From 52bbd2e8879aa10f205fe7f48f18b6b7a363750e Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sat, 20 Jun 2020 07:49:58 -0700 Subject: [PATCH 1/6] Attempt to add coverage.py to testing workflow. --- .github/workflows/python-package.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 51bd099..3874603 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -1,7 +1,7 @@ # 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 -name: Python package +name: Test coverage on: push: @@ -27,6 +27,7 @@ jobs: run: | python -m pip install --upgrade pip setuptools wheel pip install flake8 pytest + pip install coverage if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - name: Lint with flake8 run: | @@ -36,5 +37,5 @@ jobs: flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest run: | - pip install pytest - python -m pytest + coverage run -m pytest + coverage report -m From 9fcc69b9a80b6fe01d6ff11aa7efd0e5df76e7ec Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sat, 20 Jun 2020 08:10:28 -0700 Subject: [PATCH 2/6] Store coverage results as artifacts --- .github/workflows/python-package.yml | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3874603..f0c7f23 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -35,7 +35,18 @@ jobs: 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 + - name: Test with pytest and coverage run: | coverage run -m pytest - coverage report -m + coverage report -m | tee coverage.txt + coverage html + - name: Store coverage text results + uses: actions/upload-artifact@v1 + with: + name: coverage-text + path: coverage.txt + - name: Store coverage HTML results + uses: actions/upload-artifact@v1 + with: + name: coverage-html + path: htmlcov/* From 4fd012cb57152fd30b17fe56cdc5b4f971ebe701 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sat, 20 Jun 2020 08:12:31 -0700 Subject: [PATCH 3/6] Fix YAML error. --- .github/workflows/python-package.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index f0c7f23..9f43487 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -42,11 +42,11 @@ jobs: coverage html - name: Store coverage text results uses: actions/upload-artifact@v1 - with: - name: coverage-text - path: coverage.txt + with: + name: coverage-text + path: coverage.txt - name: Store coverage HTML results uses: actions/upload-artifact@v1 - with: - name: coverage-html - path: htmlcov/* + with: + name: coverage-html + path: htmlcov/* From 151125b18c8fabb0c403113c6e95d025bd6f613c Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sat, 20 Jun 2020 08:17:17 -0700 Subject: [PATCH 4/6] Update runner version. Support wildcard artifact storage. --- .github/workflows/python-package.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 9f43487..3d2cb52 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -41,12 +41,12 @@ jobs: coverage report -m | tee coverage.txt coverage html - name: Store coverage text results - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v2 with: name: coverage-text path: coverage.txt - name: Store coverage HTML results - uses: actions/upload-artifact@v1 + uses: actions/upload-artifact@v2 with: name: coverage-html path: htmlcov/* From d982745858dd59efa049e5b3b108f16d79293241 Mon Sep 17 00:00:00 2001 From: Nathan Baker Date: Sat, 20 Jun 2020 08:24:16 -0700 Subject: [PATCH 5/6] Expand tests to all branches. Also update README with testing badge. --- .github/workflows/python-package.yml | 6 +++--- README.md | 2 ++ 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 3d2cb52..2e5b461 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -1,13 +1,13 @@ # 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 -name: Test coverage +name: Tests on: push: - branches: [ master ] + branches: '**' pull_request: - branches: [ master ] + branches: '**' jobs: build: diff --git a/README.md b/README.md index 4f24163..69b71a5 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,7 @@ # PROPKA 3 +![Tests](https://github.com/jensengroup/propka/workflows/Tests/badge.svg) + PROPKA predicts the pKa values of ionizable groups in proteins (version 3.0) and protein-ligand complexes (version 3.1 and later) based on the 3D structure. From 4dc87a5a38177aacad1f05be37faffdb71347d0c Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Thu, 25 Jun 2020 17:22:45 -0700 Subject: [PATCH 6/6] upload coverage to https://codecov.io/gh/jensengroup/propka --- .github/workflows/python-package.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 2e5b461..3858d08 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -40,6 +40,8 @@ jobs: coverage run -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: