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cbouycbouy
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add notebook tests
1 parent 8bff942 commit cd18740

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lines changed

‎.github/workflows/_build-package.yml

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@@ -0,0 +1,68 @@
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name: build-package
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on:
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workflow_call:
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inputs:
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check-prerelease:
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default: false
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required: false
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type: boolean
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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build:
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name: Build mols2grid package
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Get prerelease version tags
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if: inputs.check-prerelease
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id: prerelease-check
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run: |
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py_dirty_tag=$(awk '/__version__ = "[[:digit:]+]\.[[:digit:]+]\.[[:digit:]+]\-.+"/ {print $3}' ./mols2grid/_version.py)
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py_is_pre=$(test -z "$py_dirty_tag" && echo "false" || echo "true")
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js_version_string=$(grep '"version":' ./package.json)
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js_dirty_tag=$(echo "$js_version_string" | cut -d- -f2)
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js_is_pre=$(test "$js_version_string" == "$js_dirty_tag" && echo "false" || echo "true")
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echo "py=$py_is_pre" >> $GITHUB_OUTPUT
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echo "js=$js_is_pre" >> $GITHUB_OUTPUT
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- name: Fail if prerelease is not correctly versioned
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if: (inputs.check-prerelease) && !( steps.prerelease-check.outputs.py && steps.prerelease-check.outputs.js )
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uses: actions/github-script@v3
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with:
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script: |
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core.setFailed("Versions are not tagged as a prerelease")
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: "18.12.1"
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registry-url: 'https://registry.npmjs.org/'
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cache: "yarn"
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- name: Install python with pip
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uses: actions/setup-python@v4
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with:
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python-version: 3.10
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cache: "pip"
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- name: Install dependencies for packaging
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run: |
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pip install setuptools wheel build virtualenv twine
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- name: Check python installation
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run: |
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which python
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python --version
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pip --version
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pip list
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- name: Build package
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run: |
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python -m build .

‎.github/workflows/build.yml

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@@ -17,55 +17,11 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Get prerelease version tags
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if: env.IS_PRERELEASE == 'true'
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run: |
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py_dirty_tag=$(awk '/__version__ = "[[:digit:]+]\.[[:digit:]+]\.[[:digit:]+]\-.+"/ {print $3}' ./mols2grid/_version.py)
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py_is_pre=$(test -z "$py_dirty_tag" && echo "false" || echo "true")
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js_version_string=$(grep '"version":' ./package.json)
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js_dirty_tag=$(echo "$js_version_string" | cut -d- -f2)
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js_is_pre=$(test "$js_version_string" == "$js_dirty_tag" && echo "false" || echo "true")
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echo "py_is_pre=$py_is_pre" >> $GITHUB_ENV
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echo "js_is_pre=$js_is_pre" >> $GITHUB_ENV
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- name: Fail if prerelease is not correctly versioned
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if: (env.IS_PRERELEASE == 'true') && !( env.py_is_pre && env.js_is_pre )
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uses: actions/github-script@v3
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with:
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script: |
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core.setFailed("Versions are not tagged as a prerelease")
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: 18
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registry-url: 'https://registry.npmjs.org/'
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cache: "yarn"
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- name: Install python with pip
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uses: actions/setup-python@v4
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- name: Build package
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uses: ./.github/workflows/_build-package.yml
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with:
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python-version: 3.8
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cache: "pip"
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check-prerelease: ${{ env.IS_PRERELEASE }}
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- name: Install dependencies for packaging
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run: |
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pip install setuptools wheel build virtualenv twine
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- name: Check python installation
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run: |
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which python
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python --version
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pip --version
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pip list
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- name: Build package
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run: |
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python -m build .
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- name: Publish the Python package
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env:
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TWINE_USERNAME: __token__

‎.github/workflows/ci.yml

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@@ -19,42 +19,30 @@ concurrency:
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jobs:
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tests:
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name: ${{ matrix.label }}
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runs-on: ${{ matrix.os }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- label: CI-old
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os: ubuntu-latest
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- label: rdkit-2021
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python-version: 3.8
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extra_dependencies: "rdkit==2020.03.1 boost-cpp=1.72.0=h359cf19_6"
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- label: CI-edge
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os: ubuntu-latest
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extra_dependencies: "rdkit==2021.03.1"
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- label: rdkit-latest
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python-version: "3.10"
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extra_dependencies: "rdkit"
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- label: CI-py3.9-rdkit2022
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os: ubuntu-latest
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python-version: 3.9
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extra_dependencies: "rdkit==2022.03.1"
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steps:
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- uses: actions/checkout@v3
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- name: Install node
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uses: actions/setup-node@v3
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with:
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node-version: 18
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cache: "yarn"
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- name: Install Firefox
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uses: browser-actions/setup-firefox@latest
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- run: firefox --version
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- name: Prepare Selenium
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uses: browser-actions/setup-geckodriver@latest
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with:
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geckodriver-version: "0.32.0"
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- run: geckodriver --version
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- name: Cache conda
@@ -64,15 +52,27 @@ jobs:
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with:
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path: ~/conda_pkgs_dir
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key:
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conda-${{ hashFiles('environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
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conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
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- name: Cache pip
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: pip-${{ hashFiles('setup.cfg') }}
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key: pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: pip-
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- name: Get yarn cache directory path
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id: yarn-cache-dir-path
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run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
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- name: Cache yarn
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uses: actions/cache@v3
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with:
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path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
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key: yarn-${{ hashFiles('yarn.lock') }}
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restore-keys: |
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yarn-
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- name: Setup Conda
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uses: conda-incubator/setup-miniconda@v2
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with:
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- name: Install remaining conda dependencies
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run: |
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mamba install ${{ matrix.extra_dependencies }}
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mamba install 'jupyterlab>=3,<5' ipywidgets=8 ${{ matrix.extra_dependencies }}
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mamba list
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- name: Install package through pip
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- name: Build and install package
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run: |
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pip install .[tests,build]
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jupyter labextension develop . --overwrite
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pip list
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jupyter labextension list
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- name: Run tests
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run: |
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pytest --color=yes --disable-pytest-warnings \
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fail_ci_if_error: true
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verbose: true
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- name: Prepare for build
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run: |
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pip uninstall -y mols2grid
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python -m build .
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echo "$SCRIPT" > test_install.py
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cat test_install.py
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build:
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name: Build package
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runs-on: ubuntu-latest
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steps:
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- name: Build package
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uses: ./.github/workflows/_build-package.yml
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- name: Prepare quick test script
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run: |
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echo "$SCRIPT" > test_install.py
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cat test_install.py
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env:
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SCRIPT: |
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import mols2grid as mg
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from rdkit import RDConfig
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sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf"
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mg.save(sdf, output="/dev/null")
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- name: Test tar.gz build
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run: |
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pip install dist/mols2grid-*.tar.gz
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python test_install.py
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pip uninstall -y mols2grid
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- name: Test wheel build
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run: |
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pip install dist/mols2grid-*.whl
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python test_install.py
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- name: Cache package
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uses: actions/cache@v3
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id: cache-mols2grid
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with:
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path: dist/mols2grid-*.whl
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key: ${{ runner.os }}-mols2grid-wheel
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notebook-tests:
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needs: [build]
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name: ${{ matrix.label }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- label: JLab-3-Widgets-7
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extra_dependencies: "jupyterlab>=3.2 ipywidgets=7"
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- label: JLab-4-Widgets-8
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extra_dependencies: "jupyterlab=4 ipywidgets=8"
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steps:
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- uses: actions/checkout@v3
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- name: Retrieve cached package
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uses: actions/cache@v3
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id: cache-mols2grid
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with:
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path: dist/mols2grid-*.whl
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key: ${{ runner.os }}-mols2grid-wheel
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- name: Cache conda
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uses: actions/cache@v3
129185
env:
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SCRIPT: |
131-
import mols2grid as mg
132-
from rdkit import RDConfig
133-
sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf"
134-
mg.save(sdf, output="/dev/null")
186+
CACHE_NUMBER: 0
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with:
188+
path: ~/conda_pkgs_dir
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key:
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conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
135191

136-
- name: Test tar.gz build
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- name: Cache pip
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: pip-${{ hashFiles('pyproject.toml') }}
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restore-keys: pip-
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- name: Get yarn cache directory path
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id: yarn-ui-cache-dir-path
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run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
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- name: Cache yarn
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uses: actions/cache@v3
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with:
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path: ${{ steps.yarn-ui-cache-dir-path.outputs.dir }}
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key: yarn-ui-${{ hashFiles('tests/notebooks/yarn.lock') }}
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restore-keys: |
209+
yarn-ui-
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- name: Setup Conda
212+
uses: conda-incubator/setup-miniconda@v2
213+
with:
214+
python-version: "3.10"
215+
use-only-tar-bz2: true
216+
miniforge-variant: Mambaforge
217+
miniforge-version: latest
218+
use-mamba: true
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- name: Install remaining conda dependencies
221+
run: |
222+
mamba install rdkit pandas ${{ matrix.extra_dependencies }}
223+
mamba list
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- name: Install the extension
226+
run: |
227+
pip install dist/mols2grid-*.whl[packaging]
228+
jupyter labextension list
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- name: Install Test Dependencies
137231
run: |
138-
pip install dist/mols2grid-*.tar.gz
139-
python test_install.py
140-
pip uninstall -y mols2grid
232+
jlpm --no-immutable
233+
npx playwright install chromium
234+
working-directory: tests/notebooks
141235

142-
- name: Test wheel build
236+
- name: Execute integration tests
237+
working-directory: tests/notebooks
143238
run: |
144-
pip install dist/mols2grid-*.whl
145-
python test_install.py
239+
npx playwright test
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- name: Upload Playwright Test assets
242+
if: always()
243+
uses: actions/upload-artifact@v3
244+
with:
245+
name: notebooks-test-assets
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path: |
247+
tests/notebooks/test-results
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- name: Upload Playwright Test report
250+
if: always()
251+
uses: actions/upload-artifact@v3
252+
with:
253+
name: notebooks-test-report
254+
path: |
255+
tests/notebooks/playwright-report
256+
257+
- name: Update snapshots
258+
if: failure()
259+
working-directory: tests/notebooks
260+
run: |
261+
jlpm test:update
262+
263+
- name: Upload updated snapshots
264+
if: failure()
265+
uses: actions/upload-artifact@v3
266+
with:
267+
name: notebook-updated-snapshots
268+
path: tests/notebooks/tests

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