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Improve error management #39

Improve error management

Improve error management #39

Workflow file for this run

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: CI
on:
pull_request:
branches:
- '*'
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
build:
runs-on: ubuntu-latest
defaults:
run:
shell: bash -el {0}
strategy:
fail-fast: false
matrix:
python-version: [3.8] #["3.8", "3.9", "3.10"]
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v3
# Install requirements
- uses: conda-incubator/setup-miniconda@v2
with:
mamba-version: "*"
python-version: ${{ matrix.python-version }}
channels: conda-forge,bioconda,defaults
environment-file: binette.yaml
activate-environment: binette
- name: Install binette
run: |
pip install .
binette -h
- name: Lint with flake8
run: |
mamba install flake8
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test with pytest
run: |
mamba install pytest pytest-cov
pytest --cov=binette --cov-report=html --cov-report=xml
- name: Generate coverage badge
run: |
pip install genbadge[coverage]
genbadge coverage -i coverage.xml -o htmlcov/coverage-badge.svg
rm htmlcov/.gitignore
- name: Publish coverage report to GitHub Pages
if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch)
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: htmlcov
branch: gh-pages
- name: Download test data
uses: actions/checkout@v3
with:
repository: genotoul-bioinfo/Binette_TestData
path: test_data
- name: Run simple test case
run: |
cd test_data
binette -b binning_results/* --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd -v -o test_results
- name: Compare results with expectation
run: |
cd test_data
head expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv
python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv