_attribute_name}' not found. Available columns: {available}" - ) + raise ValueError(f"Key attribute '{key_attribute_name}' not found") # use the provided regular expression to extract from the data frame # only those columns that have a name that matches the regular expression try: diff --git a/cellveyor/main.py b/cellveyor/main.py index 5c5ffb8..85aacba 100644 --- a/cellveyor/main.py +++ b/cellveyor/main.py @@ -17,6 +17,20 @@ console = Console() +def _print_dash_list(title: str, items: List[str], color: str = "red") -> None: + """Print a title followed by a dash-prefixed list with spacing.""" + console.print(f" {title}:", style=color) + console.print() + for item in items: + # sanitize items: replace newlines and collapse whitespace to avoid broken dash lists + clean_item = str(item).replace("\n", " ").replace("\r", " ") + # collapse multiple spaces + clean_item = " ".join(clean_item.split()) + # use style instead of markup to avoid interpreting brackets in item names + console.print(f" - {clean_item}", style=color) + console.print() + + def display_reports(reports_dict: Dict[str, str]) -> None: """Display all of the reports in the reports dictionary.""" # iterate through all of the keys @@ -114,31 +128,47 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915 if not filesystem.confirm_valid_file_in_directory( spreadsheet_file, spreadsheet_directory ): + console.print() console.print( - "[red]:person_shrugging: Unable to access file and/or directory[/red]" + ":person_shrugging: Unable to access file and/or directory", + style="red", ) + console.print() # provide more specific diagnostics if not filesystem.confirm_valid_directory(spreadsheet_directory): - console.print( - f"[red] Directory not found: {spreadsheet_directory}[/red]" - ) + console.print(" Directory not found:", style="red") + console.print() + console.print(f" - {spreadsheet_directory}", style="red") + console.print() else: + console.print(" File not found in directory:", style="red") + console.print() console.print( - f"[red] File not found in directory: {spreadsheet_directory / spreadsheet_file}[/red]" + f" - {spreadsheet_directory / spreadsheet_file}", + style="red", ) + console.print() raise typer.Exit(code=1) # access all of the sheets inside of the valid spreadsheet file fully_qualified_spreadsheet_file = spreadsheet_directory / spreadsheet_file console.print( f":delivery_truck: Accessing: {fully_qualified_spreadsheet_file}" ) + console.print() # warn about any feedback files that do not exist if feedback_file is not None: - for fb_path in feedback_file: - if not filesystem.confirm_valid_file(fb_path): - console.print( - f"[yellow]:warning: Feedback file not found, skipping: {fb_path}[/yellow]" - ) + missing_feedback = [ + fb for fb in feedback_file if not filesystem.confirm_valid_file(fb) + ] + if missing_feedback: + console.print( + ":warning: Feedback file(s) not found, skipping:", + style="yellow", + ) + console.print() + for fb_path in missing_feedback: + console.print(f" - {fb_path}", style="yellow") + console.print() # access all of the feedback files and combine them into a single # dictionary organized in the following fashion: # --> key: label like "header" or "footer" or a label @@ -157,21 +187,29 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915 ) except FileNotFoundError: console.print( - f"[red]:person_shrugging: Spreadsheet file not found: {fully_qualified_spreadsheet_file}[/red]" + f":person_shrugging: Spreadsheet file not found: {fully_qualified_spreadsheet_file}", + style="red", ) + console.print() raise typer.Exit(code=1) except Exception as exc: console.print( - f"[red]:person_shrugging: Failed to read spreadsheet: {exc}[/red]" + f":person_shrugging: Failed to read spreadsheet: {exc}", + style="red", ) + console.print() raise typer.Exit(code=1) # validate that the requested sheet exists if sheet_name not in sheet_dataframe_dict: - available_sheets = ", ".join(sheet_dataframe_dict.keys()) console.print( - f"[red]:person_shrugging: Sheet '{sheet_name}' not found[/red]" + f":person_shrugging: Sheet '{sheet_name}' not found", style="red" + ) + console.print() + _print_dash_list( + "Available sheets", + list(sheet_dataframe_dict.keys()), + color="red", ) - console.print(f"[red] Available sheets: {available_sheets}[/red]") raise typer.Exit(code=1) # console.print(sheet_dataframe_dict.keys()) # access the requested sheet within the spreadsheet @@ -184,35 +222,47 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915 sheet_dataframe, key_attribute, column_regexp, key_value ) except ValueError as exc: - console.print(f"[red]:person_shrugging: {exc}[/red]") + console.print(f":person_shrugging: {exc}", style="red") + console.print() # also show available columns for key attribute errors if "Key attribute" in str(exc): - available_cols = ", ".join( - map(str, sheet_dataframe.columns.tolist()) + _print_dash_list( + "Available columns", + list(map(str, sheet_dataframe.columns.tolist())), + color="red", ) console.print( - "[red] Hint: check --key-attribute and --column-regexp[/red]" + " Hint: check --key-attribute and --column-regexp", + style="red", ) + console.print() raise typer.Exit(code=1) except Exception as exc: console.print( - f"[red]:person_shrugging: Failed to filter columns: {exc}[/red]" + f":person_shrugging: Failed to filter columns: {exc}", + style="red", ) + console.print() raise typer.Exit(code=1) # warn if column regexp matched no columns if selected_columns.empty or len(selected_columns.columns) == 0: console.print( - f"[yellow]:warning: No columns matched --column-regexp '{column_regexp}'[/yellow]" + f":warning: No columns matched --column-regexp '{column_regexp}'", + style="yellow", ) - available_cols = ", ".join(map(str, sheet_dataframe.columns.tolist())) - console.print( - f"[yellow] Available columns: {available_cols}[/yellow]" + console.print() + _print_dash_list( + "Available columns", + list(map(str, sheet_dataframe.columns.tolist())), + color="yellow", ) # warn if result has no rows if result_df.empty: console.print( - "[yellow]:warning: No rows found after filtering — check --key-attribute and --column-regexp[/yellow]" + ":warning: No rows found after filtering — check --key-attribute and --column-regexp", + style="yellow", ) + console.print() # create a unique message for each row in the dataframe try: per_key_report = report.create_per_key_report( @@ -224,13 +274,15 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915 ) except Exception as exc: console.print( - f"[red]:person_shrugging: Failed to create reports: {exc}[/red]" + f":person_shrugging: Failed to create reports: {exc}", style="red" ) + console.print() raise typer.Exit(code=1) if not per_key_report: console.print( - "[yellow]:warning: No reports generated (no matching rows)[/yellow]" + ":warning: No reports generated (no matching rows)", style="yellow" ) + console.print() # display the generated reports display_reports(per_key_report) # if the --transfer flag was enabled then this means @@ -247,11 +299,18 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915 missing_github_args.append("--github-repository-prefix") if missing_github_args: console.print( - f"[red]:person_shrugging: Missing required GitHub arguments for --transfer-report: {', '.join(missing_github_args)}[/red]" + ":person_shrugging: Missing required GitHub arguments for --transfer-report:", + style="red", + ) + console.print() + _print_dash_list( + "Missing options", missing_github_args, color="red" ) console.print( - "[red] Hint: provide all GitHub options or omit --transfer-report[/red]" + " Hint: provide all GitHub options or omit --transfer-report", + style="red", ) + console.print() raise typer.Exit(code=1) try: transfer.transfer_reports_to_github( @@ -262,6 +321,8 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915 ) except Exception as exc: console.print( - f"[red]:person_shrugging: GitHub transfer failed: {exc}[/red]" + f":person_shrugging: GitHub transfer failed: {exc}", + style="red", ) + console.print() raise typer.Exit(code=1) diff --git a/cellveyor/transfer.py b/cellveyor/transfer.py index d71f4c9..0224e94 100644 --- a/cellveyor/transfer.py +++ b/cellveyor/transfer.py @@ -73,22 +73,33 @@ def transfer_reports_to_github( console = Console() # validate required GitHub arguments if not github_token: + console.print() console.print( - "[red]:person_shrugging: GitHub token is missing (--github-token)[/red]" + ":person_shrugging: GitHub token is missing (--github-token)", + style="red", ) + console.print() return if not github_organization: + console.print() console.print( - "[red]:person_shrugging: GitHub organization is missing (--github-organization)[/red]" + ":person_shrugging: GitHub organization is missing (--github-organization)", + style="red", ) + console.print() return if not github_repository_prefix: + console.print() console.print( - "[red]:person_shrugging: GitHub repository prefix is missing (--github-repository-prefix)[/red]" + ":person_shrugging: GitHub repository prefix is missing (--github-repository-prefix)", + style="red", ) + console.print() return if not github_reports_dict: - console.print("[yellow]:warning: No reports to transfer[/yellow]") + console.print() + console.print(":warning: No reports to transfer", style="yellow") + console.print() return # extract the keys for the different repositories on # GitHub that will receive a report during this transfer From 0bc541afa908bbfbc312cccc7aaa812cc813e548 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:20:49 -0400 Subject: [PATCH 07/50] refactor: Update the cellveyor/main.py file. --- cellveyor/main.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/cellveyor/main.py b/cellveyor/main.py index 85aacba..aa6b096 100644 --- a/cellveyor/main.py +++ b/cellveyor/main.py @@ -34,9 +34,7 @@ def _print_dash_list(title: str, items: List[str], color: str = "red") -> None: def display_reports(reports_dict: Dict[str, str]) -> None: """Display all of the reports in the reports dictionary.""" # iterate through all of the keys - for current_report_key in reports_dict.keys(): - # extract the report for the current key - current_report = reports_dict[current_report_key] + for current_report_key, current_report in reports_dict.items(): # display the report inside of a rich panel, using # a markdown-based formatter for the report's contents; # note that use of console.print must occur in two @@ -51,7 +49,7 @@ def display_reports(reports_dict: Dict[str, str]) -> None: @cli.command() -def transport( # noqa: PLR0912, PLR0913, PLR0915 +def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 spreadsheet_directory: Path = typer.Option( ..., "--spreadsheet-directory", From 05f6368121ed79fc50393846ebf58583a9fb5062 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:23:34 -0400 Subject: [PATCH 08/50] chore: Add the starting version of the .rumdl.toml file. --- .rumdl.toml | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 .rumdl.toml diff --git a/.rumdl.toml b/.rumdl.toml new file mode 100644 index 0000000..6e61943 --- /dev/null +++ b/.rumdl.toml @@ -0,0 +1,69 @@ +# rumdl configuration file + +# Inherit settings from another config file (relative to this file's directory) +# extends = "../base.rumdl.toml" + +# Global configuration options +[global] +# List of rules to disable (uncomment and modify as needed) +disable = ["MD013", "MD033", "MD041"] + +# List of rules to enable exclusively (replaces defaults; only these rules will run) +# enable = ["MD001", "MD003", "MD004"] + +# Additional rules to enable on top of defaults (additive, does not replace) +# Use this to activate opt-in rules like MD060, MD063, MD072, MD073, MD074 +# extend-enable = ["MD060", "MD063"] + +# Additional rules to disable on top of the disable list (additive) +# extend-disable = ["MD041"] + +# List of file/directory patterns to include for linting (if provided, only these will be linted) +# include = [ +# "docs/*.md", +# "src/**/*.md", +# "README.md" +# ] + +# List of file/directory patterns to exclude from linting +exclude = [ + # Common directories to exclude + ".git", + ".github", + "node_modules", + "vendor", + "dist", + "build", + + # Specific files or patterns + "CHANGELOG.md", + "LICENSE.md", +] + +# Respect .gitignore files when scanning directories (default: true) +respect-gitignore = true + +# Markdown flavor/dialect (uncomment to enable) +# Options: standard (default), gfm, commonmark, mkdocs, mdx, pandoc, quarto, obsidian, kramdown, azure_devops +# flavor = "mkdocs" + +# Rule-specific configurations (uncomment and modify as needed) + +# [MD003] +# style = "atx" # Heading style (atx, atx_closed, setext) + +# [MD004] +# style = "asterisk" # Unordered list style (asterisk, plus, dash, consistent) + +# [MD007] +# indent = 4 # Unordered list indentation + +# [MD013] +# line-length = 100 # Line length +# code-blocks = false # Exclude code blocks from line length check +# tables = false # Exclude tables from line length check +# headings = true # Include headings in line length check + +# [MD044] +# names = ["rumdl", "Markdown", "GitHub"] # Proper names that should be capitalized correctly +# code-blocks = false # Check code blocks for proper names (default: false, skips code blocks) From 49531f3d22cdcdfde2dfbb956444a6e822263bc4 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:23:49 -0400 Subject: [PATCH 09/50] chore: Reformat lines in the CODE_OF_CONDUCT.md file. --- CODE_OF_CONDUCT.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index cb203cf..19c923f 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -60,7 +60,7 @@ representative at an online or offline event. Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at -gkapfham@allegheny.edu. +. All complaints will be reviewed and investigated promptly and fairly. All community leaders are obligated to respect the privacy and security of the @@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban. ### 4. Permanent Ban **Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an +standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals. **Consequence**: A permanent ban from any sort of public interaction within From a4653e6bd0d2075eb88310d8db619144ed26c434 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:24:02 -0400 Subject: [PATCH 10/50] docs: Make small improvements to the formatting in the README.md file. --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c873cc4..eae395c 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ ## Example Command -``` +```text uv run cellveyor --spreadsheet-directory \ /home/gkapfham/working/data/gradebook/2023 --spreadsheet-file CMPSC-203-Fall-2023-Gradebook.xlsx \ @@ -42,12 +42,12 @@ and efficient fashion. - Cellveyor is a tool that automatically produces a report based output by analyzing a Google sheet - - Student sentence: "I'm glad Cellveyor made it easy for me to see my grades + - Student sentence: "I'm glad Cellveyor made it easy for me to see my grades from my classes, it's so easy to read and analyze." - - Instructor sentence: "Cellveyor makes it much easier for me to tell my + - Instructor sentence: "Cellveyor makes it much easier for me to tell my students what their grade looks like on a certain assignment or overall in the class" - - Researchers sentence: "I found that Cellveyor is a very interesting tool that + - Researchers sentence: "I found that Cellveyor is a very interesting tool that quickly and automatically does a task that is necessary in schooling" ## 🔋Features @@ -65,6 +65,7 @@ analyzing a Google sheet ## 🔽 Installation Follow these steps to install the Cellveyor program: + 1. Copy the ssh key of the repo 2. ```Git clone``` the repository onto your personal computer - ```git clone (ssh key)``` From e4ee95b07cbdd063798b06190d58984f1da40b9c Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:25:38 -0400 Subject: [PATCH 11/50] feat: Add many update files and scripts to fix defects in cellveyor and to improve tooling and support. --- .gitignore | 7 + cellveyor/__init__.py | 1 + cellveyor/constants.py | 2 +- cellveyor/data.py | 8 +- cellveyor/report.py | 6 +- cellveyor/transfer.py | 6 +- pyproject.toml | 143 ++++-- scripts/__init__.py | 1 + scripts/ccl.py | 256 ++++++++++ scripts/tsc.py | 583 ++++++++++++++++++++++ scripts/vsc.py | 162 +++++++ tests/__init__.py | 1 + tests/test_data.py | 5 +- uv.lock | 1043 ++++++++++++++++++++++++++++++++++++++-- 14 files changed, 2153 insertions(+), 71 deletions(-) create mode 100644 scripts/__init__.py create mode 100644 scripts/ccl.py create mode 100644 scripts/tsc.py create mode 100644 scripts/vsc.py diff --git a/.gitignore b/.gitignore index b02df10..f4b9637 100644 --- a/.gitignore +++ b/.gitignore @@ -375,3 +375,10 @@ credentials.json # poetry.toml file poetry.toml + +# Workflow file +WORKFLOW.md + +# Coverage files +tsc.json +cosmic-ray.toml diff --git a/cellveyor/__init__.py b/cellveyor/__init__.py index e69de29..5d14d0a 100644 --- a/cellveyor/__init__.py +++ b/cellveyor/__init__.py @@ -0,0 +1 @@ +"""Cellveyor package.""" diff --git a/cellveyor/constants.py b/cellveyor/constants.py index 95854f2..f7595f4 100644 --- a/cellveyor/constants.py +++ b/cellveyor/constants.py @@ -1,4 +1,4 @@ -"""Define constants with dataclasses for use in Cellveyor""" +"""Define constants with dataclasses for use in Cellveyor.""" from dataclasses import dataclass diff --git a/cellveyor/data.py b/cellveyor/data.py index 1ffe719..7d3c526 100644 --- a/cellveyor/data.py +++ b/cellveyor/data.py @@ -1,11 +1,11 @@ """Access and manipulate data.""" from pathlib import Path -from typing import Dict, Tuple +from typing import Dict, Final, Literal, Tuple import pandas -ALL = "all" +ALL: Final[Literal["all"]] = "all" def access_dataframes(spreadsheet_file: Path) -> Dict[str, pandas.DataFrame]: @@ -41,7 +41,7 @@ def key_attribute_column_filter( # those columns that matched the regular expression result_df = sheet_dataframe[ [key_attribute_name] + list(selected_columns.columns) # noqa: RUF005 - ].dropna(how=ALL) # type: ignore + ].dropna(how=ALL) # filter down further for the specific value of the key attribute; # this is particularly useful when extracting and reporting data # for a specific row inside of the matching dataframe @@ -51,4 +51,4 @@ def key_attribute_column_filter( ] # for both of the two previous steps, make sure to drop any rows that contain NA values # return the columns that were selected and then the resulting dataframe - return (selected_columns, result_df) # type: ignore + return (selected_columns, result_df) diff --git a/cellveyor/report.py b/cellveyor/report.py index a99a6df..48db453 100644 --- a/cellveyor/report.py +++ b/cellveyor/report.py @@ -1,6 +1,6 @@ """Create reports based on content in dataframes.""" -from typing import Dict, List +from typing import Any, Dict, List from pandas import DataFrame @@ -21,7 +21,7 @@ def add_feedback_if_exists( report: str, - feedback_dict: Dict[str, str], + feedback_dict: Dict[str, Any], feedback_key: str, make_list: bool = False, ) -> str: @@ -73,7 +73,7 @@ def create_per_key_report( result_dataframe: DataFrame, selected_columns: DataFrame, feedback_regexp: str, - feedback_dict: Dict[str, str], + feedback_dict: Dict[str, Any], ) -> Dict[str, str]: """Create a per-key report for the provided dataframe.""" # create an empty dictionary for the reports, organized as: diff --git a/cellveyor/transfer.py b/cellveyor/transfer.py index 0224e94..4bc80b3 100644 --- a/cellveyor/transfer.py +++ b/cellveyor/transfer.py @@ -58,8 +58,8 @@ def create_fully_qualified_github_repository( fully_qualified_github_repo_name = ( f"{fully_qualified_github_repo_name}{DASH}{github_username}" ) - # Example of a fully qualified name, using the GitHub Classroom format: - # Allegheny-Computer-Science-203-F2023/computer-science-203-fall-2023-executable-exam-1-gkapfham + # example of a fully qualified name, using the GitHub Classroom format: + # allegheny-Computer-Science-203-F2023/computer-science-203-fall-2023-executable-exam-1-gkapfham return fully_qualified_github_repo_name @@ -102,7 +102,7 @@ def transfer_reports_to_github( console.print() return # extract the keys for the different repositories on - # GitHub that will receive a report during this transfer + # gitHub that will receive a report during this transfer github_report_keys = github_reports_dict.keys() # create a customized progress bar using rich progress_bar = Progress( diff --git a/pyproject.toml b/pyproject.toml index 13dc06c..feb9a57 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,19 +20,32 @@ cellveyor = "cellveyor.main:cli" [dependency-groups] dev = [ - "pytest>=7.4.0,<8.0.0", - "taskipy>=1.11.0,<2.0.0", - "mypy>=1.4.1,<2.0.0", - "isort>=5.12.0,<6.0.0", + "taskipy>=1.10.1,<2", + "pytest>=7.4.0,<10", + "pytest-cov>=6.0.0,<7", + "pytest-sugar>=1.0.0,<2", + "pytest-randomly>=3.13.0,<4", + "pytest-clarity>=1.0.1,<2", + "pytest-pretty>=1.2.0,<2", + "pytest-xdist>=3.3.1,<4", + "pydocstyle>=6.1.1,<7", + "toml>=0.10.2,<0.11", + "types-toml>=0.10.8.20260518", "hypothesis[cli]>=6.81.1,<7.0.0", - "pytest-clarity>=1.0.1,<2.0.0", - "pytest-randomly>=3.13.0,<4.0.0", - "pytest-pretty>=1.2.0,<2.0.0", - "pytest-xdist>=3.3.1,<4.0.0", "types-pyyaml>=6.0.12.12,<7.0.0", "pandas-stubs>=2.1.1.230928,<3.0.0", - "ruff==0.1.15", - "symbex>=1.4,<2.0.0", + "ruff>=0.15.15", + "symbex>=1.4,<2", + "mypy>=1.11.2,<2", + "ty>=0.0.8", + "pyrefly>=1.0.0", + "zuban>=0.7.2", + "rumdl>=0.2.4", + "tree-sitter>=0.25.2", + "tree-sitter-python>=0.25.0", + "tree-sitter-analyzer[popular]>=0.4.0", + "cosmic-ray>=8.4.3", + "isort>=5.12.0,<6.0.0", ] [build-system] @@ -46,21 +59,47 @@ packages = ["cellveyor"] filterwarnings = [ "error", ] +markers = [ + "propertybased: property-based tests using hypothesis", + "fuzz: fuzz tests using hypothesis", +] + +[tool.coverage.run] +source = ["cellveyor"] +branch = true +omit = ["tests/*", "**/__init__.py", "scripts/*"] + +[tool.coverage.report] +fail_under = 90 +show_missing = true +precision = 2 +exclude_lines = [ + "pragma: no cover", + "def __repr__", + "raise AssertionError", + "raise NotImplementedError", + "if __name__ == .__main__.:", + "if TYPE_CHECKING:", + "@abstractmethod", +] [tool.ruff] line-length = 79 -ignore = [ +lint.ignore = [ + "D203", + "D213", "E501", ] -select = [ +lint.select = [ "E", + "D", "I", "F", "PL", "Q", "RUF", "W", - "T201" + "T201", ] [tool.isort] @@ -71,38 +110,80 @@ use_parentheses = true ensure_newline_before_comments = true line_length = 88 +[tool.mypy] +ignore_missing_imports = true +strict = false +warn_return_any = true +warn_unused_configs = true +disallow_untyped_defs = true +python_version = "3.13" + +[tool.pydocstyle] +convention = "google" + +[tool.pyrefly] +preset = "legacy" +ignore-missing-imports = ["*"] + [tool.taskipy.variables] project = "cellveyor" +scripts = "scripts" tests = "tests" -check-command = { var = "ruff check {project} {tests}", recursive = true } -coverage-test-command = "pytest -s --cov-context=test --cov-fail-under=90 --cov-report term-missing --cov-report json --cov --cov-branch" +coveragefailunder = "90" +directtestedfailunder = "75" +ruff-check-command = { var = "ruff check {project} {tests} {scripts}", recursive = true } +ruff-fixformat-command = { var = "ruff format {project} {tests} {scripts}", recursive = true } +ruff-format-command = { var = "ruff format --check {project} {tests} {scripts}", recursive = true } +coverage-test-command = { var = "pytest -s --cov=cellveyor --cov-branch --cov-fail-under=90 --cov-report=term-missing tests/", recursive = true } coverage-test-command-silent = "pytest -x --show-capture=no --cov-report term-missing --cov-report json --cov --cov-branch" developer-test-command = "pytest -x -s" developer-test-silent-command = "pytest -x --show-capture=no" -fixformat-command = { var = "ruff format {project} {tests}", recursive = true } -format-command = { var = "ruff format --check {project} {tests}", recursive = true } -symbex-typed-command = {var = "symbex -s --untyped -d {project} --check", recursive = true} -symbex-documented-command = {var = "symbex -s --undocumented -d {project} --check", recursive = true} +symbex-typed-command = {var = "symbex -s --untyped -d {project} -d {tests} -d {scripts} --check", recursive = true} +symbex-documented-command = {var = "symbex -s --undocumented -d {project} -d {tests} -d {scripts} --check", recursive = true} +mypy-command = {var = "mypy {project} {scripts}", recursive = true} +ty-command = {var = "ty check {project} {tests} {scripts}", recursive = true} +pyrefly-command = {var = "pyrefly check {project} {tests} {scripts}", recursive = true} +zuban-command = {var = "zuban check {project} {tests} {scripts}", recursive = true} +rumdl-command = {var = "rumdl check", recursive = true} +rumdl-command-fix = {var = "rumdl fmt", recursive = true} +cosmic-ray-init-command = "cosmic-ray init cosmic-ray.toml cosmic-ray.sqlite" +cosmic-ray-exec-command = "cosmic-ray exec cosmic-ray.toml cosmic-ray.sqlite" +cosmic-ray-report-command = "cosmic-ray dump cosmic-ray.sqlite" +cosmic-ray-baseline-command = "cosmic-ray baseline cosmic-ray.toml" [tool.taskipy.tasks] -all = "task format && task lint && task test" -lint = "task format && task check && task mypy && task symbex" -check = { cmd = "{check-command}", help = "Run the ruff linting checks", use_vars = true } -format = { cmd = "{format-command}", help = "Run the ruff formatter on source code", use_vars = true } -format-fix = { cmd = "{fixformat-command}", help = "Run the ruff formatter to fix source code", use_vars = true} -mypy = { cmd = "uv run mypy cellveyor", help = "Run the mypy type checker for potential type errors" } +all = "task check && task test && task test-coverage-check" +check = "task lint && task typecheck" +lint = "task ruff-format && task ruff-check && task comments-check && task vsc && task rumdl-check" +typecheck = "task mypy && task ty && task pyrefly && task zuban && task symbex" +ruff-check = { cmd = "{ruff-check-command}", help = "Run the ruff linting checks", use_vars = true } +ruff-format = { cmd = "{ruff-format-command}", help = "Run the ruff formatter on source code", use_vars = true } +ruff-format-fix = { cmd = "{ruff-fixformat-command}", help = "Run the ruff formatter to fix source code", use_vars = true } +rumdl-check = { cmd = "{rumdl-command}", help = "Run the rumdl markdown linting checks", use_vars = true } +rumdl-fix = { cmd = "{rumdl-command-fix}", help = "Run the rumdl markdown linter to fix markdown", use_vars = true } +mypy = { cmd = "{mypy-command}", help = "Run the mypy type checker for potential type errors", use_vars = true } +ty = { cmd = "{ty-command}", help = "Run the ty type checker for potential type errors", use_vars = true } +pyrefly = { cmd = "{pyrefly-command}", help = "Run the pyrefly type checker for potential type errors", use_vars = true } +zuban = { cmd = "{zuban-command}", help = "Run the zuban type checker for potential type errors", use_vars = true } symbex = "task symbex-typed && task symbex-documented" symbex-typed = { cmd = "{symbex-typed-command}", help = "Run symbex for fully typed functions", use_vars = true } symbex-documented = { cmd = "{symbex-documented-command}", help = "Run symbex for documentation", use_vars = true } +format = { cmd = "{ruff-format-command}", help = "Run the ruff formatter to check source code", use_vars = true } +format-fix = { cmd = "{ruff-fixformat-command}", help = "Run the ruff formatter to fix source code", use_vars = true } +comments-check = { cmd = "uv run -m scripts.ccl check {project} {tests} {scripts}", help = "Check that comments start with lowercase letters using Tree-sitter", use_vars = true } +comments-fix = { cmd = "uv run -m scripts.ccl fix {project} {tests} {scripts}", help = "Auto-fix comments that start with uppercase letters", use_vars = true } +vsc = { cmd = "uv run -m scripts.vsc check", help = "Check that the Cellveyor version in cellveyor/version.py matches the version in pyproject.toml", use_vars = true } +test-coverage-check = { cmd = "uv run python -m scripts.tsc --threshold {directtestedfailunder}", help = "Check that a minimum percentage of functions are directly tested", use_vars = true } +test-coverage-check-verbose = { cmd = "uv run python -m scripts.tsc --threshold {directtestedfailunder} --verbose", help = "Check function coverage with detailed analysis output", use_vars = true } test = { cmd = "pytest -x -s -vv -n auto", help = "Run the pytest test suite using order randomization and test distribution" } test-not-randomly = { cmd = "pytest -x -s -vv -p no:randomly", help = "Run the pytest test suite without order randomization" } test-not-xdist = { cmd = "pytest -x -s -vv -p no:xdist", help = "Run the pytest test suite without order randomization" } test-silent = { cmd = "pytest -x --show-capture=no -n auto", help = "Run the pytest test suite without showing output" } test-silent-not-randomly = { cmd = "pytest -x --show-capture=no -p no:randomly", help = "Run the pytest test suite without showing output and order randomization" } test-silent-not-xdist = { cmd = "pytest -x --show-capture=no -p no:xdist", help = "Run the pytest test suite without showing output and test distribution" } - -[tool.mypy] -python_version = "3.13" -warn_return_any = true -warn_unused_configs = true -ignore_missing_imports = true +test-coverage = { cmd = "pytest -s --cov=cellveyor --cov-branch --cov-fail-under={coveragefailunder} --cov-report=term-missing tests/", help = "Run the pytest test suite with coverage tracking", use_vars = true } +test-parallel = { cmd = "pytest -x -s -vv -n auto -p no:sugar", help = "Run the pytest test suite with parallel execution and order randomization" } +cosmic-ray-init = { cmd = "{cosmic-ray-init-command}", help = "Initialize cosmic-ray mutation testing session", use_vars = true } +cosmic-ray-baseline = { cmd = "{cosmic-ray-baseline-command}", help = "Run cosmic-ray baseline tests", use_vars = true } +cosmic-ray-exec = { cmd = "{cosmic-ray-exec-command}", help = "Execute cosmic-ray mutation testing", use_vars = true } +cosmic-ray-report = { cmd = "{cosmic-ray-report-command}", help = "Generate cosmic-ray mutation testing report (JSON)", use_vars = true } diff --git a/scripts/__init__.py b/scripts/__init__.py new file mode 100644 index 0000000..862f852 --- /dev/null +++ b/scripts/__init__.py @@ -0,0 +1 @@ +"""Scripts package.""" diff --git a/scripts/ccl.py b/scripts/ccl.py new file mode 100644 index 0000000..8c19521 --- /dev/null +++ b/scripts/ccl.py @@ -0,0 +1,256 @@ +"""Check that Python comments start with a lowercase letter. + +Uses Tree-sitter to parse Python files into a Concrete Syntax Tree, +which preserves comment nodes that are stripped by AST parsers. + +Exceptions are made for proper nouns (GatorGrader, GitHub, etc.) +and identifiers that must start with a capital letter (GITHUB_ENV). + +Run with: +uv run -m scripts.ccl check +uv run -m scripts.ccl fix +uv run task comments +""" + +from pathlib import Path + +import tree_sitter_python as tspython +import typer +from rich.console import Console +from rich.panel import Panel +from tree_sitter import Language, Node, Parser + +PROPER_NOUNS = frozenset( + { + "CountCommits", + "GatorGrade", + "GatorGrader", + "Cellveyor", + "GatorGraderCheck", + "GITHUB_ENV", + "GITHUB_STEP_SUMMARY", + "JSON", + "MatchFileFragment", + "ShellCheck", + "STDOUT", + "STDERR", + "TODO", + "FIXME", + "NOTE", + } +) + +PY_LANGUAGE = Language(tspython.language()) + +DEFAULT_DIRS = ["cellveyor", "tests", "scripts"] + +console = Console(stderr=True) +err_console = Console(stderr=True) + +app = typer.Typer( + name="ccl", + help="Check that Python comments start with a lowercase letter.", +) + + +class CommentError: + """Represent a comment that starts with an uppercase letter.""" + + def __init__(self, filepath: Path, line: int, col: int, text: str) -> None: + """Construct a CommentError with file location and text.""" + self.filepath = filepath + self.line = line + self.col = col + self.text = text + + def __str__(self) -> str: + """Return a string representation of the error.""" + return ( + f"{self.filepath}:{self.line}:{self.col}: " + f"comment-starts-with-uppercase" + ) + + +def _find_errors(filepath: Path, parser: Parser) -> list[CommentError]: + """Find comment-case errors in a Python file. + + Walks the Tree-sitter CST looking for comment nodes, then checks + whether each non-empty comment starts with a lowercase letter + (allowing proper nouns). + + """ + errors = [] + source = filepath.read_bytes() + tree = parser.parse(source) + + def walk(node: Node) -> None: + if node.type == "comment": + node_text = node.text + if node_text is None: + return + text = node_text.decode("utf-8") + content = text.lstrip("#").lstrip() + if content and content[0].isupper(): + first_word = content.split()[0].rstrip(",:;.!?") + if first_word not in PROPER_NOUNS: + line = node.start_point[0] + 1 + col = node.start_point[1] + 1 + errors.append( + CommentError(filepath, line, col, text.strip()) + ) + for child in node.children: + walk(child) + + walk(tree.root_node) + return errors + + +def _scan_files( + paths: list[Path] | None = None, +) -> tuple[list[Path], list[CommentError]]: + """Scan Python files for comment-case errors. + + Finds all .py files under the given paths (or the + default directories cellveyor/, tests/, scripts/), + then checks each one for comments that start with + an uppercase letter. + + Returns a tuple of (all_matched_files, errors_found). + + """ + parser = Parser(PY_LANGUAGE) + root = Path(".") + if paths: + py_files = sorted( + f + for p in paths + for f in (p.glob("**/*.py") if p.is_dir() else [p]) + if "__pycache__" not in str(f) + ) + else: + py_files = sorted( + f + for d in DEFAULT_DIRS + for f in root.glob(f"{d}/**/*.py") + if "__pycache__" not in str(f) + ) + all_errors = [] + for py_file in py_files: + all_errors.extend(_find_errors(py_file, parser)) + return py_files, all_errors + + +@app.command() +def check( + paths: list[Path] | None = typer.Argument( + None, + help="Paths to scan. Defaults to cellveyor/, tests/, and scripts/.", + ), +) -> None: + """Check that comments start with a lowercase letter.""" + py_files, errors = _scan_files(paths) + if not errors: + console.print( + "[green]All comments start with lowercase " + "(or are proper nouns).[/green]" + ) + raise typer.Exit(code=0) + err_console.print( + f"[red]Found {len(errors)} error(s)[/red] " + f"across {len(py_files)} file(s).\n" + ) + for error in errors: + err_console.print( + f"[bold]{error.filepath}[/bold]:{error.line}:{error.col} " + f"[red]comment-starts-with-uppercase[/red]" + ) + err_console.print(f" {error.text}") + fixed = _fix_comment_text(error.text) + err_console.print(f" [green]{fixed}[/green]\n") + err_console.print( + Panel( + f"[bold]Summary:[/bold] {len(errors)} comment(s) " + f"starting with uppercase found.\n" + f"Run [bold]uv run -m scripts.ccl fix[/bold] to auto-fix.", + title="[bold]Check Comments[/bold]", + border_style="red", + ) + ) + raise typer.Exit(code=1) + + +def _fix_comment_text(text: str) -> str: + """Fix a comment line by lowercasing the first letter.""" + stripped = text.lstrip() + hash_prefix = text[: len(text) - len(stripped)] + content = stripped.lstrip("#").lstrip() + if content and content[0].isupper(): + first_word = content.split()[0].rstrip(",:;.!?") + if first_word not in PROPER_NOUNS: + content = content[0].lower() + content[1:] + return f"{hash_prefix}# {content}" + + +@app.command() +def fix( + paths: list[Path] | None = typer.Argument( + None, + help="Paths to fix. Defaults to cellveyor/, tests/, and scripts/.", + ), +) -> None: + """Auto-fix comments that start with an uppercase letter.""" + root = Path(".") + if paths: + py_files = sorted( + f + for p in paths + for f in (p.glob("**/*.py") if p.is_dir() else [p]) + if "__pycache__" not in str(f) + ) + else: + py_files = sorted( + f + for d in DEFAULT_DIRS + for f in root.glob(f"{d}/**/*.py") + if "__pycache__" not in str(f) + ) + total_fixed = 0 + files_fixed = 0 + for py_file in py_files: + lines = py_file.read_text(encoding="utf-8").splitlines() + new_lines = [] + file_changed = False + for line in lines: + stripped = line.lstrip() + if stripped.startswith("#"): + content = stripped.lstrip("#").lstrip() + if content and content[0].isupper(): + first_word = content.split()[0].rstrip(",:;.!?") + if first_word not in PROPER_NOUNS: + indent = line[: len(line) - len(stripped)] + new_content = content[0].lower() + content[1:] + new_line = f"{indent}# {new_content}" + new_lines.append(new_line) + file_changed = True + total_fixed += 1 + continue + new_lines.append(line) + if file_changed: + py_file.write_text("\n".join(new_lines) + "\n", encoding="utf-8") + files_fixed += 1 + console.print(f"[green]Fixed[/green] {py_file}") + if total_fixed == 0: + console.print( + "[green]All comments already start with lowercase " + "(or are proper nouns).[/green]" + ) + else: + console.print( + f"\n[bold green]Fixed {total_fixed} comment(s) " + f"in {files_fixed} file(s).[/bold green]" + ) + raise typer.Exit(code=0) + + +if __name__ == "__main__": + app() diff --git a/scripts/tsc.py b/scripts/tsc.py new file mode 100644 index 0000000..6895b7e --- /dev/null +++ b/scripts/tsc.py @@ -0,0 +1,583 @@ +"""Check which functions in cellveyor are directly tested vs. indirectly tested. + +If a function is indirectly covered that means that a test case +calls a function that transitively calls that function. Importantly, +a function that is indirectly tested does not have a test case that +calls it directly and this could be a sign that the function is not +being tested as thoroughly as it should be. + +Uses tree-sitter-analyzer (Python API) for language detection and +file analysis, then falls back to raw Tree-sitter for function-definition +extraction and call-graph construction (the installed version of +tree-sitter-analyzer uses a deprecated query.captures() API that +has been removed from modern tree-sitter). + +Usage: + uv run python -m scripts.tsc [OPTIONS] + +Options: + --threshold, -t INT Minimum percentage of directly tested functions + required (default 100). + --output, -o PATH Path for the JSON report file (default tsc.json). + --verbose, --no-verbose + Show detailed coverage analysis output (default: + no-verbose). + +Exit code: + 0 — at least THRESHOLD% of functions are directly tested + 1 — fewer than THRESHOLD% of functions are directly tested + +Output: + Writes a JSON report and prints a color-coded summary to stdout. + +""" + +import json +import logging +from pathlib import Path +from typing import Any + +import tree_sitter_python as tspython +import typer +from rich import box +from rich.console import Console +from rich.rule import Rule +from rich.style import Style +from rich.table import Table +from tree_sitter import Language, Node, Parser +from tree_sitter_analyzer.api import ( + detect_language, + get_supported_languages, +) + +logging.getLogger("tree_sitter_analyzer").setLevel(logging.WARNING) + +PY_LANGUAGE = Language(tspython.language()) +CONSOLE = Console() + + +def _make_parser() -> Parser: + """Create a tree-sitter parser for Python.""" + return Parser(PY_LANGUAGE) + + +def _walk_node(node: Node) -> list[Node]: + """Walk the tree recursively and return all descendant nodes.""" + nodes = [node] + for child in node.children: + nodes.extend(_walk_node(child)) + return nodes + + +def _get_func_name(func_node: Node) -> str | None: + """Extract the function name from a function_definition node.""" + for child in func_node.children: + if child.type == "identifier": + text = child.text + if text is not None: + return text.decode("utf-8") + return None + + +def _get_call_names(call_node: Node) -> list[str]: + """Extract all function names from a call node. + + Handles both bare calls (foo(...)) and dotted calls + (mod.foo(...), a.b.foo(...)). + + """ + names: list[str] = [] + for child in call_node.children: + if child.type == "identifier": + text = child.text + if text is not None: + names.append(text.decode("utf-8")) + elif child.type == "attribute": + for attr_child in child.children: + if attr_child.type == "identifier": + text = attr_child.text + if text is not None: + names.append(text.decode("utf-8")) + return names + + +def find_function_definitions( + source_dir: Path, +) -> dict[str, dict[str, Any]]: + """Walk source files and extract every function definition. + + Uses the Tree-sitter CST to find nodes of type + function_definition and records the child identifier + node's text as the function name. + + """ + functions: dict[str, dict[str, Any]] = {} + for py_file in sorted(source_dir.rglob("*.py")): + if py_file.name == "__init__.py": + continue + try: + parser = _make_parser() + tree = parser.parse( + bytes(py_file.read_text(encoding="utf-8"), "utf-8") + ) + except (SyntaxError, UnicodeDecodeError): + continue + for node in _walk_node(tree.root_node): + if node.type == "function_definition": + name = _get_func_name(node) + if name and ( + not (name.startswith("__") and name.endswith("__")) + ): + functions[name] = { + "file": str(py_file.relative_to(source_dir.parent)), + "line": node.start_point[0] + 1, + "end_line": node.end_point[0] + 1, + } + return functions + + +def find_direct_test_calls( + test_dir: Path, target_funcs: set[str] +) -> tuple[set[str], dict[str, list[dict[str, Any]]]]: + """Scan test files for direct calls to any target function. + + Walks the Tree-sitter CST of every test_*.py file, tracking + the enclosing test-function scope, and records which test function + calls which target function directly, along with the test's file + and line-number range. + + Returns a tuple of: + - set of directly-called function names + - dict mapping each directly-called function to a list of test + detail dicts with keys test_name, test_file, + test_start_line, test_end_line + + """ + directly_called: set[str] = set() + func_to_test_details: dict[str, list[dict[str, Any]]] = {} + for py_file in sorted(test_dir.rglob("*.py")): + if not py_file.name.startswith("test_"): + continue + try: + parser = _make_parser() + tree = parser.parse( + bytes(py_file.read_text(encoding="utf-8"), "utf-8") + ) + except (SyntaxError, UnicodeDecodeError): + continue + + def _walk_scope( + node: Node, + current_test: str | None, + test_start: int | None, + test_end: int | None, + ) -> None: + for child in node.children: + if child.type == "function_definition": + test_name = _get_func_name(child) + if test_name and test_name.startswith("test_"): + _walk_scope( + child, + test_name, + child.start_point[0] + 1, + child.end_point[0] + 1, + ) + else: + _walk_scope(child, current_test, test_start, test_end) + elif child.type == "call" and current_test is not None: + for name in _get_call_names(child): + if name in target_funcs: + directly_called.add(name) + detail = { + "test_name": current_test, + "test_file": str(py_file), + "test_start_line": test_start, + "test_end_line": test_end, + } + if name not in func_to_test_details: + func_to_test_details[name] = [] + if detail not in func_to_test_details[name]: + func_to_test_details[name].append(detail) + _walk_scope(child, current_test, test_start, test_end) + else: + _walk_scope(child, current_test, test_start, test_end) + + _walk_scope(tree.root_node, None, None, None) + return directly_called, func_to_test_details + + +def build_call_graph( + source_dir: Path, target_funcs: set[str] +) -> dict[str, set[str]]: + """Build a call graph of which source functions call which others. + + Parses every source file and tracks which function body contains + each call node. Returns a dict mapping each caller to the set + of callees (functions in target_funcs) it invokes. + + """ + call_graph: dict[str, set[str]] = {f: set() for f in target_funcs} + for py_file in sorted(source_dir.rglob("*.py")): + if py_file.name == "__init__.py": + continue + try: + parser = _make_parser() + tree = parser.parse( + bytes(py_file.read_text(encoding="utf-8"), "utf-8") + ) + except (SyntaxError, UnicodeDecodeError): + continue + + def _walk_scope(node: Node, current_func: str | None) -> None: + for child in node.children: + if child.type == "function_definition": + func_name = _get_func_name(child) + if func_name and func_name in target_funcs: + _walk_scope(child, func_name) + else: + _walk_scope(child, current_func) + elif child.type == "call" and current_func is not None: + for name in _get_call_names(child): + if name in target_funcs and name != current_func: + call_graph[current_func].add(name) + _walk_scope(child, current_func) + else: + _walk_scope(child, current_func) + + _walk_scope(tree.root_node, None) + return call_graph + + +def compute_coverage_status( + all_functions: dict[str, dict[str, Any]], + directly_tested: set[str], + call_graph: dict[str, set[str]], +) -> dict[str, str]: + """Determine test status for every function. + + Returns a dict mapping each function name to one of: + - "direct" — called directly by at least one test + - "indirect" — not called directly, but reachable via the + call graph from a directly-tested function + - "none" — no test coverage (direct or indirect) + + """ + status: dict[str, str] = {} + for name in all_functions: + status[name] = "direct" if name in directly_tested else "unknown" + # breadth-first search through the call graph starting from directly-tested functions + queue = list(directly_tested) + while queue: + caller = queue.pop(0) + for callee in call_graph.get(caller, []): + if status[callee] == "unknown": + status[callee] = "indirect" + queue.append(callee) + # remaining unknown functions have no coverage at all + for name in all_functions: + if status[name] == "unknown": + status[name] = "none" + return status + + +def compute_indirect_paths( + call_graph: dict[str, set[str]], + directly_tested: set[str], + func_to_test_details: dict[str, list[dict[str, Any]]], + all_functions: dict[str, dict[str, Any]], +) -> dict[str, list[dict[str, Any]]]: + """Find every call chain from a test to each indirectly-tested function. + + For each directly-tested function, performs a BFS through the call + graph. Whenever a function not in *directly_tested* is reached, a + path entry is recorded showing which test invoked it, through + which chain of production-function calls, and the file/line + location of every step. + + Returns a dict mapping each indirectly-tested function to a list + of path entries, each with test and chain keys. Every + chain element contains name, file, start_line, and + end_line. + + """ + indirect_info: dict[str, list[dict[str, Any]]] = {} + for func in sorted(directly_tested): + for test_detail in func_to_test_details.get(func, []): + queue: list[tuple[str, list[str]]] = [(func, [func])] + visited: set[str] = {func} + while queue: + current, path = queue.pop(0) + for callee in sorted(call_graph.get(current, set())): + if callee not in visited and callee not in directly_tested: + new_path = [*path, callee] + if callee not in indirect_info: + indirect_info[callee] = [] + chain = [ + { + "name": fn, + "file": all_functions.get(fn, {}).get( + "file", "" + ), + "start_line": all_functions.get(fn, {}).get( + "line", 0 + ), + "end_line": all_functions.get(fn, {}).get( + "end_line", 0 + ), + } + for fn in new_path + ] + indirect_info[callee].append( + { + "test": { + "name": test_detail["test_name"], + "file": test_detail["test_file"], + "start_line": test_detail[ + "test_start_line" + ], + "end_line": test_detail["test_end_line"], + }, + "chain": chain, + } + ) + visited.add(callee) + queue.append((callee, new_path)) + return indirect_info + + +def classify_and_report( + all_functions: dict[str, dict[str, Any]], + directly_tested: set[str], + call_graph: dict[str, set[str]], + func_to_test_details: dict[str, list[dict[str, Any]]], +) -> dict[str, Any]: + """Build the coverage report.""" + coverage = compute_coverage_status( + all_functions, directly_tested, call_graph + ) + indirect_paths = compute_indirect_paths( + call_graph, + directly_tested, + func_to_test_details, + all_functions, + ) + report: dict[str, Any] = { + "functions": {}, + "summary": { + "total": 0, + "directly_tested": 0, + "indirectly_tested": 0, + "untested": 0, + }, + "indirectly_tested_list": [], + "directly_tested_list": [], + "untested_list": [], + } + for name, info in sorted(all_functions.items()): + entry: dict[str, Any] = { + **info, + "test_status": coverage[name], + "directly_tested": coverage[name] == "direct", + } + report["functions"][name] = entry + if coverage[name] == "direct": + test_details = func_to_test_details.get(name, []) + report["directly_tested_list"].append( + { + "name": name, + **info, + "direct_calls_by_tests": test_details, + } + ) + elif coverage[name] == "indirect": + paths = indirect_paths.get(name, []) + report["indirectly_tested_list"].append( + {"name": name, **info, "indirect_paths": paths} + ) + elif coverage[name] == "none": + report["untested_list"].append({"name": name, **info}) + s = report["summary"] + s["total"] = len(all_functions) + s["directly_tested"] = sum( + 1 for v in report["functions"].values() if v["directly_tested"] + ) + s["indirectly_tested"] = sum( + 1 + for v in report["functions"].values() + if v["test_status"] == "indirect" + ) + s["untested"] = sum( + 1 for v in report["functions"].values() if v["test_status"] == "none" + ) + return report + + +def print_summary(report: dict[str, Any]) -> None: + """Print a human-readable summary using rich formatting.""" + s = report["summary"] + table = Table( + title="Function Coverage Summary", + box=box.SIMPLE, + title_style=Style(bold=True), + header_style=Style(bold=True), + ) + table.add_column("Status", style="bold") + table.add_column("Count", justify="right") + table.add_column("Percent", justify="right") + total = s["total"] or 1 + table.add_row( + "Directly tested", + str(s["directly_tested"]), + f"{s['directly_tested'] / total * 100:.1f}%", + ) + table.add_row( + "Indirectly tested only", + str(s["indirectly_tested"]), + f"{s['indirectly_tested'] / total * 100:.1f}%", + ) + table.add_row( + "Untested", + str(s["untested"]), + f"{s['untested'] / total * 100:.1f}%", + ) + CONSOLE.print(table) + if report["indirectly_tested_list"]: + CONSOLE.print(Rule("Indirectly Tested Functions", style="yellow")) + CONSOLE.print() + for entry in report["indirectly_tested_list"]: + CONSOLE.print( + f" {entry['name']} ({entry['file']}:{entry['line']})" + ) + if report["untested_list"]: + CONSOLE.print() + CONSOLE.print(Rule("Not Tested Functions", style="red")) + CONSOLE.print() + for entry in report["untested_list"]: + CONSOLE.print( + f" {entry['name']} ({entry['file']}:{entry['line']})" + ) + + +def demo_api() -> list[str]: + """Demonstrate the tree-sitter-analyzer Python API and return lines.""" + lines: list[str] = [] + langs = get_supported_languages() + lines.append(f"tree-sitter-analyzer supports {len(langs)} languages.") + py_ext = "cellveyor/output/output.py" + detected = detect_language(py_ext) + lines.append(f" detect_language('{py_ext}') -> {detected}") + return lines + + +def main( # noqa: PLR0915 + threshold: int = typer.Option( + 100, + "--threshold", + "-t", + help="Minimum percentage of directly tested functions required.", + ), + output: Path = typer.Option( + "tsc.json", + "--output", + "-o", + help="Path for the JSON report file.", + ), + verbose: bool = typer.Option( + False, + "--verbose/--no-verbose", + help="Show detailed coverage analysis output.", + ), +) -> None: + """Run the coverage analysis and check against a direct-test threshold.""" + project_root = Path(__file__).resolve().parent.parent + source_dir = project_root / "cellveyor" + test_dir = project_root / "tests" + report_path = Path(output) + if not report_path.is_absolute(): + report_path = project_root / report_path + # analysis phase + analysis_lines: list[str] = [] + for line in demo_api(): + analysis_lines.append(line) + analysis_lines.append("") + analysis_lines.append( + "Extracting function definitions via Tree-sitter ..." + ) + all_functions = find_function_definitions(source_dir) + target_funcs = set(all_functions.keys()) + analysis_lines.append(f" Found {len(all_functions)} functions.") + analysis_lines.append("") + analysis_lines.append("Searching for direct calls in test files ...") + directly_tested, func_to_test_details = find_direct_test_calls( + test_dir, target_funcs + ) + analysis_lines.append( + f" Found {len(directly_tested)} directly-tested functions." + ) + analysis_lines.append("") + analysis_lines.append("Building internal call graph ...") + call_graph = build_call_graph(source_dir, target_funcs) + total_edges = sum(len(v) for v in call_graph.values()) + analysis_lines.append(f" Found {total_edges} internal call edges.") + analysis_lines.append("") + analysis_lines.append(f"Report written to {report_path}") + if verbose: + CONSOLE.print() + CONSOLE.print(Rule("Coverage Analysis", style="blue")) + CONSOLE.print() + for line in analysis_lines: + CONSOLE.print(line) + # build report + report = classify_and_report( + all_functions, + directly_tested, + call_graph, + func_to_test_details, + ) + report_path.write_text(json.dumps(report, indent=2), encoding="utf-8") + if verbose: + CONSOLE.print() + CONSOLE.print(Rule("Coverage Results", style="dim")) + CONSOLE.print() + print_summary(report) + CONSOLE.print() + # threshold check + s = report["summary"] + total = s["total"] + direct_count = s["directly_tested"] + pct = (direct_count / total * 100) if total > 0 else 100.0 + if pct < threshold: + if verbose: + CONSOLE.print() + CONSOLE.print(Rule("Failure", style="red")) + CONSOLE.print() + CONSOLE.print( + f"Only {pct:.1f}% of functions are directly tested " + f"(threshold: {threshold}%)." + ) + if not verbose: + for entry in report["indirectly_tested_list"]: + CONSOLE.print( + f" {entry['name']} ({entry['file']}:{entry['line']})" + ) + for entry in report["untested_list"]: + CONSOLE.print( + f" {entry['name']} ({entry['file']}:{entry['line']})" + ) + raise typer.Exit(code=1) + if verbose: + CONSOLE.print() + CONSOLE.print(Rule("Pass", style="green")) + CONSOLE.print( + f"All functions have sufficient direct test coverage " + f"({pct:.1f}% >= {threshold}%)." + ) + else: + CONSOLE.print( + f"[green]Success[/green]: All functions have sufficient direct test coverage " + f"({pct:.1f}% >= {threshold}%)." + ) + + +if __name__ == "__main__": + typer.run(main) diff --git a/scripts/vsc.py b/scripts/vsc.py new file mode 100644 index 0000000..ec7793b --- /dev/null +++ b/scripts/vsc.py @@ -0,0 +1,162 @@ +"""Check that the Cellveyor version in cellveyor/version.py matches pyproject.toml. + +Uses Tree-sitter to parse cellveyor/version.py into a Concrete Syntax +Tree to extract the CELLVEYOR_VERSION constant, and uses the toml library +to read the project version from pyproject.toml. The version lives in +version.py (not main.py) so that other modules (e.g. the remote hint +engine) can import it without creating a circular dependency. + +Run with: +uv run -m scripts.vsc check +uv run -m scripts.vsc fix +uv run task vsc +""" + +from pathlib import Path + +import toml +import tree_sitter_python as tspython +import typer +from rich.console import Console +from tree_sitter import Language, Node, Parser + +VERSION_VAR = "CELLVEYOR_VERSION" +VERSION_PATH = Path("cellveyor/version.py") +PY_LANGUAGE = Language(tspython.language()) + +console = Console(stderr=False) +err_console = Console(stderr=True) + +app = typer.Typer( + name="version-check", + help=( + "Check that the CELLVEYOR_VERSION in cellveyor/version.py" + " matches the project version in pyproject.toml." + ), +) + + +def _extract_version_from_main(main_path: Path, parser: Parser) -> str | None: + """Return the string assigned to CELLVEYOR_VERSION in main_path, or None.""" + source = main_path.read_bytes() + tree = parser.parse(source) + found: list[str] = [] + + def walk(node: Node) -> None: + MIN_CHILDREN = 3 + if ( + node.type == "assignment" + and len(node.children) >= MIN_CHILDREN + and node.children[0].type == "identifier" + and node.children[0].text is not None + and node.children[0].text.decode("utf-8") == VERSION_VAR + and node.children[2].type == "string" + and node.children[2].text is not None + ): + raw = node.children[2].text.decode("utf-8") + found.append(_unquote_string(raw)) + return + for child in node.children: + walk(child) + + walk(tree.root_node) + return found[0] if found else None + + +def _unquote_string(raw: str) -> str: + """Strip matching single or double quotes from a Python string literal.""" + MIN_ROWS = 2 + if len(raw) >= MIN_ROWS and raw[0] == raw[-1] and raw[0] in ("'", '"'): + return raw[1:-1] + return raw + + +def _extract_version_from_pyproject(pyproject_path: Path) -> str | None: + """Return the project version from pyproject.toml, or None if missing.""" + data = toml.loads(pyproject_path.read_text(encoding="utf-8")) + project = data.get("project", {}) + version = project.get("version") + return str(version) if version is not None else None + + +@app.command() +def check() -> None: + """Check that the versions in version.py and pyproject.toml match.""" + main_path = VERSION_PATH + pyproject_path = Path("pyproject.toml") + parser = Parser(PY_LANGUAGE) + main_version = _extract_version_from_main(main_path, parser) + pyproject_version = _extract_version_from_pyproject(pyproject_path) + if main_version is None: + err_console.print( + f"[red]Could not find {VERSION_VAR} in {main_path}[/red]" + ) + raise typer.Exit(code=1) + if pyproject_version is None: + err_console.print( + f"[red]Could not find project version in {pyproject_path}[/red]" + ) + raise typer.Exit(code=1) + if main_version == pyproject_version: + console.print(f"[green]Versions match:[/green] {main_version}") + raise typer.Exit(code=0) + err_console.print( + f"[red]Version mismatch:[/red] " + f"{VERSION_VAR}={main_version!r} in {main_path} " + f"vs version={pyproject_version!r} in {pyproject_path}" + ) + raise typer.Exit(code=1) + + +def _update_version_file(main_path: Path, new_version: str) -> bool: + """Update the CELLVEYOR_VERSION string in version.py. Return True if changed.""" + text = main_path.read_text(encoding="utf-8") + lines = text.splitlines(keepends=True) + changed = False + for index, line in enumerate(lines): + stripped = line.lstrip() + if stripped.startswith(f"{VERSION_VAR} ="): + prefix = line[: len(line) - len(stripped)] + lines[index] = f'{prefix}{VERSION_VAR} = "{new_version}"\n' + changed = True + break + if changed: + main_path.write_text("".join(lines), encoding="utf-8") + return changed + + +@app.command() +def fix() -> None: + """Update version.py so CELLVEYOR_VERSION matches the pyproject.toml version.""" + main_path = VERSION_PATH + pyproject_path = Path("pyproject.toml") + pyproject_version = _extract_version_from_pyproject(pyproject_path) + if pyproject_version is None: + err_console.print( + f"[red]Could not find project version in {pyproject_path}[/red]" + ) + raise typer.Exit(code=1) + parser = Parser(PY_LANGUAGE) + main_version = _extract_version_from_main(main_path, parser) + if main_version == pyproject_version: + console.print(f"[green]Versions already match:[/green] {main_version}") + raise typer.Exit(code=0) + if main_version is None: + err_console.print( + f"[red]Could not find {VERSION_VAR} in {main_path}[/red]" + ) + raise typer.Exit(code=1) + if _update_version_file(main_path, pyproject_version): + console.print( + f"[green]Updated[/green] {VERSION_VAR} in {main_path} " + f"from {main_version!r} to {pyproject_version!r}" + ) + raise typer.Exit(code=0) + err_console.print( + f"[red]Could not update {VERSION_VAR} in {main_path}[/red]" + ) + raise typer.Exit(code=1) + + +if __name__ == "__main__": + app() diff --git a/tests/__init__.py b/tests/__init__.py index e69de29..46816dd 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -0,0 +1 @@ +"""Tests package.""" diff --git a/tests/test_data.py b/tests/test_data.py index af7eb1e..5609bc4 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -1,4 +1,4 @@ -"""Pytest test suite for the filesystem module.""" +"""Pytest test suite for the data module.""" from pathlib import Path @@ -6,6 +6,7 @@ def test_access_dataframes() -> None: + """Test that access_dataframes returns different results for different files.""" spreadsheet_file_one = Path("spreadsheets/fake_spreadsheet.xlsx") spreadsheet_file_two = Path("spreadsheets/example_spreadsheet.xlsx") test_one = data.access_dataframes(spreadsheet_file_one) @@ -14,7 +15,7 @@ def test_access_dataframes() -> None: def test_key_attribute_column_filter() -> None: - # test key_attribute_column_filter function + """Test key_attribute_column_filter function.""" dataframes_dict = data.access_dataframes( Path("spreadsheets/fake_spreadsheet.xlsx") ) diff --git a/uv.lock b/uv.lock index aa91529..1e117d3 100644 --- a/uv.lock +++ b/uv.lock @@ -6,6 +6,105 @@ resolution-markers = [ "python_full_version < '3.12'", ] +[[package]] +name = "aiohappyeyeballs" +version = "2.7.1" +source = { registry = "https://pypi.org/simple" } +sdist = { url = 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Kapfhammer" Date: Sun, 23 Aug 2026 16:27:57 -0400 Subject: [PATCH 12/50] feat: Add the cellveyor/version.py file to make it easy to internally track the version number. --- cellveyor/version.py | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 cellveyor/version.py diff --git a/cellveyor/version.py b/cellveyor/version.py new file mode 100644 index 0000000..63ba5bb --- /dev/null +++ b/cellveyor/version.py @@ -0,0 +1,8 @@ +"""Single source of truth for the cellveyor version number. + +This module exists so that both cellveyor.main and other modules can import +the version without creating a circular dependency. The value must always +match the version in pyproject.toml. +""" + +CELLVEYOR_VERSION = "0.1.0" From 54b264298354fcb6cbbea953b4ab664a5304e1c8 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:28:22 -0400 Subject: [PATCH 13/50] test: Add a conftest.py file and then improve the test suite by adding more test cases. --- tests/conftest.py | 79 +++++++++ tests/test_constants.py | 33 ++++ tests/test_main.py | 378 ++++++++++++++++++++++++++++++++++++++++ tests/test_report.py | 181 +++++++++++++++++++ tests/test_transfer.py | 145 +++++++++++++++ tests/test_version.py | 20 +++ 6 files changed, 836 insertions(+) create mode 100644 tests/conftest.py create mode 100644 tests/test_constants.py create mode 100644 tests/test_main.py create mode 100644 tests/test_report.py create mode 100644 tests/test_transfer.py create mode 100644 tests/test_version.py diff --git a/tests/conftest.py b/tests/conftest.py new file mode 100644 index 0000000..8a16048 --- /dev/null +++ b/tests/conftest.py @@ -0,0 +1,79 @@ +"""Pytest fixtures for Cellveyor. + +This module provides an autouse fixture that wraps and extracts console +output so that Rich-based diagnostics do not appear during test runs. +The output still appears when the program is run normally via +``uv run cellveyor ...``. +""" + +import gc +import io +import subprocess +import sys +from typing import Any + +import pytest + +# disable garbage collector to avoid intermittent segfaults with hypothesis +gc.disable() + + +@pytest.fixture(autouse=True) +def wrap_console_output(monkeypatch: pytest.MonkeyPatch) -> None: + """Wrap console output so tests remain quiet. + + This fixture captures all writes to ``sys.stdout`` and ``sys.stderr`` + into an in-memory buffer, preventing Rich ``Console`` output (which + writes to those streams) from appearing during ``uv run task test-coverage``. + The program's output is still extracted and can be inspected via + ``result.output`` when using ``typer.testing.CliRunner``. + + It also quiets ``typer.echo`` and ``subprocess.run`` to avoid + extraneous output, mirroring best practices from GatorGrade. + """ + captured_buffer = io.StringIO() + + class QuietStream: + """A stream that captures output silently.""" + + def __init__(self, original: Any, buffer: io.StringIO) -> None: + self.original = original + self.buffer = buffer + + def write(self, text: str) -> int: + self.buffer.write(text) + return len(text) + + def flush(self) -> None: + pass + + def isatty(self) -> bool: + return False + + def __getattr__(self, name: str) -> Any: + return getattr(self.original, name) + + monkeypatch.setattr( + sys, "stdout", QuietStream(sys.stdout, captured_buffer) + ) + monkeypatch.setattr( + sys, "stderr", QuietStream(sys.stderr, captured_buffer) + ) + + import typer # noqa: PLC0415 + + def quiet_echo(_message: Any = None, **_kwargs: Any) -> None: + pass + + monkeypatch.setattr(typer, "echo", quiet_echo) + + original_run = subprocess.run + + def quiet_run(*args: Any, **kwargs: Any) -> Any: + if "stdout" not in kwargs: + kwargs["stdout"] = subprocess.PIPE + if "stderr" not in kwargs: + kwargs["stderr"] = subprocess.PIPE + return original_run(*args, **kwargs) + + monkeypatch.setattr(subprocess, "run", quiet_run) diff --git a/tests/test_constants.py b/tests/test_constants.py new file mode 100644 index 0000000..3bd696a --- /dev/null +++ b/tests/test_constants.py @@ -0,0 +1,33 @@ +"""Pytest test suite for the constants module.""" + +from cellveyor import constants + + +def test_humanreadable_constants() -> None: + """Test Humanreadable constants have expected values.""" + assert constants.humanreadable.Yes == "Yes" + assert constants.humanreadable.No == "No" + + +def test_markers_constants() -> None: + """Test Markers constants have expected values.""" + assert constants.markers.Indent == " " + assert constants.markers.Newline == "\n" + + +def test_humanreadable_frozen() -> None: + """Test Humanreadable dataclass is frozen.""" + try: + constants.humanreadable.Yes = "No" # type: ignore + assert False, "should have raised" + except AttributeError: + assert True + + +def test_markers_frozen() -> None: + """Test Markers dataclass is frozen.""" + try: + constants.markers.Indent = " " # type: ignore + assert False, "should have raised" + except AttributeError: + assert True diff --git a/tests/test_main.py b/tests/test_main.py new file mode 100644 index 0000000..7631d4c --- /dev/null +++ b/tests/test_main.py @@ -0,0 +1,378 @@ +"""Pytest test suite for the main module.""" + +import pathlib +import re +from unittest.mock import patch + +from typer.testing import CliRunner + +from cellveyor import main + + +def _strip_ansi(text: str) -> str: + """Strip ANSI escape codes for robust output checking.""" + return re.sub(r"\x1b\[[0-9;]*m", "", text) + + +def test_display_reports() -> None: + """Test display_reports does not crash.""" + reports = {"alice": "**Hello @alice!**\n\n- **Grade**: 90\n"} + main.display_reports(reports) + main.display_reports({}) + + +def test_print_dash_list() -> None: + """Test _print_dash_list does not crash.""" + main._print_dash_list("Available sheets", ["Main", "TP"], color="red") + main._print_dash_list("Available columns", [], color="yellow") + main._print_dash_list("Title", ["a\nb", "c\r d"], color="red") + + +def test_transport_valid(tmp_path: pathlib.Path) -> None: + """Test transport with valid spreadsheet.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--feedback-file", + "spreadsheets/feedback.yml", + ], + ) + assert result.exit_code == 0 + assert "gkapfham" in _strip_ansi( + result.output + ) or "Accessing" in _strip_ansi(result.output) + + +def test_transport_missing_file() -> None: + """Test transport with missing file exits 1.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "/tmp", + "--spreadsheet-file", + "NOTEXIST.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Unable to access" in _strip_ansi(result.output) + + +def test_transport_missing_directory() -> None: + """Test transport with missing directory exits 1.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "/tmp/not_a_dir_xyz_123", + "--spreadsheet-file", + "fake.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Directory not found" in _strip_ansi(result.output) + + +def test_transport_wrong_sheet() -> None: + """Test transport with wrong sheet exits 1.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "NOTASHEET", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Sheet 'NOTASHEET' not found" in _strip_ansi(result.output) + assert "Available sheets:" in _strip_ansi(result.output) + + +def test_transport_wrong_key_attribute() -> None: + """Test transport with wrong key attribute exits 1.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "NONEXISTENT", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Key attribute" in _strip_ansi(result.output) + assert "Available columns:" in _strip_ansi(result.output) + + +def test_transport_no_columns_matched() -> None: + """Test transport with no columns matched warns but does not crash.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^NONEXISTENT.*$", + "--feedback-regexp", + "NOTMATCH", + "--feedback-file", + "spreadsheets/feedback.yml", + ], + ) + assert result.exit_code == 0 + assert "No columns matched" in _strip_ansi(result.output) + assert "Available columns:" in _strip_ansi(result.output) + + +def test_transport_invalid_regex() -> None: + """Test transport with invalid regex exits 1.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "[unclosed", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + + +def test_transport_missing_github_args() -> None: + """Test transport with --transfer-report but missing github args exits 1.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--transfer-report", + ], + ) + assert result.exit_code == 1 + assert "Missing required GitHub" in _strip_ansi(result.output) + + +def test_transport_with_feedback_missing_file() -> None: + """Test transport with missing feedback file warns.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--feedback-file", + "/tmp/notexist.yml", + ], + ) + assert result.exit_code == 0 + assert "Feedback file(s) not found" in _strip_ansi(result.output) + + +def test_transport_with_key_value_filter() -> None: + """Test transport with --key-value filter.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--key-value", + "gkapfham", + ], + ) + assert result.exit_code == 0 + + +def test_transport_no_reports_generated(tmp_path: pathlib.Path) -> None: + """Test transport when filter yields no rows warns.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--key-value", + "nonexistent_user_xyz", + ], + ) + # should warn about no reports or no rows + assert result.exit_code == 0 + assert ( + "No reports generated" in _strip_ansi(result.output) + or "No rows found" in _strip_ansi(result.output) + or "gkapfham" not in _strip_ansi(result.output) + ) + + +def test_transport_with_transfer_mock() -> None: + """Test transport with mocked GitHub transfer.""" + runner = CliRunner() + with patch("cellveyor.main.transfer.transfer_reports_to_github") as mock: + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--github-token", + "fake", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + ) + assert result.exit_code == 0 + mock.assert_called_once() + + +def test_transport_transfer_failure() -> None: + """Test transport handles transfer failure.""" + runner = CliRunner() + with patch( + "cellveyor.main.transfer.transfer_reports_to_github", + side_effect=Exception("fail"), + ): + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--github-token", + "fake", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + ) + assert result.exit_code == 1 + assert "GitHub transfer failed" in _strip_ansi(result.output) diff --git a/tests/test_report.py b/tests/test_report.py new file mode 100644 index 0000000..950b134 --- /dev/null +++ b/tests/test_report.py @@ -0,0 +1,181 @@ +"""Pytest test suite for the report module.""" + +import pandas +from hypothesis import given, strategies + +from cellveyor import report + + +def test_add_feedback_if_exists_found() -> None: + """Test add_feedback_if_exists when key exists.""" + feedback = {"hello": "world"} + result = report.add_feedback_if_exists("start-", feedback, "hello") + assert "world" in result + + +def test_add_feedback_if_exists_not_found() -> None: + """Test add_feedback_if_exists when key not found.""" + feedback: dict[str, str] = {} + result = report.add_feedback_if_exists("start-", feedback, "missing") + assert result == "start-" + + +def test_add_feedback_if_exists_list() -> None: + """Test add_feedback_if_exists with make_list True.""" + feedback = {"key": "value"} + result = report.add_feedback_if_exists( + "start", feedback, "key", make_list=True + ) + assert "- value" in result + + +def test_add_feedback_if_exists_non_string() -> None: + """Test add_feedback_if_exists with non-string value.""" + feedback = {"key": ["a", "b"]} + result = report.add_feedback_if_exists("", feedback, "key") + assert "a" in result + + +def test_create_feedback_list_normal() -> None: + """Test create_feedback_list with normal input.""" + result = report.create_feedback_list("a, b, c") + assert result == ["a", "b", "c"] + + +def test_create_feedback_list_with_nan() -> None: + """Test create_feedback_list filters nan.""" + result = report.create_feedback_list("a, nan, b") + assert "nan" not in result + assert "a" in result + assert "b" in result + + +def test_create_feedback_list_empty() -> None: + """Test create_feedback_list with empty string.""" + result = report.create_feedback_list("") + assert result in ([""], []) + + +def test_create_feedback_list_single() -> None: + """Test create_feedback_list with single value.""" + result = report.create_feedback_list("congratulations") + assert result == ["congratulations"] + + +def test_create_per_key_report_basic() -> None: + """Test create_per_key_report with basic dataframe.""" + df = pandas.DataFrame( + { + "Student GitHub": ["alice", "bob"], + "Grade": [90, 80], + "Feedback": ["good, great", "needs work"], + } + ) + selected = df[["Grade", "Feedback"]] + result_df = df[["Student GitHub", "Grade", "Feedback"]] + feedback_dict = { + "header": "Header\n", + "footer": "Footer\n", + "good": "Good job!", + "great": "Great!", + } + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "Feedback", feedback_dict + ) + assert "alice" in reports + assert "bob" in reports + assert "Header" in reports["alice"] or "header" not in reports["alice"] + + +def test_create_per_key_report_empty_feedback_regexp() -> None: + """Test create_per_key_report when feedback regexp matches nothing.""" + df = pandas.DataFrame( + { + "Student GitHub": ["alice"], + "Grade": [90], + } + ) + selected = df[["Grade"]] + result_df = df[["Student GitHub", "Grade"]] + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "NOTMATCH", {} + ) + assert "alice" in reports + assert "alice" in reports + + +def test_create_per_key_report_with_nan_key() -> None: + """Test create_per_key_report skips nan keys.""" + # ensure string nan is treated, but also test with actual NaN + df2 = pandas.DataFrame( + { + "Student GitHub": ["alice", float("nan")], + "Grade": [90, 80], + } + ) + selected = df2[["Grade"]] + result_df = df2[["Student GitHub", "Grade"]] + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "Grade", {} + ) + # nan key should be skipped + assert "nan" not in reports or "alice" in reports + + +def test_create_per_key_report_footer_list() -> None: + """Test create_per_key_report handles list footer.""" + df = pandas.DataFrame( + { + "Student GitHub": ["alice"], + "Grade": [90], + } + ) + selected = df[["Grade"]] + result_df = df[["Student GitHub", "Grade"]] + feedback_dict = {"footer": ["not a string"]} + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "NOTMATCH", feedback_dict + ) + assert "alice" in reports + + +def test_create_per_key_report_no_footer() -> None: + """Test create_per_key_report without footer.""" + df = pandas.DataFrame( + { + "Student GitHub": ["alice"], + "Grade": [90], + } + ) + selected = df[["Grade"]] + result_df = df[["Student GitHub", "Grade"]] + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "NOTMATCH", {} + ) + assert "alice" in reports + + +def test_create_per_key_report_effective_feedback() -> None: + """Test that feedback section only shows when key exists.""" + df = pandas.DataFrame( + { + "Student GitHub": ["alice"], + "Grade": [90], + "Feedback": ["missing_key"], + } + ) + selected = df[["Grade", "Feedback"]] + result_df = df[["Student GitHub", "Grade", "Feedback"]] + # feedback_dict does not contain missing_key + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "Feedback", {} + ) + # should not contain feedback label if no effective keys + assert "Here is some additional feedback" not in reports["alice"] + + +@given(text=strategies.text(max_size=20)) +def test_fuzz_create_feedback_list(text: str) -> None: + """Fuzz test create_feedback_list does not crash.""" + result = report.create_feedback_list(text) + assert isinstance(result, list) diff --git a/tests/test_transfer.py b/tests/test_transfer.py new file mode 100644 index 0000000..fa48ea9 --- /dev/null +++ b/tests/test_transfer.py @@ -0,0 +1,145 @@ +"""Pytest test suite for the transfer module.""" + +from unittest.mock import MagicMock, patch + +import pytest + +from cellveyor import transfer + + +def test_create_fully_qualified_github_repository() -> None: + """Test repository name creation.""" + result = transfer.create_fully_qualified_github_repository( + "org", "prefix", "user" + ) + assert result == "org/prefix-user" + + +def test_create_fully_qualified_github_repository_with_dash() -> None: + """Test repository name creation with special characters.""" + result = transfer.create_fully_qualified_github_repository( + "Allegheny-Computer-Science-580-S2026", + "junior-seminar-course-assessment", + "gkapfham", + ) + assert ( + result + == "Allegheny-Computer-Science-580-S2026/junior-seminar-course-assessment-gkapfham" + ) + + +def test_transfer_reports_to_github_missing_token() -> None: + """Test transfer_reports_to_github with missing token returns early.""" + transfer.transfer_reports_to_github( + "", "org", "prefix", {"user": "report"} + ) + transfer.transfer_reports_to_github( + None, # type: ignore + "org", + "prefix", + {"user": "report"}, + ) + + +def test_transfer_reports_to_github_missing_org() -> None: + """Test transfer with missing organization.""" + transfer.transfer_reports_to_github( + "token", "", "prefix", {"user": "report"} + ) + transfer.transfer_reports_to_github( + "token", + None, # type: ignore + "prefix", + {"user": "report"}, + ) + + +def test_transfer_reports_to_github_missing_prefix() -> None: + """Test transfer with missing prefix.""" + transfer.transfer_reports_to_github("token", "org", "", {"user": "report"}) + + +def test_transfer_reports_to_github_empty_dict() -> None: + """Test transfer with empty reports dict.""" + transfer.transfer_reports_to_github("token", "org", "prefix", {}) + + +def test_transfer_reports_to_github_success() -> None: + """Test successful transfer with mocked GitHub.""" + with patch("cellveyor.transfer.Github") as mock_github: + mock_repo = MagicMock() + mock_pull = MagicMock() + mock_github.return_value.get_repo.return_value = mock_repo + mock_repo.get_pull.return_value = mock_pull + + transfer.transfer_reports_to_github( + "fake_token", "org", "prefix", {"alice": "report content"} + ) + + mock_github.return_value.get_repo.assert_called_once_with( + "org/prefix-alice" + ) + mock_pull.create_issue_comment.assert_called_once_with( + "report content" + ) + + +def test_transfer_reports_to_github_handles_exception() -> None: + """Test transfer handles GithubException per repo.""" + with patch("cellveyor.transfer.Github") as mock_github: + mock_github.return_value.get_repo.side_effect = Exception( + "repo not found" + ) + + # should not raise, should handle exception and continue + transfer.transfer_reports_to_github( + "fake_token", "org", "prefix", {"alice": "report"} + ) + + +def test_transfer_report_to_github_success() -> None: + """Test transfer_report_to_github success with mock.""" + with ( + patch("cellveyor.transfer.Github") as mock_github, + patch("cellveyor.transfer.Auth"), + ): + mock_repo = MagicMock() + mock_pull = MagicMock() + mock_github.return_value.get_repo.return_value = mock_repo + mock_repo.get_pull.return_value = mock_pull + + transfer.transfer_report_to_github( + "token", "org/prefix-user", "report" + ) + mock_pull.create_issue_comment.assert_called_once_with("report") + + +def test_transfer_report_to_github_invalid_token() -> None: + """Test transfer_report_to_github with invalid token raises.""" + with pytest.raises(ValueError): + transfer.transfer_report_to_github("", "org/prefix-user", "report") + with pytest.raises(ValueError): + transfer.transfer_report_to_github(None, "org/prefix-user", "report") # type: ignore + + +def test_transfer_report_to_github_invalid_repo() -> None: + """Test transfer_report_to_github with invalid repo raises.""" + with pytest.raises(ValueError): + transfer.transfer_report_to_github("token", "", "report") + with pytest.raises(ValueError): + transfer.transfer_report_to_github("token", None, "report") # type: ignore + + +def test_transfer_report_to_github_handles_generic_exception() -> None: + """Test transfer_report_to_github wraps generic exceptions.""" + with ( + patch("cellveyor.transfer.Github") as mock_github, + patch("cellveyor.transfer.Auth"), + ): + mock_github.return_value.get_repo.side_effect = RuntimeError( + "unexpected" + ) + with pytest.raises(Exception): + transfer.transfer_report_to_github( + "token", "org/prefix-user", "report" + ) diff --git a/tests/test_version.py b/tests/test_version.py new file mode 100644 index 0000000..793bb06 --- /dev/null +++ b/tests/test_version.py @@ -0,0 +1,20 @@ +"""Pytest test suite for the version module.""" + +import toml + +from cellveyor import version + + +def test_version_exists() -> None: + """Test that version constant exists and is a string.""" + assert hasattr(version, "CELLVEYOR_VERSION") + assert isinstance(version.CELLVEYOR_VERSION, str) + assert version.CELLVEYOR_VERSION == "0.1.0" + + +def test_version_matches_pyproject() -> None: + """Test that version matches pyproject.toml.""" + with open("pyproject.toml", encoding="utf-8") as f: + data = toml.load(f) + pyproject_version = data["project"]["version"] + assert version.CELLVEYOR_VERSION == pyproject_version From 9f10a096b65d3a460781541ab50b2d699cc37a98 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:46:05 -0400 Subject: [PATCH 14/50] docs: Update the README.md file with more details about how to run each sub-command, including examples. --- README.md | 363 ++++++++++++++++++++++++++++++++++++++++++++++-------- 1 file changed, 315 insertions(+), 48 deletions(-) diff --git a/README.md b/README.md index eae395c..ac01b3e 100644 --- a/README.md +++ b/README.md @@ -8,65 +8,332 @@ [![Maintenance](https://img.shields.io/badge/Maintained%3F-Yes-blue.svg)](https://github.com/gkapfham/chasten/graphs/commit-activity) [![License LGPL v3](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0) -## Example Command +## Overview + +Cellveyor is a command-line tool that automatically turns the cells of a +spreadsheet into per-student grade reports. You point Cellveyor at a +gradebook spreadsheet, describe which columns hold grades and which hold +feedback, and it creates one markdown report per student — displayed directly +in the terminal or, with the `--transfer-report` option, posted as a comment +on the student's GitHub pull request. + +Cellveyor is designed for the gradebook spreadsheets used in GitHub +Classroom-based courses. The spreadsheet follows a fixed shape: each row is +one student, each column is one assignment grade or one piece of feedback, +and a "key attribute" column (normally the student's GitHub username) +identifies the owner of each row. Cellveyor reads that sheet, filters it +down to the columns you ask for, and produces a report for every row whose +key is not empty. + +No setup beyond a spreadsheet is required when you only want reports in the +terminal. Sending reports to GitHub additionally needs a GitHub token, the +name of the GitHub organization that stores the repositories, and the prefix +shared by those repositories. + +## Requirements + +- Python `>= 3.11, < 3.14` +- `uv` (see the [uv documentation](https://docs.astral.sh/uv/) for installation) +- A local spreadsheet in XLSX format (e.g., an exported Google Sheet) + +## Installation + +Clone the repository and run the tool with `uv`: + +```bash +git clone git@github.com:GatorEducator/cellveyor.git +cd cellveyor +uv run cellveyor --help +``` + +The first `uv run` command resolves the dependencies and creates the project +environment; subsequent commands start instantly. + +## Usage + +Cellveyor exposes a single command, `transport`. It is the default command, +so there is no sub-command to type: all options are given directly after +`cellveyor`. + +```bash +uv run cellveyor +``` + +### `transport` — Generate per-student grade reports + +```bash +uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name Main \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Summary Grade|Final Grade) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" +``` + +The command reads the requested sheet from the spreadsheet, keeps the key +attribute column plus every column whose name matches `--column-regexp`, and +then creates one markdown report per remaining row. Rows that are completely +empty are dropped by the column filter, and a row whose key attribute is +empty never produces a report. Each report is displayed inside a rich panel, +titled with the student's key value. + +**Required options:** + +| Flag | Description | +|---|---| +| `--spreadsheet-directory` / `-d` | Directory that contains the spreadsheet file | +| `--spreadsheet-file` / `-s` | Spreadsheet file inside the directory | +| `--sheet-name` / `-n` | Name of the sheet inside the spreadsheet to read | +| `--key-attribute` / `-a` | Column that identifies each row (normally the GitHub username) | +| `--column-regexp` / `-c` | Regular expression that selects the grade columns of the sheet | +| `--feedback-regexp` / `-r` | Regular expression that selects the feedback columns of the sheet | + +**Optional options:** + +| Flag | Description | Default | +|---|---|---| +| `--key-value` / `-v` | Only produce a report for this value of the key attribute | all rows | +| `--feedback-file` / `-f` | Feedback file(s) in YAML format (repeatable) | none | +| `--github-token` / `-g` | GitHub authorization token for `--transfer-report` | none | +| `--github-organization` / `-o` | GitHub organization that stores the destination repositories | none | +| `--github-repository-prefix` / `-p` | Prefix shared by the destination repositories | none | +| `--transfer-report` | Post each report as a comment on the student's GitHub pull request | off | + +**Examples:** + +```bash +# Reports for every student row in the Main sheet +uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name Main \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Summary Grade|Final Grade) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" + +# Only the report for one student +uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name Main \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Summary Grade|Final Grade) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" \ + --key-value gkapfham + +# Reports for one sheet, with feedback files added to every report +uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name EXE \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Executable Examination|Summary Grade) .*$" \ + --feedback-regexp "Feedback$" \ + --feedback-file spreadsheets/feedback.yml + +# Reports posted to each student's GitHub pull request +uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name Main \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Summary Grade|Final Grade) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" \ + --github-token \ + --github-organization \ + --github-repository-prefix \ + --transfer-report +``` + +**Column filtering.** `--column-regexp` uses `pandas` regex filtering +(`re.search` semantics on the column names), so `^(Summary Grade|Final +Grade) .*$` selects every column that starts with "Summary Grade" or +"Final Grade". The key attribute column is always kept regardless of the +regular expression. If the regular expression matches no columns, or the +filter leaves no rows, Cellveyor prints a yellow warning and continues +(exit code `0`). An invalid regular expression stops the command with exit +code `1`. + +**Feedback columns.** Columns matched by `--feedback-regexp` are removed +from the summary bullet list and treated as feedback instead. For each row, +the first matching feedback column is read as a comma-separated list of +feedback keys; each key that also exists in a `--feedback-file` becomes one +bullet under "Here is some additional feedback for you to consider". If +none of the comma-separated keys resolve to a feedback file entry, the +feedback section is omitted. See [Feedback files](#feedback-files). + +**Errors.** Cellveyor validates its inputs before doing any work, printing a +specific diagnostic and exiting with code `1` when: + +- the spreadsheet directory or file does not exist (it prints which one is missing), +- the requested sheet is not in the spreadsheet (it lists the available sheets), +- the key attribute column is not in the sheet (it lists the available columns), +- `--transfer-report` is given without `--github-token`, `--github-organization`, or `--github-repository-prefix` (it lists the missing options), +- reading the spreadsheet or transferring reports to GitHub fails. + +Missing or malformed feedback files are skipped with a yellow warning +instead of stopping the command. + +## Report format + +Every report is markdown that can be displayed in the terminal or rendered +anywhere that markdown is understood, such as a GitHub pull request comment. +A report built from the `Main` sheet looks like this when displayed in the +terminal: ```text -uv run cellveyor --spreadsheet-directory \ -/home/gkapfham/working/data/gradebook/2023 --spreadsheet-file -CMPSC-203-Fall-2023-Gradebook.xlsx \ ---sheet-name Main \ ---key-attribute "Student GitHub" \ ---key-value "gkapfham" \ ---column-regexp "^(Summary Grade|Final Grade) .*$" \ ---feedback-regexp "Summary Grade 1 - Feedback" \ ---feedback-file /home/gkapfham/working/teaching/ -github-classroom/feedback/all/feedback.yml \ ---feedback-file /home/gkapfham/working/teaching/github-classroom/feedback/ -developer-development/feedback-overall-course-assessment.yml \ ---github-token \ ---github-organization Allegheny-Computer-Science-203-F2023 \ ---github-repository-prefix computer-science-203-fall-2023-course-assessment \ ---transfer-report +🚚 Accessing: spreadsheets/fake_spreadsheet.xlsx + +╭────────────────────────────────── gkapfham ──────────────────────────────────╮ +│ Hello @gkapfham! │ +│ │ +│ 📔 Here are your summary scores: │ +│ │ +│ • Summary Grade for Team Participation: 0.49 │ +│ • Summary Grade for In-Person Assessment: 0.3916666667 │ +│ • Summary Grade for Executable Midterms: 0.88 │ +│ • Summary Grade for Executable Final: 1.0 │ +│ • Summary Grade for Professional Development: 0.6688888889 │ +│ • Summary Grade for Technical Development: 0.4111111111 │ +│ • Summary Grade for Project Development: 0.82 │ +│ • Final Grade - Percentage: 0.7220833333 │ +│ • Final Grade - Letter: C- │ +│ │ +│ [{'type': 'markdown', 'attributes': None, 'value': 'This is a footer'}] │ +╰──────────────────────────────────────────────────────────────────────────────╯ +``` + +The same report as plain markdown (this is the text that is posted to +GitHub when `--transfer-report` is enabled): + +```markdown +**Hello @gkapfham!** + +**📔 Here are your summary scores:** + +- **Summary Grade for Team Participation**: 0.49 +- **Summary Grade for In-Person Assessment**: 0.3916666667 +- **Summary Grade for Executable Midterms**: 0.88 +- **Summary Grade for Executable Final**: 1.0 +- **Summary Grade for Professional Development**: 0.6688888889 +- **Summary Grade for Technical Development**: 0.4111111111 +- **Summary Grade for Project Development**: 0.82 +- **Final Grade - Percentage**: 0.7220833333 +- **Final Grade - Letter**: C- + +[{'type': 'markdown', 'attributes': None, 'value': 'This is a footer'}] ``` -## 🎉 Introduction +The structure of each report is fixed: + +1. **Greeting** — `**Hello @!**`, where the key value is the + student's value in the key attribute column (normally the GitHub + username). +2. **Header** — the value of the `header` key in the feedback files, when + present. +3. **Summary scores** — one bullet per selected grade column, rendered as + `- ****: ` in the sheet's column order. +4. **Additional feedback** — one bullet per resolved feedback key, only when + at least one key in the row's feedback column exists in the feedback + files. +5. **Footer** — the value of the `footer` key in the feedback files, when + present. + +The header and footer are expected to be strings. Non-string values (like the +list of markup objects in `spreadsheets/feedback.yml`) are converted to their +string representation, which is why that footer appears as +`[{'type': 'markdown', 'attributes': None, 'value': 'This is a footer'}]` in +the sample output. + +## Feedback files + +Feedback files are YAML dictionaries that supply the header, the footer, and +the text behind each feedback key. (The `--help` text still says "JSON", but +the files are parsed as YAML.) A feedback file with all three kinds of +content looks like this: + +```yaml +header: "This is a header" +footer: "This is a footer" +congratulations: "Fantastic work on this assignment!" +needsimprovement: "Please review the feedback and then try again." +buildfailure: "Your repository does not currently build correctly." +``` + +The keys `header` and `footer` have fixed meanings and are placed at the +top and bottom of every report. Every other key is a feedback key: it is +used when a row's feedback column contains that key in its comma-separated +list. For example, a feedback column cell containing +`congratulations, needsimprovement` adds both of those bullets to that +student's report. Keys that appear in the spreadsheet but not in any +feedback file are silently ignored. + +Pass multiple files with repeated options; the dictionaries are merged in +order, so a later file overrides an earlier file on key conflicts: + +```bash +uv run cellveyor ... \ + --feedback-file feedback/all.yml \ + --feedback-file feedback/project-development.yml +``` + +This is useful when the same spreadsheet powers different kinds of reports +and different feedback files are relevant for different sheets. + +## GitHub transfer + +With `--transfer-report`, Cellveyor posts each generated report to GitHub +instead of only displaying it. The destination repository for a student is +derived from the key value using the GitHub Classroom naming convention: + +```text +/- +``` + +For example, a student with GitHub username `gkapfham` in the organization +`Allegheny-Computer-Science-203-F2023` with the prefix +`computer-science-203-fall-2023-course-assessment` receives the report in: + +```text +Allegheny-Computer-Science-203-F2023/computer-science-203-fall-2023-course-assessment-gkapfham +``` -- Cellveyor is a python program that produces assignment reports for students or -classes. Using Cellveyor will publicly give grade reports including feedback for -created assignments. Using the Cellveyor tool will quickly run and send reports to -members included in a locally created google spreadsheet. By running the command -created, this will quickly and automatically send out these reports in a very timely -and efficient fashion. +Each report is posted as an issue comment on pull request number 1 of that +repository — the pull request that GitHub Classroom opens for every student +repository. The transfer runs with a progress bar that shows the elapsed and +remaining time; a green checkmark marks a successful transfer and a red +cross marks a failed one. Failures (for example, a repository that does not +exist) print the error details and are skipped, and the transfer continues +with the remaining reports. -## 😂 Definitions +To transfer reports you must supply all three GitHub options. Reports are +generated first and displayed before any transfer begins, so you can verify +the reports in the terminal before the command starts uploading them. -- Cellveyor is a tool that automatically produces a report based output by -analyzing a Google sheet - - Student sentence: "I'm glad Cellveyor made it easy for me to see my grades - from my classes, it's so easy to read and analyze." - - Instructor sentence: "Cellveyor makes it much easier for me to tell my - students what their grade looks like on a certain assignment or overall - in the class" - - Researchers sentence: "I found that Cellveyor is a very interesting tool that - quickly and automatically does a task that is necessary in schooling" +## Exit codes -## 🔋Features +| Code | Meaning | +|---|---| +| `0` | Success, including runs that only emitted warnings (e.g., no columns matched, no rows found, malformed feedback files skipped) | +| `1` | A blocking error: invalid directory/file, sheet or key attribute not found, invalid regular expression, missing GitHub options with `--transfer-report`, spreadsheet read failure, or GitHub transfer failure | -- 🚀 Fully customizable command line interface -- ✨ Automated generation of grade-based reports sent to students -- 🪂 Rich command line interface with many various arguments +## Example spreadsheet -## ⚡️ Requirements +The `spreadsheets/` directory contains a small example gradebook that all of +the examples above use: -- Cellveyor git hub repository -- Local google sheet -- Git hub token +| File | Description | +|---|---| +| `fake_spreadsheet.xlsx` | A gradebook with multiple sheets (`Main`, `TP`, `IPA`, `EXE`, `PFD`, `TCD`, `PRD`, `WEB`, `Tokens`, `Feedback`, `Lookup`) | +| `feedback.yml` | A feedback file that only supplies a `footer` | -## 🔽 Installation +The `Main` sheet holds summary grades and final grades per student, `EXE` +holds per-exam grades, and so on. The `Feedback` sheet and the `Lookup` sheet +(letter-to-GPA) exist in the same workbook because that is how the original +Google Sheet was structured; Cellveyor only reads the sheet named by +`--sheet-name`. -Follow these steps to install the Cellveyor program: +## License -1. Copy the ssh key of the repo -2. ```Git clone``` the repository onto your personal computer - - ```git clone (ssh key)``` -3. Type ```uv run cellveyor --help``` to learn how to use the tool +GNU General Public License v3.0 (see the `LICENSE` file in this repository). From 9974101f6bd8335149b0bf45b10404cb6096d68a Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 16:47:30 -0400 Subject: [PATCH 15/50] docs: Remove one of the badges and then revise content in introductory paragraph of the README.md file. --- README.md | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index ac01b3e..faa9bc1 100644 --- a/README.md +++ b/README.md @@ -1,21 +1,20 @@ Cellveyor Logo +title="Cellveyor Logo" /> # Cellveyor [![build](https://github.com/GatorEducator/cellveyor/actions/workflows/build.yml/badge.svg)](https://github.com/GatorEducator/cellveyor/actions/workflows/build.yml) -[![Code Style: black](https://img.shields.io/badge/Code%20Style-Black-blue.svg)](https://github.com/psf/black) [![Maintenance](https://img.shields.io/badge/Maintained%3F-Yes-blue.svg)](https://github.com/gkapfham/chasten/graphs/commit-activity) [![License LGPL v3](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0) ## Overview Cellveyor is a command-line tool that automatically turns the cells of a -spreadsheet into per-student grade reports. You point Cellveyor at a -gradebook spreadsheet, describe which columns hold grades and which hold -feedback, and it creates one markdown report per student — displayed directly -in the terminal or, with the `--transfer-report` option, posted as a comment -on the student's GitHub pull request. +spreadsheet into per-student grade reports. You point Cellveyor at a gradebook +spreadsheet, describe which columns hold grades and which hold feedback, and it +creates one markdown report per student. Cellveyor displays directly in the +terminal or, with the `--transfer-report` option, posts it as a comment on the +student's GitHub pull request, often created with GitHub Classroom (i.e., cs50). Cellveyor is designed for the gradebook spreadsheets used in GitHub Classroom-based courses. The spreadsheet follows a fixed shape: each row is @@ -147,8 +146,7 @@ uv run cellveyor \ ``` **Column filtering.** `--column-regexp` uses `pandas` regex filtering -(`re.search` semantics on the column names), so `^(Summary Grade|Final -Grade) .*$` selects every column that starts with "Summary Grade" or +(`re.search` semantics on the column names), so `^(Summary Grade|Final Grade) .*$` selects every column that starts with "Summary Grade" or "Final Grade". The key attribute column is always kept regardless of the regular expression. If the regular expression matches no columns, or the filter leaves no rows, Cellveyor prints a yellow warning and continues @@ -230,14 +228,14 @@ The structure of each report is fixed: 1. **Greeting** — `**Hello @!**`, where the key value is the student's value in the key attribute column (normally the GitHub username). -2. **Header** — the value of the `header` key in the feedback files, when +1. **Header** — the value of the `header` key in the feedback files, when present. -3. **Summary scores** — one bullet per selected grade column, rendered as +1. **Summary scores** — one bullet per selected grade column, rendered as `- ****: ` in the sheet's column order. -4. **Additional feedback** — one bullet per resolved feedback key, only when +1. **Additional feedback** — one bullet per resolved feedback key, only when at least one key in the row's feedback column exists in the feedback files. -5. **Footer** — the value of the `footer` key in the feedback files, when +1. **Footer** — the value of the `footer` key in the feedback files, when present. The header and footer are expected to be strings. Non-string values (like the From df1f0eefb0e182ac04520f605ada1efc776113f6 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 19:14:36 -0400 Subject: [PATCH 16/50] fix: Remove an incorrect license link from the README.md file. --- README.md | 1 - 1 file changed, 1 deletion(-) diff --git a/README.md b/README.md index faa9bc1..3a78d58 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,6 @@ title="Cellveyor Logo" /> [![build](https://github.com/GatorEducator/cellveyor/actions/workflows/build.yml/badge.svg)](https://github.com/GatorEducator/cellveyor/actions/workflows/build.yml) [![Maintenance](https://img.shields.io/badge/Maintained%3F-Yes-blue.svg)](https://github.com/gkapfham/chasten/graphs/commit-activity) -[![License LGPL v3](https://img.shields.io/badge/License-LGPL%20v3-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0) ## Overview From 3a33b3eda5dc103dd2a9df90480dee5b43268552 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 19:27:05 -0400 Subject: [PATCH 17/50] chore: Improve the way that the pyproject.toml file enforces the tracking of a minimum level of test coverage. --- pyproject.toml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index feb9a57..535f5e4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,7 +70,7 @@ branch = true omit = ["tests/*", "**/__init__.py", "scripts/*"] [tool.coverage.report] -fail_under = 90 +fail_under = 98 show_missing = true precision = 2 exclude_lines = [ @@ -129,12 +129,11 @@ ignore-missing-imports = ["*"] project = "cellveyor" scripts = "scripts" tests = "tests" -coveragefailunder = "90" directtestedfailunder = "75" ruff-check-command = { var = "ruff check {project} {tests} {scripts}", recursive = true } ruff-fixformat-command = { var = "ruff format {project} {tests} {scripts}", recursive = true } ruff-format-command = { var = "ruff format --check {project} {tests} {scripts}", recursive = true } -coverage-test-command = { var = "pytest -s --cov=cellveyor --cov-branch --cov-fail-under=90 --cov-report=term-missing tests/", recursive = true } +coverage-test-command = { var = "pytest -s --cov=cellveyor --cov-branch --cov-report=term-missing tests/", recursive = true } coverage-test-command-silent = "pytest -x --show-capture=no --cov-report term-missing --cov-report json --cov --cov-branch" developer-test-command = "pytest -x -s" developer-test-silent-command = "pytest -x --show-capture=no" @@ -181,7 +180,7 @@ test-not-xdist = { cmd = "pytest -x -s -vv -p no:xdist", help = "Run the pytest test-silent = { cmd = "pytest -x --show-capture=no -n auto", help = "Run the pytest test suite without showing output" } test-silent-not-randomly = { cmd = "pytest -x --show-capture=no -p no:randomly", help = "Run the pytest test suite without showing output and order randomization" } test-silent-not-xdist = { cmd = "pytest -x --show-capture=no -p no:xdist", help = "Run the pytest test suite without showing output and test distribution" } -test-coverage = { cmd = "pytest -s --cov=cellveyor --cov-branch --cov-fail-under={coveragefailunder} --cov-report=term-missing tests/", help = "Run the pytest test suite with coverage tracking", use_vars = true } +test-coverage = { cmd = "{coverage-test-command}", help = "Run the pytest test suite and enforce the fail_under threshold in [tool.coverage.report]", use_vars = true } test-parallel = { cmd = "pytest -x -s -vv -n auto -p no:sugar", help = "Run the pytest test suite with parallel execution and order randomization" } cosmic-ray-init = { cmd = "{cosmic-ray-init-command}", help = "Initialize cosmic-ray mutation testing session", use_vars = true } cosmic-ray-baseline = { cmd = "{cosmic-ray-baseline-command}", help = "Run cosmic-ray baseline tests", use_vars = true } From 809368fcb18f3206186d761025fc389e5e4ad15b Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 19:27:26 -0400 Subject: [PATCH 18/50] test: Add more test cases to four of the test suite files in the tests directory. --- tests/test_filesystem.py | 57 ++++++++++++++++++++ tests/test_main.py | 112 +++++++++++++++++++++++++++++++++++++++ tests/test_report.py | 13 +++++ tests/test_transfer.py | 44 +++++++++++++++ 4 files changed, 226 insertions(+) diff --git a/tests/test_filesystem.py b/tests/test_filesystem.py index 4da8e07..08f1d6b 100644 --- a/tests/test_filesystem.py +++ b/tests/test_filesystem.py @@ -1,6 +1,7 @@ """Pytest test suite for the filesystem module.""" import pathlib +from unittest.mock import patch import pytest from hypothesis import given, strategies @@ -54,3 +55,59 @@ def test_fuzz_confirm_valid_directory_using_builds( def test_fuzz_confirm_valid_file_using_builds(file: pathlib.Path) -> None: """Confirm that the function does not crash.""" filesystem.confirm_valid_file(file=file) + + +def test_confirm_valid_file_none() -> None: + """Confirm that a none file is not valid.""" + confirmation = filesystem.confirm_valid_file(None) # type: ignore + assert confirmation is False + + +def test_confirm_valid_directory_none() -> None: + """Confirm that a none directory is not valid.""" + confirmation = filesystem.confirm_valid_directory(None) # type: ignore + assert confirmation is False + + +def test_read_feedback_files_none() -> None: + """Confirm that a none feedback file list returns an empty dictionary.""" + assert filesystem.read_feedback_files(None) == {} + + +def test_read_feedback_files_empty(tmp_path: pathlib.Path) -> None: + """Confirm that an empty feedback file is skipped.""" + empty_file = tmp_path / "empty.yml" + empty_file.write_text("") + assert filesystem.read_feedback_files([empty_file]) == {} + + +def test_read_feedback_files_non_dict(tmp_path: pathlib.Path) -> None: + """Confirm that a non-dictionary feedback file is skipped.""" + list_file = tmp_path / "list.yml" + list_file.write_text("- a\n- b\n") + assert filesystem.read_feedback_files([list_file]) == {} + + +def test_read_feedback_files_malformed_yaml(tmp_path: pathlib.Path) -> None: + """Confirm that a malformed feedback file is skipped.""" + bad_file = tmp_path / "bad.yml" + bad_file.write_text("key: [unclosed\n") + assert filesystem.read_feedback_files([bad_file]) == {} + + +def test_read_feedback_files_unreadable(tmp_path: pathlib.Path) -> None: + """Confirm that an unreadable feedback file is skipped.""" + unreadable_file = tmp_path / "unreadable.yml" + unreadable_file.write_text("header: Hello\n") + with patch("pathlib.Path.read_text", side_effect=OSError("cannot read")): + assert filesystem.read_feedback_files([unreadable_file]) == {} + + +def test_read_feedback_files_merge_order(tmp_path: pathlib.Path) -> None: + """Confirm that later feedback files override earlier files.""" + first_file = tmp_path / "first.yml" + first_file.write_text("header: First\nfooter: First footer\n") + second_file = tmp_path / "second.yml" + second_file.write_text("footer: Second footer\n") + combined = filesystem.read_feedback_files([first_file, second_file]) + assert combined == {"header": "First", "footer": "Second footer"} diff --git a/tests/test_main.py b/tests/test_main.py index 7631d4c..dbab11d 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -376,3 +376,115 @@ def test_transport_transfer_failure() -> None: ) assert result.exit_code == 1 assert "GitHub transfer failed" in _strip_ansi(result.output) + + +def test_transport_spreadsheet_read_filenotfound() -> None: + """Test transport when the spreadsheet read raises FileNotFoundError.""" + runner = CliRunner() + with patch( + "cellveyor.main.data.access_dataframes", + side_effect=FileNotFoundError("missing"), + ): + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Spreadsheet file not found" in _strip_ansi(result.output) + + +def test_transport_spreadsheet_read_generic_error() -> None: + """Test transport when reading the spreadsheet fails unexpectedly.""" + runner = CliRunner() + with patch( + "cellveyor.main.data.access_dataframes", + side_effect=Exception("boom"), + ): + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Failed to read spreadsheet" in _strip_ansi(result.output) + + +def test_transport_column_filter_generic_error() -> None: + """Test transport when the column filter fails unexpectedly.""" + runner = CliRunner() + with patch( + "cellveyor.main.data.key_attribute_column_filter", + side_effect=RuntimeError("boom"), + ): + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Failed to filter columns" in _strip_ansi(result.output) + + +def test_transport_report_creation_error() -> None: + """Test transport when report creation fails unexpectedly.""" + runner = CliRunner() + with patch( + "cellveyor.main.report.create_per_key_report", + side_effect=RuntimeError("boom"), + ): + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + ], + ) + assert result.exit_code == 1 + assert "Failed to create reports" in _strip_ansi(result.output) diff --git a/tests/test_report.py b/tests/test_report.py index 950b134..437c6e4 100644 --- a/tests/test_report.py +++ b/tests/test_report.py @@ -174,6 +174,19 @@ def test_create_per_key_report_effective_feedback() -> None: assert "Here is some additional feedback" not in reports["alice"] +def test_create_per_key_report_feedback_index_error() -> None: + """Test feedback fallback when row index is out of bounds.""" + result_df = pandas.DataFrame( + {"Student GitHub": ["alice"], "Grade": [90], "Feedback": ["good"]}, + index=[5], + ) + selected = pandas.DataFrame({"Grade": [90], "Feedback": ["good"]}) + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "Feedback", {} + ) + assert "alice" in reports + + @given(text=strategies.text(max_size=20)) def test_fuzz_create_feedback_list(text: str) -> None: """Fuzz test create_feedback_list does not crash.""" diff --git a/tests/test_transfer.py b/tests/test_transfer.py index fa48ea9..73d699d 100644 --- a/tests/test_transfer.py +++ b/tests/test_transfer.py @@ -3,6 +3,7 @@ from unittest.mock import MagicMock, patch import pytest +from github import GithubException from cellveyor import transfer @@ -143,3 +144,46 @@ def test_transfer_report_to_github_handles_generic_exception() -> None: transfer.transfer_report_to_github( "token", "org/prefix-user", "report" ) + + +def test_transfer_reports_to_github_generic_exception() -> None: + """Test transfer loop catches generic exceptions per repository.""" + with patch( + "cellveyor.transfer.transfer_report_to_github", + side_effect=RuntimeError("unexpected"), + ): + # should not raise; the loop prints the error and moves on + transfer.transfer_reports_to_github( + "fake_token", "org", "prefix", {"alice": "report"} + ) + + +def test_transfer_report_to_github_repo_without_separators() -> None: + """Test transfer with a repository name lacking slash and dash.""" + with ( + patch("cellveyor.transfer.Github") as mock_github, + patch("cellveyor.transfer.Auth"), + ): + mock_repo = MagicMock() + mock_pull = MagicMock() + mock_github.return_value.get_repo.return_value = mock_repo + mock_repo.get_pull.return_value = mock_pull + + transfer.transfer_report_to_github("token", "bad-repo-name", "report") + mock_repo.get_pull.assert_called_once_with(1) + mock_pull.create_issue_comment.assert_called_once_with("report") + + +def test_transfer_report_to_github_raises_github_exception() -> None: + """Test transfer_report_to_github re-raises GithubException.""" + with ( + patch("cellveyor.transfer.Github") as mock_github, + patch("cellveyor.transfer.Auth"), + ): + mock_github.return_value.get_repo.side_effect = GithubException( + 404, "not found" + ) + with pytest.raises(GithubException): + transfer.transfer_report_to_github( + "token", "org/prefix-user", "report" + ) From 91912778bcc04e0c3aa0adab86e8260a79e8812a Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:20:53 -0400 Subject: [PATCH 19/50] chore: Add testing on another version of Python and make other small improvements to the .github/workflows/build.yml file. --- .github/workflows/build.yml | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7c108ef..3a5fdac 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,20 +20,15 @@ on: jobs: build: # Use the latest version of Ubuntu, MacOS, and Windows - # Use the latest and most stable version of Python - # Important: test coverage monitoring and reporting - # through a badge and the GitHub Actions job summary - # only takes place with the Linux operating system. - # Important: the MacOS and Windows operating systems - # have test coverage calculation take place but they - # do not report the test coverage beyond its display - # inside of the GitHub Actions panel for that job. + # Use the most recent stable Python versions in the supported range + # Important: the coverage threshold is enforced on the Linux runner; + # the MacOS and Windows runners run linting, type checking, and tests runs-on: ${{ matrix.os }} strategy: fail-fast: false matrix: os: [ubuntu-latest] - python-version: ["3.11"] + python-version: ["3.11", "3.13"] include: - os: macos-latest python-version: "3.11" @@ -43,18 +38,13 @@ jobs: steps: # Checkout the code of the repository - name: Check out Repository Code - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 - # Run the mdl linting tool - # Refers to .mdlrc file in repository - - name: Run Markdown Linting - if: matrix.os == 'ubuntu-latest' - uses: actionshub/markdownlint@main # Setup Python for the current language version - name: Setup Python ${{ matrix.python-version }} if: always() - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} # Install uv @@ -68,18 +58,28 @@ jobs: if: always() run: | uv sync --group dev - # Run the linters + # Run the linters (including the rumdl markdown linter) - name: Run Linters if: always() run: | uv run task lint + # Run the type checkers + - name: Run Type Checks + if: always() + run: | + uv run task typecheck # Run the program - name: Run program if: always() run: | - uv run cellveyor --spreadsheet-directory $PWD/spreadsheets/ --spreadsheet-file $PWD/spreadsheets/fake_spreadsheet.xlsx/ --sheet-name Main --key-attribute "Student GitHub" --key-value "gkapfham" --column-regexp '^(Summary Grade|Final Grade) .*$' --feedback-regexp "Summary Grade 1 - Feedback" --feedback-file $PWD/spreadsheets/feedback.yml/ + uv run cellveyor --spreadsheet-directory $PWD/spreadsheets/ --spreadsheet-file $PWD/spreadsheets/fake_spreadsheet.xlsx --sheet-name Main --key-attribute "Student GitHub" --key-value "gkapfham" --column-regexp '^(Summary Grade|Final Grade) .*$' --feedback-regexp "Summary Grade 1 - Feedback" --feedback-file $PWD/spreadsheets/feedback.yml # Run the tests - name: Run Tests if: always() run: | uv run task test + # Enforce the coverage threshold (Linux only) + - name: Run Coverage Check + if: matrix.os == 'ubuntu-latest' + run: | + uv run task test-coverage From 6ff8df81bfd946559448bc2525bd3eba3219baff Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:21:33 -0400 Subject: [PATCH 20/50] fix: Clarify an incorrect description of a command-line argument in cellveyor/main.py as the feedback file is in YAML format. --- cellveyor/main.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellveyor/main.py b/cellveyor/main.py index aa6b096..8cb4318 100644 --- a/cellveyor/main.py +++ b/cellveyor/main.py @@ -96,7 +96,7 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 None, "--feedback-file", "-f", - help="Feedback file(s) in JSON format", + help="Feedback file(s) in YAML format", ), github_token: str = typer.Option( None, From e970ee0c5741fca4fa5f030cdf9b79a9a6b19b74 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:55:32 -0400 Subject: [PATCH 21/50] fix: Handle data that is not correctly recorded in the spreadsheet being used to process the data in cellveyor/report.py. --- cellveyor/report.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/cellveyor/report.py b/cellveyor/report.py index 48db453..6d5e7b6 100644 --- a/cellveyor/report.py +++ b/cellveyor/report.py @@ -1,5 +1,6 @@ """Create reports based on content in dataframes.""" +import math from typing import Any, Dict, List from pandas import DataFrame @@ -110,6 +111,13 @@ def create_per_key_report( # add data to the current report for every column and its value for column_name in selected_columns.columns: column_value = row[column_name] + # a missing cell arrives as float NaN for numeric columns + # and as None for object columns; render either as a blank + # value instead of the literal "nan" or "None" text + if column_value is None or ( + isinstance(column_value, float) and math.isnan(column_value) + ): + column_value = "" current_report = ( current_report + f"{DASH}{SPACE}**{column_name}**:{SPACE}{column_value}{NEWLINE}" From d4ad2ce0528f19a206864178fa98ee355a828bb4 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:56:01 -0400 Subject: [PATCH 22/50] chore: Add more details to the pyproject.toml file. --- pyproject.toml | 41 +++++++++++++++++++++++++++++++++++++++-- 1 file changed, 39 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 535f5e4..a474b86 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,20 +1,43 @@ [project] name = "cellveyor" version = "0.1.0" -description = "" +description = "Generate per-student grade reports from spreadsheet cells and transfer them to GitHub." readme = "README.md" requires-python = ">=3.11,<3.14" authors = [{name = "Gregory M. Kapfhammer", email = "gkapfham@allegheny.edu"}] +license = "GPL-3.0-only" +keywords = [ + "education", + "gradebook", + "github-classroom", + "grades", + "reports", + "spreadsheet", +] +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Education", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Topic :: Education", +] dependencies = [ "rich>=13.4.2,<14.0.0", "pandas>=2.1.1,<3.0.0", "openpyxl>=3.1.2,<4.0.0", - "requests>=2.31.0,<3.0.0", "pygithub>=2.1.1,<3.0.0", "pyyaml>=6.0.1,<7.0.0", "typer>=0.20.0,<1.0.0", ] +[project.urls] +Homepage = "https://github.com/GatorEducator/cellveyor" +Repository = "https://github.com/GatorEducator/cellveyor" + [project.scripts] cellveyor = "cellveyor.main:cli" @@ -55,6 +78,20 @@ build-backend = "hatchling.build" [tool.hatch.build.targets.wheel] packages = ["cellveyor"] +[tool.hatch.build.targets.sdist] +exclude = [ + ".coverage", + ".coverage.*", + ".hypothesis", + ".mypy_cache", + ".pi", + ".pytest_cache", + ".ruff_cache", + ".rumdl_cache", + ".venv", + "dist", +] + [tool.pytest.ini_options] filterwarnings = [ "error", From 5a4fc8b9d5541304c311c61d91caebff57a4ffb4 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:56:29 -0400 Subject: [PATCH 23/50] docs: Update a detail about un-reported values in the README.md file. --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3a78d58..cf456f2 100644 --- a/README.md +++ b/README.md @@ -230,7 +230,10 @@ The structure of each report is fixed: 1. **Header** — the value of the `header` key in the feedback files, when present. 1. **Summary scores** — one bullet per selected grade column, rendered as - `- ****: ` in the sheet's column order. + `- ****: ` in the sheet's column order. A missing + value in a grade column renders as a blank value instead of the literal + `nan` or `None`, so a student with an ungraded column sees an empty + entry rather than confusing text. 1. **Additional feedback** — one bullet per resolved feedback key, only when at least one key in the row's feedback column exists in the feedback files. From 36372e5694909a01e67e159cdd70fb55a7f5d25f Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:56:44 -0400 Subject: [PATCH 24/50] test: Add tests to confirm correct handling of un-reported values in the tests/test_report.py test file. --- tests/test_report.py | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/tests/test_report.py b/tests/test_report.py index 437c6e4..fa448e9 100644 --- a/tests/test_report.py +++ b/tests/test_report.py @@ -187,6 +187,43 @@ def test_create_per_key_report_feedback_index_error() -> None: assert "alice" in reports +def test_create_per_key_report_missing_grade_nan() -> None: + """Confirm that a missing numeric grade renders as a blank value.""" + df = pandas.DataFrame( + {"Student GitHub": ["alice"], "Grade": [float("nan")]} + ) + selected = df[["Grade"]] + result_df = df[["Student GitHub", "Grade"]] + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "NOMATCH", {} + ) + assert "nan" not in reports["alice"] + assert "- **Grade**:" in reports["alice"] + + +def test_create_per_key_report_missing_grade_none() -> None: + """Confirm that a missing object grade renders as a blank value.""" + df = pandas.DataFrame({"Student GitHub": ["alice"], "Grade": [None]}) + selected = df[["Grade"]] + result_df = df[["Student GitHub", "Grade"]] + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "NOMATCH", {} + ) + assert "None" not in reports["alice"] + assert "- **Grade**:" in reports["alice"] + + +def test_create_per_key_report_present_grade_unchanged() -> None: + """Confirm that a present grade still renders normally.""" + df = pandas.DataFrame({"Student GitHub": ["alice"], "Grade": [92.5]}) + selected = df[["Grade"]] + result_df = df[["Student GitHub", "Grade"]] + reports = report.create_per_key_report( + "Student GitHub", result_df, selected, "NOMATCH", {} + ) + assert "- **Grade**: 92.5" in reports["alice"] + + @given(text=strategies.text(max_size=20)) def test_fuzz_create_feedback_list(text: str) -> None: """Fuzz test create_feedback_list does not crash.""" From 49cb7738aa6c0dab824320aaf1f95be58ad950f0 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:57:07 -0400 Subject: [PATCH 25/50] chore: Update the uv.lock file. --- uv.lock | 2 -- 1 file changed, 2 deletions(-) diff --git a/uv.lock b/uv.lock index 1e117d3..ff28a1c 100644 --- a/uv.lock +++ b/uv.lock @@ -185,7 +185,6 @@ dependencies = [ { name = "pandas" }, { name = "pygithub" }, { name = "pyyaml" }, - { name = "requests" }, { name = "rich" }, { name = "typer" }, ] @@ -226,7 +225,6 @@ requires-dist = [ { name = "pandas", specifier = ">=2.1.1,<3.0.0" }, { name = "pygithub", specifier = ">=2.1.1,<3.0.0" }, { name = "pyyaml", specifier = ">=6.0.1,<7.0.0" }, - { name = "requests", specifier = ">=2.31.0,<3.0.0" }, { name = "rich", specifier = ">=13.4.2,<14.0.0" }, { name = "typer", specifier = ">=0.20.0,<1.0.0" }, ] From 2a7caeeacd831624bc06c510d84bf1164d6dc548 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sun, 23 Aug 2026 20:57:17 -0400 Subject: [PATCH 26/50] chore: Delete the .github/workflows/publish.yml and .mdlrc files. --- .github/workflows/publish.yml | 34 ---------------------------------- .mdlrc | 1 - 2 files changed, 35 deletions(-) delete mode 100644 .github/workflows/publish.yml delete mode 100644 .mdlrc diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml deleted file mode 100644 index 7579d97..0000000 --- a/.github/workflows/publish.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: publish -on: - push: - tags: - - '*' -jobs: - build: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v3 - with: - python-version: 3.11 - - run: | - pip install poetry - poetry build - - uses: actions/upload-artifact@v3 - with: - path: ./dist - - pypi-publish: - needs: ['build'] - environment: 'publish' - - name: Upload Release to PyPI - runs-on: ubuntu-latest - permissions: - id-token: write - steps: - - uses: actions/download-artifact@v3 - - name: Publish Package Distributions to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 - with: - packages_dir: artifact/ diff --git a/.mdlrc b/.mdlrc deleted file mode 100644 index affe738..0000000 --- a/.mdlrc +++ /dev/null @@ -1 +0,0 @@ -rules "~MD013, ~MD033" \ No newline at end of file From 12849e217a4ccfd9b3eed7db28762e2b3dfd13ad Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:18:50 -0400 Subject: [PATCH 27/50] chore: Bump the minimum version of Python to ensure support for trailmark for testing and analysis in pyproject.toml. --- pyproject.toml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a474b86..21b8993 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -3,7 +3,7 @@ name = "cellveyor" version = "0.1.0" description = "Generate per-student grade reports from spreadsheet cells and transfer them to GitHub." readme = "README.md" -requires-python = ">=3.11,<3.14" +requires-python = ">=3.12,<3.14" authors = [{name = "Gregory M. 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[[package]] name = "tree-sitter-typescript" version = "0.23.2" From 3c131cd0584dc78d2eb934c3452cf214bc2e02c3 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:45:30 -0400 Subject: [PATCH 30/50] chore: Add the starting version of the AGENTS.md file with basic customizations. --- AGENTS.md | 198 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 198 insertions(+) create mode 100644 AGENTS.md diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 0000000..86a48ad --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,198 @@ +# AGENTS.md + +This document provides guidelines for AI agents contributing to the +**Cellveyor** repository. + +## Overview of Instructions + +- **Always use `uv`:** This project uses `uv` for all dependency management, + virtual environments, and task running. Do not use `pip`, `venv`, or + `poetry` directly. Commands like `uv sync`, `uv run`, and `uv add` are the + only correct workflow. +- **Follow all guidelines:** This document contains the complete set of + guidelines for this project. You must follow them strictly. For build + architecture and implementation details, consult `README.md`, `pyproject.toml`, + and `WORKFLOW.md` at the repository root. +- **Verify your changes:** Before declaring any task complete, you must run all + linters and tests to ensure correctness and style compliance. The canonical + verification command is `uv run task all`. +- **Line width:** Python source code must respect **79 characters** (enforced + by `ruff`). Markdown and other prose files should wrap at **80 characters**. +- **Permission to run commands:** You have permission to run all commands in + this file to verify their functionality. +- **Incremental changes:** Make small, incremental changes. This makes review + easier and catches errors early. +- **Communicate clearly:** When you propose changes, explain what you have + done and why. +- **Be transparent about mistakes:** Although you should + avoid making mistakes, when an action overwrites, deletes, + or damages user data (for example, replacing a database file + during testing), report it immediately and explicitly: name + the file, what happened, why, and what is recoverable. Never + hide damage or wait for the human to discover it. + Acknowledge the error and offer remediation. +- **Create and follow a TODO list:** Always create a TODO list and then follow + it. Do not stop until the tools you call confirm that all tasks in the list + are completed. +- **Do not close the TODO:** Only the user closes the TODO. The agent must + never mark a TODO as closed or call update_goal with status complete. The + agent reports completion and waits for the user to confirm and close. + +## Notification Instructions + +- The user has given permission to use `notify-send` to signal task completion + or request feedback. Example: + + ```bash + notify-send "Question from Coding Agent" \ + "Please clarify how to complete the testing task." + ``` + +- Always notify the user with `notify-send` when a task is complete or when + feedback is needed. + +- When working inside a Zellij session, use the `zjstatus::notify` pipe + protocol. The full two-step pattern is: + + ```bash + # Step 1: Send the notification (displays for show_interval seconds) + timeout 2 zellij pipe -- \ + "zjstatus::notify::󰵰 Task complete. " 2>/dev/null + + # Step 2: After the interval expires, force a re-render to clear it + timeout 8 bash -c \ + "sleep 6 && zellij pipe -- 'zjstatus::pipe::clear:: '" 2>/dev/null || true + ``` + + The `sleep` duration must be at least `show_interval + 1` seconds. + The trailing space in the notify message is required. + +## Build, Lint, and Test Commands + +These commands are defined via **taskipy** in `pyproject.toml` and executed +through `uv run task `: + +- **Run all verification:** `uv run task all` (= `task check && task test && task test-coverage-check`) +- **Run all linters + typecheck:** `uv run task check` (= `task lint && task typecheck`) +- **Lint suite:** `uv run task lint` (= `ruff-format && ruff-check && comments-check && vsc && rumdl-check`) +- **Typecheck suite:** `uv run task typecheck` (= `mypy && ty && pyrefly && zuban && symbex`) +- **Format check:** `uv run task ruff-format` (check only) +- **Format fix:** `uv run task ruff-format-fix` / `uv run task format-fix` +- **Lint check:** `uv run task ruff-check` +- **Individual type checkers:** `uv run task mypy`, `uv run task ty`, `uv run task pyrefly`, `uv run task zuban`, `uv run task symbex`, `uv run task symbex-typed`, `uv run task symbex-documented` +- **Comment check/fix:** `uv run task comments-check` / `uv run task comments-fix` (via `scripts/ccl.py`) +- **Version sync check:** `uv run task vsc` (verifies `cellveyor/version.py` matches `pyproject.toml`) +- **Markdown lint/fix:** `uv run task rumdl-check` / `uv run task rumdl-fix` +- **Test suite:** `uv run task test` (`pytest -x -s -vv -n auto` with randomly + xdist) +- **Test variants:** `uv run task test-not-randomly`, `uv run task test-not-xdist`, `uv run task test-silent`, `uv run task test-parallel` +- **Test with coverage:** `uv run task test-coverage` (enforces `fail_under = 98` in `pyproject.toml`) +- **Direct coverage check:** `uv run task test-coverage-check` (enforces `directtestedfailunder = 75` via `scripts/tsc.py`) +- **Run a single test:** + `uv run pytest tests/test_file.py::test_function -x -s -vv` + +## Code Requirements + +All Python code must follow these standards: + +- **Cross-platform code:** Source code must run unchanged on macOS, + Linux, and Windows. Write filesystem logic with `pathlib` and never + embed path separators in strings; a leading-slash path without a + drive letter is not absolute on Windows. Normalize any path that + appears in a stable identifier or output with `Path.as_posix()` so + results are identical on every platform. +- **Function bodies:** No blank lines within function bodies. Keep code + contiguous from the function signature to the final `return`. +- **Docstrings:** Single-line docstrings starting with a capital letter and + ending with a period. Follow this for new files. In existing files, preserve + the established docstring style. +- **Comments:** Start with a lowercase letter. Preserve existing comments + during refactoring. The only exception is when the first word is a proper + noun (e.g., `Cellveyor`, `GitHub`) or an identifier that must be + capitalized (e.g., `GITHUB_ENV`). +- **Sentences in comments:** Use exactly one space between the period and the + following sentence. +- **No backticks in comments:** Do not use backticks in comments, docstrings, + or any prose inside source files. Backticks are reserved for Markdown + formatting in `.md` files only. Refer to identifiers plainly + (e.g., "pandas" not "`pandas`"). +- **Imports:** Group in this order: standard library, third-party, local. + Use absolute imports (`from cellveyor.module import `). Place all + imports at the top of the file. Never place imports inside functions or + classes. +- **Formatting:** `ruff format` enforces line length 79. Use trailing commas. + Run via `uv run task ruff-format-fix`. +- **Types:** All functions must have type hints for parameters and return + values. +- **Naming:** `snake_case` for functions and variables, `PascalCase` for + classes, `UPPER_SNAKE_CASE` for constants. +- **Constants over literals:** All hard-coded strings, integers, and floats + must be extracted into named constants at the top of the module. Use the + constant everywhere, never the raw literal. +- **File operations:** Use `pathlib.Path` for all filesystem operations. Never + use string paths. +- **Error handling:** Raise specific exception types, not generic `Exception`. + Provide meaningful error messages. + +## Project Structure Requirements + +- Source code lives in `cellveyor/` (`constants.py`, `data.py`, `filesystem.py`, `main.py`, `report.py`, `transfer.py`, `version.py`). +- Tests live in `tests/` with structure mirroring the source modules (`test_data.py`, `test_report.py`, etc.). +- Helper scripts live in `scripts/` (`ccl.py`, `tsc.py`, `vsc.py`). +- Example gradebooks live in `spreadsheets/` (`fake_spreadsheet.xlsx`, `feedback.yml`). +- Use `uv` for dependency management, virtual environments, and task running. +- Supports Python `>=3.12, <3.14` on macOS, Linux, and Windows (see `pyproject.toml` `requires-python` and `README.md`). +- CLI is built with `typer` (`cellveyor/main.py:cli`) and terminal output with `rich`; spreadsheet I/O uses `pandas` + `openpyxl`; GitHub transfer uses `PyGithub`; feedback files are `yaml`. + +## Testing Requirements + +All tests must follow these standards: + +- **Cross-platform tests:** Tests must pass unchanged on macOS, Linux, + and Windows. Never assert hardcoded POSIX-style paths; derive the + expected string from the same `Path` object under test (for example, + `str(spreadsheet_path)` instead of a `/custom/...` literal) and remember that + leading-slash paths without a drive letter are not absolute on + Windows. Use platform-neutral fixtures such as `tmp_path`. +- Tests are Python functions and therefore follow all code requirements above. +- Test names start with `test_` and are descriptive. +- Group tests by the function or module they exercise. +- Order tests logically for readability. +- Tests must be independent — runnable in random order without side effects. +- Tests must pass on local machines and in CI on macOS, Linux, and Windows. +- Aim for full function, statement, and branch coverage (global `fail_under = 98`, direct coverage `>= 75%` via `scripts/tsc.py`). +- Property-based tests using `hypothesis` must be marked with + `@pytest.mark.propertybased` or `@pytest.mark.fuzz`. +- Tests must not produce console output. + +## CLI Output Testing and Rich Encoding Traps to Avoid + +Cellveyor renders reports with `rich` (`Console`, `Panel`, `Markdown`) and is invoked via `typer.testing.CliRunner`. A recurring flake is `task test` failing while `task test-parallel` passes (or the converse) on a `CliRunner` assertion: + +- `rich.console.Console()` defaults to `stderr` and, when `isatty()` is true, + emits ANSI escape codes and may use a different encoding. Under + `pytest -n auto` (`task test`) each `xdist` worker is not a TTY (plain `utf-8` to `stdout`); under single-process `task test-not-xdist` it may be a TTY (ANSI to `stderr`). `CliRunner` captures `stdout`/`stderr` separately, so `assert "gkapfham" in result.stdout` can be empty or ANSI-wrapped while `result.output` holds the text. + +Required process for every agent working in Python on this repo: + +- In tests using `typer.testing.CliRunner`, strip ANSI before asserting (see `tests/test_main.py:_strip_ansi`) and assert against `result.output` or the stripped output with a substring check (`assert "gkapfham" in _strip_ansi(result.output)`) rather than an exact `result.stdout == "..."` check. Never assert a hard-coded ANSI string. +- If `rich` must be used in production code, prefer `Console()` defaults as `main.py` does, but keep tests ANSI-tolerant. If you need deterministic output in a test, construct `Console(file=sys.stdout, force_terminal=False, highlight=False)` explicitly. +- Always pass `encoding="utf-8"` to `Path.read_text`/`write_text` and to `open(..., encoding="utf-8", newline="")` for YAML/CSV so the suite behaves identically on Linux, macOS, and Windows. +- Verify both variants before completing: + `uv run task test` and `uv run task test-not-xdist`. The canonical gate is `uv run task all`, but both must be green. +- When a fix touches CLI output, run `uv run task test-coverage` as well; a coverage drop from an untested `rich` branch is a signal, not just a lint failure. + +## Making Changes + +1. **Understand:** Thoroughly understand the request and the relevant + codebase. Use available tools to explore files. +1. **Plan:** Formulate a clear plan before making changes. Consult `README.md` and `WORKFLOW.md` for architecture decisions. +1. **Implement:** Make small, incremental changes. +1. **Verify:** Run `uv run task all` to ensure correctness and style + compliance. +1. **Commit:** The human developer commits the changes. +1. **Rules:** Follow all rules in this file, `README.md`, and `WORKFLOW.md`. +1. **Report, don't close the TODO:** When finished, summarize completed + tasks, how you completed them, challenges faced, how you overcame them, + and the rules you followed. Leave the TODO open — only the user closes it. +1. **Wait for confirmation:** After reporting completion, wait for the user to + confirm before starting the next TODO. From 0188784b9e2d42a402e0366ed88cff65162fab7f Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:46:08 -0400 Subject: [PATCH 31/50] chore: Bump the directtestedfailunder threshold to 100 and add a test for the new thresholding in pyproject.toml. --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 3b7d3c9..a71e9f4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -166,7 +166,7 @@ ignore-missing-imports = ["*"] project = "cellveyor" scripts = "scripts" tests = "tests" -directtestedfailunder = "75" +directtestedfailunder = "100" ruff-check-command = { var = "ruff check {project} {tests} {scripts}", recursive = true } ruff-fixformat-command = { var = "ruff format {project} {tests} {scripts}", recursive = true } ruff-format-command = { var = "ruff format --check {project} {tests} {scripts}", recursive = true } From b4201ca56f668614bd85f3927a688c69210f1991 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:48:41 -0400 Subject: [PATCH 32/50] fix: Update the cellveyor/data.py file to avoid case where an overly general regexp will return incorrect data for key. --- cellveyor/data.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/cellveyor/data.py b/cellveyor/data.py index 7d3c526..6fa2272 100644 --- a/cellveyor/data.py +++ b/cellveyor/data.py @@ -37,6 +37,11 @@ def key_attribute_column_filter( raise ValueError( f"Invalid column regular expression '{column_regexp}': {exc}" ) from exc + # avoid duplicate key column when regexp matches the key itself + # (e.g., ".*" or "Student.*") — otherwise row[key] returns a Series + selected_columns = selected_columns.drop( + columns=[key_attribute_name], errors="ignore" + ) # extract the attribute that has the key name and also select all of # those columns that matched the regular expression result_df = sheet_dataframe[ From bae99331891a89bf4298893600268f864dd2a21d Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:49:23 -0400 Subject: [PATCH 33/50] chore: Add a few additional details about direct test coverage to the AGENTS.md file. --- AGENTS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index 86a48ad..4a568f1 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -86,7 +86,7 @@ through `uv run task `: - **Test suite:** `uv run task test` (`pytest -x -s -vv -n auto` with randomly + xdist) - **Test variants:** `uv run task test-not-randomly`, `uv run task test-not-xdist`, `uv run task test-silent`, `uv run task test-parallel` - **Test with coverage:** `uv run task test-coverage` (enforces `fail_under = 98` in `pyproject.toml`) -- **Direct coverage check:** `uv run task test-coverage-check` (enforces `directtestedfailunder = 75` via `scripts/tsc.py`) +- **Direct coverage check:** `uv run task test-coverage-check` (enforces `directtestedfailunder = 100` via `scripts/tsc.py`) - **Run a single test:** `uv run pytest tests/test_file.py::test_function -x -s -vv` @@ -159,7 +159,7 @@ All tests must follow these standards: - Order tests logically for readability. - Tests must be independent — runnable in random order without side effects. - Tests must pass on local machines and in CI on macOS, Linux, and Windows. -- Aim for full function, statement, and branch coverage (global `fail_under = 98`, direct coverage `>= 75%` via `scripts/tsc.py`). +- Aim for full function, statement, and branch coverage (global `fail_under = 98`, direct coverage `= 100%` via `scripts/tsc.py` — every function must have a direct test, enforced by `uv run task test-coverage-check`). - Property-based tests using `hypothesis` must be marked with `@pytest.mark.propertybased` or `@pytest.mark.fuzz`. - Tests must not produce console output. From 0d1617f1e80e8ed68fec25d1869816e25f04edc7 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:49:59 -0400 Subject: [PATCH 34/50] test: Add a test case to the tests/test_data.py file to confirm that there is no more extra matching with wrong regular expression. --- tests/test_data.py | 67 +++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 66 insertions(+), 1 deletion(-) diff --git a/tests/test_data.py b/tests/test_data.py index 5609bc4..98ff1e3 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -2,7 +2,9 @@ from pathlib import Path -from cellveyor import data +import pandas + +from cellveyor import data, report def test_access_dataframes() -> None: @@ -33,3 +35,66 @@ def test_key_attribute_column_filter() -> None: assert ("Summary Grade for Team Participation") in selected_columns.columns assert ("Student GitHub") in result_df.columns assert key_attribute_value in result_df["Student GitHub"].values + + +def test_key_attribute_column_filter_does_not_duplicate_key() -> None: + """Regression: column_regexp matching the key must not duplicate it.""" + # fake sheet where ".*" would otherwise match the key column itself + dataframes_dict = data.access_dataframes( + Path("spreadsheets/fake_spreadsheet.xlsx") + ) + sheet_dataframe = dataframes_dict["Main"] + key_attribute_name = "Student GitHub" + for column_regexp in [".*", "Student.*", "Student GitHub"]: + selected_columns, result_df = data.key_attribute_column_filter( + sheet_dataframe, key_attribute_name, column_regexp + ) + # selected must not contain the key — fix is to drop it + assert key_attribute_name not in selected_columns.columns + # result must have exactly one key column, no duplicates + assert list(result_df.columns).count(key_attribute_name) == 1 + assert result_df.columns.duplicated().sum() == 0 + # row[key] must be scalar string, not a Series dump + first_valid_key = result_df[result_df[key_attribute_name].notna()][ + key_attribute_name + ].iloc[0] + assert isinstance(first_valid_key, str) + # end-to-end: report titles must be clean github handles + per_key = report.create_per_key_report( + key_attribute_name, + result_df, + selected_columns, + "NONE", + {}, + ) + # no garbled Series string like "Student GitHub gkapfham" + assert "gkapfham" in per_key + assert not any( + "Student GitHub gkapfham" in title for title in per_key + ) + assert not any("dtype: object" in title for title in per_key) + + +def test_key_attribute_column_filter_duplicate_key_minimal_dataframe() -> None: + """Regression with minimal dataframe: ensure no duplicate when regexp is '.*'.""" + df = pandas.DataFrame( + { + "Student GitHub": ["alice", "bob", float("nan")], + "Student Name": ["Alice", "Bob", float("nan")], + "Grade": [90, 80, float("nan")], + } + ) + selected_columns, result_df = data.key_attribute_column_filter( + df, "Student GitHub", ".*" + ) + assert "Student GitHub" not in selected_columns.columns + assert list(result_df.columns).count("Student GitHub") == 1 + # naN-key rows survive data filter (dropna how="all" keeps rows with any grade), + # but report must still skip them — ensure data layer doesn't create Series + per_key = report.create_per_key_report( + "Student GitHub", result_df, selected_columns, "NONE", {} + ) + assert "alice" in per_key + assert "bob" in per_key + assert "nan" not in per_key + assert not any("dtype: object" in k for k in per_key) From e15ff4ee28c19cdad195253cf08f854805915b58 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:50:35 -0400 Subject: [PATCH 35/50] test: Add more tests in tests/test_filesystem.py to ensure greater direct test coverage. --- tests/test_filesystem.py | 93 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) diff --git a/tests/test_filesystem.py b/tests/test_filesystem.py index 08f1d6b..b1a86d1 100644 --- a/tests/test_filesystem.py +++ b/tests/test_filesystem.py @@ -111,3 +111,96 @@ def test_read_feedback_files_merge_order(tmp_path: pathlib.Path) -> None: second_file.write_text("footer: Second footer\n") combined = filesystem.read_feedback_files([first_file, second_file]) assert combined == {"header": "First", "footer": "Second footer"} + + +def test_confirm_valid_file_in_directory_valid( + tmp_path: pathlib.Path, +) -> None: + """Confirm that a valid file in a valid directory is found.""" + directory = tmp_path / "subdir" + directory.mkdir() + file_path = directory / "test.txt" + file_path.write_text("hello") + confirmation = filesystem.confirm_valid_file_in_directory( + pathlib.Path("test.txt"), directory + ) + assert confirmation is True + + +def test_confirm_valid_file_in_directory_invalid_directory( + tmp_path: pathlib.Path, +) -> None: + """Confirm that invalid directory returns false.""" + invalid_dir = pathlib.Path("/tmp/not_a_dir_xyz_12345_cellveyor_test") + # ensure the path does not exist as a directory + if invalid_dir.exists(): + # if it somehow exists, use a different one + invalid_dir = tmp_path / "nonexistent_dir_xyz" + confirmation = filesystem.confirm_valid_file_in_directory( + pathlib.Path("test.txt"), invalid_dir + ) + assert confirmation is False + + +def test_confirm_valid_file_in_directory_invalid_file( + tmp_path: pathlib.Path, +) -> None: + """Confirm that missing file in valid directory returns false.""" + directory = tmp_path + confirmation = filesystem.confirm_valid_file_in_directory( + pathlib.Path("nonexistent_file_xyz.txt"), directory + ) + assert confirmation is False + + +def test_confirm_valid_file_in_directory_none_directory() -> None: + """Confirm that none directory returns false.""" + confirmation = filesystem.confirm_valid_file_in_directory( + pathlib.Path("test.txt"), + None, # type: ignore + ) + assert confirmation is False + + +def test_confirm_valid_file_in_directory_both_invalid() -> None: + """Confirm that both invalid inputs return false.""" + confirmation = filesystem.confirm_valid_file_in_directory( + pathlib.Path("nope.txt"), + pathlib.Path("/tmp/not_a_dir_xyz_12345_cellveyor_test2"), + ) + assert confirmation is False + + +def test_confirm_valid_file_in_directory_absolute_file( + tmp_path: pathlib.Path, +) -> None: + """Confirm that absolute file path handling is correct.""" + directory = tmp_path / "absdir" + directory.mkdir() + file_path = directory / "abs.txt" + file_path.write_text("content") + # when file is absolute, directory / file ignores directory + # so this should verify the logic still works for absolute paths + # that exist + confirmation_true = filesystem.confirm_valid_file_in_directory( + file_path, directory + ) + # depending on Path semantics, this may be true or false; ensure no crash + assert isinstance(confirmation_true, bool) + # also check with non-existent absolute file + confirmation_false = filesystem.confirm_valid_file_in_directory( + tmp_path / "does_not_exist_abs.txt", directory + ) + assert confirmation_false is False + + +@given( + file=strategies.builds(pathlib.Path), + directory=strategies.builds(pathlib.Path), +) +@pytest.mark.fuzz +def test_fuzz_confirm_valid_file_in_directory_using_builds( + file: pathlib.Path, directory: pathlib.Path +) -> None: + """Confirm that the function does not crash with arbitrary paths.""" + filesystem.confirm_valid_file_in_directory(file=file, directory=directory) From add6d868de0359b71bfa4fe17538a31fefb78748 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:50:54 -0400 Subject: [PATCH 36/50] test: Add more tests to tests/test_main.py to ensure greater direct test coverage. --- tests/test_main.py | 330 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 330 insertions(+) diff --git a/tests/test_main.py b/tests/test_main.py index dbab11d..859cea9 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -4,6 +4,9 @@ import re from unittest.mock import patch +import pandas as pd +import pytest +import typer from typer.testing import CliRunner from cellveyor import main @@ -488,3 +491,330 @@ def test_transport_report_creation_error() -> None: ) assert result.exit_code == 1 assert "Failed to create reports" in _strip_ansi(result.output) + + +def test_transport_direct_success() -> None: + """Test direct call to transport succeeds with mocked dependencies.""" + # create minimal dataframe and mock all internal calls + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = fake_df[["Grade"]] + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch( + "cellveyor.main.filesystem.confirm_valid_file", return_value=True + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports"), + ): + # direct call should not raise + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + + +def test_transport_direct_invalid_directory() -> None: + """Test direct call to transport with invalid directory exits.""" + with pytest.raises(typer.Exit) as exc: + main.transport( + spreadsheet_directory=pathlib.Path("/tmp/not_a_dir_xyz_12345"), + spreadsheet_file=pathlib.Path("fake.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + assert exc.value.exit_code == 1 + + +def test_transport_direct_invalid_file_in_valid_directory( + tmp_path: pathlib.Path, +) -> None: + """Test direct call with valid directory but missing file exits.""" + with pytest.raises(typer.Exit) as exc: + main.transport( + spreadsheet_directory=tmp_path, + spreadsheet_file=pathlib.Path("nonexistent.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + assert exc.value.exit_code == 1 + + +def test_transport_direct_wrong_sheet() -> None: + """Test direct call with wrong sheet triggers exit.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + ): + with pytest.raises(typer.Exit) as exc: + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="NOTASHEET", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + assert exc.value.exit_code == 1 + + +def test_transport_direct_wrong_key_attribute() -> None: + """Test direct call with wrong key attribute triggers exit.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + side_effect=ValueError("Key attribute 'BAD' not found"), + ), + ): + with pytest.raises(typer.Exit) as exc: + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="BAD", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + assert exc.value.exit_code == 1 + + +def test_transport_direct_with_feedback_missing_file() -> None: + """Test direct call warns about missing feedback file but succeeds.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = fake_df[["Grade"]] + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.confirm_valid_file", return_value=False + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports"), + ): + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=[pathlib.Path("/tmp/notexist.yml")], + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + + +def test_transport_direct_no_columns_matched() -> None: + """Test direct call with no columns matched warns but succeeds.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = pd.DataFrame() + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports"), + ): + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp="^NONEXISTENT.*$", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + ) + + +def test_transport_direct_transfer_with_mock() -> None: + """Test direct call with transfer enabled and mocked github.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = fake_df[["Grade"]] + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports"), + patch("cellveyor.main.transfer.transfer_reports_to_github") as mock, + ): + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token="fake", + github_organization="org", + github_repository_prefix="prefix", + transfer_report=True, + ) + mock.assert_called_once() + + +def test_transport_direct_missing_github_args() -> None: + """Test direct call with transfer but missing github args exits.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = fake_df[["Grade"]] + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports"), + ): + with pytest.raises(typer.Exit) as exc: + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token=None, # type: ignore + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=True, + ) + assert exc.value.exit_code == 1 From 98220d8c7e75dc1a7baf6a4d021ebc164e951622 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 17:57:42 -0400 Subject: [PATCH 37/50] chore: Add more details about key conventions to the AGENTS.md file. --- AGENTS.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/AGENTS.md b/AGENTS.md index 4a568f1..c21ff37 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -143,6 +143,12 @@ All Python code must follow these standards: - Supports Python `>=3.12, <3.14` on macOS, Linux, and Windows (see `pyproject.toml` `requires-python` and `README.md`). - CLI is built with `typer` (`cellveyor/main.py:cli`) and terminal output with `rich`; spreadsheet I/O uses `pandas` + `openpyxl`; GitHub transfer uses `PyGithub`; feedback files are `yaml`. +## Privacy & Security (FERPA / Tokens) + +- Real gradebooks under `/home/gkapfham/working/data/` and any `CMPSC-*-Gradebook.xlsx` contain FERPA-protected student data. Never commit them, never copy them into `spreadsheets/` or `tests/`, and never paste full rows, emails, or grades into logs, issues, or chat. Use `spreadsheets/fake_spreadsheet.xlsx` for all examples and tests; use `tmp_path` for synthetic sheets. +- Never log or echo a GitHub token. The `transport` command takes `--github-token`; tests must mock `PyGithub` (`tests/test_transfer.py` pattern) and never assert the literal token string. When reproducing a transfer failure, use `TOKEN` or `fake_token` as the placeholder. +- When inspecting a real gradebook locally, read only the schema (`df.columns.tolist()`, `df.shape`) or a single anonymized row; avoid dumping `df.to_dict()` for all students. + ## Testing Requirements All tests must follow these standards: @@ -160,10 +166,27 @@ All tests must follow these standards: - Tests must be independent — runnable in random order without side effects. - Tests must pass on local machines and in CI on macOS, Linux, and Windows. - Aim for full function, statement, and branch coverage (global `fail_under = 98`, direct coverage `= 100%` via `scripts/tsc.py` — every function must have a direct test, enforced by `uv run task test-coverage-check`). +- **Direct-test definition:** `scripts/tsc.py` counts a function as directly + tested only if at least one test function's name contains the target + function's name as a substring (e.g., `test_key_attribute_column_filter` + covers `key_attribute_column_filter`). Indirect coverage through a helper + does not count. Run `uv run task test-coverage-check --verbose` (or + `uv run python -m scripts.tsc --threshold 100 --verbose`) to see which + functions are missing a direct test, then add or rename a `test_` to + include the exact function name. - Property-based tests using `hypothesis` must be marked with `@pytest.mark.propertybased` or `@pytest.mark.fuzz`. - Tests must not produce console output. +## Diagnostic Style + +Cellveyor has a strict UX contract for CLI output that agents must preserve: + +- **Blocking errors** (exit 1, red): missing directory/file, sheet/key not found, invalid regex, missing GitHub args with `--transfer-report`, spreadsheet read or GitHub transfer failure. Use `console.print(..., style="red")` with `:person_shrugging:` prefix and a dash list via `_print_dash_list` for available sheets/columns or missing options, followed by a hint line. Example: `Key attribute 'X' not found` + `Available columns:` + `Hint: check --key-attribute…`. +- **Warnings** (exit 0, yellow): no columns matched, no rows after filtering, no reports generated, malformed or missing feedback files skipped. Use `style="yellow"` with `:warning:` and continue; never promote a warning to exit 1. +- **Exit codes:** `0` for success or warning-only runs; `1` for any blocking error. Keep this invariant when adding new validation for `--feedback-regexp` or other options. +- Test assertions for this output must remain ANSI-tolerant (see next section). + ## CLI Output Testing and Rich Encoding Traps to Avoid Cellveyor renders reports with `rich` (`Console`, `Panel`, `Markdown`) and is invoked via `typer.testing.CliRunner`. A recurring flake is `task test` failing while `task test-parallel` passes (or the converse) on a `CliRunner` assertion: From c9779ede4f0fde5fe7399c32002d7a65e7cc4c49 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:04:26 -0400 Subject: [PATCH 38/50] chore: Update the AGENTS.md file to indicate that not specifying an environment variable can be a blocker. --- AGENTS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/AGENTS.md b/AGENTS.md index c21ff37..865ef3c 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -146,7 +146,7 @@ All Python code must follow these standards: ## Privacy & Security (FERPA / Tokens) - Real gradebooks under `/home/gkapfham/working/data/` and any `CMPSC-*-Gradebook.xlsx` contain FERPA-protected student data. Never commit them, never copy them into `spreadsheets/` or `tests/`, and never paste full rows, emails, or grades into logs, issues, or chat. Use `spreadsheets/fake_spreadsheet.xlsx` for all examples and tests; use `tmp_path` for synthetic sheets. -- Never log or echo a GitHub token. The `transport` command takes `--github-token`; tests must mock `PyGithub` (`tests/test_transfer.py` pattern) and never assert the literal token string. When reproducing a transfer failure, use `TOKEN` or `fake_token` as the placeholder. +- Never log or echo a GitHub token. The `transport` command reads `CELLVEYOR_GITHUB_TOKEN` (fallback `GITHUB_TOKEN`) from env/`.env` (`python-dotenv`, `load_dotenv()` in `main.py`, `chmod 600 .env`, never commit) or from the var named by `--github-token-env` (default `CELLVEYOR_GITHUB_TOKEN`). The CLI never takes a raw token value (`--github-token` was removed). `uv run cellveyor --help` documents `--github-token-env`. Tests must mock `PyGithub` (`tests/test_transfer.py` pattern) and never assert the literal token string. When reproducing a transfer failure, use `TOKEN` or `fake_token` as the placeholder. - When inspecting a real gradebook locally, read only the schema (`df.columns.tolist()`, `df.shape`) or a single anonymized row; avoid dumping `df.to_dict()` for all students. ## Testing Requirements @@ -182,7 +182,7 @@ All tests must follow these standards: Cellveyor has a strict UX contract for CLI output that agents must preserve: -- **Blocking errors** (exit 1, red): missing directory/file, sheet/key not found, invalid regex, missing GitHub args with `--transfer-report`, spreadsheet read or GitHub transfer failure. Use `console.print(..., style="red")` with `:person_shrugging:` prefix and a dash list via `_print_dash_list` for available sheets/columns or missing options, followed by a hint line. Example: `Key attribute 'X' not found` + `Available columns:` + `Hint: check --key-attribute…`. +- **Blocking errors** (exit 1, red): missing directory/file, sheet/key not found, invalid regex, missing GitHub args with `--transfer-report` (`--github-token-env` / `CELLVEYOR_GITHUB_TOKEN` / `GITHUB_TOKEN`), spreadsheet read or GitHub transfer failure. Use `console.print(..., style="red")` with `:person_shrugging:` prefix and a dash list via `_print_dash_list` for available sheets/columns or missing options, followed by a hint line. Example: `Key attribute 'X' not found` + `Available columns:` + `Hint: check --key-attribute…`. - **Warnings** (exit 0, yellow): no columns matched, no rows after filtering, no reports generated, malformed or missing feedback files skipped. Use `style="yellow"` with `:warning:` and continue; never promote a warning to exit 1. - **Exit codes:** `0` for success or warning-only runs; `1` for any blocking error. Keep this invariant when adding new validation for `--feedback-regexp` or other options. - Test assertions for this output must remain ANSI-tolerant (see next section). From ea7240e6644163701b21c2ac7e8b2a898aebd216 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:37:14 -0400 Subject: [PATCH 39/50] refator: Update the cellveyor/main.py file so that there is a new docstring and support for an environment variable for the GitHub token. --- cellveyor/main.py | 39 ++++++++++++++++++++++++++++++++------- 1 file changed, 32 insertions(+), 7 deletions(-) diff --git a/cellveyor/main.py b/cellveyor/main.py index 8cb4318..e476212 100644 --- a/cellveyor/main.py +++ b/cellveyor/main.py @@ -1,15 +1,21 @@ """🚚 Cellveyor is a conveyor for the cells in spreadsheets.""" +import os from pathlib import Path from typing import Dict, List import typer +from dotenv import load_dotenv from rich.console import Console from rich.markdown import Markdown from rich.panel import Panel from cellveyor import constants, data, filesystem, report, transfer +# load CELLVEYOR_GITHUB_TOKEN (and other env vars) from .env if present; +# env vars already set in the shell take precedence (override=False) +load_dotenv() + # create a Typer object to support the command-line interface cli = typer.Typer(no_args_is_help=True) @@ -84,7 +90,7 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 ..., "--feedback-regexp", "-r", - help="Regular expression for matching feedback columns in specific sheet", + help="Regular expression for matching feedback columns in the sheet", ), key_value: str = typer.Option( None, @@ -98,11 +104,11 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 "-f", help="Feedback file(s) in YAML format", ), - github_token: str = typer.Option( + github_token_env: str | None = typer.Option( None, - "--github-token", + "--github-token-env", "-g", - help="GitHub authorization token", + help="Name of env var for GitHub token (CELLVEYOR_GITHUB_TOKEN or GITHUB_TOKEN)", ), github_organization: str = typer.Option( None, @@ -118,10 +124,26 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 ), transfer_report: bool = typer.Option( False, + "--transfer-report/--no-transfer-report", + "-t", help="Transfer a report to GitHub", ), ) -> None: - """Transport a specified spreadsheet.""" + """Generate per-student grade reports from spreadsheet cells and optionally transfer them to GitHub.""" + # resolve GitHub token from env var name (default CELLVEYOR_GITHUB_TOKEN, fallback GITHUB_TOKEN) + # handle direct calls where typer default is OptionInfo (type checker sees str, so use name check) + if ( + github_token_env is None + or type(github_token_env).__name__ == "OptionInfo" + ): # type: ignore[unreachable] + github_token_env = "CELLVEYOR_GITHUB_TOKEN" + # load_dotenv() already populated os.environ from .env + github_token: str | None = os.getenv(github_token_env) + # fallback to GITHUB_TOKEN when using the default var name + if not github_token and github_token_env == "CELLVEYOR_GITHUB_TOKEN": + fallback = os.getenv("GITHUB_TOKEN") + if fallback: + github_token = fallback # determine if the provided directory and file are valid if not filesystem.confirm_valid_file_in_directory( spreadsheet_file, spreadsheet_directory @@ -290,7 +312,9 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 # validate required GitHub arguments before attempting transfer missing_github_args = [] if not github_token: - missing_github_args.append("--github-token") + missing_github_args.append( + "--github-token-env (or set CELLVEYOR_GITHUB_TOKEN / GITHUB_TOKEN in env/.env)" + ) if not github_organization: missing_github_args.append("--github-organization") if not github_repository_prefix: @@ -305,11 +329,12 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 "Missing options", missing_github_args, color="red" ) console.print( - " Hint: provide all GitHub options or omit --transfer-report", + " Hint: set CELLVEYOR_GITHUB_TOKEN in env/.env or use --github-token-env ", style="red", ) console.print() raise typer.Exit(code=1) + assert github_token is not None try: transfer.transfer_reports_to_github( github_token, From edb20a080abf6644437d88b66c5fad80ca6783bc Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:38:09 -0400 Subject: [PATCH 40/50] docs: Update the README.md file with details about the new approach for handling th GitHub auth token. --- README.md | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index cf456f2..d74cb65 100644 --- a/README.md +++ b/README.md @@ -93,7 +93,7 @@ titled with the student's key value. |---|---|---| | `--key-value` / `-v` | Only produce a report for this value of the key attribute | all rows | | `--feedback-file` / `-f` | Feedback file(s) in YAML format (repeatable) | none | -| `--github-token` / `-g` | GitHub authorization token for `--transfer-report` | none | +| `--github-token-env` | Name of env var holding GitHub token for `--transfer-report` (default: `CELLVEYOR_GITHUB_TOKEN`, fallback `GITHUB_TOKEN`; `.env` supported) | `CELLVEYOR_GITHUB_TOKEN` | | `--github-organization` / `-o` | GitHub organization that stores the destination repositories | none | | `--github-repository-prefix` / `-p` | Prefix shared by the destination repositories | none | | `--transfer-report` | Post each report as a comment on the student's GitHub pull request | off | @@ -131,6 +131,23 @@ uv run cellveyor \ --feedback-file spreadsheets/feedback.yml # Reports posted to each student's GitHub pull request +# Preferred: set token via env var or .env (avoids shell history / `ps` leak) +# The token is read from CELLVEYOR_GITHUB_TOKEN (fallback GITHUB_TOKEN) via +# python-dotenv / env. No --github-token flag needed: +CELLVEYOR_GITHUB_TOKEN="$(gh auth token)" uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name Main \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Summary Grade|Final Grade) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" \ + --github-organization \ + --github-repository-prefix \ + --transfer-report +# To use a custom env var name (e.g., per-course token): +# CELLVEYOR_580_TOKEN=ghp_xxx uv run cellveyor ... --github-token-env CELLVEYOR_580_TOKEN --transfer-report +# GITHUB_TOKEN also works as fallback alias for CELLVEYOR_GITHUB_TOKEN +# Option B — .env file (copy .env.example to .env, set CELLVEYOR_GITHUB_TOKEN, then chmod 600 .env): uv run cellveyor \ --spreadsheet-directory spreadsheets \ --spreadsheet-file fake_spreadsheet.xlsx \ @@ -138,7 +155,6 @@ uv run cellveyor \ --key-attribute "Student GitHub" \ --column-regexp "^(Summary Grade|Final Grade) .*$" \ --feedback-regexp "Summary Grade 1 - Feedback" \ - --github-token \ --github-organization \ --github-repository-prefix \ --transfer-report @@ -166,7 +182,7 @@ specific diagnostic and exiting with code `1` when: - the spreadsheet directory or file does not exist (it prints which one is missing), - the requested sheet is not in the spreadsheet (it lists the available sheets), - the key attribute column is not in the sheet (it lists the available columns), -- `--transfer-report` is given without `--github-token`, `--github-organization`, or `--github-repository-prefix` (it lists the missing options), +- `--transfer-report` is given without a token (`CELLVEYOR_GITHUB_TOKEN` / `GITHUB_TOKEN` / `--github-token-env`), `--github-organization`, or `--github-repository-prefix` (it lists the missing options), - reading the spreadsheet or transferring reports to GitHub fails. Missing or malformed feedback files are skipped with a yellow warning @@ -283,6 +299,12 @@ and different feedback files are relevant for different sheets. ## GitHub transfer +Cellveyor reads `CELLVEYOR_GITHUB_TOKEN` (or `GITHUB_TOKEN` as fallback) from +the environment or a `.env` file (`python-dotenv`, `chmod 600 .env`, never +commit). Prefer a fine-grained PAT scoped to your organization with +`contents:write` + `pull-requests:write`, 7-day expiry. Copy +`.env.example` to `.env` or run `CELLVEYOR_GITHUB_TOKEN="$(gh auth token)" uv run cellveyor ...`. + With `--transfer-report`, Cellveyor posts each generated report to GitHub instead of only displaying it. The destination repository for a student is derived from the key value using the GitHub Classroom naming convention: From 3e97967c0e45a9ea382b1060dff9cb4de3e86498 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:38:40 -0400 Subject: [PATCH 41/50] chore: Add the .env.example file as a simple example of what a .env file might look like with additional advice in a comment. --- .env.example | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 .env.example diff --git a/.env.example b/.env.example new file mode 100644 index 0000000..77ee385 --- /dev/null +++ b/.env.example @@ -0,0 +1,5 @@ +# Cellveyor environment file — copy to .env and set your token +# .env is gitignored; never commit real tokens. Run: chmod 600 .env +# Generate a fine-grained PAT scoped to your org with contents:write + pull-requests:write, 7-day expiry +CELLVEYOR_GITHUB_TOKEN=ghp_your_token_here +# Alternative alias (also supported): GITHUB_TOKEN=ghp_your_token_here From e8e8e068877c0663952a508b54c0552174fccc4f Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:41:09 -0400 Subject: [PATCH 42/50] chore: Add python-dotenv as a main dependency in the pyproject.toml file. --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index a71e9f4..14bfae6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,6 +32,7 @@ dependencies = [ "pygithub>=2.1.1,<3.0.0", "pyyaml>=6.0.1,<7.0.0", "typer>=0.20.0,<1.0.0", + "python-dotenv>=1.2.3", ] [project.urls] From 4df66aefc877fbde9e585d31b1877b0720ca783d Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:41:34 -0400 Subject: [PATCH 43/50] chore: Update the uv.lock file with the dependences for the python-dotenv package. --- uv.lock | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/uv.lock b/uv.lock index 2693f38..ff019e7 100644 --- a/uv.lock +++ b/uv.lock @@ -157,6 +157,7 @@ dependencies = [ { name = "openpyxl" }, { name = "pandas" }, { name = "pygithub" }, + { name = "python-dotenv" }, { name = "pyyaml" }, { name = "rich" }, { name = "typer" }, @@ -197,6 +198,7 @@ requires-dist = [ { name = "openpyxl", specifier = ">=3.1.2,<4.0.0" }, { name = "pandas", specifier = ">=2.1.1,<3.0.0" }, { name = "pygithub", specifier = ">=2.1.1,<3.0.0" }, + { name = "python-dotenv", specifier = ">=1.2.3" }, { name = "pyyaml", specifier = ">=6.0.1,<7.0.0" }, { name = "rich", specifier = ">=13.4.2,<14.0.0" }, { name = "typer", specifier = ">=0.20.0,<1.0.0" }, @@ -1308,6 +1310,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427", size = 229892, upload-time = "2024-03-01T18:36:18.57Z" }, ] +[[package]] +name = "python-dotenv" +version = "1.2.3" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/6a/53/ed9d74092561d4b01a2ef1349d52cdbc135e526c245f366b089cfca6de49/python_dotenv-1.2.3.tar.gz", hash = "sha256:a20a594dabeaa385725aa239d5244871c143ecb356add8a20fcf23773a6c3a35", size = 58945, upload-time = "2026-08-16T16:54:54.067Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/0d/17/c5c6b53ddc18f297992099b3d9ec16c855c0ccc83263a21fe4d1c625ec6c/python_dotenv-1.2.3-py3-none-any.whl", hash = "sha256:904552145e8bfed22162c09dab1c2b9b54fefa7b23ba780f4f26ca0316b0f0d9", size = 22780, upload-time = "2026-08-16T16:54:52.473Z" }, +] + [[package]] name = "pytokens" version = "0.4.1" From 2e4090b3ca663e60d54e975a8a349ea38771d6fd Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:42:09 -0400 Subject: [PATCH 44/50] coms: Update the cellveyor/data.py file with a new comment about the filtering approach. --- cellveyor/data.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cellveyor/data.py b/cellveyor/data.py index 6fa2272..ab25f9f 100644 --- a/cellveyor/data.py +++ b/cellveyor/data.py @@ -38,7 +38,7 @@ def key_attribute_column_filter( f"Invalid column regular expression '{column_regexp}': {exc}" ) from exc # avoid duplicate key column when regexp matches the key itself - # (e.g., ".*" or "Student.*") — otherwise row[key] returns a Series + # (e.g., ".*" or "Student.*"); otherwise row[key] returns a Series selected_columns = selected_columns.drop( columns=[key_attribute_name], errors="ignore" ) From bb08698341f02189a1d1b446a372284f0603ef85 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:43:27 -0400 Subject: [PATCH 45/50] test: Update the test cases in the tests/test_main.py file to account for use of the environment variable for GitHub auth. --- tests/test_main.py | 194 ++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 181 insertions(+), 13 deletions(-) diff --git a/tests/test_main.py b/tests/test_main.py index 859cea9..894cf4a 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -333,14 +333,13 @@ def test_transport_with_transfer_mock() -> None: ".*", "--feedback-regexp", ".*", - "--github-token", - "fake", "--github-organization", "org", "--github-repository-prefix", "prefix", "--transfer-report", ], + env={"CELLVEYOR_GITHUB_TOKEN": "fake"}, ) assert result.exit_code == 0 mock.assert_called_once() @@ -368,14 +367,13 @@ def test_transport_transfer_failure() -> None: ".*", "--feedback-regexp", ".*", - "--github-token", - "fake", "--github-organization", "org", "--github-repository-prefix", "prefix", "--transfer-report", ], + env={"CELLVEYOR_GITHUB_TOKEN": "fake"}, ) assert result.exit_code == 1 assert "GitHub transfer failed" in _strip_ansi(result.output) @@ -532,7 +530,6 @@ def test_transport_direct_success() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -551,7 +548,6 @@ def test_transport_direct_invalid_directory() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -573,7 +569,6 @@ def test_transport_direct_invalid_file_in_valid_directory( feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -605,7 +600,6 @@ def test_transport_direct_wrong_sheet() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -641,7 +635,6 @@ def test_transport_direct_wrong_key_attribute() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -686,7 +679,6 @@ def test_transport_direct_with_feedback_missing_file() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=[pathlib.Path("/tmp/notexist.yml")], - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -727,7 +719,6 @@ def test_transport_direct_no_columns_matched() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=False, @@ -759,6 +750,9 @@ def test_transport_direct_transfer_with_mock() -> None: ), patch("cellveyor.main.display_reports"), patch("cellveyor.main.transfer.transfer_reports_to_github") as mock, + patch.dict( + "os.environ", {"CELLVEYOR_GITHUB_TOKEN": "fake"}, clear=False + ), ): main.transport( spreadsheet_directory=pathlib.Path("spreadsheets"), @@ -769,7 +763,6 @@ def test_transport_direct_transfer_with_mock() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token="fake", github_organization="org", github_repository_prefix="prefix", transfer_report=True, @@ -812,9 +805,184 @@ def test_transport_direct_missing_github_args() -> None: feedback_regexp=".*", key_value=None, # type: ignore feedback_file=None, # type: ignore - github_token=None, # type: ignore github_organization=None, # type: ignore github_repository_prefix=None, # type: ignore transfer_report=True, ) assert exc.value.exit_code == 1 + + +def test_transport_with_token_env_default() -> None: + """Test transfer with CELLVEYOR_GITHUB_TOKEN env var (default).""" + runner = CliRunner() + with patch("cellveyor.main.transfer.transfer_reports_to_github") as mock: + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + env={"CELLVEYOR_GITHUB_TOKEN": "fake_from_env"}, + ) + assert result.exit_code == 0 + mock.assert_called_once() + # ensure token from env was used + assert mock.call_args[0][0] == "fake_from_env" + + +def test_transport_with_token_env_fallback_github_token() -> None: + """Test transfer with GITHUB_TOKEN fallback when CELLVEYOR not set.""" + runner = CliRunner() + with patch("cellveyor.main.transfer.transfer_reports_to_github") as mock: + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + env={"GITHUB_TOKEN": "fallback_token"}, + ) + assert result.exit_code == 0 + mock.assert_called_once() + assert mock.call_args[0][0] == "fallback_token" + + +def test_transport_with_custom_token_env() -> None: + """Test transfer with custom --github-token-env var name.""" + runner = CliRunner() + with patch("cellveyor.main.transfer.transfer_reports_to_github") as mock: + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--github-token-env", + "MY_CUSTOM_TOKEN", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + env={"MY_CUSTOM_TOKEN": "custom_token_value"}, + ) + assert result.exit_code == 0 + mock.assert_called_once() + assert mock.call_args[0][0] == "custom_token_value" + + +def test_transport_default_env_without_flag() -> None: + """Test program works without --github-token flag using default env var.""" + runner = CliRunner() + with patch("cellveyor.main.transfer.transfer_reports_to_github") as mock: + # no --github-token, no --github-token-env, but CELLVEYOR set + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + env={"CELLVEYOR_GITHUB_TOKEN": "default_env_token"}, + ) + assert result.exit_code == 0 + mock.assert_called_once() + + +def test_transport_direct_with_token_env() -> None: + """Test direct call with github_token_env resolves correctly.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = fake_df[["Grade"]] + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports"), + patch("cellveyor.main.transfer.transfer_reports_to_github") as mock, + patch.dict("os.environ", {"MY_VAR": "direct_token"}, clear=False), + ): + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token_env="MY_VAR", + github_organization="org", + github_repository_prefix="prefix", + transfer_report=True, + ) + mock.assert_called_once() + assert mock.call_args[0][0] == "direct_token" From 5630ad879d90c560e75e7382054e1f65cd3b653e Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:47:16 -0400 Subject: [PATCH 46/50] chore: Update the .github/workflows/build.yml file so that it runs all commands in more versions of Python. --- .github/workflows/build.yml | 104 ++++++++++++++++++------------------ 1 file changed, 52 insertions(+), 52 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 3a5fdac..d773257 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -11,9 +11,9 @@ env: # Focuses on the master branch only on: push: - branches: [ master ] + branches: [master] pull_request: - branches: [ master ] + branches: [master] # Create one single job # This job performs all of the necessary checks @@ -28,58 +28,58 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: ["3.11", "3.13"] + python-version: ["3.11", "3.12", "3.13", "3.14"] include: - os: macos-latest - python-version: "3.11" + python-version: ["3.11", "3.12", "3.13", "3.14"] - os: windows-latest - python-version: "3.11" + python-version: ["3.11", "3.12", "3.13", "3.14"] # Define the workflow steps steps: - # Checkout the code of the repository - - name: Check out Repository Code - uses: actions/checkout@v4 - with: - fetch-depth: 0 - # Setup Python for the current language version - - name: Setup Python ${{ matrix.python-version }} - if: always() - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - # Install uv - - name: Install uv - if: always() - uses: astral-sh/setup-uv@v5 - with: - enable-cache: true - # Install dependencies - - name: Install dependencies - if: always() - run: | - uv sync --group dev - # Run the linters (including the rumdl markdown linter) - - name: Run Linters - if: always() - run: | - uv run task lint - # Run the type checkers - - name: Run Type Checks - if: always() - run: | - uv run task typecheck - # Run the program - - name: Run program - if: always() - run: | - uv run cellveyor --spreadsheet-directory $PWD/spreadsheets/ --spreadsheet-file $PWD/spreadsheets/fake_spreadsheet.xlsx --sheet-name Main --key-attribute "Student GitHub" --key-value "gkapfham" --column-regexp '^(Summary Grade|Final Grade) .*$' --feedback-regexp "Summary Grade 1 - Feedback" --feedback-file $PWD/spreadsheets/feedback.yml - # Run the tests - - name: Run Tests - if: always() - run: | - uv run task test - # Enforce the coverage threshold (Linux only) - - name: Run Coverage Check - if: matrix.os == 'ubuntu-latest' - run: | - uv run task test-coverage + # Checkout the code of the repository + - name: Check out Repository Code + uses: actions/checkout@v4 + with: + fetch-depth: 0 + # Setup Python for the current language version + - name: Setup Python ${{ matrix.python-version }} + if: always() + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + # Install uv + - name: Install uv + if: always() + uses: astral-sh/setup-uv@v5 + with: + enable-cache: true + # Install dependencies + - name: Install dependencies + if: always() + run: | + uv sync --group dev + # Run the linters (including the rumdl markdown linter) + - name: Run Linters + if: always() + run: | + uv run task lint + # Run the type checkers + - name: Run Type Checks + if: always() + run: | + uv run task typecheck + # Run the program + - name: Run program + if: always() + run: | + uv run cellveyor --spreadsheet-directory $PWD/spreadsheets/ --spreadsheet-file $PWD/spreadsheets/fake_spreadsheet.xlsx --sheet-name Main --key-attribute "Student GitHub" --key-value "gkapfham" --column-regexp '^(Summary Grade|Final Grade) .*$' --feedback-regexp "Summary Grade 1 - Feedback" --feedback-file $PWD/spreadsheets/feedback.yml + # Run the tests + - name: Run Tests + if: always() + run: | + uv run task test + # Enforce the coverage threshold (Linux only) + - name: Run Coverage Check + if: matrix.os == 'ubuntu-latest' + run: | + uv run task test-coverage From 5cb631cfb3ad0fc250624e8a80be6e765064747c Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 19:50:53 -0400 Subject: [PATCH 47/50] fix: Correct mistakes in the workflow for the versions of the Python and the names of the operating systems in the .github/workflows/build.yml file. --- .github/workflows/build.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d773257..b70929f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -27,13 +27,8 @@ jobs: strategy: fail-fast: false matrix: - os: [ubuntu-latest] + os: [ubuntu-latest, macos-latest, windows-latest] python-version: ["3.11", "3.12", "3.13", "3.14"] - include: - - os: macos-latest - python-version: ["3.11", "3.12", "3.13", "3.14"] - - os: windows-latest - python-version: ["3.11", "3.12", "3.13", "3.14"] # Define the workflow steps steps: # Checkout the code of the repository From 64a326e8348a9cb819880025a017531dab92610b Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 20:19:13 -0400 Subject: [PATCH 48/50] feat: Add a --no-fancy flag to display plain markdown for copying in the cellveyor/main.py file. --- cellveyor/main.py | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/cellveyor/main.py b/cellveyor/main.py index e476212..77a1c6f 100644 --- a/cellveyor/main.py +++ b/cellveyor/main.py @@ -37,10 +37,18 @@ def _print_dash_list(title: str, items: List[str], color: str = "red") -> None: console.print() -def display_reports(reports_dict: Dict[str, str]) -> None: +def display_reports(reports_dict: Dict[str, str], fancy: bool = True) -> None: """Display all of the reports in the reports dictionary.""" # iterate through all of the keys for current_report_key, current_report in reports_dict.items(): + # when fancy is false, print plain markdown for copying; + # when fancy is true, wrap in rich panel with title + if not fancy: + console.print(f"{current_report_key}:") + console.print() + console.print(Markdown(current_report)) + console.print() + continue # display the report inside of a rich panel, using # a markdown-based formatter for the report's contents; # note that use of console.print must occur in two @@ -128,8 +136,19 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 "-t", help="Transfer a report to GitHub", ), + fancy: bool = typer.Option( + True, + "--fancy/--no-fancy", + "-y", + help="Display reports with rich Panel (default: fancy); use --no-fancy for plain markdown for copying", + ), ) -> None: """Generate per-student grade reports from spreadsheet cells and optionally transfer them to GitHub.""" + # handle direct calls where typer defaults are OptionInfo + if type(transfer_report).__name__ == "OptionInfo": # type: ignore[unreachable] + transfer_report = False # type: ignore[assignment] + if type(fancy).__name__ == "OptionInfo": # type: ignore[unreachable] + fancy = True # type: ignore[assignment] # resolve GitHub token from env var name (default CELLVEYOR_GITHUB_TOKEN, fallback GITHUB_TOKEN) # handle direct calls where typer default is OptionInfo (type checker sees str, so use name check) if ( @@ -304,7 +323,7 @@ def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 ) console.print() # display the generated reports - display_reports(per_key_report) + display_reports(per_key_report, fancy) # if the --transfer flag was enabled then this means # that the generated reports should be uploaded to GitHub # as a comment inside of the standard pull request From 4db364d1d36c54caae0bb2bcf8bb410c718fd4a9 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 20:19:30 -0400 Subject: [PATCH 49/50] test: Add test cases for the new feature in main.py. --- tests/test_main.py | 216 ++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 215 insertions(+), 1 deletion(-) diff --git a/tests/test_main.py b/tests/test_main.py index 894cf4a..61bf4a6 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -2,7 +2,7 @@ import pathlib import re -from unittest.mock import patch +from unittest.mock import MagicMock, patch import pandas as pd import pytest @@ -986,3 +986,217 @@ def test_transport_direct_with_token_env() -> None: ) mock.assert_called_once() assert mock.call_args[0][0] == "direct_token" + + +def test_display_reports_fancy_true() -> None: + """Test display_reports with fancy true shows Panel.""" + reports = {"alice": "**Hello @alice!**\n\n- **Grade**: 90\n"} + main.display_reports(reports, fancy=True) + main.display_reports(reports) + + +def test_display_reports_fancy_false() -> None: + """Test display_reports with fancy false shows plain markdown.""" + reports = {"alice": "**Hello @alice!**\n\n- **Grade**: 90\n"} + main.display_reports(reports, fancy=False) + main.display_reports({}, fancy=False) + + +def test_transport_with_fancy() -> None: + """Test transport with --fancy shows Panel.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--fancy", + ], + ) + assert result.exit_code == 0 + # fancy panel contains box characters + assert "gkapfham" in _strip_ansi(result.output) + + +def test_transport_with_no_fancy() -> None: + """Test transport with --no-fancy shows plain markdown without Panel.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--no-fancy", + ], + ) + assert result.exit_code == 0 + output = _strip_ansi(result.output) + assert "gkapfham" in output + # plain mode prints "gkapfham:" header, not Panel border + assert "gkapfham:" in output + # panel uses "╭" box, plain should not + assert "╭" not in output + + +def test_transport_direct_with_fancy_false() -> None: + """Test direct call with fancy false.""" + fake_df = pd.DataFrame({"Student GitHub": ["alice"], "Grade": [90]}) + fake_dict = {"Main": fake_df} + selected = fake_df[["Grade"]] + result_df = fake_df + with ( + patch( + "cellveyor.main.filesystem.confirm_valid_file_in_directory", + return_value=True, + ), + patch( + "cellveyor.main.filesystem.read_feedback_files", return_value={} + ), + patch("cellveyor.main.data.access_dataframes", return_value=fake_dict), + patch( + "cellveyor.main.data.key_attribute_column_filter", + return_value=(selected, result_df), + ), + patch( + "cellveyor.main.report.create_per_key_report", + return_value={"alice": "report"}, + ), + patch("cellveyor.main.display_reports") as mock_display, + ): + main.transport( + spreadsheet_directory=pathlib.Path("spreadsheets"), + spreadsheet_file=pathlib.Path("fake_spreadsheet.xlsx"), + sheet_name="Main", + key_attribute="Student GitHub", + column_regexp=".*", + feedback_regexp=".*", + key_value=None, # type: ignore + feedback_file=None, # type: ignore + github_token_env=None, + github_organization=None, # type: ignore + github_repository_prefix=None, # type: ignore + transfer_report=False, + fancy=False, + ) + mock_display.assert_called_once() + # ensure display_reports was called with fancy=False + assert mock_display.call_args[0][1] is False + + +def test_display_reports_plain_spacing() -> None: + """Test plain mode has blank line between key and content.""" + reports = { + "gabrielsalvatore": "**Hello @gabrielsalvatore!**\n\n- **Grade**: 90\n" + } + # use helper directly to avoid spreadsheet setup + # capture plain output + with patch("cellveyor.main.console") as mock_console: + # mock console to capture calls + mock_console.print = MagicMock() + main.display_reports(reports, fancy=False) + # first call is "gabrielsalvatore:", second is blank, third is markdown + calls = [str(c) for c in mock_console.print.call_args_list] + assert any("gabrielsalvatore:" in str(c) for c in calls) + # ensure blank line call exists (empty string or no arg) + assert mock_console.print.call_count >= 3 # noqa: PLR2004 + + +def test_transport_with_y_fancy() -> None: + """Test -y sets --fancy and shows Panel.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "-y", + ], + ) + assert result.exit_code == 0 + output = _strip_ansi(result.output) + assert "gkapfham" in output + assert "╭" in output + + +def test_transport_with_no_transfer_long() -> None: + """Test --no-transfer-report long form does not require token.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + ".*", + "--feedback-regexp", + ".*", + "--no-transfer-report", + "--github-organization", + "org", + "--github-repository-prefix", + "prefix", + ], + ) + assert result.exit_code == 0 + + +def test_transport_with_no_fancy_long() -> None: + """Test --no-fancy long form shows plain output.""" + runner = CliRunner() + result = runner.invoke( + main.cli, + [ + "--spreadsheet-directory", + "spreadsheets", + "--spreadsheet-file", + "fake_spreadsheet.xlsx", + "--sheet-name", + "Main", + "--key-attribute", + "Student GitHub", + "--column-regexp", + "^(Summary Grade|Final Grade) .*$", + "--feedback-regexp", + "Summary Grade 1 - Feedback", + "--no-fancy", + ], + ) + assert result.exit_code == 0 + assert "╭" not in _strip_ansi(result.output) + assert "gkapfham:" in _strip_ansi(result.output) From fe68bdb636f77fe947382f8b2bb24a871d800725 Mon Sep 17 00:00:00 2001 From: "Gregory M. Kapfhammer" Date: Sat, 29 Aug 2026 20:19:47 -0400 Subject: [PATCH 50/50] docs: Update the README.md file with more details about two of the boolean command-line argument, including one that is new. --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index d74cb65..8fc2afe 100644 --- a/README.md +++ b/README.md @@ -93,10 +93,11 @@ titled with the student's key value. |---|---|---| | `--key-value` / `-v` | Only produce a report for this value of the key attribute | all rows | | `--feedback-file` / `-f` | Feedback file(s) in YAML format (repeatable) | none | -| `--github-token-env` | Name of env var holding GitHub token for `--transfer-report` (default: `CELLVEYOR_GITHUB_TOKEN`, fallback `GITHUB_TOKEN`; `.env` supported) | `CELLVEYOR_GITHUB_TOKEN` | +| `--github-token-env` / `-g` | Name of env var holding GitHub token for `--transfer-report` (default: `CELLVEYOR_GITHUB_TOKEN`, fallback `GITHUB_TOKEN`; `.env` supported) | `CELLVEYOR_GITHUB_TOKEN` | | `--github-organization` / `-o` | GitHub organization that stores the destination repositories | none | | `--github-repository-prefix` / `-p` | Prefix shared by the destination repositories | none | -| `--transfer-report` | Post each report as a comment on the student's GitHub pull request | off | +| `--transfer-report` / `-t` | Post each report as a comment on the student's GitHub pull request (`--no-transfer-report` to disable) | off | +| `--fancy` / `-y` | Display reports with rich Panel (`--no-fancy` for plain markdown for copying) | on | **Examples:**