Switch to pixi and rattler-build

.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: somd2-build
     defaults:
@@ -32,30 +30,43 @@ 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: somd2_build
-          miniforge-version: latest
-#
-      - name: Clone the devel branch
-        run: git clone -b devel https://github.com/openbiosim/somd2
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/somd2/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 }}/somd2/recipes/somd2
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/somd2/actions/upload_package.py
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        shell: bash
+        run: python actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-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/somd2" -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

@@ -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: somd2-build
     defaults:
@@ -33,30 +33,45 @@ 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: somd2_build
-          miniforge-version: latest
-#
-      - name: Clone the main branch
-        run: git clone -b main https://github.com/openbiosim/somd2
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/somd2/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 }}/somd2/recipes/somd2
-#
-      - name: Upload Conda package
-        run: python ${{ github.workspace }}/somd2/actions/upload_package.py
+          ref: main
+          fetch-depth: 0
+      #
+      - name: Compute version info
+        shell: bash
+        run: python actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-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/somd2" -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

@@ -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: somd2-build
     defaults:
@@ -33,31 +31,39 @@ 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:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-          activate-environment: somd2_build
-          miniforge-version: latest
-#
-      - name: Clone the feature branch
-        run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} somd2
-#
-      - name: Setup Conda
-        run: conda install -y -c conda-forge boa anaconda-client packaging
-#
-      - name: Update Conda recipe
-        run: python ${{ github.workspace }}/somd2/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
+        shell: bash
+        run: python actions/update_recipe.py
+      #
+      - name: Create sdist
+        run: pip install build && python -m build --sdist && mv dist/*.tar.gz somd2-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 (main channel)
         if: ${{ github.base_ref == 'main' }}
-        run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/somd2/recipes/somd2
-#
-      - name: Build Conda package using conda build using dev channel
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -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 ${{ github.workspace }}/somd2/recipes/somd2
+        shell: bash
+        run: rattler-build build --recipe "${{ github.workspace }}/recipes/somd2" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

.gitignore

@@ -20,7 +20,6 @@ setup.err
 dist/
 build/
 somd2.egg-info
-src/somd2/_version.py
 
 # Test output.
 output.yaml
@@ -35,5 +34,5 @@ output.yaml
 # VSCode config
 .vscode/
 
-# Conda recipe (it is auto-generated)
-recipes/somd2/meta.yaml
+# Auto-generated version file
+src/somd2/_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

README.md

@@ -9,42 +9,91 @@ simulations. Built on top of [Sire](https://github.com/OpenBioSim/sire) and [Ope
 
 ## Installation
 
-First create a conda environment using the provided environment file:
+### Conda package
+
+Install `somd2` directly from the `openbiosim` channel:
 
 ```
-conda env create -f environment.yaml
+conda install -c conda-forge -c openbiosim somd2
 ```
 
-(We recommend using [Miniforge](https://github.com/conda-forge/miniforge).)
+Or, for the development version:
 
-> [!NOTE]
-> On macOS, you will need to use the `environment_macos.yaml` file instead.
+```
+conda install -c conda-forge -c openbiosim/label/dev somd2
+```
 
-Now install `somd2` into the environment:
+### 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),
+[BioSimSpace](https://github.com/OpenBioSim/biosimspace),
+[Ghostly](https://github.com/OpenBioSim/ghostly), and
+[Loch](https://github.com/OpenBioSim/loch)):
 
 ```
-conda activate somd2
-pip install --editable .
+git clone https://github.com/openbiosim/somd2
+cd somd2
+pixi install
+pixi shell
+pip install -e .
 ```
 
-Alternatively, to install into an existing conda environment:
+### 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 somd2
+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),
+[Ghostly](https://github.com/OpenBioSim/ghostly), and
+[Loch](https://github.com/OpenBioSim/loch):
 
 ```
-conda install -c conda-forge -c openbiosim/label/dev somd2
+pip install -e /path/to/biosimspace
+pip install -e /path/to/ghostly
+pip install -e /path/to/loch
+```
+
+Then install `somd2` into the environment:
+
 ```
+pip install -e .
+```
+
+### Testing
 
 You should now have a `somd2` executable in your path. To test, run:
 
 ```
 somd2 --help
 ```
 
+## Development
+
+Pre-commit hooks are used to ensure consistent code formatting and linting.
+To set up pre-commit in your development environment:
+
+```
+pixi shell -e dev
+pre-commit install
+```
+
+This will run [ruff](https://docs.astral.sh/ruff/) formatting and linting
+checks automatically on each commit. To run the checks manually against all
+files:
+
+```
+pre-commit run --all-files
+```
+
 ## Usage
 
 In order to run an alchemical free-energy simulation you will need to