feat: Add competing risks models and enhance data visualization

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 120
+extend-ignore = E501,W291,W293,W391,F401,F841,E402,E302,E305

.github/workflows/bump-version.yml

@@ -1,67 +1,26 @@
 # .github/workflows/bump-version.yml
-name: Bump Version on Merge to Main
- 
+name: Tag Version on Merge to Main
+
 on:
   push:
     branches:
       - main
 
 jobs:
-  bump-version:
+  tag-version:
     runs-on: ubuntu-latest
     permissions:
       contents: write
-      id-token: write
 
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: 0  # Fetch all history for all branches and tags
+          fetch-depth: 0
 
       - uses: actions/setup-python@v5
         with:
           python-version: "3.11"
 
-      - run: pip install python-semantic-release
-
-      - name: Configure Git
-        run: |
-          git config user.name "github-actions[bot]"
-          git config user.email "github-actions[bot]@users.noreply.github.com"
-
-      - name: Run Semantic Release
-        env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: semantic-release version
+      - name: Tag repository from pyproject
+        run: python scripts/check_version_match.py --fix
 
-      - name: Push changes
-        run: |
-          git push --follow-tags
-      - name: "Install Poetry"
-        run: pip install poetry
-      - name: "Determine version bump type"
-        run: |
-            git fetch --tags
-            # This defaults to a patch type, unless a feature commit was pushed, then set type to minor
-            LAST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
-            LAST_COMMIT=$(git log -1 --format='%H')
-            echo "Last git tag: $LAST_TAG"
-            echo "Last git commit: $LAST_COMMIT"
-            echo "Commits:"
-            git log --no-merges --pretty=oneline $LAST_TAG...$LAST_COMMIT
-            git log --no-merges --pretty=format:"%s" $LAST_TAG...$LAST_COMMIT | grep -q ^feat: && BUMP_TYPE="minor" || BUMP_TYPE="patch"
-            echo "Version bump type: $BUMP_TYPE"
-            echo "BUMP_TYPE=$BUMP_TYPE" >> $GITHUB_ENV
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: "Version bump"
-        run: |
-            poetry version $BUMP_TYPE
-      - name: "Push new version"
-        run: |
-            git add pyproject.toml
-            git commit -m "Update version to $(poetry version -s)"
-            git pull --ff-only origin main
-            git push origin main --follow-tags
-        env:
-            GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci.yml

@@ -0,0 +1,65 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    name: Test with Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: poetry install --with dev
+
+      - name: Run tests with coverage
+        run: poetry run pytest --cov=gen_surv --cov-report=xml --cov-report=term
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: coverage.xml
+          token: ${{ secrets.CODECOV_TOKEN }}  # optional if public repo
+
+  lint:
+    name: Code Quality
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: poetry install --with dev
+
+      - name: Run pre-commit checks
+        run: poetry run pre-commit run --all-files

.github/workflows/docs.yml

@@ -0,0 +1,27 @@
+name: Documentation Build
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install Poetry
+        run: pip install poetry
+      - name: Install dependencies
+        run: poetry install --with docs
+      - name: Build documentation
+        run: poetry run sphinx-build -W -b html docs/source docs/build
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build/

.github/workflows/test.yml

@@ -9,6 +9,9 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - name: Checkout code
@@ -17,15 +20,15 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: ${{ matrix.python-version }}
 
       - name: Install Poetry
         run: |
           curl -sSL https://install.python-poetry.org | python3 -
           echo "$HOME/.local/bin" >> $GITHUB_PATH
 
       - name: Install dependencies
-        run: poetry install
+        run: poetry install --with dev
 
       - name: Run tests
         run: poetry run pytest --cov=gen_surv --cov-report=xml --cov-report=term

.gitignore

@@ -50,3 +50,4 @@ dist/
 # Temporary
 *.log
 *.tmp
+.hypothesis/

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 24.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.15.0
+    hooks:
+      - id: mypy

.readthedocs.yml

@@ -4,10 +4,22 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
+  jobs:
+    post_create_environment:
+      - pip install poetry
+    post_install:
+      - poetry config virtualenvs.create false
+      - poetry install --with docs
 
 python:
   install:
-    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
 
 sphinx:
   configuration: docs/source/conf.py
+  fail_on_warning: false
+
+formats:
+  - pdf
+  - epub

CHANGELOG.md

@@ -1,5 +1,40 @@
 # CHANGELOG
 
+## v1.0.9 (2025-08-02)
+
+### Features
+- export datasets to RDS files
+- test workflow runs on a Python version matrix
+- scikit-learn compatible data generator
+- compatibility helpers for lifelines and scikit-survival
+
+### Documentation
+- updated usage examples and tutorials
+- document optional scikit-survival dependency throughout the docs
+
+### Continuous Integration
+- auto-tag releases using the version check script
+
+### Misc
+- README quick example uses `covariate_range`
+
+## v1.0.8 (2025-07-30)
+
+### Documentation
+- ensure absolute path resolution in `conf.py`
+- drop unsupported theme option
+- define bibliography anchors and headings
+- fix tutorial links to non-existing docs
+- add additional references to the bibliography
+
+### Testing
+- add CLI integration test
+- expand piecewise generator test coverage
+
+### Misc
+- remove fix_recommendations.md
+
+
 
 ## v1.0.0 (2025-06-06)
 

CHECKLIST.md

@@ -0,0 +1,102 @@
+# ✅ Python Package Development Checklist
+
+A checklist to ensure quality, maintainability, and usability of your Python package.
+
+---
+
+## 1. Purpose & Scope
+
+- [ ] Clear purpose and use cases defined  
+- [ ] Scoped to a specific problem/domain  
+- [ ] Project name is meaningful and not taken on PyPI  
+
+---
+
+## 2. Project Structure
+
+- [ ] Uses `src/` layout or appropriate flat structure  
+- [ ] All package folders contain `__init__.py`  
+- [ ] Main configuration handled via `pyproject.toml`  
+- [ ] Includes standard files: `README.md`, `LICENSE`, `.gitignore`, `CHANGELOG.md`  
+
+---
+
+## 3. Dependencies
+
+- [ ] All dependencies declared in `pyproject.toml` or `requirements.txt`  
+- [ ] Development dependencies separated from runtime dependencies  
+- [ ] Uses minimal, necessary dependencies only  
+
+---
+
+## 4. Code Quality
+
+- [ ] Follows PEP 8 formatting  
+- [ ] Imports sorted with `isort` or `ruff`  
+- [ ] No linter warnings (`ruff`, `flake8`, etc.)  
+- [ ] Fully typed using `typing` module  
+- [ ] No unresolved TODOs or FIXME comments  
+
+---
+
+## 5. Function & Module Design
+
+- [ ] Functions are small, pure, and single-responsibility  
+- [ ] Classes follow clear and simple roles  
+- [ ] Global state is avoided  
+- [ ] Public API defined explicitly (e.g. via `__all__`)  
+
+---
+
+## 6. Documentation
+
+- [ ] `README.md` includes overview, install, usage, contributing  
+- [ ] All functions/classes include docstrings (Google/NumPy style)  
+- [ ] API reference documentation auto-generated (e.g., Sphinx, MkDocs)  
+- [ ] Optional: `docs/` folder for additional documentation or site generator  
+
+---
+
+## 7. Testing
+
+- [ ] Unit and integration tests implemented  
+- [ ] Test coverage > 80% verified by `coverage`  
+- [ ] Tests are fast and deterministic  
+- [ ] Continuous Integration (CI) configured to run tests  
+
+---
+
+## 8. Versioning & Releases
+
+- [ ] Uses semantic versioning (MAJOR.MINOR.PATCH)  
+- [ ] Git tags created for releases  
+- [ ] `CHANGELOG.md` updated with each release  
+- [ ] Local build verified (`poetry build`, `hatch build`, or equivalent)  
+- [ ] Can be published to PyPI and/or TestPyPI  
+
+---
+
+## 9. CLI or Scripts (Optional)
+
+- [ ] CLI entrypoint works correctly (`__main__.py` or `entry_points`)  
+- [ ] CLI provides helpful messages (`--help`) and handles errors gracefully  
+
+---
+
+## 10. Examples / Tutorials
+
+- [ ] Usage examples included in `README.md` or `examples/`  
+- [ ] Optional: Jupyter notebooks with demonstrations  
+- [ ] Optional: Colab or Binder links for live usage  
+
+---
+
+## 11. Licensing & Attribution
+
+- [ ] LICENSE file included (MIT, Apache 2.0, GPL, etc.)  
+- [ ] Author and contributors credited in `README.md`  
+- [ ] Optional: `CITATION.cff` file for academic citation  
+
+---
+
+> You can duplicate this file for each new package or use it as a GitHub issue template for release checklists.