Use Pixi for environment and task management

.codecov.yml

@@ -13,4 +13,5 @@ comment:
   flags: []
   paths: []
 ignore:
-  - "openff/pablo/_version.py"
+  - "examples/"
+  - "docs/"

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+
+    groups:
+      dependencies:
+        patterns:
+          - "*"

.github/workflows/lint.yaml

@@ -0,0 +1,47 @@
+name: GH Actions Lints
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  # Specific group naming so CI is only cancelled
+  # within same PR or on merge to main
+  group: ${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+jobs:
+  lints:
+    if: "github.repository == 'openforcefield/openff-pablo'"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build information
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      - uses: prefix-dev/[email protected]
+        with:
+          pixi-version: v0.50.0
+          activate-environment: lint
+
+      - run: ruff check openff
+
+      - run: pixi r typecheck

.github/workflows/gh-ci.yaml → .github/workflows/tests.yaml

@@ -1,4 +1,4 @@
-name: GH Actions CI
+name: GH Actions Tests
 on:
   push:
     branches:
@@ -23,14 +23,13 @@ defaults:
     shell: bash -l {0}
 
 jobs:
-  main-tests:
+  tests:
     if: "github.repository == 'openforcefield/openff-pablo'"
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.11"]
 
     steps:
       - uses: actions/checkout@v4
@@ -43,38 +42,18 @@ jobs:
           df -h
           ulimit -a
 
-      - name: Install environment
-        uses: mamba-org/setup-micromamba@v2
+      - uses: prefix-dev/[email protected]
         with:
-          environment-file: devtools/conda-envs/test_env.yaml
-          create-args: >-
-            python=${{ matrix.python-version }}
+          pixi-version: v0.52.0
+          environments: test
 
-      - name: Install package
-        run: |
-          python --version
-          python -m pip install .
-
-      - name: Python information
-        run: |
-          which python
-          which pip
-          pip list
-          micromamba info
-          micromamba list
+      - run: pixi r slowtest -v --color=yes --cov=openff/pablo --cov-append --cov-report=xml
 
-      - name: Type check
-        if: runner.os == 'Linux'
-        run: |
-          basedpyright openff
+      - run: pixi r doctest -v --color=yes
 
-      - name: Run tests
-        run: |
-          pytest -n auto -v --color=yes
-
-    # - name: codecov
-    #   uses: codecov/codecov-action@v3
-    #   with:
-    #     file: coverage.xml
-    #     name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
-    #     verbose: True
+      - name: Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./coverage.xml
+          disable_search: true
+          fail_ci_if_error: false

.gitignore

@@ -116,4 +116,8 @@ poetry.lock
 # zed
 .zed/
 
+# pixi
+.pixi
+pixi.lock
+
 .ccd_cache

openff/pablo/_utils.py

@@ -18,7 +18,6 @@
 import rdkit.Chem.Draw
 import rdkit.Chem.rdDepictor
 import rdkit.Geometry
-from IPython.display import SVG
 from openff.toolkit import Molecule
 from openff.toolkit.topology._mm_molecule import _SimpleMolecule
 from openff.toolkit.topology.molecule import MoleculeLike
@@ -348,7 +347,7 @@ def draw_molecule(
     emphasize_atoms: list[int] | None = None,
     explicit_hydrogens: bool | None = None,
     color_by_element: bool | None = None,
-) -> SVG:
+):
     """Draw a molecule
 
     Parameters
@@ -392,6 +391,7 @@ def draw_molecule(
         When an atom or bond in highlight_atoms or highlight_bonds is missing
         from the image, including when it is present in the molecule but hidden.
     """
+    from IPython.display import SVG
 
     # We're working in RDKit
     try:

openff/pablo/residue.py

@@ -542,6 +542,41 @@ def from_smiles(
         virtual_sites
             Virtual sites expected by the residue. See
             :py:data:`openff.pablo.ResidueDefinition.virtual_sites`
+
+        Examples
+        --------
+
+        To create a ``ResidueDefinition`` for a neutral cysteine residue:
+
+        >>> from openff.pablo.residue import ResidueDefinition
+        >>> from openff.pablo.chem import DISULFIDE_BOND, PEPTIDE_BOND
+        >>>
+        >>> ResidueDefinition.from_smiles(
+        ...     residue_name="CYS",
+        ...     mapped_smiles=r"[N:1]([C@@:2]([C:5]([S:6][H:13])([H:11])[H:12])([C:3]([O:7][H:14])=[O:4])[H:10])([H:8])[H:9]",
+        ...     atom_names={
+        ...         1: "N",
+        ...         2: "CA",
+        ...         3: "C",
+        ...         4: "O",
+        ...         5: "CB",
+        ...         6: "SG",
+        ...         7: "OXT",
+        ...         8: "H",
+        ...         9: "H2",
+        ...         10: "HA",
+        ...         11: "HB2",
+        ...         12: "HB3",
+        ...         13: "HG",
+        ...         14: "HXT",
+        ...     },
+        ...     leaving_atoms={7, 14, 13, 9},
+        ...     crosslink=DISULFIDE_BOND,
+        ...     linking_bond=PEPTIDE_BOND,
+        ...     description="CYSTEINE",
+        ... )
+        ResidueDefinition(...)
+
         """
         molecule = Molecule.from_mapped_smiles(
             mapped_smiles,