Add Python 3.12 to officially supported versions and test it in CI (#139

) * add python 3.12 to officially supported versions and test it in CI * explicit setuptools install in test.yml * split release.yml workflow out from test.yml * fix release wf name * remove PR and push triggers from release.yml * refactor CrystalGraphConverter._create_graph_fast
CederGroupHub · Mar 11, 2024 · 6f35990 · 6f35990
1 parent 6a5d96a
commit 6f35990
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,85 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      task:
+        type: choice
+        options: [release, test-release]
+        default: test-release
+        description: Release to PyPI or TestPyPI.
+
+jobs:
+  tests:
+    # run test.yml first to ensure that the test suite is passing
+    uses: ./.github/workflows/test.yml
+
+  build_source_dist:
+    name: Build source distribution
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: "3.10"
+
+      - name: Build source distribution
+        run: |
+          pip install build
+          python -m build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz
+
+  build_wheels:
+    name: Build wheels for Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    needs: tests
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-14, windows-latest]
+        python-version: ["39", "310", "311", "312"]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/[email protected]
+        env:
+          CIBW_BUILD: cp${{ matrix.python-version }}-*
+          CIBW_ARCHS_MACOS: universal2
+
+      - name: Save artifact
+        uses: actions/upload-artifact@v3
+        with:
+          path: wheelhouse
+
+  release:
+    name: Release wheels and source distribution to PyPI
+    needs: [build_wheels, build_source_dist]
+    runs-on: ubuntu-latest
+    permissions:
+      # For pypi trusted publishing
+      id-token: write
+    steps:
+      - name: Download build artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish to PyPi or TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          verbose: true
+          # set the repository URL to the test PyPI repository if the task is 'test-release'
+          # else empty string defaults to production PyPI
+          repository-url: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.task == 'test-release' && 'https://test.pypi.org/legacy/' || '' }}
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -4,22 +4,16 @@ on:
   push:
     branches: [main]
   pull_request:
-  release:
-    types: [published]
   workflow_dispatch:
-    inputs:
-      task:
-        type: choice
-        options: [tests, release, test-release]
-        default: tests
-        description: Run tests, release to PyPI, or release to TestPyPI.
+  workflow_call:
 
 jobs:
   tests:
     strategy:
       fail-fast: true
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]
+        python-version: ["3.10", "3.12"]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -29,7 +23,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -38,15 +32,17 @@ jobs:
 
       - name: Install dependencies
         run: |
-          uv pip install cython --system
-          # install ase from main branch until FrechetCellFilter is released
-          # TODO remove uv pip install git+https://gitlab.com/ase/ase
+          uv pip install cython setuptools --system
+
           python setup.py build_ext --inplace
+
           uv pip install -e .[test] --system
+
+          # TODO remove next line installing ase from main branch when FrechetCellFilter is released
           uv pip install --upgrade 'ase@git+https://gitlab.com/ase/ase' --system
 
       - name: Run Tests
-        run: pytest --capture=no --cov --cov-report=xml .
+        run: pytest --capture=no --cov --cov-report=xml
         env:
           CHGNET_DEVICE: cpu
 
@@ -56,71 +52,3 @@ jobs:
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: coverage.xml
-
-  build_source_dist:
-    name: Build source distribution
-    needs: tests
-    runs-on: ubuntu-latest
-    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
-    steps:
-      - name: Check out repo
-        uses: actions/checkout@v4
-
-      - uses: actions/setup-python@v5
-        name: Install Python
-        with:
-          python-version: "3.10"
-
-      - name: Build source distribution
-        run: |
-          pip install build
-          python -m build --sdist
-
-      - uses: actions/upload-artifact@v3
-        with:
-          path: dist/*.tar.gz
-
-  build_wheels:
-    name: Build wheels for Python ${{ matrix.python-version }} on ${{ matrix.os }}
-    needs: tests
-    if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
-    strategy:
-      matrix:
-        os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["39", "310", "311"]
-    runs-on: ${{ matrix.os }}
-    steps:
-      - name: Check out repo
-        uses: actions/checkout@v4
-
-      - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_BUILD: cp${{ matrix.python-version }}-*
-          CIBW_ARCHS_MACOS: universal2
-
-      - name: Save artifact
-        uses: actions/upload-artifact@v3
-        with:
-          path: wheelhouse
-
-  release:
-    name: Release wheels and source distribution to PyPI
-    needs: [build_wheels, build_source_dist]
-    runs-on: ubuntu-latest
-    permissions:
-      # For pypi trusted publishing
-      id-token: write
-    steps:
-      - name: Download build artifacts
-        uses: actions/download-artifact@v3
-        with:
-          name: artifact
-          path: dist
-
-      - name: Publish to PyPi or TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          skip-existing: true
-          verbose: true
-          repository-url: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.task == 'test-release' && 'https://test.pypi.org/legacy/' || '' }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.0
+    rev: v0.3.2
     hooks:
       - id: ruff
         args: [--fix]
@@ -46,7 +46,7 @@ repos:
           - svelte
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v9.0.0-beta.1
+    rev: v9.0.0-beta.2
     hooks:
       - id: eslint
         types: [file]

diff --git a/chgnet/graph/converter.py b/chgnet/graph/converter.py
@@ -250,25 +250,19 @@ def _create_graph_fast(
         distance = np.ascontiguousarray(distance)
         gc_saved = gc.get_threshold()
         gc.set_threshold(0)
-        (
-            nodes,
-            directed_edges_list,
-            undirected_edges_list,
-            undirected_edges,
-        ) = make_graph(
+        nodes, dir_edges_list, undir_edges_list, undirected_edges = make_graph(
             center_index, len(center_index), neighbor_index, image, distance, n_atoms
         )
         graph = Graph(nodes=nodes)
-        graph.directed_edges_list = directed_edges_list
-        graph.undirected_edges_list = undirected_edges_list
+        graph.directed_edges_list = dir_edges_list
+        graph.undirected_edges_list = undir_edges_list
         graph.undirected_edges = undirected_edges
         gc.set_threshold(gc_saved[0])
 
         return graph
 
     def set_isolated_atom_response(
-        self,
-        on_isolated_atoms: Literal["ignore", "warn", "error"],
+        self, on_isolated_atoms: Literal["ignore", "warn", "error"]
     ) -> None:
         """Set the graph converter's response to isolated atom graph
         Args:
@@ -282,7 +276,7 @@ def set_isolated_atom_response(
         self.on_isolated_atoms = on_isolated_atoms
         return
 
-    def as_dict(self) -> dict[str, float]:
+    def as_dict(self) -> dict[str, str | float]:
         """Save the args of the graph converter."""
         return {
             "atom_graph_cutoff": self.atom_graph_cutoff,
@@ -291,6 +285,6 @@ def as_dict(self) -> dict[str, float]:
         }
 
     @classmethod
-    def from_dict(cls, dict) -> CrystalGraphConverter:
+    def from_dict(cls, dct: dict) -> CrystalGraphConverter:
         """Create converter from dictionary."""
-        return CrystalGraphConverter(**dict)
+        return CrystalGraphConverter(**dct)
diff --git a/chgnet/model/dynamics.py b/chgnet/model/dynamics.py
@@ -52,7 +52,7 @@
 class CHGNetCalculator(Calculator):
     """CHGNet Calculator for ASE applications."""
 
-    implemented_properties = ("energy", "forces", "stress", "magmoms")  # type: ignore
+    implemented_properties = ("energy", "forces", "stress", "magmoms")
 
     def __init__(
         self,

diff --git a/pyproject.toml b/pyproject.toml
@@ -24,6 +24,7 @@ classifiers = [
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
     "Topic :: Scientific/Engineering :: Chemistry",