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Merge pull request #48 from brainprepdesk/dev
Release 2.0.0
2 parents f533c35 + ec3ce1c commit aa5b129

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‎.github/codespellignore.txt‎

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licences

‎.github/run_examples.py‎

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‎.github/run_unitests.py‎

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‎.github/workflows/codespell.yml‎

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---
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# Workflow to check common misspellings in text files.
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#
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# To run this check locally from the repository folder:
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#
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# .. code-block:: bash
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#
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# $ codespell --toml pyproject.toml brainprep examples
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###
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name: "SpellLinter[codespell]"
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on:
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push:
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branches:
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- "master"
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- "main"
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- "dev"
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pull_request:
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branches:
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- "*"
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workflow_dispatch:
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jobs:
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codespell:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: [3.12]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Codespell
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uses: codespell-project/actions-codespell@v2
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with:
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path: examples,brainprep
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builtin: clear,rare,en-GB_to_en-US
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ignore_words_file: ./.github/codespellignore.txt
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skip: ./.git,*.bib,./brainprep/resources/*,./AUTHORS.rst

‎.github/workflows/documentation.yml‎

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name: "DOCUMENTATION"
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# Workflow to build doc, upload it as artifact, and deploy it for the
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# master, main and dev branches.
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#
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# To run this check locally from the `doc` folder:
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#
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# .. code-block:: bash
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#
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# $ sphinxdoc -v 2 -p $MODULE_DIR -n brainprep -o $MODULE_DIR/doc
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# $ cd $MODULE_DIR/doc
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# $ make html-strict
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###
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name: "DocumentationBuilder"
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on:
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push:
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branches:
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- "master"
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- "main"
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- "dev"
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pull_request:
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branches:
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- "*"
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workflow_dispatch:
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env:
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MIN_PYTHON_VERSION: "3.12"
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jobs:
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build_and_deploy:
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runs-on: ${{ matrix.os }}
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if: ${{ github.ref == 'refs/heads/master' }}
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runs-on: "ubuntu-latest"
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: [3.12]
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env:
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FREESURFER_HOME: "/freesurfer/home"
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permissions:
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contents: write
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steps:
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- name: Extract branch name
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id: extract-branch
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shell: bash
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run: echo "BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
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- name: Identify deploy type
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id: deploy-type
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run: |
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if ${{ github.ref == 'refs/heads/master' ||
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github.ref == 'refs/heads/main' }}; then
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echo "DEPLOY_TYPE=stable" >> $GITHUB_OUTPUT
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elif ${{ github.ref == 'refs/heads/dev' }}; then
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echo "DEPLOY_TYPE=dev" >> $GITHUB_OUTPUT
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else
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echo "DEPLOY_TYPE=pr" >> $GITHUB_OUTPUT
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fi
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- name: Checkout repository
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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python-version: ${{ env.MIN_PYTHON_VERSION }}
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cache: "pip"
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --progress-bar off .
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python -m pip install git+https://github.com/AGrigis/pysphinxdoc.git
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python -m pip install requests "scipy<=1.15" statsmodels
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python -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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python -m pip install git+https://github.com/neurospin-deepinsight/brainrise.git
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python -m pip install --progress-bar off ".[ci,doc]"
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- name: Install apt packages
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uses: awalsh128/cache-apt-pkgs-action@latest
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with:
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packages: dvipng texlive-latex-base texlive-latex-extra build-essential
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version: 1.0
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- name: Install documentation resources
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run: |
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DIR=$(pwd)
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which python
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sphinxdoc -v 2 -p $DIR -n brainprep -o $DIR/doc
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- name: Compute documentation
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run: |
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mkdir -p tmp/doc
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sphinxdoc -v 2 -p . -n brainprep -o tmp/doc
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cd tmp/doc
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make raw-html
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ls source/_static
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ls build/html/_static
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cp -r source/_static/* build/html/_static
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cd ../..
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DIR=$(pwd)
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cd $DIR/doc
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echo "Documentation folder: $DIR/doc"
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make html-strict
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cd $DIR
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- name: Upload documentation as an artifact
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uses: actions/upload-artifact@v4
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env:
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DEPLOY_TYPE: ${{ steps.deploy-type.outputs.DEPLOY_TYPE }}
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with:
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name: html-documentation
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retention-days: 15
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name: doc-${{ env.DEPLOY_TYPE }}
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retention-days: 1
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path: |
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tmp/doc/build/html
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doc/_build/html
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- name: Deploy
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env:
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DEPLOY_TYPE: ${{ steps.deploy-type.outputs.DEPLOY_TYPE }}
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if: env.DEPLOY_TYPE != 'pr'
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: tmp/doc/build/html
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build:
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runs-on: ${{ matrix.os }}
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if: ${{ github.ref != 'refs/heads/master' }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: [3.12]
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permissions:
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contents: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install --progress-bar off .
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python -m pip install git+https://github.com/AGrigis/pysphinxdoc.git
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python -m pip install requests "scipy<=1.15" statsmodels
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python -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
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python -m pip install git+https://github.com/neurospin-deepinsight/brainrise.git
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- name: Compute documentation
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run: |
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mkdir -p tmp/doc
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sphinxdoc -v 2 -p . -n brainprep -o tmp/doc
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cd tmp/doc
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make raw-html
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ls source/_static
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ls build/html/_static
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cp -r source/_static/* build/html/_static
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cd ../..
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publish_dir: doc/_build/html
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destination_dir: ./${{ env.DEPLOY_TYPE }}

‎.github/workflows/pep8.yml‎

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‎.github/workflows/pycodestyle.yml‎

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---
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# Workflow to check code format.
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#
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# To run this check locally from the repository folder:
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#
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# .. code-block:: bash
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#
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# $ pycodestyle brainprep --ignore="E121,E123,E126,E226,E24,E704,E402,E731,E722,E741,W503,W504,W605,E305,E125"
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###
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name: "PythonLinter[pycodestyle]"
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on:
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push:
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branches:
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- "master"
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- "main"
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- "dev"
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pull_request:
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branches:
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- "*"
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workflow_dispatch:
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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python-version: [3.12]
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install pycodestyle
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pip install --progress-bar off .
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- name: Check Python syntax
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run: |
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pycodestyle brainprep --ignore="E121,E123,E126,E226,E24,E704,E402,E731,E722,E741,W503,W504,W605,E305,E125"

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