(v2.1.1.9094) fix antibiotics

.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,66 @@
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+on:
+  push:
+    # only on main
+    branches: 'main_UPDATE_THIS'
+
+name: Publish Python Package to PyPI
+
+jobs:
+  update-pypi:
+    runs-on: ubuntu-latest
+    
+    steps:
+      
+      - name: Checkout code
+        uses: actions/checkout@v3
+      
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+        
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+        
+      - name: Build the package
+        run: python -m build
+      
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: "msberends"
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          python -m twine upload dist/*
+        # for test server:
+        # python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*