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ci.yml
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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