Migrate project to pixi (#1093)

* MAINT: Add `pixi` configuration

* Invest more

* Syntax

* Add Linux platform

* Add openeye channel

* Fix

* Always install OpenEye?

* Try `pixi install`

* Try running through pixi shell?

* Update

* Remove examples workflow

* Empty commit

* Bump

* Fix

* Expose openeye channel everywhere

* Move dependencies around

* Hack

* Update

* Syntax

* Simplify

* Add pip haha

* Set up test-only dependencies

* Run tests in environment

* Add engines

* Also install test plugins

* Ensure other features are not grabbed from PyPI

* Run commands under `pixi`

* Run in environment

* Add InterMol

* lol toml doesn't support multi-line tables

* Run commands in environment

* Fix typo

* Always install regression test dependencies

* More cleanly use tasks

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Add examples environments/workflow

* Lint

* Slim CI matrix

* Fix

* Bump toolkit

* Fix

* Update

* Other updates

* Fixes

* Debug

* Also run examples

* Fix `run_examples`

* Revert OE change

* Fix?

* Add `jax` to examples environment

* Use `contains`

* Try building out matrix again

* Fix

* A PEP 695 fix?

* Add MoSDeF stack

* Add beta workflow, debug

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Lint

* Fix license setup

* Track lock file

* Fix silly typo

* Revert other changes

* Remove environment files

* Update environments

* Update environments

* Revamp

* Update development docs

* Fix link

* Also run on macOS

* Add back JAX, update release history

* Add lockfile

* Turn on Foyer + GROMACS combination

* Add 'etc' environment

* Fix test, run more tests

* Fix type-checking

* Fixes

* One more fix

* Another fix

* Debug

* Skip Amber example

* Debug

* Foyer + GROMACS

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: mattwthompson

.github/workflows/beta.yaml

@@ -8,44 +8,34 @@ on:
     branches:
       - main
   schedule:
-    - cron: "0 5 * * *"
+    - cron: "0 6 * * *"
   workflow_dispatch:
 
 defaults:
   run:
-    shell: bash -e -l {0}
+    shell: pixi run bash -e {0}
 
 jobs:
   test:
-    name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}, OpenEye ${{ matrix.openeye }}, RDKit ${{ matrix.rdkit }}, AmberTools ${{ matrix.ambertools }}, NAGL ${{ matrix.nagl }}
+    name: Test on ${{ matrix.os }}, ${{ matrix.environment }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os:
-          - macos-latest
           - ubuntu-latest
-        python-version:
-          - "3.11"
-          - "3.12"
-          - "3.13"
-        openeye:
-          - true
-          - false
-        rdkit:
-          - true
-        ambertools:
-          - true
-          - false
-        nagl:
-          - true
-          - false
-        openmm:
-          - true
-        exclude:
-          - python-version: "3.13"
-            openeye: true
-          - ambertools: false
-            openeye: false
+          - macos-latest
+        environment:
+          - py311amber
+          - py311openeye
+          - py311examples
+          - py311etc
+          - py311amber
+          - py312openeye
+          - py312examples
+          - py312etc
+          - py313openeye
+          - py313examples
+          - betas
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
@@ -54,87 +44,35 @@ jobs:
     steps:
     - uses: actions/checkout@v6
 
-    - name: Install conda environment
-      uses: mamba-org/setup-micromamba@v2
+    - name: Set up virtual environment
+      uses: prefix-dev/setup-pixi@v0.8.4
       with:
-        environment-file: devtools/conda-envs/test_env.yaml
-        create-args: >-
-          python=${{ matrix.python-version }}
+        pixi-version: v0.41.4
+        environments: ${{ matrix.environment }}
 
     - name: Install and license OpenEye Toolkits
-      if: ${{ matrix.openeye == true }}
+      if: ${{ !contains(matrix.environment, 'amber') }}
       run: |
-        micromamba install "openeye-toolkits =2025" -c openeye
         echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
-        python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
+        pixi run -e ${{ matrix.environment }} python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
       env:
         SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
-    - name: Install OpenMM
-      if: ${{ matrix.openmm == true }}
-      run: |
-        micromamba install openmm -c conda-forge
-
-    - name: Install RDKit
-      if: ${{ matrix.rdkit == true }}
-      run: |
-        micromamba install rdkit "ambertools =24" intermol -c conda-forge
-
-    - name: Remove AmberTools
-      if: ${{ matrix.ambertools == false }}
-      run: |
-        micromamba remove ambertools parmed
-        micromamba install "packmol >=20.15.0" "lammps>=2024" "numpy>=2.4"
-
-    - name: Install OpenFF NAGL
-      if: ${{ matrix.nagl == true }}
-      run: |
-        micromamba install openff-nagl -c conda-forge
-
-    - name: Install Python <3.13 dependencies
-      if: ${{ matrix.python-version != '3.13' && matrix.ambertools == true }}
-      run: micromamba install --file devtools/conda-envs/test_not_py313.yaml python=${{ matrix.python-version }}
-
-    - name: Install package
-      run: python -m pip install . plugins/
+    - name: Run mypy
+      if: ${{ !contains(matrix.environment, 'examples') }}
+      run: pixi run -e ${{ matrix.environment }} run_mypy
 
     - name: Run tests
-      run: python -m pytest $COV openff/interchange/ -r fExs -n logical --durations=10
-
-    - name: Run small molecule regression tests
-      if: ${{ matrix.openeye == true && matrix.openmm == true }}
-      run: |
-        micromamba install "openmm=8.4.0" "deepdiff <=8" rich click -c conda-forge
-        python -m pip install git+https://github.com/openforcefield/interchange-regression-testing.git@443480732f5caf3fc63f5442fdd763176c63e72f
-
-        create_openmm_systems \
-          --input             "regression_tests/small-molecule/input-topologies.json" \
-          --output            "regression_tests/small-molecule/" \
-          --using-interchange \
-          --force-field       "openff-2.0.0.offxml" \
-          --n-procs           4
+      if: ${{ !contains(matrix.environment, 'examples') }}
+      run: pixi run -e ${{ matrix.environment }} run_tests
 
-        # Don't trust the interchange version here, for some reason, just put it in a new directory
-        mkdir regression_tests/small-molecule/omm-systems-interchange-latest/
-        mv regression_tests/small-molecule/omm-systems-interchange-*/*xml regression_tests/small-molecule/omm-systems-interchange-latest/
+    - name: Run examples
+      if: ${{ contains(matrix.environment, 'examples') }}
+      run: pixi run -e ${{ matrix.environment }} run_examples
 
-        compare_openmm_systems \
-          --input-dir-a       "regression_tests/small-molecule/omm-systems-toolkit-0.10.6" \
-          --input-dir-b       "regression_tests/small-molecule/omm-systems-interchange-latest" \
-          --output            "regression_tests/differences.json" \
-          --settings          "regression_tests/default-comparison-settings.json" \
-          --expected-changes  "regression_tests/toolkit-to-interchange.json" \
-          --n-procs           4
-
-        python devtools/scripts/molecule-regressions.py
-
-    - name: Run mypy
-      run: |
-        # As of 01/23, JAX with mypy is too slow to use without a pre-built cache
-        # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875
-        micromamba remove jax
-        python -m mypy -p "openff.interchange" --exclude "openff/interchange/_tests/"
-        python -m mypy plugins/nonbonded_plugins/
+    - name: Run small molecule regression tests
+      if: ${{ contains(matrix.environment, 'openeye') }}
+      run: pixi run -e ${{ matrix.environment }} run_regression_tests
 
     - name: Codecov
       uses: codecov/codecov-action@v5

.github/workflows/ci.yaml

@@ -135,3 +135,7 @@ tmp.in
 .Trashes
 ehthumbs.db
 Thumbs.db
+
+# pixi environments
+.pixi
+*.egg-info

.github/workflows/examples.yaml

@@ -67,6 +67,10 @@ For more information, please consult the [full documentation](https://openff-int
 
 For more examples specific to Interchange, navigate to the `examples/` directory.
 
+## Developing
+
+See the [Development guide](docs/developing.md).
+
 ## Copyright
 
 Copyright (c) 2020, Open Force Field Initiative