refactor: residual coverage, uv, and migration

.github/workflows/mkdocs-build.yml

@@ -0,0 +1,11 @@
+name: MkDocs Build (RationAI Standard)
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+jobs:
+  run:
+    uses: RationAI/.github/.github/workflows/mkdocs-build.yml@main

.github/workflows/python-lint.yml

@@ -0,0 +1,11 @@
+name: Python Lint (RationAI Standard)
+on:
+  push:
+    branches: ["master"]
+  pull_request:
+    branches: ["master"]
+  workflow_dispatch:
+
+jobs:
+  run:
+    uses: RationAI/.github/.github/workflows/python-lint.yml@main

.markdownlint.yaml

@@ -0,0 +1,6 @@
+MD013: false  # Line length
+MD023: false  # Heading start left
+MD024: false  # Duplicate headings
+MD033: false  # Inline HTML
+MD041: false  # First line in file should be a top level heading
+MD046: false  # Fenced code blocks

.mypy.ini

@@ -3,4 +3,8 @@ strict = True
 ignore_missing_imports = True
 disallow_untyped_calls = False
 disable_error_code = no-any-return
-explicit_package_bases = True
+explicit_package_bases = True
+
+# Ignore type errors in the external piqe.py file
+[mypy-rationai.qc.blur.piqe]
+ignore_errors = True

.pre-commit-config.yaml

@@ -8,16 +8,15 @@ repos:
         args: [--unsafe]
 
   - repo: https://github.com/commitizen-tools/commitizen
-    rev: v4.8.3
+    rev: v4.10.0
     hooks:
       - id: commitizen
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.10
+    rev: v0.14.10
     hooks:
       # Run the linter.
-      - id: ruff
-        entry: pdm lint --force-exclude
+      - id: ruff-check
+        args: [--fix]
       # Run the formatter.
       - id: ruff-format
-        entry: pdm format --force-exclude

.ruff.toml

@@ -2,6 +2,8 @@ fix = true
 line-length = 88
 target-version = "py311"
 
+extend-exclude = ["rationai/qc/blur/piqe.py"]
+
 [format]
 # Enable reformatting of code snippets in docstrings.
 docstring-code-format = true
@@ -20,10 +22,10 @@ extend-select = [
     "PGH", # pygrep
     "RUF", # ruff checks
     "SIM", # flake8-simplify
-    "TCH", # flake8-type-checking
+    "TC",  # flake8-type-checking
     "TID", # flake8-tidy-imports
     "UP",  # pyupgrade
-    "D",   # pydocstyle 
+    "D",   # pydocstyle    
 ]
 extend-ignore = [
     "ERA001", # commented out code
@@ -36,7 +38,7 @@ extend-ignore = [
     "D106",   # missing docstring in public nested class
     "D107",   # missing docstring in __init__
     "N812",   # lowercase imported as non lowercase
-    "TCH002", # move third-party into a type-checking block
+    "TC002",  # move third-party into a type-checking block
     "F722",   # jaxtyping
 ]
 

README.md

@@ -5,4 +5,21 @@ for QC methods** developed at RationAI. These functions are meant to be run on s
 regions and they **offer a straightforward and well-documented access** to the key parts
 of the complete QC methods to allow for easier debugging and experimenting.
 
-TODO: Add link to mkdocs documentation
+## Documentation
+
+**[`RationAI Quality Control`](https://rationai.github.io/quality-control/)**
+
+## Setting up a Development Environment
+
+1. Create the development environment (including all optional and development dependencies):
+
+    ```bash
+    uv sync --all-groups
+    ```
+
+2. Install pre-commit hooks:
+
+    ```bash
+    uv run pre-commit install
+    uv run pre-commit install --hook-type commit-msg
+    ```

docs/getting-started/installation.md

@@ -1,4 +1,4 @@
-1.  ### Install **pyvips** for Efficient Image Processing
+1. ### Install **pyvips** for Efficient Image Processing
 
     [Pyvips](https://pypi.org/project/pyvips/2.0.2/) is a powerful and fast image processing library, particularly suited for working with large images like WSIs. To install `pyvips`, ensure that the `libvips` system dependencies are installed first:
 
@@ -18,41 +18,21 @@
 
     Follow the instructions on the official [libvips installation page](https://www.libvips.org/install.html).
 
-
-2.  ### Install the Core Quality Control Library
+2. ### Install the Core Quality Control Library
 
     You can install the core library using one of the following methods, depending on your package manager:
 
-    === "pdm"
-
-        ```bash
-        pdm add git+https://gitlab.ics.muni.cz/rationai/digital-pathology/quality-control/quality-control.git
-        ```
-
-    === "pip"
-
-        ```bash
-        pip install git+https://gitlab.ics.muni.cz/rationai/digital-pathology/quality-control/quality-control.git
-        ```
-
-    #### Installing a Specific Version
-
-    To install a specific version of the **Quality Control** library, use the following command, replacing `v1.0.0` with your desired version.
-
-    === "pdm"
+    === "uv"
+        (*Note that this command assumes an existing uv project.*)
 
         ```bash
-        pdm add git+https://gitlab.ics.muni.cz/rationai/digital-pathology/quality-control/quality-control.git@v1.0.0
+        uv add git+https://github.com/RationAI/quality-control.git
         ```
 
     === "pip"
 
         ```bash
-        pip install git+https://gitlab.ics.muni.cz/rationai/digital-pathology/quality-control/quality-control.git@v1.0.0
+        pip install git+https://github.com/RationAI/quality-control.git
         ```
 
-    !!! info
-
-        Replace `v1.0.0` with the specific version you want to install.
-
 Once **pyvips**, and the core library are installed, you're ready to start using QC functions.