Release 2025.4.0

.github/workflows/Sandpit_exs.yml

@@ -41,9 +41,7 @@ jobs:
       - name: Install the dev version
         run: |
           conda remove --force biosimspace
-          cd python
-          python setup.py develop
-          cd ..
+          pip install -e .
 
       - name: Run tests
         run: |

.github/workflows/devel.yaml

@@ -3,7 +3,7 @@ name: Release Devel
 on:
   workflow_dispatch:
   push:
-    branches: [ devel ]
+    branches: [devel]
 
 jobs:
   build:
@@ -15,18 +15,21 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
         platform:
-          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
         exclude:
           # Exclude all but the latest Python from all
           # 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
-          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
             python-version: "3.10"
-          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - platform:
+              { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
+            python-version: "3.11"
+          - platform: { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
+            python-version: "3.10"
+          - platform: { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
             python-version: "3.11"
     environment:
       name: biosimspace-build
@@ -37,30 +40,44 @@ jobs:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      #
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        shell: bash
+        run: python actions/update_recipe.py
+      #
+      - name: Create sdist
+        shell: bash
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz biosimspace-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: bss_build
-          miniforge-version: latest
-#
-      - name: Clone the devel branch
-        run: git clone -b devel https://github.com/openbiosim/biosimspace
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/biosimspace/actions/upload_package.py
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/biosimspace" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Install anaconda-client
+        shell: bash
+        run: python -m pip install anaconda-client
+      #
+      - name: Upload package
+        shell: bash
+        run: python actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: dev

.github/workflows/main.yaml

@@ -18,13 +18,10 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
         platform:
-          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
           - { 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: biosimspace-build
     defaults:
@@ -34,30 +31,46 @@ jobs:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      #
+      - uses: actions/checkout@v4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: bss_build
-          miniforge-version: latest
-#
-      - name: Clone the main branch
-        run: git clone -b main https://github.com/openbiosim/biosimspace
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build
-        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/biosimspace/actions/upload_package.py
+          ref: main
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        shell: bash
+        run: python actions/update_recipe.py
+      #
+      - name: Create sdist
+        shell: bash
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz biosimspace-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/biosimspace" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Install anaconda-client
+        shell: bash
+        run: python -m pip install anaconda-client
+        if: github.event.inputs.upload_packages == 'true'
+      #
+      - name: Upload package
+        shell: bash
+        run: python actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main

.github/workflows/pr.yaml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         python-version: ["3.10", "3.11", "3.12"]
         platform:
-          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          - { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
         exclude:
@@ -23,12 +23,12 @@ 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...
-          - platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
+            python-version: "3.11"
+          - platform: { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
+            python-version: "3.10"
+          - platform: { name: "windows", os: "windows-latest", shell: "bash -l {0}" }
             python-version: "3.11"
     environment:
       name: biosimspace-build
@@ -38,31 +38,40 @@ jobs:
     env:
       SIRE_DONT_PHONEHOME: 1
       SIRE_SILENT_PHONEHOME: 1
-      REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
     steps:
-      - uses: conda-incubator/setup-miniconda@v3
+      #
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        shell: bash
+        run: python actions/update_recipe.py
+      #
+      - name: Create sdist
+        shell: bash
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz biosimspace-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install pixi
+        uses: prefix-dev/setup-pixi@v0.9.4
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: bss_build
-          miniforge-version: latest
-#
-      - name: Clone the feature branch
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} biosimspace
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/biosimspace/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build using main channel
+          run-install: false
+      #
+      - name: Install rattler-build
+        shell: bash
+        run: pixi global install rattler-build
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build (main channel)
         if: ${{ github.base_ref == 'main' }}
-        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/biosimspace/recipes/biosimspace
-#
-      - name: Build Conda package using conda build using dev channel
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/biosimspace" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Build package using rattler-build (dev channel)
         if: ${{ github.base_ref != 'main' }}
-        run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/biosimspace/recipes/biosimspace
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/biosimspace" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

.gitignore

@@ -34,5 +34,5 @@ output.yaml
 # VSCode config
 .vscode/
 
-# Conda recipe (it is auto-generated)
-recipes/biosimspace/meta.yaml
+# Auto-generate version file.
+src/BioSimSpace/_version.py

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+files: ^(src|tests)/
+exclude: ^tests/(input|output)/
+
+repos:
+  # General file quality checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
+        args: [--maxkb=1000]  # Prevent files larger than 1MB
+      - id: check-merge-conflict
+
+  # Python formatting and linting
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.4
+    hooks:
+      # Run the formatter
+      - id: ruff-format
+      # Run the linter (optional - remove if too strict)
+      - id: ruff
+        args: [--fix, --exit-zero]  # Auto-fix but don't block commits

MANIFEST.in

@@ -0,0 +1 @@
+graft tests