GitHub Actions

.github/env.yaml

@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   - python >=3.7,<3.10
-  - biobb_common ==3.9.0
+  - biobb_common ==4.0.0
   - gfortran ==8.5.0
   - flexserv ==1.0.2
   - pcasuite ==1.0.0

.github/workflows/linting_and_testing.yml

@@ -20,7 +20,7 @@ jobs:
       matrix:
         os: [self-hosted]
         python-version: ["3.7", "3.8", "3.9"]
-    runs-on: self-hosted
+    runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code
         uses: actions/checkout@v3
@@ -43,8 +43,14 @@ jobs:
             python=${{ matrix.python-version }}
             pytest
             pytest-cov
+            pytest-html
             flake8
+            pip
       
+      - name: Install genbadge from pip
+        shell: bash -l {0}  # necessary for conda env to be active
+        run: pip install genbadge[all]
+
       - name: List installed package versions
         shell: bash -l {0}  # necessary for conda env to be active
         run: micromamba list
@@ -57,9 +63,17 @@ jobs:
 
           # Workflow fails: Stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --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
+          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: bash -l {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
@@ -72,13 +86,33 @@ jobs:
         run: |
           # Ignoring docker and singularity tests
           export PYTHONPATH=.:./biobb_common:$PYTHONPATH
+
+          # Create directory for tests reports
+          mkdir -p ./reports/junit
+
           # Production one
-          pytest biobb_flexserv/test/unitests/ --cov=./ --cov-report=xml --ignore-glob=*container.py --ignore-glob=*pmemd*
+          pytest biobb_flexserv/test/unitests/ --cov=./ --cov-report=xml --junit-xml=./reports/junit/junit.xml --html=./reports/junit/report.html
+
+      - name: Generate Tests badge
+        shell: bash -l {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: bash -l {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: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v3
+      - name: Publish coverage report to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          folder: ./reports
 
       - name: Restore .bash_profile
         run: cp ~/.bash_profile_orig ~/.bash_profile

README.md

@@ -1,12 +1,26 @@
-[![](https://github.com/bioexcel/biobb_flexserv/actions/workflows/linting_and_testing.yml/badge.svg)](https://github.com/bioexcel/biobb_flexserv/actions/workflows/linting_and_testing.yml)
-[![](https://codecov.io/gh/bioexcel/biobb_flexserv/branch/master/graph/badge.svg?token=1WU81J2VLP)](https://codecov.io/gh/bioexcel/biobb_flexserv)
-[![](https://readthedocs.org/projects/biobb-flexserv/badge/?version=latest)](https://biobb-flexserv.readthedocs.io/en/latest/?badge=latest)
-
-[![](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](https://anaconda.org/bioconda/biobb_flexserv)
-[![](https://img.shields.io/badge/docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_flexserv?tab=tags)
-[![](https://img.shields.io/badge/singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexserv:3.9.0--pyhdfd78af_0)
-
+[![](https://img.shields.io/github/v/tag/bioexcel/biobb_flexserv?label=Version)](https://GitHub.com/bioexcel/biobb_flexserv/tags/)
+[![](https://img.shields.io/pypi/v/biobb-flexserv.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-flexserv/)
+[![](https://img.shields.io/conda/vn/bioconda/biobb_flexserv?label=Conda)](https://anaconda.org/bioconda/biobb_flexserv)
+[![](https://img.shields.io/conda/dn/bioconda/biobb_flexserv?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_flexserv)
+[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_flexserv?tab=tags)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_flexserv:4.0.0--pyhdfd78af_0)
+
+[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_flexserv)
+[![](https://img.shields.io/pypi/pyversions/biobb-flexserv.svg?label=Python%20Versions)](https://pypi.org/project/biobb-flexserv/)
 [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_flexserv)
+
+[![](https://readthedocs.org/projects/biobb-flexserv/badge/?version=latest&label=Docs)](https://biobb-flexserv.readthedocs.io/en/latest/?badge=latest)
+[![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
+[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
+[![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
+
+[![](https://docs.bioexcel.eu/biobb_flexserv/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_flexserv/junit/report.html)
+[![](https://docs.bioexcel.eu/biobb_flexserv/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_flexserv/coverage/)
+[![](https://docs.bioexcel.eu/biobb_flexserv/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_flexserv/flake8/)
+[![](https://img.shields.io/github/last-commit/bioexcel/biobb_flexserv?label=Last%20Commit)](https://github.com/bioexcel/biobb_flexserv/commits/master)
+[![](https://img.shields.io/github/issues/bioexcel/biobb_flexserv.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_flexserv/issues/)
 
 
 # biobb_flexserv