refactor: update regex for seqid #165 (#166) #381
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name: ci | |
on: [push, pull_request] | |
jobs: | |
static-code-analysis: | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
steps: | |
- name: check out repository | |
uses: actions/checkout@v4 | |
- name: set up miniconda and env | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: "3.9" | |
mamba-version: "*" | |
auto-update-conda: true | |
activate-environment: htsinfer | |
environment-file: environment-dev.yml | |
auto-activate-base: false | |
- name: display env info | |
run: | | |
conda info -a | |
conda list | |
- name: flake8 | |
run: flake8 | |
- name: pylint | |
run: pylint --rcfile pylint.cfg setup.py htsinfer/ | |
- name: mypy | |
run: mypy htsinfer | |
unit-testing: | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: [ '3.8', '3.9', '3.10' ] | |
name: unit-testing-Python-${{ matrix.python-version }} | |
steps: | |
- name: check out repository | |
uses: actions/checkout@v3 | |
- name: set up miniconda and env | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
mamba-version: "*" | |
auto-update-conda: true | |
activate-environment: htsinfer | |
environment-file: environment-dev.yml | |
auto-activate-base: false | |
- name: display env info | |
run: | | |
conda info -a | |
conda list | |
- name: run unit tests | |
run: | | |
coverage run --source htsinfer -m pytest | |
coverage xml | |
- name: submit coverage report | |
uses: codecov/codecov-action@v2 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
files: ./coverage.xml | |
fail_ci_if_error: true | |
verbose: true | |
integration-testing: | |
runs-on: ubuntu-latest | |
defaults: | |
run: | |
shell: bash -l {0} | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: [ '3.8', '3.9', '3.10' ] | |
name: integration-testing-Python-${{ matrix.python-version }} | |
steps: | |
- name: check out repository | |
uses: actions/checkout@v4 | |
- name: set up miniconda and env | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
mamba-version: "*" | |
auto-update-conda: true | |
activate-environment: htsinfer | |
environment-file: environment-dev.yml | |
auto-activate-base: false | |
- name: display env info | |
run: | | |
conda info -a | |
conda list | |
- name: integration test - help screen | |
run: htsinfer --help | |
- name: integration test - single-ended library | |
run: htsinfer --cleanup-regime=KEEP_NONE --verbosity=DEBUG tests/files/adapter_single.fastq | |
- name: integration test - paired-ended library | |
run: htsinfer --cleanup-regime=KEEP_NONE --verbosity=DEBUG tests/files/adapter_{1,2}.fastq | |
publish: | |
name: build and publish app image | |
runs-on: ubuntu-latest | |
if: | | |
github.event_name == 'push' && | |
github.ref == format('refs/heads/{0}', github.event.repository.default_branch) | |
steps: | |
- name: check out repository | |
uses: actions/checkout@v3 | |
- name: generate tag | |
run: | | |
echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV | |
- name: build and publish image | |
id: docker | |
uses: philips-software/docker-ci-scripts@v5.1.0 | |
with: | |
dockerfile: . | |
image-name: "htsinfer" | |
tags: "latest ${{ env.TAG }}" | |
push-branches: "${{ github.event.repository.default_branch }}" | |
env: | |
REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }} | |
REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}" | |
DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }} | |
GITHUB_ORGANIZATION: ${{ github.repository_owner }} | |
- name: Verify that image was pushed | |
run: | | |
echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}" | |
echo "# Set to 'true' if image was pushed, empty string otherwise" | |
test "${{ steps.docker.outputs.push-indicator }}" == "true" |