update version [skip ci]

.github/workflows/publish.yaml

@@ -30,10 +30,32 @@ jobs:
       
       - name: Create a release tag
         id: tag
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
+          # git config http.sslVerify false
+          # repo="https://${GITHUB_ACTOR}:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git"
           git config --local user.email "[email protected]"
           git config --local user.name "ersilia-bot"
           git tag -a "v${{ steps.version.outputs.VERSION }}" -m "v${{ steps.version.outputs.VERSION }}"
+          # git push "${repo}" origin "v${{ steps.version.outputs.VERSION }}"
+
+      - name: Update version in CITATION.cff
+        id: update-citation
+        env:
+          VERSION: ${{ steps.version.outputs.VERSION }}
+        run: |
+          pip install PyYAML
+          python -c "
+          import os
+          import yaml
+          with open('CITATION.cff', 'r') as file:
+              content = file.read()
+          citation = yaml.safe_load(content)
+          citation['version'] = os.environ['VERSION']
+          with open('CITATION.cff', 'w') as file:
+              yaml.dump(citation, file, default_flow_style=False, sort_keys=False)
+          "
 
       - name: Commit and push changes done to the static version file and pyproject.toml
         uses: actions-js/push@5a7cbd780d82c0c937b5977586e641b2fd94acc5 # [email protected]
@@ -46,51 +68,51 @@ jobs:
           amend: true
           force: true
           branch: "master"
+          tags: true
 
   gh-release:
     runs-on: ubuntu-latest
     needs: version
     env:
       GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
+      - uses: actions/checkout@v4
       - name: Create GitHub release
         id: gh_release
         run: |
           # Get the version file that we updated in the previous job
           wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/ersilia/_static_version.py
-
+        
           month=$(date +'%B')
           year=$(date +'%Y')
-          title="Release $month $year"
+          title="$month $year"
           version=`sed -n 's/.*version = "\([^"]*\)".*/\1/p' _static_version.py`
-          gh release create "v$version" --title "$title" --notes-from-tag
+          git fetch --tags
+          gh release create "v$version" --title "$title" --generate-notes
 
   pypi-release:
     runs-on: ubuntu-latest
     needs: version
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # [email protected]
+        with:
+          ref: master
 
       - name: Set up Python
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # [email protected]
         with:
           python-version: '3.8'
           # cache: 'pip' # caching pip dependencies
 
-      - name: Get version
-        run: |
-          wget https://raw.githubusercontent.com/ersilia-os/ersilia/master/ersilia/_static_version.py
-          mv _static_version.py ersilia/.
-
       - name: Python Poetry Action
         uses: abatilo/[email protected]
 
       - name: Build and publish
         env:
           PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
           PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-
         run: |
+          git pull origin master 
           poetry config -- http-basic.pypi $PYPI_USERNAME $PYPI_PASSWORD
           poetry --build publish 
 

CITATION.cff

@@ -1,17 +1,17 @@
 cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
+message: If you use this software, please cite it as below.
 authors:
-- family-names: "Turon"
-  given-names: "Gemma"
-  orcid: "https://orcid.org/0000-0001-6798-0275"
-- family-names: "Arora"
-  given-names: "Dhanshree"
-  orcid: "https://orcid.org/0009-0005-1303-4044"
-- family-names: "Duran-Frigola"
-  given-names: "Miquel"
-  orcid: "https://orcid.org/0000-0002-9906-6936"
-title: "Ersilia Model Hub: a repository of AI/ML models for neglected tropical diseases"
-version: 1.0.0
-doi: 10.5281/zenodo.7274646
+- family-names: Turon
+  given-names: Gemma
+  orcid: https://orcid.org/0000-0001-6798-0275
+- family-names: Arora
+  given-names: Dhanshree
+  orcid: https://orcid.org/0009-0005-1303-4044
+- family-names: Duran-Frigola
+  given-names: Miquel
+  orcid: https://orcid.org/0000-0002-9906-6936
+title: 'Ersilia Model Hub: a repository of AI/ML models for neglected tropical diseases'
+version: 0.1.36
+doi: 10.5281/zenodo.7274645
 date-released: 2022-11-02
-url: "https://github.com/ersilia-os/ersilia"
+url: https://github.com/ersilia-os/ersilia

ersilia/_static_version.py

@@ -1 +1 @@
-version = "0.1.35"
+version = "0.1.36"