Align prepmd Packaging and Release Workflow with Other CCPBioSim Repositories

.github/workflows/release.yml

@@ -16,82 +16,90 @@ jobs:
     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: 3.13.0
-
-    - 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 ${{ github.event.inputs.version }}
-#    needs: checks
-#    runs-on: ubuntu-24.04
-#    steps:
-
-#      - name: checkout
-#        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
-
-#      - name: Change version in repo and CITATION.cff
-#        run: |
+      - name: Checkout repository
+        id: repo
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+        with:
+          python-version: 3.13.0
+
+      - name: Get latest release tag
+        id: latestreleased
+        run: |
+          PREVIOUS_VERSION=$(git tag --sort=-version:refname | head -n 1)
+          PREVIOUS_VERSION=${PREVIOUS_VERSION#v}
+
+          if [ -z "$PREVIOUS_VERSION" ]; then
+            PREVIOUS_VERSION="0.0.0"
+          fi
+
+          echo "release_tag=$PREVIOUS_VERSION" >> "$GITHUB_OUTPUT"
+          echo "$PREVIOUS_VERSION"
+
+      - name: version comparison
+        id: compare
+        run: |
+          pip3 install semver
+          output=$(pysemver compare ${{ steps.latestreleased.outputs.release_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
+          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: ${{ secrets.GITHUB_TOKEN }}
+          if [ -f CITATION.cff ]; then
+            sed -i -E "s/^(version:\s*).*/\1${{ 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
+    needs: version
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout repository
@@ -113,12 +121,12 @@ jobs:
     steps:
 
       - name: create release
-        uses: softprops/action-gh-release@v3
+        uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2.5.0
         with:
           name: v${{ github.event.inputs.version }}
           generate_release_notes: true
           tag_name: ${{ github.event.inputs.version }}
-          
+
   conda:
     name: publish conda to anaconda.org
     needs: [tag, release]
@@ -129,13 +137,12 @@ jobs:
         uses: actions/checkout@v4
         with:
           ref: main
-
-#      - name: Update modeller key
-#        shell: bash -l {0}
-#        run: |
-#          sed -i -e 's/SECRET-MODELLER-LICENSE-KEY/${{ secrets.MODELLER_KEY }}/g' $GITHUB_WORKSPACE/conda-recipe/meta.yml
-#          sed -i -e 's/SECRET-MODELLER-LICENSE-KEY/${{ secrets.MODELLER_KEY }}/g' $GITHUB_WORKSPACE/conda-recipe/build.sh
-
+
+      - name: Set version in conda recipe
+        run: |
+          sed -i "s/^{% set version = \".*\" %}$/{% set version = \"${{ github.event.inputs.version }}\" %}/" conda-recipe/meta.yaml
+          grep '{% set version' conda-recipe/meta.yaml
+
       - name: Setup Conda (conda-forge only)
         uses: conda-incubator/setup-miniconda@v3
         with:
@@ -144,25 +151,30 @@ jobs:
           auto-activate: true
           activate-environment: base
           conda-remove-defaults: true
-          channels: conda-forge,salilab
+          channels: conda-forge
           channel-priority: strict
 
       - name: Install build tools
         shell: bash -l {0}
         run: |
-          conda install -y conda-build anaconda-client
+          conda install -y \
+            --override-channels \
+            --channel conda-forge \
+            conda-build \
+            anaconda-client
+
           conda config --set anaconda_upload no
           conda list conda-build
           conda build --help
 
       - name: Build package
         shell: bash -l {0}
-        env:
-          PIP_NO_INDEX: "0"
         run: |
-          PKG_PATH=$(conda build conda-recipe --output)
+          PKG_PATH=$(conda build conda-recipe --output --override-channels --channel conda-forge)
           echo "PKG_PATH=$PKG_PATH" >> "$GITHUB_ENV"
-          conda build conda-recipe
+
+          conda build conda-recipe --override-channels --channel conda-forge
+
           test -f "$PKG_PATH"
           echo "Built: $PKG_PATH"
 

CITATION.cff

@@ -17,6 +17,11 @@ authors:
     email: harry.swift@stfc.ac.uk
     affiliation: 'STFC, Scientific Computing'
     orcid: 'https://orcid.org/0009-0007-3323-753X'
+  - given-names: Jas
+    family-names: Kalayan
+    email: jas.kalayan@stfc.ac.uk
+    affiliation: 'STFC, Scientific Computing'
+    orcid: 'https://orcid.org/0000-0002-6833-1864'
 repository-code: 'https://github.com/CCPBioSim/prepmd'
 abstract: >-
   A utility to automatically prepare structures from the PDB

conda-recipe/meta.yaml

@@ -1,39 +1,62 @@
+{% set name = "prepmd" %}
+{% set version = "0.0.0" %}
+
 package:
-  name: prepmd
-  version: 1.0.1
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  #git_url: https://www.github.com/ccpbiosim/prepmd.git
   path: ..
 
 build:
   noarch: python
+  script: |
+    {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  entry_points:
+    - prepmd=prepmd.prep:entry_point
+    - runmd=prepmd.run:entry_point
+    - prep-license=prepmd.add_modeller_license:entry_point
 
 requirements:
-  build:
-    - python
+  host:
+    - python >=3.13,<3.14
     - pip
-    - setuptools
+    - flit-core >=3.4,<4
+
   run:
-    - python=3.13
+    - python >=3.13,<3.14
     - requests
     - openmm
     - pdbfixer
-    - modeller
     - biopython
+    - pdb2pqr
     - mdanalysis
-    - openmmtools
     - rdkit
+    - openmmforcefields
     - openff-toolkit
-    - pdb2pqr
+
 test:
-#  commands:
-#    - prep-license SECRET-MODELLER-LICENSE-KEY
   imports:
     - prepmd
 
+  commands:
+    - python -c "import prepmd; print(prepmd.__version__)"
+    - prepmd --help
+    - runmd --help
+
 about:
-  summary: A utility to automatically prepare structures from the PDB for molecular dynamics simulation
-  dev_url: https://github.com/CCPBioSim/prepmd
-  license: GNU Affero General Public License v3.0
+  home: https://github.com/CCPBioSim/prepmd
+  license: AGPL-3.0-or-later
+  license_family: AGPL
   license_file: LICENSE
+  license_url: https://github.com/CCPBioSim/prepmd/blob/main/LICENSE
+  summary: Automatically prepare PDB and mmCIF structures for molecular dynamics simulations.
+  description: >-
+    prepmd is a Python utility for automatically preparing PDB and mmCIF
+    structures for molecular dynamics simulations. It provides tools for
+    preparing, repairing, and processing molecular structures using OpenMM,
+    PDBFixer, Biopython, MDAnalysis, RDKit, PDB2PQR, OpenMMForceFields,
+    and the OpenFF Toolkit.
+  dev_url: https://github.com/CCPBioSim/prepmd
+  doc_url: https://prepmd.readthedocs.io/en/latest/
+  doc_source_url: https://github.com/CCPBioSim/prepmd/blob/main/README.md

prepmd/__init__.py

@@ -1,14 +1,11 @@
-from . import fix
-from . import download
-from . import run
-from . import get_residues
-from . import util
-from . import prep
-from . import model
-from . import metadynamics
-from . import align_together
-from . import add_modeller_license
-from . import point_cloud
-from . import lib
-from . import ligand
-__version__ = "1.0.0"
+"""
+prepmd
+
+prepmd is a Python package for automatically preparing PDB and mmCIF
+structures for molecular dynamics simulations. It provides tools for
+preparing, repairing, and processing molecular structures using OpenMM,
+PDBFixer, Biopython, MDAnalysis, RDKit, PDB2PQR, OpenMMForceFields,
+and the OpenFF Toolkit.
+"""
+
+__version__ = "1.0.0"