Release 2025.4.0

.github/workflows/choose_branch.yaml

@@ -2,8 +2,8 @@ name: Release Branch
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 on:
   workflow_dispatch:
@@ -31,11 +31,11 @@ jobs:
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
             python-version: "3.10"
-          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.11"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.11"
     environment:
@@ -50,31 +50,36 @@ jobs:
       REPO: "${{ github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.inputs.branch }}
+          fetch-depth: 0
+      #
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sire_build
-          miniforge-version: latest
+          run-install: false
       #
-      - name: Clone the desired branch
-        run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
       #
-      - name: Upload Conda package
-        # Maybe add the logic here that this is a dev package?
-        run: python ${{ github.workspace }}/sire/actions/upload_package.py
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
-          SRC_DIR: ${{ github.workspace }}/sire
+          SRC_DIR: ${{ github.workspace }}
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}

.github/workflows/devel.yaml

@@ -2,8 +2,8 @@ name: Release Devel
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 on:
   workflow_dispatch:
@@ -28,7 +28,10 @@ jobs:
           # but Linux
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet... We want 3.10 and 3.11
+            python-version: "3.10"
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.11"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
@@ -45,31 +48,35 @@ jobs:
       REPO: "${{ github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      #
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sire_build
-          miniforge-version: latest
+          run-install: false
       #
-      - name: Clone the devel branch (push to devel)
-        run: git clone https://github.com/${{ env.REPO }} sire
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
       #
-      - name: Upload Conda package
-        # Maybe add the logic here that this is a dev package?
-        run: python ${{ github.workspace }}/sire/actions/upload_package.py
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
-          SRC_DIR: ${{ github.workspace }}/sire
+          SRC_DIR: ${{ github.workspace }}
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}

.github/workflows/main.yaml

@@ -2,8 +2,8 @@ name: Release Main
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 # Only allow this action to run on a manual run.
 # We should specify when run whether or not we want
@@ -29,10 +29,7 @@ jobs:
           - { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-        exclude:
-          - platform:
-              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+        # No exclusions - release builds all combinations
     environment:
       name: sire-build
     defaults:
@@ -45,32 +42,39 @@ jobs:
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sire_build
-          miniforge-version: latest
+          ref: main
+          fetch-depth: 0
       #
-      - name: Clone the main branch (push to main)
-        run: git clone -b main https://github.com/openbiosim/sire sire
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
+        if: github.event.inputs.upload_packages == 'yes'
       #
-      - name: Upload Conda package
+      - name: Upload package
         # upload to the 'test' channel
-        run: python ${{ github.workspace }}/sire/actions/upload_package.py test
+        run: python ${{ github.workspace }}/actions/upload_package.py test
         env:
-          SRC_DIR: ${{ github.workspace }}/sire
+          SRC_DIR: ${{ github.workspace }}
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
         if: github.event.inputs.upload_packages == 'yes'

.github/workflows/pr.yaml

@@ -2,8 +2,8 @@ name: Pull-Request
 
 # Note that push and pull-request builds are automatically
 # now skipped by GitHub if
-# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
-# are in the commit message. We don't need to check for this ourselves.
+# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip]
+# are in the commit message. We don't need to check for this ourselves.
 
 on:
   pull_request:
@@ -28,11 +28,11 @@ jobs:
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
             python-version: "3.10"
-          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
-            python-version: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.11"
+          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.10"
           - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.11"
     environment:
@@ -47,24 +47,26 @@ jobs:
       REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
       #
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: sire_build
-          miniforge-version: latest
+          fetch-depth: 0
       #
-      - name: Clone the feature branch (pull request to devel)
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          run-install: false
       #
-      - name: Setup Conda
-        run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
       #
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/sire/actions/update_recipe.py
+      - name: Generate recipe
+        run: python ${{ github.workspace }}/actions/generate_recipe.py --features obs emle
       #
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
       #
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/sire" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

.gitignore

@@ -10,7 +10,7 @@ build/wrapper/*
 build/module/*
 build/downloads/*
 recipes/sire/meta.yaml
-#files for wrapper
+# files for wrappers
 module_info
 active_headers.data
 exposed_decl.pypp.txt
@@ -57,12 +57,15 @@ tests/cache/*
 # Python autogenerated backup wrappers
 *~
 
-#Atom
+# Atom
 .idea
 
-#VS Code
+# VS Code
 .vscode
 
 .DS_Store
 
 .coverage
+
+# Pixi startup file
+pixi.sh