Merge pull request #19 from GuilhemSempere/feat/actions

added github actions to create release / build & publish pypi package

.github/workflows/release.yaml

@@ -0,0 +1,53 @@
+name: Publish Python 🐍 mbctools 📦 to PyPI
+
+permissions:
+ contents: write
+
+on:
+ workflow_dispatch:
+
+jobs:
+ build-n-publish:
+ name: Build and publish Python 🐍 mbctools 📦 to PyPI
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@v4
+
+ - name: Set up Python
+ uses: actions/setup-python@v5
+ with:
+ python-version: "3.x"
+
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install setuptools wheel twine
+
+ - name: Extract version
+ id: get_version
+ run: |
+ VERSION=$(grep -oP "__version__ = \"\K[^\"]*" mbctools.py)
+ echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
+
+ - name: Build and publish
+ env:
+ TWINE_USERNAME: __token__
+ TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+ run: |
+ python setup.py sdist bdist_wheel
+ twine upload dist/*
+
+ - name: Create Release
+ uses: actions/create-release@v1
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+ with:
+ tag_name: v${{ steps.get_version.outputs.VERSION }}
+ release_name: ${{ steps.get_version.outputs.VERSION }}
+ body: |
+ New release of mbctools version ${{ steps.get_version.outputs.VERSION }}
+ 
+ PyPI package: https://pypi.org/project/mbctools/${{ steps.get_version.outputs.VERSION }}/
+ draft: false
+ prerelease: false

mbctools.py

@@ -1,7 +1,6 @@
 #!/usr/bin/python3
 
-"""
-mbctools a cross-platform toolkit to make use of VSEARCH easier and interactive, thus helping analyze
+"""mbctools a cross-platform toolkit to make use of VSEARCH easier and interactive, thus helping analyze
 metabarcoding data in the best conditions. It assumes VSEARCH is pre-installed and consists in the following MAIN MENU:
 
 1 -> INITIAL ANALYSIS (mandatory)
@@ -36,12 +35,7 @@
 
 VSEARCH reference:
 Rognes T, Flouri T, Nichols B, Quince C, Mahe F (2016). VSEARCH: a versatile open source tool for metagenomics
-PeerJ 4:e2584 doi: https://doi.org/10.7717/peerj.2584
-
-metaXplor reference:
-Sempéré G, Pétel A, Abbé M, et al (2021) metaXplor: an interactive viral and microbial metagenomic data manager
-GigaScience 10:giab001 doi: https://doi.org/10.1093/gigascience/giab001
-
+PeerJ 4:e2584 doi: 10.7717/peerj.2584 https://doi.org/10.7717/peerj.2584
 
 Usage:
 =====
@@ -1839,7 +1833,7 @@ def quit_mbctools():
 def printHowToCite():
  print(warningStyle + "\nPlease cite this software as follows:" +
  citationStyle + "\nmbctools:\tA User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing\n\t\tMultiple Amplicon Sequencing Data across a Large Diversity of Organisms" + normalStyle
- + "\nC. Barnabé, G. Sempéré, V. Manzanilla, J. Moo-Millan, A. Amblard-Rambert and E. Waleckx\n" + citationStyle + "bioRxiv, 2024.02.08.579441, https://doi.org/10.1101/2024.02.08.579441" + normalStyle + "\n\n")
+ + "\nChristian Barnabé, Guilhem Sempéré, Vincent Manzanilla and Etienne Waleckx.\n" + citationStyle + "https://github.com/GuilhemSempere/mbctools" + normalStyle + "\n\n")
 
 
 def main_menu1():