Add Conda packaging and release workflow for SIST

.github/workflows/pr.yaml

@@ -20,33 +20,32 @@ jobs:
       - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
         with:
-          python-version: "3.14"
+          miniforge-variant: Miniforge3
+          auto-activate: true
+          activate-environment: base
+          conda-remove-defaults: true
+          channels: conda-forge,bioconda
+          channel-priority: strict
 
-      - name: Install testing dependencies
+      - name: Install conda-build
+        shell: bash -l {0}
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e '.[testing]'
+          conda install -y \
+            --override-channels \
+            -c conda-forge \
+            conda-build
 
-      - name: Run regression tests
+      - name: Build and run regression tests
+        shell: bash -l {0}
         run: |
-          python -m pytest tests \
-            -m regression \
-            -vv \
-            --durations=20 \
-            --basetemp=.testdata
-
-      - name: Upload regression artefacts on failure
-        if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
-        with:
-          name: pr-regression-failure
-          path: .testdata/
-          if-no-files-found: ignore
-          include-hidden-files: true
-          retention-days: 7
+          conda build conda-recipe \
+            --override-channels \
+            -c conda-forge \
+            -c bioconda \
+            --no-anaconda-upload
 
   docs:
     name: Docs

.github/workflows/regression-tests.yaml

@@ -25,30 +25,29 @@ jobs:
       - name: Checkout
         uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8
 
-      - name: Set up Python 3.14
-        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
         with:
-          python-version: "3.14"
-
-      - name: Install testing dependencies
+          miniforge-variant: Miniforge3
+          auto-activate: true
+          activate-environment: base
+          conda-remove-defaults: true
+          channels: conda-forge,bioconda
+          channel-priority: strict
+
+      - name: Install conda-build
+        shell: bash -l {0}
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install -e '.[testing]'
+          conda install -y \
+            --override-channels \
+            -c conda-forge \
+            conda-build
 
-      - name: Run regression tests
+      - name: Build and run regression tests
+        shell: bash -l {0}
         run: |
-          python -m pytest tests \
-            -m regression \
-            -vv \
-            --durations=20 \
-            --basetemp=.testdata
-
-      - name: Upload regression artefacts on failure
-        if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
-        with:
-          name: sist-regression-failure
-          path: .testdata/
-          if-no-files-found: ignore
-          include-hidden-files: true
-          retention-days: 7
+          conda build conda-recipe \
+            --override-channels \
+            -c conda-forge \
+            -c bioconda \
+            --no-anaconda-upload

.github/workflows/release.yaml

@@ -0,0 +1,229 @@
+name: Release SIST
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        required: true
+        default: 'x.y.z'
+
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  checks:
+    name: Version check
+    runs-on: ubuntu-24.04
+    steps:
+    - name: Checkout repository
+      id: repo
+      uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7.0.0
+      with:
+        python-version: 3.14.6
+
+    - name: Get latest release
+      id: latestreleased
+      run: |
+        PREVIOUS_VERSION=$(git tag --sort=-v:refname | head -n 1)
+        echo "release_tag=$PREVIOUS_VERSION" >> "$GITHUB_OUTPUT"
+        echo "$PREVIOUS_VERSION"
+
+    - name: version comparison
+      id: compare
+      run: |
+        python -m pip install semver
+
+        PREVIOUS_VERSION="${{ steps.latestreleased.outputs.release_tag }}"
+        NEW_VERSION="${{ github.event.inputs.version }}"
+
+        if [ -z "$PREVIOUS_VERSION" ]; then
+          echo "No previous release found"
+          exit 0
+        fi
+
+        output=$(pysemver compare "$PREVIOUS_VERSION" "$NEW_VERSION")
+
+        if [ "$output" -ge 0 ]; then
+          exit 1
+        fi
+
+  version:
+    name: prepare ${{ github.event.inputs.version }}
+    needs: checks
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: checkout
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+
+      - name: Change version in repo and CITATION.cff
+        run: |
+          # Update Conda package version
+          sed -i \
+            "s/{% set version = \".*\" %}/{% set version = \"${{ github.event.inputs.version }}\" %}/" \
+            conda-recipe/meta.yaml
+
+          # 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@5f6978faf089d4d20b00c7766989d076bb2fc7f1 # v8.1.1
+        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 Conda recipe 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
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PR_NUMBER: ${{ steps.pr_id.outputs.pull-request-number }}
+        run: |
+          gh pr merge \
+            --merge \
+            --delete-branch \
+            --auto \
+            "$PR_NUMBER"
+
+          while true; do
+            STATE=$(gh pr view "$PR_NUMBER" --json state --jq '.state')
+
+            if [ "$STATE" = "MERGED" ]; then
+              echo "Version bump PR merged"
+              break
+            fi
+
+            if [ "$STATE" = "CLOSED" ]; then
+              echo "Version bump PR was closed without merging"
+              exit 1
+            fi
+
+            sleep 10
+          done
+
+  tag:
+    name: tag release
+    needs: version
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        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 ${{ github.event.inputs.version }}
+
+  release:
+    name: make github release
+    needs: tag
+    runs-on: ubuntu-24.04
+    steps:
+
+      - name: create release
+        uses: softprops/action-gh-release@3d0d9888cb7fd7b750713d6e236d1fcb99157228 # v3.0.2
+        with:
+          name: v${{ github.event.inputs.version }}
+          generate_release_notes: true
+          tag_name: ${{ github.event.inputs.version }}
+
+  conda:
+    name: publish conda to anaconda.org
+    needs: [tag, release]
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          ref: ${{ github.event.inputs.version }}
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
+        with:
+          miniforge-variant: Miniforge3
+          python-version: "3.14"
+          auto-activate: true
+          activate-environment: base
+          conda-remove-defaults: true
+          channels: conda-forge,bioconda
+          channel-priority: strict
+
+      - name: Install build tools
+        shell: bash -l {0}
+        run: |
+          conda install -y \
+            --override-channels \
+            -c conda-forge \
+            conda-build \
+            anaconda-client
+
+          conda config --set anaconda_upload no
+          conda list conda-build
+          conda build --help
+
+      - name: Build package
+        shell: bash -l {0}
+        run: |
+          PKG_PATH=$(conda build conda-recipe \
+            --output \
+            --override-channels \
+            -c conda-forge \
+            -c bioconda)
+
+          echo "PKG_PATH=$PKG_PATH" >> "$GITHUB_ENV"
+
+          conda build conda-recipe \
+            --override-channels \
+            -c conda-forge \
+            -c bioconda \
+            --no-anaconda-upload
+
+          test -f "$PKG_PATH"
+          echo "Built: $PKG_PATH"
+
+      - name: Upload to Anaconda
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        run: |
+          anaconda \
+            -t "$ANACONDA_API_TOKEN" \
+            upload "$PKG_PATH" \
+            --user CCPBioSim \
+            --force

CITATION.cff

@@ -0,0 +1,36 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: SIST
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+
+authors:
+
+repository-code: 'https://github.com/CCPBioSim/SIST'
+url: 'https://sist.readthedocs.io/en/latest/'
+
+abstract: >-
+  SIST (Stress-Induced Structural Transitions) calculates
+  stress-induced structural transition probabilities in
+  superhelical DNA, including strand separation, Z-DNA
+  formation, cruciform extrusion, and competition between
+  these transitions.
+
+keywords:
+  - DNA
+  - superhelical DNA
+  - DNA supercoiling
+  - strand separation
+  - Z-DNA
+  - cruciform extrusion
+  - structural transitions
+  - statistical mechanics
+  - biomolecular simulations
+
+license: MIT
+version: 0.0.0
+date-released: '2026-08-14'