mod pr template #171
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# This workflow will install Python dependencies, run tests and lint with a single version of Python | |
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
name: "CI" | |
env: | |
REGISTRY: ghcr.io | |
IMAGE_NAME: ${{ github.repository }} | |
on: | |
push: | |
branches: [ "*" ] | |
pull_request: | |
types: [opened, ready_for_review] | |
concurrency: | |
group: ${{ github.ref }} | |
cancel-in-progress: true | |
jobs: | |
build-and-ci: | |
name: miniconda build | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: [3.6, 3.7, 3.8] | |
env: | |
SETUPTOOLS_USE_DISTUTILS: stdlib | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- uses: actions/checkout@v2 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
activate-environment: test-environment | |
python-version: ${{ matrix.python-version }} | |
channels: bioconda,default,anaconda,r,conda-forge | |
allow-softlinks: true | |
channel-priority: 'flexible' | |
show-channel-urls: true | |
use-only-tar-bz2: true | |
auto-update-conda: true | |
- name: setup conda | |
run: | | |
conda config --set always_yes yes --set changeps1 no | |
conda info -a | |
conda list | |
conda config --show-sources | |
conda config --show | |
- name: Install dependencies | |
run: | | |
conda install mamba | |
mamba install pandas tzlocal rpy2 biopython ReportLab pytest-cov codecov bioconductor-deseq2 gfortran_linux-64 bioconductor-apeglm | |
- name: hack for missing sysconfigdata (py3.7 and py3.8, doing nothing really) | |
if: matrix.python-version != '3.6' | |
run: | | |
ls $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda*.py | |
- name: hack for missing sysconfigdata (py3.6) | |
if: matrix.python-version == '3.6' | |
run: | | |
ls $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64*.py | |
cp $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda_cos6_linux_gnu.py $CONDA_PREFIX/lib/python${{ matrix.python-version }}/_sysconfigdata_x86_64_conda_linux_gnu.py | |
- name: install package | |
run: | | |
conda activate test-environment | |
pip install . | |
- name: install R packages | |
run: | | |
Rscript setup.R | |
- name: Test with pytest | |
run: | | |
coverage run -m pytest -vvv | |
- name: codecov | |
run: | | |
bash <(curl -s https://codecov.io/bash) | |
build-and-push-image: | |
runs-on: ubuntu-latest | |
needs: build-and-ci | |
permissions: | |
contents: read | |
packages: write | |
steps: | |
- name: Checkout repository | |
uses: actions/checkout@v3 | |
- name: Log in to the Container registry | |
uses: docker/login-action@v2 | |
with: | |
registry: ${{ env.REGISTRY }} | |
username: ${{ github.actor }} | |
password: ${{ secrets.GITHUB_TOKEN }} | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v2 | |
- name: Build and push Docker image | |
if: github.ref_name == 'master' | |
uses: docker/build-push-action@v3 | |
with: | |
context: . | |
push: true | |
target: diffexpr | |
cache-from: type=gha | |
cache-to: type=gha,mode=max | |
tags: | | |
${{ env.REGISTRY }}/${{ github.repository }}/diffexpr:${{ github.ref_name }} | |
${{ env.REGISTRY }}/${{ github.repository }}/diffexpr:${{ github.sha }} | |
- name: Build and push Dev Docker image | |
uses: docker/build-push-action@v3 | |
with: | |
context: . | |
push: true | |
target: diffexpr_dev | |
cache-from: type=gha | |
cache-to: type=gha,mode=max | |
tags: | | |
${{ env.REGISTRY }}/${{ github.repository }}/diffexpr-dev:${{ github.ref_name }} | |
${{ env.REGISTRY }}/${{ github.repository }}/diffexpr-dev:${{ github.sha }} |