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Update github workflow
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‎.github/workflows/lint.yml

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@@ -11,4 +11,6 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: chartboost/ruff-action@v1
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- uses: chartboost/ruff-action@v1
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with:
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src: './modules'

‎.github/workflows/test_codebase.yml

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@@ -27,34 +27,31 @@ jobs:
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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: ["3.10", "3.11"]
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torch-version: [2.0.1]
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include:
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- torch-version: 2.0.1
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python-version: [3.11.3]
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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- uses: actions/checkout@v4
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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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cache: "pip"
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cache-dependency-path: '**/pyproject.toml'
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python-version: ${{matrix.python-version}}
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- name: Install PyTorch ${{ matrix.torch-version }}+cpu
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run: |
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pip install --upgrade pip setuptools wheel
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pip install torch==${{ matrix.torch-version}} --extra-index-url https://download.pytorch.org/whl/cpu
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pip install torch-scatter -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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pip install torch-sparse -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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pip install torch-cluster -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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pip show pip
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- name: Install main package
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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: ${{matrix.os}}-${{matrix.python-version}}-${{ hashFiles('pyproject.toml') }}
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- name: Install dependencies
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run: |
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pip install -e .[all]
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- name: Run tests for codebase [pytest]
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python -m pip install --upgrade pip
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pip install pytest
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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source env_setup.shs
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- name: Test with pytest
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run: |
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pytest -n 2 --cov --cov-report=xml:coverage.xml test/transforms/feature_liftings test/transforms/liftings
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pytest test/tutorials/test_tutorials.py
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- name: Upload coverage
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uses: codecov/codecov-action@v3
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with:

‎.github/workflows/test_tutorials.yml

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@@ -1,59 +1,59 @@
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name: "Testing Tutorials"
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# name: "Testing Tutorials"
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on:
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workflow_dispatch:
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push:
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branches: [main,github-actions-test]
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paths-ignore:
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- 'docs/**'
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- 'README.md'
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- 'LICENSE.txt'
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- '.gitignore'
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# on:
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# workflow_dispatch:
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# push:
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# branches: [main,github-actions-test]
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# paths-ignore:
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# - 'docs/**'
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# - 'README.md'
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# - 'LICENSE.txt'
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# - '.gitignore'
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pull_request:
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branches: [main]
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paths-ignore:
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- 'docs/**'
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- 'README.md'
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- 'LICENSE.txt'
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- '.gitignore'
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# pull_request:
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# branches: [main]
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# paths-ignore:
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# - 'docs/**'
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# - 'README.md'
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# - 'LICENSE.txt'
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# - '.gitignore'
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# Disable debugger's warnings from nbconvert in test_tutorials.py
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env:
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PYDEVD_DISABLE_FILE_VALIDATION: 1
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# # Disable debugger's warnings from nbconvert in test_tutorials.py
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# env:
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# PYDEVD_DISABLE_FILE_VALIDATION: 1
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jobs:
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test-all-tutorials-pytest:
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runs-on: ${{ matrix.os }}
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# jobs:
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# test-all-tutorials-pytest:
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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: ["3.10", "3.11"]
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torch-version: [2.0.1]
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include:
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- torch-version: 2.0.1
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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: ["3.10", "3.11"]
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# torch-version: [2.0.1]
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# include:
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# - torch-version: 2.0.1
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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cache-dependency-path: "pyproject.toml"
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# steps:
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# - uses: actions/checkout@v3
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# - name: Set up Python ${{ matrix.python-version }}
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# uses: actions/setup-python@v4
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# with:
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# python-version: ${{ matrix.python-version }}
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# cache: "pip"
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# cache-dependency-path: "pyproject.toml"
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- name: Install PyTorch ${{ matrix.torch-version }}+cpu
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run: |
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pip install --upgrade pip setuptools wheel
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pip install torch==${{ matrix.torch-version}} --extra-index-url https://download.pytorch.org/whl/cpu
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pip install torch-scatter -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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pip install torch-sparse -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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pip install torch-cluster -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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- name: Install main package
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run: |
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pip install -e .[all]
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- name: Run tests for tutorials on all domains [pytest]
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run: |
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pytest test/tutorials/test_tutorials.py
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# - name: Install PyTorch ${{ matrix.torch-version }}+cpu
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# run: |
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# pip install --upgrade pip setuptools wheel
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# pip install torch==${{ matrix.torch-version}} --extra-index-url https://download.pytorch.org/whl/cpu
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# pip install torch-scatter -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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# pip install torch-sparse -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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# pip install torch-cluster -f https://data.pyg.org/whl/torch-${{ matrix.torch-version }}+cpu.html
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# - name: Install main package
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# run: |
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# pip install -e .[all]
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# - name: Run tests for tutorials on all domains [pytest]
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# run: |
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# pytest test/tutorials/test_tutorials.py

‎.pre-commit-config.yaml

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@@ -17,25 +17,12 @@ repos:
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- id: trailing-whitespace
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- id: requirements-txt-fixer
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- repo: https://github.com/psf/black
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rev: 23.3.0
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.4.4
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hooks:
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- id: black-jupyter
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- id: ruff-format
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- repo: https://github.com/pycqa/isort
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rev: 5.12.0
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- repo: https://github.com/numpy/numpydoc
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rev: v1.6.0
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hooks:
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- id : isort
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args : ["--profile=black", "--filter-files"]
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#- repo: https://github.com/asottile/blacken-docs
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# rev: 1.13.0
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# hooks:
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# - id: blacken-docs
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# additional_dependencies: [black==23.3.0]
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# - repo: https://github.com/pycqa/flake8
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# rev: 6.0.0
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# hooks:
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# - id: flake8
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# additional_dependencies: [flake8-docstrings, Flake8-pyproject]
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- id: numpydoc-validation

‎env_setup.sh

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#!/bin/bash -l
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pip install --upgrade pip
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pip install -e '.[all]'
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# Note that not all combinations of torch and CUDA are available
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# See https://github.com/pyg-team/pyg-lib to check the configuration that works for you
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TORCH="2.3.0" # available options: 1.12.0, 1.13.0, 2.0.0, 2.1.0, 2.2.0, or 2.3.0
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CUDA="cpu" # if available, select the CUDA version suitable for your system
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# available options: cpu, cu102, cu113, cu116, cu117, cu118, or cu121
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pip install torch==${TORCH} --extra-index-url https://download.pytorch.org/whl/${CUDA}
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pip install pyg-lib torch-scatter torch-sparse torch-cluster -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html
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#pytest
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pre-commit install

‎pyproject.toml

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"matplotlib",
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"networkx",
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"pandas",
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"pyg-nightly",
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"decorator",
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"hypernetx < 2.0.0",
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"omegaconf",
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"trimesh",
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"spharapy",
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"wandb",
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"einops==0.7.0",
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"tabulate",
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"ipykernel",
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"notebook",
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"jupyterlab",
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"rich",
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"rootutils",
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"pytest",
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"toponetx @ git+https://github.com/pyt-team/TopoNetX.git",
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"topomodelx @ git+https://github.com/pyt-team/TopoModelX.git",
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"topoembedx @ git+https://github.com/pyt-team/TopoEmbedX.git",
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]
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@@ -78,42 +80,22 @@ all = ["challenge-icml-2024[dev, doc]"]
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homepage="https://github.com/pyt-team/challenge-icml-2024.git"
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repository="https://github.com/pyt-team/challenge-icml-2024.git"
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[tool.ruff]
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[tool.black]
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line-length = 79 # PEP 8 standard for maximum line length
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target-version = ['py310']
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# Same as Black.
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line-length = 88
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indent-width = 4
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[tool.docformatter]
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wrap-summaries = 79
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wrap-descriptions = 79
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[tool.ruff]
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target-version = "py310"
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extend-include = ["*.ipynb"]
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[lint]
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# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default.
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select = ["E4", "E7", "E9", "F"]
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ignore = []
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# Allow fix for all enabled rules (when `--fix`) is provided.
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fixable = ["ALL"]
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unfixable = []
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# Allow unused variables when underscore-prefixed.
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dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
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[format]
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# Like Black, use double quotes for strings.
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quote-style = "double"
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# Like Black, indent with spaces, rather than tabs.
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indent-style = "space"
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# Like Black, respect magic trailing commas.
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skip-magic-trailing-comma = false
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# Like Black, automatically detect the appropriate line ending.
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line-ending = "auto"
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#extend-include = ["*.ipynb"]
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extend-exclude = ["test", "tutorials"]
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line-length = 79 # PEP 8 standard for maximum line length
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[tool.ruff.format]
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docstring-code-format = true
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docstring-code-format = false
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[tool.ruff.lint]
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select = [

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