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 diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index f454f37..b70929f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -11,80 +11,70 @@ 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 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"] - include: - - os: macos-latest - python-version: "3.11" - - os: windows-latest - python-version: "3.11" + os: [ubuntu-latest, macos-latest, windows-latest] + 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@v3 - 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 - with: - python-version: ${{ matrix.python-version }} - # Install pip - - name: Install Pip - if: always() - run: | - python -m pip install --upgrade pip - # Install poetry - - name: Install Poetry - if: always() - uses: abatilo/actions-poetry@v2.0.0 - with: - poetry-version: 1.4.0 - # Install dependencies - - name: Install dependencies - if: always() - run: | - poetry install - # Run the linters - - name: Run Linters - if: always() - run: | - poetry 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/ - # Run the tests - - name: Run Tests - if: always() - run: | - poetry run task test + # 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 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/.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/.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 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) diff --git a/AGENTS.md b/AGENTS.md new file mode 100644 index 0000000..865ef3c --- /dev/null +++ b/AGENTS.md @@ -0,0 +1,221 @@ +# 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 = 100` 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`. + +## 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 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 + +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 `= 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` (`--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). + +## 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. 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 diff --git a/README.md b/README.md index 843404d..8fc2afe 100644 --- a/README.md +++ b/README.md @@ -1,71 +1,362 @@ 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) -## 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. 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 +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 ``` -poetry 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 + +### `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-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` / `-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:** + +```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$" \ + --feedback-file spreadsheets/feedback.yml + +# Reports posted to each student's GitHub pull request +# Preferred: set token via env var or .env (avoids shell history / `ps` leak) +# The token is read from CELLVEYOR_GITHUB_TOKEN (fallback GITHUB_TOKEN) via +# python-dotenv / env. No --github-token flag needed: +CELLVEYOR_GITHUB_TOKEN="$(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) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" \ + --github-organization \ + --github-repository-prefix \ + --transfer-report +# To use a custom env var name (e.g., per-course token): +# CELLVEYOR_580_TOKEN=ghp_xxx uv run cellveyor ... --github-token-env CELLVEYOR_580_TOKEN --transfer-report +# GITHUB_TOKEN also works as fallback alias for CELLVEYOR_GITHUB_TOKEN +# Option B — .env file (copy .env.example to .env, set CELLVEYOR_GITHUB_TOKEN, then chmod 600 .env): +uv run cellveyor \ + --spreadsheet-directory spreadsheets \ + --spreadsheet-file fake_spreadsheet.xlsx \ + --sheet-name Main \ + --key-attribute "Student GitHub" \ + --column-regexp "^(Summary Grade|Final Grade) .*$" \ + --feedback-regexp "Summary Grade 1 - Feedback" \ + --github-organization \ + --github-repository-prefix \ + --transfer-report +``` + +**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 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 +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 +🚚 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'}] +``` + +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). +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. 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. +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 +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 + +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: + +```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 ``` -## 🎉 Introduction +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. -- 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. +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. -## 😂 Definitions +## Exit codes -- 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" +| 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 | -## 🔋Features +## Example spreadsheet -- 🚀 Fully customizable command line interface -- ✨ Automated generation of grade-based reports sent to students -- 🪂 Rich command line interface with many various arguments +The `spreadsheets/` directory contains a small example gradebook that all of +the examples above use: -## ⚡️ Requirements +| 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` | -- Cellveyor git hub repository -- Local google sheet -- Git hub token +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`. -## 🔽 Installation +## License -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 +GNU General Public License v3.0 (see the `LICENSE` file in this repository). 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 adfd3a3..ab25f9f 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]: @@ -26,15 +26,27 @@ 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: + 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 - # 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 + # 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[ [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 @@ -44,4 +56,4 @@ 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/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..77a1c6f 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) @@ -17,12 +23,32 @@ console = Console() -def display_reports(reports_dict: Dict[str, str]) -> None: +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], fancy: bool = True) -> 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(): + # 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 @@ -37,7 +63,7 @@ def display_reports(reports_dict: Dict[str, str]) -> None: @cli.command() -def transport( # noqa: PLR0913 +def transport( # noqa: PLR0912, PLR0913, PLR0915, PLR0917 spreadsheet_directory: Path = typer.Option( ..., "--spreadsheet-directory", @@ -72,7 +98,7 @@ def transport( # noqa: PLR0913 ..., "--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, @@ -84,13 +110,13 @@ def transport( # noqa: PLR0913 None, "--feedback-file", "-f", - help="Feedback file(s) in JSON format", + 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, @@ -106,22 +132,82 @@ def transport( # noqa: PLR0913 ), transfer_report: bool = typer.Option( False, + "--transfer-report/--no-transfer-report", + "-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: - """Transport a specified spreadsheet.""" + """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 ( + 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 ): + console.print() console.print( - ":person_shrugging: Unable to access file and/or directory" + ":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(" 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" - {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: + 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 @@ -134,35 +220,151 @@ 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":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":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: + console.print( + f":person_shrugging: Sheet '{sheet_name}' not found", style="red" + ) + console.print() + _print_dash_list( + "Available sheets", + list(sheet_dataframe_dict.keys()), + color="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":person_shrugging: {exc}", style="red") + console.print() + # also show available columns for key attribute errors + if "Key attribute" in str(exc): + _print_dash_list( + "Available columns", + list(map(str, sheet_dataframe.columns.tolist())), + color="red", + ) + console.print( + " Hint: check --key-attribute and --column-regexp", + style="red", + ) + console.print() + raise typer.Exit(code=1) + except Exception as exc: + console.print( + 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":warning: No columns matched --column-regexp '{column_regexp}'", + style="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( + ":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 - 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":person_shrugging: Failed to create reports: {exc}", style="red" + ) + console.print() + raise typer.Exit(code=1) + if not per_key_report: + console.print( + ":warning: No reports generated (no matching rows)", style="yellow" + ) + 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 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-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: + missing_github_args.append("--github-repository-prefix") + if missing_github_args: + console.print( + ":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( + " 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, + github_organization, + github_repository_prefix, + per_key_report, + ) + except Exception as exc: + console.print( + f":person_shrugging: GitHub transfer failed: {exc}", + style="red", + ) + console.print() + raise typer.Exit(code=1) diff --git a/cellveyor/report.py b/cellveyor/report.py index 4773eb6..6d5e7b6 100644 --- a/cellveyor/report.py +++ b/cellveyor/report.py @@ -1,6 +1,7 @@ """Create reports based on content in dataframes.""" -from typing import Dict, List +import math +from typing import Any, Dict, List from pandas import DataFrame @@ -21,7 +22,7 @@ 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: @@ -34,6 +35,9 @@ 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 +47,8 @@ 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 @@ -69,7 +74,7 @@ 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: @@ -106,24 +111,47 @@ 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}" ) # 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 +159,14 @@ 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..4bc80b3 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, @@ -57,8 +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 @@ -69,8 +70,39 @@ 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() + console.print( + ":person_shrugging: GitHub token is missing (--github-token)", + style="red", + ) + console.print() + return + if not github_organization: + console.print() + console.print( + ":person_shrugging: GitHub organization is missing (--github-organization)", + style="red", + ) + console.print() + return + if not github_repository_prefix: + console.print() + console.print( + ":person_shrugging: GitHub repository prefix is missing (--github-repository-prefix)", + style="red", + ) + console.print() + return + if not github_reports_dict: + 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 + # 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( @@ -127,25 +159,49 @@ 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/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. 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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", + "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", +] -[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" - 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= 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 = [ - "E501", # do not check line length +lint.ignore = [ + "D203", + "D213", + "E501", ] -select = [ - "E", # pycodestyle errors - "I", # isort - "F", # Pyflakes - "PL", # pylint - "Q", # flake8-quotes - "RUF", # ruff-specific - "W", # pycodestyle warnings - "T201" # flake8-print +lint.select = [ + "E", + "D", + "I", + "F", + "PL", + "Q", + "RUF", + "W", + "T201", ] [tool.isort] @@ -62,36 +148,82 @@ 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" +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 } +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" -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 = "poetry 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" } +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 } +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 } -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +[tool.uv.sources] +pytest-intentional = { path = "/home/gkapfham/working/source/pytest-intentional", editable = 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/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_data.py b/tests/test_data.py index af7eb1e..98ff1e3 100644 --- a/tests/test_data.py +++ b/tests/test_data.py @@ -1,11 +1,14 @@ -"""Pytest test suite for the filesystem module.""" +"""Pytest test suite for the data module.""" from pathlib import Path -from cellveyor import data +import pandas + +from cellveyor import data, report 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 +17,7 @@ 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") ) @@ -32,3 +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) diff --git a/tests/test_filesystem.py b/tests/test_filesystem.py index 4da8e07..b1a86d1 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 +55,152 @@ 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"} + + +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) diff --git a/tests/test_main.py b/tests/test_main.py new file mode 100644 index 0000000..61bf4a6 --- /dev/null +++ b/tests/test_main.py @@ -0,0 +1,1202 @@ +"""Pytest test suite for the main module.""" + +import pathlib +import re +from unittest.mock import MagicMock, patch + +import pandas as pd +import pytest +import typer +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-organization", + "org", + "--github-repository-prefix", + "prefix", + "--transfer-report", + ], + env={"CELLVEYOR_GITHUB_TOKEN": "fake"}, + ) + 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-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) + + +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) + + +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_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_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_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_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_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_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_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, + patch.dict( + "os.environ", {"CELLVEYOR_GITHUB_TOKEN": "fake"}, 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_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_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" + + +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) diff --git a/tests/test_report.py b/tests/test_report.py new file mode 100644 index 0000000..fa448e9 --- /dev/null +++ b/tests/test_report.py @@ -0,0 +1,231 @@ +"""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"] + + +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 + + +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.""" + 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..73d699d --- /dev/null +++ b/tests/test_transfer.py @@ -0,0 +1,189 @@ +"""Pytest test suite for the transfer module.""" + +from unittest.mock import MagicMock, patch + +import pytest +from github import GithubException + +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" + ) + + +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" + ) 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() 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