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CI #165

Workflow file for this run

name: CI
on:
push:
branches:
- "master"
workflow_dispatch:
pull_request:
branches:
- "master"
- "dev"
schedule:
# Run a cron job once daily, weekdays only
- cron: "0 3 1,15 * *"
jobs:
test:
name: Pytest
runs-on: ${{ matrix.cfg.os }}
strategy:
fail-fast: false
matrix:
cfg:
- os: ubuntu-latest
python-version: "3.8"
- os: ubuntu-latest
python-version: "3.9"
#- os: macos-latest
# python-version: "3.9"
#- os: windows-latest
# python-version: "3.9"
steps:
- uses: actions/checkout@v4
# More info on options: https://github.com/conda-incubator/setup-miniconda
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.cfg.python-version }}
miniforge-variant: Mambaforge
miniforge-version: latest
environment-file: environment.yml
channels: conda-forge,defaults
activate-environment: kinfraglib
#auto-update-conda: false
#auto-activate-base: false
#show-channel-urls: true
- name: Additional info about the build
shell: bash
run: |
uname -a
df -h
ulimit -a
- name: Environment Information
shell: bash -l {0}
run: |
conda info --all
conda list
- name: Download external data
shell: bash -l {0}
run: |
echo "Download combinatorial library from zenodo..."
wget -q -O data/combinatorial_library/combinatorial_library.tar.bz2 https://zenodo.org/record/10843763/files/combinatorial_library.tar.bz2?download=1
ls -l data/combinatorial_library/
echo "Decompress selected files..."
tar -xvf data/combinatorial_library/combinatorial_library.tar.bz2 combinatorial_library_deduplicated.json chembl_standardized_inchi.csv
mv combinatorial_library_deduplicated.json data/combinatorial_library/
mv chembl_standardized_inchi.csv data/combinatorial_library/
ls -l data/combinatorial_library/
- name: Run tests
shell: bash -l {0}
run: |
PYTEST_ARGS="--nbval-lax --nbval-current-env --nbval-cell-timeout=1800"
pytest $PYTEST_ARGS