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chore: finalize 1.0.9 release metadata (#58)
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‎.github/workflows/bump-version.yml‎

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# .github/workflows/bump-version.yml
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name: Bump Version on Merge to Main
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name: Tag Version on Merge to Main
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on:
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push:
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branches:
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- main
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jobs:
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bump-version:
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tag-version:
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runs-on: ubuntu-latest
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permissions:
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contents: write
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id-token: write
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0 # Fetch all history for all branches and tags
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fetch-depth: 0
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- uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install Poetry
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run: pip install poetry
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- name: Install python-semantic-release
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run: pip install python-semantic-release
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- name: Configure Git
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run: |
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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- name: Run Semantic Release
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env:
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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# Run semantic-release to get the next version
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semantic-release version
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- name: Tag repository from pyproject
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run: python scripts/check_version_match.py --fix
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- name: Push changes
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run: |
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git push --follow-tags

‎.github/workflows/ci.yml‎

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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Install dependencies
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run: poetry install
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run: poetry install --with dev
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- name: Run tests with coverage
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run: poetry run pytest --cov=gen_surv --cov-report=xml --cov-report=term
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Install dependencies
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run: poetry install
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run: poetry install --with dev
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- name: Run black
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run: poetry run black --check gen_surv tests examples
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- name: Run isort
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run: poetry run isort --check gen_surv tests examples
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- name: Run flake8
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run: poetry run flake8 gen_surv tests examples
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- name: Run mypy
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run: poetry run mypy gen_surv
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- name: Run pre-commit checks
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run: poetry run pre-commit run --all-files

‎.github/workflows/test.yml‎

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echo "$HOME/.local/bin" >> $GITHUB_PATH
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- name: Install dependencies
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run: poetry install
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run: poetry install --with dev
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- name: Run tests
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run: poetry run pytest --cov=gen_surv --cov-report=xml --cov-report=term

‎.pre-commit-config.yaml‎

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

‎CHANGELOG.md‎

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# CHANGELOG
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## v1.0.9 (Unreleased)
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## v1.0.9 (2025-08-02)
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### Features
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- export datasets to RDS files
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### Documentation
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- updated usage examples and tutorials
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- document optional scikit-survival dependency throughout the docs
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### Continuous Integration
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- auto-tag releases using the version check script
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### Misc
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- README quick example uses `covariate_range`

‎CHECKLIST.md‎

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

‎CITATION.cff‎

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preferred-citation:
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type: software
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title: "gen_surv"
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version: "1.0.8"
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version: "1.0.9"
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url: "https://github.com/DiogoRibeiro7/genSurvPy"
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authors:
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- family-names: Ribeiro
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affiliation: "ESMAD - Instituto Politécnico do Porto"
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email: "[email protected]"
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license: "MIT"
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date-released: "2024-01-01"
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date-released: "2025-08-02"
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‎CONTRIBUTING.md‎

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## Getting Started
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1. Fork the repository and create your feature branch from `main`.
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2. Install dependencies with `poetry install`.
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3. Ensure the test suite passes with `poetry run pytest`.
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4. If you add a feature or fix a bug, update `CHANGELOG.md` accordingly.
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2. Install dependencies with `poetry install --with dev`.
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This installs all packages needed for development, including
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the optional dependency `scikit-survival`.
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On Debian/Ubuntu you may need `build-essential gfortran libopenblas-dev`
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to build it.
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3. Run `pre-commit install` to enable style checks and execute them with `pre-commit run --all-files`.
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4. Ensure the test suite passes with `poetry run pytest`.
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5. If you add a feature or fix a bug, update `CHANGELOG.md` accordingly.
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## Version Consistency
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‎LICENCE‎ renamed to ‎LICENSE‎

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‎README.md‎

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```bash
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git clone https://github.com/DiogoRibeiro7/genSurvPy.git
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cd genSurvPy
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poetry install
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# Install runtime and development dependencies
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# (scikit-survival is optional but required for integration tests).
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# On Debian/Ubuntu you may need ``build-essential gfortran libopenblas-dev`` to
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# build scikit-survival.
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poetry install --with dev
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```
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Integration tests that rely on scikit-survival are automatically skipped if the
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package is not installed.
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## Development Setup
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Before committing changes, install the pre-commit hooks:
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```bash
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pre-commit install
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pre-commit run --all-files
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```
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## Quick Example
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## License
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This project is licensed under the MIT License. See [LICENCE](LICENCE) for details.
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This project is licensed under the MIT License. See [LICENSE](LICENSE) for details.
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## Citation
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