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add notebook test
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@cbouy
cbouy committed Dec 25, 2023
1 parent f3a890b commit c8ef811
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18 changes: 16 additions & 2 deletions .github/workflows/_build-package.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,10 @@ on:
default: false
required: false
type: boolean
upload-package:
default: false
required: false
type: boolean

defaults:
run:
Expand Down Expand Up @@ -78,9 +82,19 @@ jobs:
- name: Cache package
if: inputs.cache-package
uses: actions/cache/save@v3
id: cache-mols2grid
with:
path: |
dist/mols2grid-*.whl
dist/mols2grid-*.tar.gz
key: mols2grid-${{ runner.os }}-${{ github.sha }}
key: mols2grid-${{ runner.os }}-${{ github.sha }}

- name: Expose package as artifact
if: inputs.upload-package
uses: actions/upload-artifact@v4
with:
name: mols2grid-package
path: |
dist/mols2grid-*.whl
dist/mols2grid-*.tar.gz
if-no-files-found: error
retention-days: 20
321 changes: 180 additions & 141 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,117 +17,118 @@ concurrency:
# cancel-in-progress: true

jobs:
tests:
name: ${{ matrix.label }}
runs-on: ubuntu-latest
strategy:
matrix:
include:
- label: rdkit-2021
python-version: 3.8
extra_dependencies: "rdkit==2021.03.1"
- label: rdkit-latest
python-version: "3.10"
extra_dependencies: "rdkit"
# unit-tests:
# name: ${{ matrix.label }}
# runs-on: ubuntu-latest
# strategy:
# matrix:
# include:
# - label: rdkit-2021
# python-version: 3.8
# extra_dependencies: "rdkit==2021.03.1"
# - label: rdkit-latest
# python-version: "3.10"
# extra_dependencies: "rdkit"

steps:
- uses: actions/checkout@v3
# steps:
# - uses: actions/checkout@v3

- name: Install Firefox
uses: browser-actions/setup-firefox@latest
# - name: Install Firefox
# uses: browser-actions/setup-firefox@latest

- run: firefox --version
# - run: firefox --version

- name: Prepare Selenium
uses: browser-actions/setup-geckodriver@latest
with:
geckodriver-version: "0.32.0"
# - name: Prepare Selenium
# uses: browser-actions/setup-geckodriver@latest
# with:
# geckodriver-version: "0.32.0"

- run: geckodriver --version
# - run: geckodriver --version

- name: Cache conda
uses: actions/cache@v3
env:
CACHE_NUMBER: 0
with:
path: ~/conda_pkgs_dir
key:
conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
# - name: Cache conda
# uses: actions/cache@v3
# env:
# CACHE_NUMBER: 0
# with:
# path: ~/conda_pkgs_dir
# key:
# conda-${{ hashFiles('tests/environment.yml') }}-${{ matrix.label }}-${{ env.CACHE_NUMBER }}

- name: Cache pip
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: pip-${{ hashFiles('pyproject.toml') }}
restore-keys: pip-
# - name: Cache pip
# uses: actions/cache@v3
# with:
# path: ~/.cache/pip
# key: pip-${{ hashFiles('pyproject.toml') }}
# restore-keys: pip-

- name: Get yarn cache directory path
id: yarn-cache-dir-path
run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
# - name: Get yarn cache directory path
# id: yarn-cache-dir-path
# run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT

- name: Cache yarn
uses: actions/cache@v3
with:
path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
key: yarn-${{ hashFiles('yarn.lock') }}
restore-keys: |
yarn-
# - name: Cache yarn
# uses: actions/cache@v3
# with:
# path: ${{ steps.yarn-cache-dir-path.outputs.dir }}
# key: yarn-${{ hashFiles('yarn.lock') }}
# restore-keys: |
# yarn-

- name: Setup Conda
uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: tests/environment.yml
use-only-tar-bz2: true
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
# - name: Setup Conda
# uses: conda-incubator/setup-miniconda@v2
# with:
# python-version: ${{ matrix.python-version }}
# environment-file: tests/environment.yml
# use-only-tar-bz2: true
# miniforge-variant: Mambaforge
# miniforge-version: latest
# use-mamba: true

- name: Check conda and pip
run: |
which python
python --version
pip --version
conda --version
mamba --version
# - name: Check conda and pip
# run: |
# which python
# python --version
# pip --version
# conda --version
# mamba --version

- name: Install remaining conda dependencies
run: |
mamba install 'jupyterlab>=3,<5' ipywidgets=8 ${{ matrix.extra_dependencies }}
mamba list
# - name: Install remaining conda dependencies
# run: |
# mamba install 'jupyterlab>=3,<5' ipywidgets=8 ${{ matrix.extra_dependencies }}
# mamba list

- name: Build and install package
run: |
pip install .[tests,build]
jupyter labextension develop . --overwrite
pip list
jupyter labextension list
# - name: Build and install package
# run: |
# pip install .[tests,build]
# jupyter labextension develop . --overwrite
# pip list
# jupyter labextension list

- name: Run tests
run: |
pytest --color=yes --disable-pytest-warnings \
--cov=mols2grid --cov-report=xml \
tests/ -m "not webdriver"
# - name: Run tests
# run: |
# pytest --color=yes --disable-pytest-warnings \
# --cov=mols2grid --cov-report=xml \
# tests/ -m "not webdriver"

- name: Run webdriver tests
run: |
pytest --color=yes --disable-pytest-warnings \
--cov=mols2grid --cov-report=xml --cov-append \
tests/ -m "webdriver"
# - name: Run webdriver tests
# run: |
# pytest --color=yes --disable-pytest-warnings \
# --cov=mols2grid --cov-report=xml --cov-append \
# tests/ -m "webdriver"

- name: Measure tests coverage
uses: codecov/codecov-action@v3
with:
files: ./coverage.xml
fail_ci_if_error: true
verbose: true
# - name: Measure tests coverage
# uses: codecov/codecov-action@v3
# with:
# files: ./coverage.xml
# fail_ci_if_error: true
# verbose: true

build:
uses: ./.github/workflows/_build-package.yml
with:
cache-package: true
upload-package: true

test-build:
build-test:
name: Test build
needs: [build]
runs-on: ubuntu-latest
Expand Down Expand Up @@ -170,61 +171,99 @@ jobs:
pip install dist/mols2grid-*.whl \
&& python test_install.py
# notebook-tests:
# needs: [build]
# name: ${{ matrix.label }}
# runs-on: ubuntu-latest
# strategy:
# matrix:
# include:
# - label: JLab-3-Widgets-7
# extra_dependencies: "'jupyterlab~=3.2' 'ipywidgets~=7.6'"
# - label: JLab-4-Widgets-8
# extra_dependencies: "'jupyterlab~=4.0' 'ipywidgets~=8.1'"

# steps:
# - uses: actions/checkout@v3

# - name: Retrieve cached package
# uses: actions/cache/restore@v3
# id: cache-mols2grid
# with:
# path: |
# dist/mols2grid-*.whl
# dist/mols2grid-*.tar.gz
# key: mols2grid-${{ runner.os }}-${{ github.sha }}
ui-tests:
needs: [build]
name: ${{ matrix.label }}
runs-on: ubuntu-latest
strategy:
matrix:
include:
- label: JLab-3-Widgets-7
extra_dependencies: "'jupyterlab~=3.2' 'ipywidgets~=7.6'"
- label: JLab-4-Widgets-8
extra_dependencies: "'jupyterlab~=4.0' 'ipywidgets~=8.1'"

# - name: Cache conda
# uses: actions/cache@v3
# env:
# CACHE_NUMBER: 2
# with:
# path: ~/conda_pkgs_dir
# key:
# conda-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
steps:
- uses: actions/checkout@v3

# - name: Setup Conda
# uses: conda-incubator/setup-miniconda@v2
# with:
# python-version: "3.10"
# miniforge-variant: Mambaforge
# miniforge-version: latest
# use-mamba: true
- name: Retrieve cached package
uses: actions/cache/restore@v3
id: cache-mols2grid
with:
path: |
dist/mols2grid-*.whl
dist/mols2grid-*.tar.gz
key: mols2grid-${{ runner.os }}-${{ github.sha }}

# - name: Install remaining conda dependencies
# run: |
# mamba install rdkit pandas ${{ matrix.extra_dependencies }}
# mamba list
- name: Cache conda
uses: actions/cache@v3
env:
CACHE_NUMBER: 2
with:
path: ~/conda_pkgs_dir
key:
conda-${{ matrix.label }}-${{ env.CACHE_NUMBER }}

# - name: Get wheel absolute path
# id: wheel-path
# run: echo "value=$(ls -d $PWD/dist/mols2grid-*.whl)" >> $GITHUB_OUTPUT
- name: Setup Conda
uses: conda-incubator/setup-miniconda@v2
with:
python-version: "3.10"
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true

# - name: Install the extension
# run: |
# pip install 'mols2grid[packaging] @ file://${{ steps.wheel-path.outputs.value }}'
# jupyter labextension list
- name: Install remaining conda dependencies
run: |
mamba install \
rdkit pandas playwright \
${{ matrix.extra_dependencies }}
mamba list
- name: Install XeLatex
run: sudo apt-get install texlive-xetex

- name: Install Ghostscript for ImageMagick
run: sudo apt-get install ghostscript

- name: Install the extension
run: |
pip install dist/mols2grid-*.whl
jupyter labextension list
- name: Run test notebook and convert to PDF
working-directory: tests/notebooks/
run: |
jupyter nbconvert --execute --no-input \
--allow-chromium-download --to webpdf \
filtering.ipynb
- name: Change ImageMagick policy to allow pdf->png conversion
run: |
sudo sed -i 's/^.*policy.*coder.*none.*PDF.*//' /etc/ImageMagick-6/policy.xml
- name: Convert to PNG
id: png-conv
working-directory: tests/notebooks/
run: |
mv filtering.pdf ${{ matrix.label }}.pdf
convert -density 192 ${{ matrix.label }}.pdf \
-quality 100 -alpha remove ${{ matrix.label }}.png
ls
- name: Run diff
id: diff-test
working-directory: tests/notebooks/
run: |
delta=$(compare -metric AE -fuzz 10% ref-${{ matrix.label }}.png ${{ matrix.label }}.png null:)
echo "Delta: $delta"
[[ $delta -eq 0 ]]
# - name: Run test
# run: |
# echo TODO
- name: Upload output if fail
if: always()
uses: actions/upload-artifact@v4
with:
name: notebook-${{ matrix.label }}
path: |
tests/notebooks/${{ matrix.label }}*
if-no-files-found: error
retention-days: 5
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