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Fix test for python 3.13 (#116)
* update * update * upadte * update * update * update * update * fail fast * fix CI * update * update * update * update * update * update * fix * update * update * update * update * update * update * update * update * fix * fix doc --------- Co-authored-by: Nathanael Perraudin <nathanael.perraudin@synthesia.io>
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [ main, master]
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pull_request:
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branches: [ main, master]
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: true
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up conda
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uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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channels: conda-forge,defaults
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channel-priority: strict
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- name: Install system dependencies
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run: |
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# Install system packages for Qt6 and OpenGL
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sudo apt-get update
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sudo apt-get install -y \
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qt6-base-dev \
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libqt6gui6 \
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libqt6widgets6 \
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libqt6opengl6-dev \
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xvfb \
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libegl1-mesa-dev \
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libgl1-mesa-dev \
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libglu1-mesa-dev \
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freeglut3-dev \
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libxkbcommon-x11-0 \
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libxcb-icccm4 \
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libxcb-image0 \
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libxcb-keysyms1 \
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libxcb-randr0 \
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libxcb-render-util0 \
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libxcb-shape0 \
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libxcb-xfixes0 \
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libxcb-xinerama0
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- name: Install graph-tool via conda
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shell: bash -l {0}
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run: |
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conda install -c conda-forge graph-tool
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- name: Verify graph-tool installation
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shell: bash -l {0}
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run: |
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python -c "import graph_tool.all as gt; print('✅ graph-tool imported successfully')"
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- name: Cache pip packages
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uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }}
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restore-keys: |
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${{ runner.os }}-pip-${{ matrix.python-version }}-
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${{ runner.os }}-pip-
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- name: Install Python dependencies
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shell: bash -l {0}
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run: |
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python -m pip install --upgrade pip setuptools wheel
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pip install --upgrade --upgrade-strategy eager .[dev]
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- name: Set up virtual display
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run: |
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export DISPLAY=:99
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Xvfb :99 -screen 0 800x600x24 > /dev/null 2>&1 &
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echo "DISPLAY=:99" >> $GITHUB_ENV
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echo "QT_QPA_PLATFORM=offscreen" >> $GITHUB_ENV
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echo "QT_QPA_FONTDIR=/usr/share/fonts" >> $GITHUB_ENV
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echo "MESA_GL_VERSION_OVERRIDE=3.3" >> $GITHUB_ENV
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echo "MESA_GLSL_VERSION_OVERRIDE=330" >> $GITHUB_ENV
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# - name: Run linting
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# shell: bash -l {0}
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# run: |
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# flake8 --doctests --exclude=doc
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- name: Run tests with coverage
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shell: bash -l {0}
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run: |
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export MPLBACKEND=agg
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coverage run --branch --source pygsp -m pytest
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coverage report
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coverage xml
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- name: Upload coverage to Coveralls
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if: matrix.python-version == '3.11' # Only upload once
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uses: coverallsapp/github-action@v2
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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file: coverage.xml
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docs:
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runs-on: ubuntu-latest
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needs: test
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steps:
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- uses: actions/checkout@v4
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- name: Set up conda
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uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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python-version: "3.11"
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channels: conda-forge,defaults
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channel-priority: strict
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- name: Install graph-tool via conda
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shell: bash -l {0}
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run: |
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conda install -c conda-forge graph-tool
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- name: Verify graph-tool installation
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shell: bash -l {0}
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run: |
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python -c "import graph_tool.all as gt; print('✅ graph-tool imported successfully')"
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- name: Install Python dependencies
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shell: bash -l {0}
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run: |
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python -m pip install --upgrade pip setuptools wheel
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pip install --upgrade --upgrade-strategy eager .[dev,doc]
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- name: Build documentation
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shell: bash -l {0}
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run: |
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export MPLBACKEND=agg
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sphinx-build -b html -d doc/_build/doctrees doc doc/_build/html
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sphinx-build -b linkcheck -d doc/_build/doctrees doc doc/_build/linkcheck
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- name: Upload documentation artifacts
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uses: actions/upload-artifact@v4
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with:
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name: documentation
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path: doc/_build/html/

‎.gitignore‎

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.venv/
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uv.lock
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__pycache__/
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# Packages

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.5.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- id: check-case-conflict
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- id: check-merge-conflict
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- id: check-toml
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- id: debug-statements
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- id: detect-private-key
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- repo: https://github.com/psf/black
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rev: 23.12.1
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hooks:
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- id: black
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language_version: python3
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args: [--line-length=88]
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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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args: [--profile=black, --line-length=88]
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# - repo: https://github.com/pycqa/flake8
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# rev: 7.0.0
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# hooks:
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# - id: flake8
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# additional_dependencies: [flake8-docstrings]
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# args: [--max-line-length, "88", --extend-ignore, "E203,W503,D100,D101,D102,D103,D104,D105,D107,D200,D202,D205,D209,D400,D401,D402,D412,D414"]
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# - repo: https://github.com/PyCQA/bandit
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# rev: 1.7.5
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# hooks:
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# - id: bandit
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# args: [--skip=B101,B601]
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# - repo: https://github.com/pre-commit/mirrors-mypy
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# rev: v1.8.0
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# hooks:
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# - id: mypy
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# additional_dependencies: [types-all]
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# args: [--ignore-missing-imports, --no-strict-optional]
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# files: ^pygsp/
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# - repo: https://github.com/pycqa/pydocstyle
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# rev: 6.3.0
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# hooks:
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# - id: pydocstyle
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# args: [--convention=numpy]
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# files: ^pygsp/
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.15.0
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hooks:
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- id: pyupgrade
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args: [--py38-plus]
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default_language_version:
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python: python3
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ci:
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autofix_commit_msg: |
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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for more information, see https://pre-commit.ci
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autofix_prs: true
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autoupdate_branch: ''
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autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
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autoupdate_schedule: weekly
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skip: []
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submodules: false

‎.travis.yml‎

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‎CHANGELOG.rst‎

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Unreleased
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----------
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* Upgrade from PyQt5 to PyQt6.
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* ``print(graph)`` and ``print(filters)`` now show valuable information.
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* Building a graph object is much faster.
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* New rectangular filter (low-pass and band-pass).

‎CONTRIBUTING.rst‎

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Update ``README.rst`` and ``CHANGELOG.rst`` if applicable.
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After making any change, please check the style, run the tests, and build the
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documentation with the following (enforced by Travis CI)::
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documentation with the following (enforced by GitHub Actions)::
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$ make lint
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$ make test
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To iterate faster, you can partially run the test suite, at various degrees of
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granularity, as follows::
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$ python -m unittest pygsp.tests.test_docstrings.suite_reference
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$ python -m unittest pygsp.tests.test_graphs.TestImportExport
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$ python -m unittest pygsp.tests.test_graphs.TestImportExport.test_save_load
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$ python -m pytest pygsp/tests/test_docstrings.py
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$ python -m pytest pygsp/tests/test_graphs.py::TestGraphs
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$ python -m pytest pygsp/tests/test_graphs.py::test_save_load
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Making a release
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----------------
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Makefile Targets for make
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setup.py Meta information about package (published on PyPI)
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.gitignore Files ignored by the git revision control system
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.travis.yml Defines testing on Travis continuous integration
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.github/workflows/ Defines testing on GitHub Actions continuous integration
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pygsp/ Contains the modules (the actual toolbox implementation)
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__init.py__ Load modules at package import

‎Makefile‎

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git clean -Xdf
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jupyter nbconvert --inplace --ClearOutputPreprocessor.enabled=True $(NB)
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lint:
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flake8 --doctests --exclude=doc
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flake8 --doctests --exclude=doc,.venv,build --max-line-length=88 --extend-ignore=E203
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# Matplotlib doesn't print to screen. Also faster.
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export MPLBACKEND = agg
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test:
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Xvfb $$DISPLAY -screen 0 800x600x24 &
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coverage run --branch --source pygsp setup.py test
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coverage run --branch --source pygsp -m pytest
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coverage report
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coverage html
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killall Xvfb

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