Introduce CITATION.cff file to formalise citation of the repository

.github/workflows/release.yml

@@ -12,9 +12,103 @@ permissions:
   pull-requests: write
 
 jobs:
+  checks:
+    name: Version check
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Checkout repository
+      id: repo
+      uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+    - name: Set up Python
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+      with:
+        python-version: 3.14.0
+
+    - name: Get latest release from pip
+      id: latestreleased
+      run: |
+        PREVIOUS_VERSION=$(python -m pip index versions prepmd | grep "prepmd" | cut -d "(" -f2 | cut -d ")" -f1)
+        echo "pip_tag=$PREVIOUS_VERSION" >> "$GITHUB_OUTPUT"
+        echo $PREVIOUS_VERSION
+
+    - name: version comparison
+      id: compare
+      run: |
+        pip3 install semver
+        output=$(pysemver compare ${{ steps.latestreleased.outputs.pip_tag }} ${{ github.event.inputs.version }})
+        if [ $output -ge 0 ]; then exit 1; fi
+
+  version:
+    name: prepare ${{ github.event.inputs.version }}
+    needs: checks
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: checkout
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+
+      - name: Change version in repo and CITATION.cff
+        run: |
+          # Update Python package version
+          sed -i "s/__version__ =.*/__version__ = \"${{ github.event.inputs.version }}\"/g" prepmd/__init__.py
+
+          # Update CITATION.cff version and date-released
+          if [ -f CITATION.cff ]; then
+            sed -i -E "s/^(version:\s*).*/\1${{ github.event.inputs.version }}/" CITATION.cff
+            sed -i -E "s/^(date-released:\s*).*/\1'$(date -u +%F)'/" CITATION.cff
+          fi
+
+      - name: send PR
+        id: pr_id
+        uses: peter-evans/create-pull-request@c0f553fe549906ede9cf27b5156039d195d2ece0 # v8.1.0
+        with:
+          commit-message: Update version to ${{ github.event.inputs.version }}
+          branch: version-update
+          title: "Update to version ${{ github.event.inputs.version }}"
+          body: |
+            Update version
+            - Update the __init__.py with new release
+            - Update CITATION.cff version & date-released
+            - Auto-generated by [CI]
+          committer: version-updater <vu.bot@users.noreply.github.com>
+          author: version-updater <vu.bot@users.noreply.github.com>
+          base: main
+          signoff: false
+          draft: false
+
+      - name: auto approve review
+        uses: hmarr/auto-approve-action@f0939ea97e9205ef24d872e76833fa908a770363 # v4.0.0
+        with:
+          pull-request-number: ${{ steps.pr_id.outputs.pull-request-number }}
+          review-message: "Auto approved version bump PR"
+          github-token: ${{ secrets.AUTO_PR_MERGE }}
+
+      - name: merge PR
+        run: gh pr merge --merge --delete-branch --auto "${{ steps.pr_id.outputs.pull-request-number }}"
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  tag:
+    name: tag release
+    needs: version
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        with:
+          ref: main
+
+      - name: tag v${{ github.event.inputs.version }}
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git tag ${{ github.event.inputs.version }}
+          git push origin tag ${{ github.event.inputs.version }}
 
   release:
     name: make github release
+    needs: tag
     runs-on: ubuntu-24.04
     steps:
 
@@ -27,7 +121,7 @@ jobs:
 
   conda:
     name: publish conda to anaconda.org
-    needs: release
+    needs: [tag, release]
     runs-on: ubuntu-24.04
 
     steps:

CITATION.cff

@@ -0,0 +1,30 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: prepmd
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Robert
+    family-names: Welch
+    email: robert.welch@stfc.ac.uk
+    affiliation: 'STFC, Scientific Computing'
+  - given-names: Harry
+    family-names: Swift
+    email: harry.swift@stfc.ac.uk
+    affiliation: 'STFC, Scientific Computing'
+    orcid: 'https://orcid.org/0009-0007-3323-753X'
+repository-code: 'https://github.com/CCPBioSim/prepmd'
+abstract: >-
+  A utility to automatically prepare structures from the PDB
+  for molecular dynamics simulation and perform
+  minimisations and simple MD simulations.
+keywords:
+  - PDB
+  - MD simulations
+license: AGPL-3.0
+version: 1.0.0
+date-released: '2026-04-14'