A new start

.flake8

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+[flake8]
+max-line-length = 88
+ignore = D105, E731, W503, F821, E203
+docstring-convention = numpy
+per-file-ignores = __init__.py:F401
+exclude =
+    .git
+    .github
+    .dvc
+    __pycache__
+    .venv
+    .mypy_cache
+    .pytest_cache
+    conf.py

.github/CODEOWNERS

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+* @jeandut @mandreux-owkin @qklopfenstein-owkin

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help improve the code
+title: "[BUG] "
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Provide snippets of code and steps on how to reproduce the behavior.
+Please also specify the version you are using.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+- OS: [e.g. iOS]
+- Python version
+- Code version [e.g. 0.02 or commit hash]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/PULL_REQUEST_TEMPLATE.md

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+<!--
+Thanks for contributing a pull request!
+This template is designed to help save time for reviewers and yourself.
+
+1. If your PR is not ready for review yet, please do not hesitate to publish it
+as a draft to run the CI.
+
+2. You can prefix the title of the PR with an acronym that indicates the
+type of PR, e.g. CI if related to the CI, DOC for the documentation,
+FIX if there is a bug fix, FEAT if a new feature is added, EXP if a new
+experiment is added.
+-->
+
+#### Reference Issue or PRs
+<!--
+If this PR is related to an existing issue or PR please reference it, eg:
+Fixes #1234.
+You can use github keywords as described:
+https://github.com/blog/1506-closing-issues-via-pull-requests
+-->
+
+
+#### What does your PR implement? Please be specific
+
+
+
+
+#### Checklist
+
+Have you:
+- [ ] Added unit tests under `tests/` (if you modified the `fedeca` folder)?
+- [ ] Added docstrings for all functions?
+- [ ] Added instructions on how to run your experimental file, and the
+expected results (e.g. in a README or in the file itself)?

.github/workflows/docs.yml

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+name: build_docs
+
+# Controls when the workflow will run
+on:
+  push:
+    branches:
+      - 'main'
+  pull_request:
+    branches:
+      - 'main'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  build_docs:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.9"]
+        # python: ["3.9", "3.10", "3.11"]  # TODO: expand to other pythons
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install dependencies
+        env:
+          GIT_TOKEN: ${{ secrets.GIT_TOKEN }}
+          GIT_USERNAME: ${{ secrets.GIT_USERNAME }}
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[all_extra]"
+      - name: Compile docs
+        run: |
+          cd docs
+          make clean html
+      - name: Publish docs to gh-pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html/
+          force_orphan: true

.github/workflows/flake8.yml

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+name: linter
+
+on:
+  push:
+    branches:
+      - 'main'
+  pull_request:
+    branches:
+      - 'main'
+
+jobs:
+  lint:
+    name: Lint code base
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Lint with flake
+        run: |
+          pip install flake8
+          pip install flake8-docstrings
+          flake8 fedeca/ --max-line-length=88 --append-config .flake8

.github/workflows/pr_validation.yml

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+name: pr-validation
+
+# Controls when the workflow will run
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths-ignore:
+    - 'experiments/**'  # if only the exps are modified, no need to run it
+    - 'docs/**'  # if only the docs are modified, no need to run it
+  schedule:
+    # Every monday at 3h30 UTC
+    - cron: '30 3 * * 1'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  run_tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.9"]
+        # python: ["3.9", "3.10", "3.11"]  # TODO: expand to other pythons
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install dependencies
+        env:
+          GIT_TOKEN: ${{ secrets.GIT_TOKEN }}
+          GIT_USERNAME: ${{ secrets.GIT_USERNAME }}
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[all_extra]"
+      - name: Testing with pytest
+        run: |
+          coverage run -m pytest -v fedeca
+      - name: Generate code coverage report
+        run: |
+          coverage html --omit="*/local-worker/*"
+      - name: Upload coverage artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: test-coverage-report
+          path: htmlcov/
+          retention-days: 20

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+tmp/
+local-worker/
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# other files
+.DS_Store
+
+# substra
+temp/
+
+# fedeca
+tokens/
+iptw_experiment/

.isort.cfg

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+[settings]
+profile = black
+skip=__init__.py