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Merge pull request #71 from jensengroup/nathan/coverage

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- add coverage.py to testing workflow
- use https://codecov.io/gh/jensengroup/propka
This commit is contained in:
Oliver Beckstein
2020-06-25 17:29:23 -07:00
committed by GitHub
parent 831e738068 4dc87a5a38
commit 58b6e652c6
2 changed files with 22 additions and 6 deletions
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26
.github/workflows/python-package.yml vendored
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@@ -1,13 +1,13 @@
# This workflow will install Python dependencies, run tests and lint with a variety of Python versions # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Python package name: Tests
on: on:
push: push:
branches: [ master ] branches: '**'
pull_request: pull_request:
branches: [ master ] branches: '**'
jobs: jobs:
build: build:
@@ -27,6 +27,7 @@ jobs:
run: | run: |
python -m pip install --upgrade pip setuptools wheel python -m pip install --upgrade pip setuptools wheel
pip install flake8 pytest pip install flake8 pytest
pip install coverage
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Lint with flake8 - name: Lint with flake8
run: | run: |
@@ -34,7 +35,20 @@ jobs:
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide # 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 flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test with pytest - name: Test with pytest and coverage
run: | run: |
pip install pytest coverage run -m pytest
python -m pytest coverage report -m | tee coverage.txt
coverage html
- name: Upload coverage to https://codecov.io/gh/jensengroup/propka
run: bash <(curl -s https://codecov.io/bash)
- name: Store coverage text results
uses: actions/upload-artifact@v2
with:
name: coverage-text
path: coverage.txt
- name: Store coverage HTML results
uses: actions/upload-artifact@v2
with:
name: coverage-html
path: htmlcov/*

2
README.md
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@@ -1,5 +1,7 @@
# PROPKA 3 # PROPKA 3
![Tests](https://github.com/jensengroup/propka/workflows/Tests/badge.svg)
PROPKA predicts the pKa values of ionizable groups in proteins PROPKA predicts the pKa values of ionizable groups in proteins
(version 3.0) and protein-ligand complexes (version 3.1 and later) (version 3.0) and protein-ligand complexes (version 3.1 and later)
based on the 3D structure. based on the 3D structure.