Merge pull request #130 from materialsproject/chores/pre-commit

[Chores] pre-commit + docs

Author: jmmshn

.github/workflows/python-publish.yml

@@ -22,16 +22,13 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v5
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
+        python-version: '3.13'
     - name: Build package
-      run: python -m build
+      run: uv build
     - name: >-
         Publish Python 🐍 distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/testing.yml

@@ -1,67 +1,60 @@
+name: Testing
+
 on:
   push:
     branches:
       - main
     tags:
-      - 'v*'
+      - "v*"
   pull_request:
     branches:
       - main
+
 jobs:
   lint:
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
-          cache: pip
-          cache-dependency-path: pyproject.toml
+          python-version: "3.13"
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[tests,dev]
+        run: uv pip install --system .[tests,dev]
 
       - name: Lint
-        run: |
-          pre-commit run --all-files --show-diff-on-failure
+        run: pre-commit run --all-files --show-diff-on-failure
 
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v4
-
-    - uses: actions/setup-python@v5
-      with:
-        python-version:  ${{ matrix.python-version }}
-
-    - uses: actions/cache@v2
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ hashFiles('**/setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-${{ matrix.python-version }}-pip-
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install .[tests]
-
-    - name: Test
-      run: |
-        pytest --cov=pyrho --cov-report=xml
-
-    - uses: codecov/codecov-action@v1
-      if: matrix.python-version == 3.11
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        file: ./coverage.xml
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv pip install --system .[tests]
+
+      - name: Test
+        run: pytest --cov=pyrho --cov-report=xml
+
+      - uses: codecov/codecov-action@v4
+        if: matrix.python-version == 3.13
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
 
   docs:
     runs-on: ubuntu-latest
@@ -72,14 +65,18 @@ jobs:
       - name: Install pandoc
         run: sudo apt-get install pandoc
 
+      - uses: astral-sh/setup-uv@v5
+        with:
+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"
+
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.13
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip lxml[html_clean]
-          pip install -e .[docs]
+        run: uv pip install --system -e .[docs]
+
       - name: Build
         run: sphinx-build docs/source _build
 

.github/workflows/update-precommit.yml

@@ -4,26 +4,30 @@ on:
   schedule:
     - cron: '0 0 1,14,28 * *'
 
+permissions:
+  contents: write
+  pull-requests: write
 
 jobs:
   auto-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v4
+      - uses: astral-sh/setup-uv@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v2.2.2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.13
 
       - name: Install pre-commit
-        run: pip install pre-commit
+        run: uv pip install --system pre-commit
 
       - name: Run pre-commit autoupdate
         run: pre-commit autoupdate
 
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v7
         with:
           branch: update/pre-commit-autoupdate
           title: Auto-update pre-commit hooks

.pre-commit-config.yaml

@@ -1,17 +1,18 @@
 default_language_version:
   python: python3
+exclude: ^notebooks/
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.8
+  rev: v0.13.3
   hooks:
     # Run the linter.
-    - id: ruff
+    - id: ruff-check
       args: [ --fix ]
     # Run the formatter.
     - id: ruff-format
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.5.1
+  rev: v1.18.2
   hooks:
   - id: mypy
     files: ^src/
@@ -22,7 +23,7 @@ repos:
     - tokenize-rt==4.1.0
     - types-pkg_resources==0.1.2
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.4.1
   hooks:
   - id: codespell
     name: codespell

mkdocs.yml

@@ -30,17 +30,18 @@ requires-python = ">=3.9"
 [tool.setuptools_scm]
 
 [project.optional-dependencies]
-dev = ["pre-commit==3.6.2"]
+dev = ["pre-commit==4.3.0"]
 docs = [
-  "numpydoc==1.6.0",
-  "sphinx==7.2.6",
-  "furo==2024.1.29",
-  "m2r2==v0.3.3.post2",
-  "ipython==8.4.0",
-  "nbsphinx==0.8.9",
-  "nbsphinx-link==1.3.0",
-  "sphinx-autodoc-typehints==2.0.0",
-  "sphinx-autoapi==3.0.0",
+  "numpydoc==1.9.0",
+  "sphinx==8.2.3",
+  "furo==2025.9.25",
+  "m2r2==0.3.4",
+  "ipython==9.6.0",
+  "nbsphinx==0.9.6",
+  "nbsphinx-link==1.3.1",
+  "sphinx-autodoc-typehints==3.5.1",
+  "sphinx-autoapi==3.6.1",
+  "lxml_html_clean==0.4.3",
 ]
 tests = [
   "pytest>=7.1.2",

pyproject.toml

@@ -1,4 +1,5 @@
 """Chang Density Objects: Periodic Grid + Lattice / Atoms."""
+
 from __future__ import annotations
 
 import math
@@ -232,7 +233,7 @@ def get_transformed(
         if isinstance(grid_out, int):
             ngrid = grid_out / new_structure.volume
             mult = (np.prod(lengths) / ngrid) ** (1 / 3)
-            grid_out = [int(math.floor(max(l_ / mult, 1))) for l_ in lengths]
+            grid_out = [math.floor(max(l_ / mult, 1)) for l_ in lengths]
 
         pgrids = {}
         for k, pgrid in self.normalized_pgrids.items():
@@ -436,18 +437,18 @@ def multiply_aug(data_aug: list[str], factor: int) -> list[str]:
             if cur_block:
                 for _ in range(factor):
                     cnt += 1
-                    cur_block[
-                        0
-                    ] = f"augmentation occupancies{cnt:>4}{cur_block[0].split()[-1]:>4}\n"
+                    cur_block[0] = (
+                        f"augmentation occupancies{cnt:>4}{cur_block[0].split()[-1]:>4}\n"
+                    )
                     res.extend(cur_block)
             cur_block = [ll]
         else:
             cur_block.append(ll)
     for _ in range(factor):
         cnt += 1
-        cur_block[
-            0
-        ] = f"augmentation occupancies{cnt:>4}{cur_block[0].split()[-1]:>4}\n"
+        cur_block[0] = (
+            f"augmentation occupancies{cnt:>4}{cur_block[0].split()[-1]:>4}\n"
+        )
         res.extend(cur_block)
     return res
 

src/pyrho/charge_density.py

@@ -1,4 +1,5 @@
 """Util Functions."""
+
 from __future__ import annotations
 
 from itertools import combinations
@@ -12,15 +13,15 @@
     from numpy.typing import ArrayLike, NDArray
 
 __all__ = [
-    "pad_arr",
-    "interpolate_fourier",
-    "roll_array",
-    "get_sc_interp",
+    "gaussian_smear",
     "get_padded_array",
     "get_plane_spacing",
+    "get_sc_interp",
     "get_ucell_frac_fit_sphere",
     "get_ucell_frac_fit_sphere",
-    "gaussian_smear",
+    "interpolate_fourier",
+    "pad_arr",
+    "roll_array",
 ]
 
 
@@ -75,7 +76,7 @@ def get_slice(idig, idim, bound_pairs):
         for i_dim, j_dim in zip(dimensions, shape)
     ]
     dim = len(dimensions)
-    fmt = f"#0{dim+2}b"
+    fmt = f"#0{dim + 2}b"
     corners = [format(itr, fmt)[-dim:] for itr in range(2**dim)]
     arr_out = np.zeros(shape, dtype=arr_in.dtype)
 
@@ -291,7 +292,7 @@ def get_plane_spacing(lattice: NDArray) -> List[float]:
             if j != idir
         ]
         v_perp_subspace = lattice[idir] - sum(idir_proj)
-        spacing.append(np.linalg.norm(v_perp_subspace))
+        spacing.append(float(np.linalg.norm(v_perp_subspace)))
     return spacing
 
 

src/pyrho/utils.py

@@ -1,4 +1,5 @@
 """Helper functions to visualize the data in plotly."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING