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Added references

Added references #13

name: tests
on:
# workflow_dispatch
push:
branches: [ master ]
paths-ignore:
- '.gitignore'
- '.readthedocs.yaml'
- 'LICENSE'
- 'setup.py'
- 'README.md'
- 'references.html'
- '**/docs/**'
- '**/json_schemas/**'
jobs:
# Name of the Job
lint_and_test:
strategy:
matrix:
os: [self-hosted]
python-version: ["3.8", "3.9", "3.10"]
runs-on: ${{ matrix.os }}
steps:
- name: Check out repository code
uses: actions/checkout@v3
- run: echo "Repository -> ${{ github.repository }}"
- run: echo "Branch -> ${{ github.ref }}"
- run: echo "Trigger event -> ${{ github.event_name }}"
- run: echo "Runner OS -> ${{ runner.os }}"
- name: List files in the repository
run: |
ls ${{ github.workspace }}
- name: Remove all micromamba installations
run: |
rm -rf /home/user/.bash_profile /home/user/.conda /home/user/micromamba /home/user/micromamba-bin 2>/dev/null
touch /home/user/.bash_profile
- name: provision-with-micromamba
uses: mamba-org/setup-micromamba@v1
with:
generate-run-shell: true
post-cleanup: all
environment-file: .github/env.yaml
create-args: >-
python=${{ matrix.python-version }}
pytest
pytest-cov
pytest-html
flake8
pip
- name: Install genbadge from pip
shell: micromamba-shell {0} # necessary for conda env to be active
run: pip install genbadge[all]
- name: List installed package versions
shell: micromamba-shell {0} # necessary for conda env to be active
run: micromamba list
- name: Lint with flake8
shell: micromamba-shell {0} # necessary for conda env to be active
run: |
# F Codes: https://flake8.pycqa.org/en/latest/user/error-codes.html
# E Code: https://pycodestyle.pycqa.org/en/latest/intro.html#error-codes
# Workflow fails: Stop the build if there are Python syntax errors or undefined names
# flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# Do not check for undefined names fix_pdb_utils.py should be fixed
flake8 . --count --select=E9,F63,F7 --show-source --statistics
# Create directory for flake8 reports
mkdir -p ./reports/flake8
# Exit-zero treats all errors as warnings, workflow will not fail:
flake8 . --exclude=docs --ignore=C901,E226 --count --exit-zero --max-complexity=10 --max-line-length=999 --statistics --format=html --htmldir=./reports/flake8/ --tee --output-file=./reports/flake8/flake8stats.txt
- name: Generate Flake8 badge
shell: micromamba-shell {0} # necessary for conda env to be active
run: |
genbadge flake8 --name "Flake8" --input-file ./reports/flake8/flake8stats.txt --output-file ./reports/flake8/flake8badge.svg
- name: Checkout biobb_common
uses: actions/checkout@v3
with:
repository: bioexcel/biobb_common
path: './biobb_common'
- name: Run tests
shell: micromamba-shell {0} # necessary for conda env to be active
run: |
# Ignoring docker and singularity tests
export PYTHONPATH=.:./biobb_common:$PYTHONPATH
# Create directory for tests reports
mkdir -p ./reports/junit
# Producction one
# pytest biobb_model/test/unitests/ --cov=./ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
# Avoiding fix_backbone because of the modeller installation
pytest biobb_model/test/unitests/ --cov=./ --cov-report=xml --ignore-glob=*fix_backbone.py --ignore-glob=*container.py --ignore-glob=*docker.py --ignore-glob=*singularity.py --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
- name: Generate Tests badge
shell: micromamba-shell {0} # necessary for conda env to be active
run: |
genbadge tests --name "Tests" --input-file ./reports/junit/junit.xml --output-file ./reports/junit/testsbadge.svg
- name: Generate Coverage badge
shell: micromamba-shell {0} # necessary for conda env to be active
run: |
# Create directory for flake8 reports
mkdir -p ./reports/coverage
coverage xml -o ./reports/coverage/coverage.xml
coverage html -d ./reports/coverage/
genbadge coverage --name "Coverage" --input-file ./reports/coverage/coverage.xml --output-file ./reports/coverage/coveragebadge.svg
- name: Publish coverage report to GitHub Pages
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: ./reports