Switch to pixi

.devcontainer/Dockerfile

@@ -1,5 +1,4 @@
-FROM --platform=linux/x86_64 condaforge/mambaforge:latest
+FROM --platform=linux/x86_64 ghcr.io/prefix-dev/pixi:latest
 
-RUN    apt update                               \
-    && apt install -y git make build-essentials \
-    && rm -rf /var/lib/apt/lists/*
+# Install git (required by setuptools_scm)
+RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*

.devcontainer/devcontainer.json

@@ -1,4 +1,4 @@
 {
   "build": { "dockerfile": "Dockerfile" },
-  "postCreateCommand": "make env"
-}
+  "postCreateCommand": "pixi install && pixi run pre-commit install"
+}

.github/PULL_REQUEST_TEMPLATE.md

@@ -2,4 +2,4 @@
 Provide a brief description of the PR's purpose here.
 
 ## Status
-- [ ] Ready to go
+- [ ] Ready to go

.github/workflows/ci.yaml

@@ -1,53 +1,80 @@
 name: CI
 
 concurrency:
-  group: ${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 on:
   push: { branches: [ "main" ] }
   pull_request: { branches: [ "main" ] }
 
 jobs:
-  test:
-
+  pre-commit:
     runs-on: ubuntu-latest
-    container: condaforge/mambaforge:latest
 
     steps:
-    - uses: actions/checkout@v3.3.0
+    - name: Checkout
+      uses: actions/checkout@v4
 
-    - name: Setup Conda Environment
-      run: |
-        apt update && apt install -y git make
+    - name: Run pre-commit
+      uses: pre-commit/action@v3.0.1
 
-        make env
+  test-matrix:
+    needs: pre-commit
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            pixi-platform: linux-64
+          - os: macos-latest
+            pixi-platform: osx-arm64
+      fail-fast: false
 
-    - name: Lint
-      run: make lint
-
-    - name: Test
-      run: make test
+    runs-on: ${{ matrix.os }}
 
-    - name: Test Examples
-      run: make test-examples
-
-    - name: Build Docs
-      run: make docs
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
 
-    - name: Reconstruct environment with Pydantic 1.0
+    - name: Setup pixi
+      uses: prefix-dev/setup-pixi@v0.9.3
+      with:
+        pixi-version: v0.62.2
+        cache: true
+        environments: default pydantic-1-cpu
+
+    - name: Run tests with pydantic >=2
+      run: |
+        pixi run test
+
+    - name: Run tests with pydantic <2
       run: |
-        # TODO: Remove this once pydantic 1.0 support is dropped
-        #       We remove absolv as femto needs pydantic >=2
-        mamba remove  --name smee --yes "absolv" "absolv-base" "femto" "pint" --force
-        mamba install --name smee --yes "pydantic <2"
+        pixi run --environment pydantic-1-cpu test
 
-    - name: Test with Pydantic 1.0
-      run: make test
+    - name: Test examples with pydantic >=2
+      run: |
+        pixi run test-examples
+
+    - name: Build docs
+      run: |
+        pixi run docs
 
     - name: CodeCov
       uses: codecov/codecov-action@v4.1.1
       with:
         file: ./coverage.xml
         flags: unittests
         token: ${{ secrets.CODECOV_TOKEN }}
+
+  test:
+    needs: test-matrix
+    runs-on: ubuntu-latest
+    if: always()
+
+    steps:
+    - name: Check test matrix result
+      run: |
+        if [[ "${{ needs.test-matrix.result }}" != "success" ]]; then
+          echo "One or more test matrix jobs failed or were cancelled."
+          exit 1
+        fi

.github/workflows/docs.yaml

@@ -9,15 +9,17 @@ jobs:
   deploy-docs:
 
     runs-on: ubuntu-latest
-    container: condaforge/mambaforge:latest
 
     steps:
-    - name: Prepare container
-      run: |
-        apt update && apt install -y git make
-
     - name: Checkout
-      uses: actions/checkout@v3.3.0
+      uses: actions/checkout@v4
+
+    - name: Setup pixi
+      uses: prefix-dev/setup-pixi@v0.9.3
+      with:
+        pixi-version: v0.62.2
+        cache: true
+        environments: cpu pydantic-1-cpu
 
     - name: Determine Version
       shell: bash
@@ -42,5 +44,4 @@ jobs:
         git fetch --all --prune
         git pull origin gh-pages --allow-unrelated-histories
 
-        make env
-        make docs-deploy VERSION="$VERSION"
+        pixi run -e cpu mike deploy --push --update-aliases $VERSION

.pre-commit-config.yaml

@@ -4,12 +4,17 @@ repos:
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
+        exclude: ".*\\.offxml$"
 
--   repo: local
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.15.1
     hooks:
-    -   id: ruff
-        name: Autoformat python code
-        language: system
-        entry: ruff
-        args: [check]
-        files: \.py$
+      # Run the linter.
+      - id: ruff-check
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
+        files: "smee|examples"
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]

README.md

@@ -16,12 +16,12 @@
 
 ---
 
-The `smee` framework aims to offer a simple API for differentiably evaluating the energy of [SMIRNOFF](https://openforcefield.github.io/standards/standards/smirnoff/) 
+The `smee` framework aims to offer a simple API for differentiably evaluating the energy of [SMIRNOFF](https://openforcefield.github.io/standards/standards/smirnoff/)
 force fields applied to molecules using `pytorch`.
 
-The package currently supports evaluating the energy of force fields that contain: 
+The package currently supports evaluating the energy of force fields that contain:
 
-* `Bonds`, `Angles`, `ProperTorsions` and `ImproperTorsions` 
+* `Bonds`, `Angles`, `ProperTorsions` and `ImproperTorsions`
 * `vdW`, `Electrostatics`, `ToolkitAM1BCC`, `LibraryCharges`
 * `VirtualSites`
 
@@ -33,14 +33,26 @@ It further supports a number of functional forms included in `smirnoff-plugins`,
 
 ## Installation
 
-This package can be installed using `conda` (or `mamba`, a faster version of `conda`):
+This package can be installed using `pixi`:
+
+```shell
+pixi add smee
+```
+
+or using `conda` / `mamba`:
 
 ```shell
 mamba install -c conda-forge smee
 ```
 
 The example notebooks further require you install `jupyter`, `nglview`, and `smirnoff-plugins`:
 
+```shell
+pixi add jupyter nglview "smirnoff-plugins >=0.0.4"
+```
+
+or with conda/mamba:
+
 ```shell
 mamba install -c conda-forge jupyter nglview "smirnoff-plugins >=0.0.4"
 ```