refactor: make pydcmqi robust and usable

.github/workflows/cd.yml

@@ -25,11 +25,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: hynek/build-and-inspect-python-package@v2
+      - uses: hynek/build-and-inspect-python-package@v2.15.0
 
   publish:
     needs: [dist]
@@ -41,12 +41,12 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v8
         with:
           name: Packages
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@release/v1
+      - uses: pypa/gh-action-pypi-publish@v1.13.0
         if: github.event_name == 'release' && github.event.action == 'published'
         with:
           # Remember to tell (test-)pypi about this repo before publishing

.github/workflows/ci.yml

@@ -21,10 +21,10 @@ jobs:
     name: Format
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.x"
       - uses: pre-commit/action@v3.0.1
@@ -42,19 +42,15 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.12"]
+        python-version: ["3.10", "3.12"]
         runs-on: [ubuntu-latest, macos-latest, windows-latest]
 
-        include:
-          - python-version: pypy-3.10
-            runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           allow-prereleases: true
@@ -68,6 +64,6 @@ jobs:
           --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v5.1.2
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -73,6 +73,15 @@ repos:
         entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
         exclude: .pre-commit-config.yaml
 
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: python
+        types: [python]
+        files: ^src/
+        require_serial: true
+        additional_dependencies: ["pylint", "numpy", "SimpleITK"]
+
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: "v0.16"
     hooks:

CLAUDE.md

@@ -0,0 +1,52 @@
+# CLAUDE.md
+
+## Project
+
+pydcmqi — Python API wrapper for dcmqi (DICOM quantitative imaging) CLI tools.
+
+## Development
+
+- Python 3.10+
+- Uses `hatchling` + `hatch-vcs` for build/versioning
+- Install for development: `.venv/bin/pip install -e ".[test]"`
+- Pre-commit hooks configured (ruff, mypy, pylint, prettier, codespell, etc.)
+
+## Before committing
+
+Always run pre-commit hooks before committing:
+
+```bash
+.venv/bin/pre-commit run --all-files
+```
+
+Fix any failures before creating the commit. Do not skip hooks with
+`--no-verify`.
+
+## Testing
+
+```bash
+.venv/bin/pytest tests/
+```
+
+Integration tests (TestSegimageRead, TestSegimageWrite) require network access
+to download DICOM data from IDC.
+
+## Linting
+
+```bash
+.venv/bin/pre-commit run --all-files   # all hooks including mypy and pylint
+.venv/bin/ruff check src/ tests/       # ruff only
+.venv/bin/mypy src/ tests/             # mypy only
+```
+
+## Project structure
+
+```
+src/pydcmqi/
+├── __init__.py      # Public API exports
+├── types.py         # TypedDicts, Literal types
+├── exceptions.py    # DcmqiError
+├── triplet.py       # Triplet class (DICOM code triplet)
+├── segment.py       # SegmentData, Segment
+├── segimage.py      # SegImageData, SegImageFiles, SegImage (orchestrator)
+```