Fix issue #6 and switch to pixi + rattler build system

.github/workflows/devel.yaml

@@ -3,7 +3,7 @@ name: Release Devel
 on:
   workflow_dispatch:
   push:
-    branches: [ devel ]
+    branches: [devel]
 
 jobs:
   build:
@@ -18,11 +18,9 @@ jobs:
           - { 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
+            python-version: "3.12"  # MacOS can't run 3.12 yet... We want 3.10 and 3.11
     environment:
       name: ghostly-build
     defaults:
@@ -32,30 +30,38 @@ 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: ghostly_build
-          miniforge-version: latest
-#
-      - name: Clone the devel branch
-        run: git clone -b devel https://github.com/openbiosim/ghostly
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/ghostly/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 }}/ghostly/recipes/ghostly
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        run: python ${{ github.workspace }}/actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ 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/ghostly" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
+        if: ${{ matrix.platform.name == 'linux' && matrix.python-version == '3.11' }}
+      #
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: dev

.github/workflows/main.yaml

@@ -23,7 +23,7 @@ jobs:
         exclude:
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: ghostly-build
     defaults:
@@ -33,30 +33,39 @@ 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: ghostly_build
-          miniforge-version: latest
-#
-      - name: Clone the main branch
-        run: git clone -b main https://github.com/openbiosim/ghostly
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/ghostly/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 }}/ghostly/recipes/ghostly
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
+          ref: main
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        run: python ${{ github.workspace }}/actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ 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/ghostly" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
+      #
+      - name: Install anaconda-client
+        run: python -m pip install anaconda-client
+        if: github.event.inputs.upload_packages == 'true' && matrix.platform.name == 'linux' && matrix.python-version == '3.11'
+      #
+      - name: Upload package
+        run: python ${{ github.workspace }}/actions/upload_package.py
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
           ANACONDA_LABEL: main

.github/workflows/pr.yaml

@@ -17,14 +17,12 @@ jobs:
           - { 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: "3.10"
           - platform:
               { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
-            python-version: "3.12"  # MacOS can't run 3.12 yet...
+            python-version: "3.12"  # MacOS can't run 3.12 yet...
     environment:
       name: ghostly-build
     defaults:
@@ -35,29 +33,34 @@ jobs:
       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:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: ghostly_build
-          miniforge-version: latest
-#
-      - name: Clone the feature branch
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} ghostly
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
-#
-      - name: Prepare build location
-        run: mkdir ${{ github.workspace }}/build
-#
-      - name: Build Conda package using conda build using main channel
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        run: python ${{ github.workspace }}/actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
+        working-directory: ${{ github.workspace }}
+      #
+      - name: Install rattler-build
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          tool-version: latest
+          build-args: --help
+      #
+      - name: Write Python variant config
+        shell: bash
+        run: printf 'python:\n  - "${{ 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 ${{ github.workspace }}/ghostly/recipes/ghostly
-#
-      - name: Build Conda package using conda build using dev channel
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -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 ${{ github.workspace }}/ghostly/recipes/ghostly
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

.gitignore

@@ -40,3 +40,6 @@ recipes/ghostly/meta.yaml
 
 # Sire cache files.
 cache/
+
+# Auto-generated version file.
+src/ghostly/_version.py

README.md

@@ -30,41 +30,60 @@ See the [examples](examples) directory for more details.
 
 ## Installation
 
-First create a conda environment using the provided environment file:
+### Conda package
+
+Install `ghostly` directly from the `openbiosim` channel:
 
 ```
-conda env create -f environment.yaml
+conda install -c conda-forge -c openbiosim ghostly
 ```
 
-(We recommend using [Miniforge](https://github.com/conda-forge/miniforge).)
-
-Now install `ghostly` into the environment:
+Or, for the development version:
 
 ```
-conda activate ghostly
-pip install .
+conda install -c conda-forge -c openbiosim/label/dev ghostly
 ```
 
-Or, for an editable install (useful for development):
+### Installing from source (standalone)
+
+To install from source using [pixi](https://pixi.sh), which will
+automatically create an environment with all required dependencies
+(including pre-built [Sire](https://github.com/OpenBioSim/sire) and
+[BioSimSpace](https://github.com/OpenBioSim/biosimspace)):
 
 ```
-conda activate ghostly
+git clone https://github.com/openbiosim/ghostly
+cd ghostly
+pixi install
+pixi shell
 pip install -e .
 ```
 
-For an existing conda environment, you can also install `ghostly` directly from
-the `openbiosim` channel:
+### Installing from source (full OpenBioSim development)
+
+If you are developing across the full OpenBioSim stack, first install
+[Sire](https://github.com/OpenBioSim/sire) from source by following the
+instructions [here](https://github.com/OpenBioSim/sire#installation), then
+activate its pixi environment:
 
 ```
-conda install -c conda-forge -c openbiosim ghostly
+pixi shell --manifest-path /path/to/sire/pixi.toml -e dev
 ```
 
-Or, for the development version:
+You may also need to install other packages from source, e.g.
+[BioSimSpace](https://github.com/OpenBioSim/biosimspace):
 
 ```
-conda install -c conda-forge -c openbiosim/label/dev ghostly
+pip install -e /path/to/biosimspace/python
+```
+
+Then install `ghostly` into the environment:
+
+```
+pip install -e .
 ```
 
+### Testing
 
 You should now have a `ghostly` executable in your path. To test, run: