Merge remote-tracking branch 'trunk/master'

.github/CODEOWNERS

@@ -2,3 +2,5 @@
 pymatgen/io/ase.py @Andrew-S-Rosen
 pymatgen/io/abinit/* @gmatteo
 pymatgen/io/lobster/* @JaGeo
+pymatgen/ext/* @ml-evs
+tests/ext/* @ml-evs

.github/release.yml

@@ -14,6 +14,8 @@ changelog:
       labels: [housekeeping]
     - title: 🚀 Performance
       labels: [performance]
+    - title: 🚧 CI
+      labels: [ci]
     - title: 💡 Refactoring
       labels: [refactor]
     - title: 🧪 Tests

.github/workflows/issue-metrics.yml

@@ -0,0 +1,42 @@
+name: Monthly issue metrics
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '3 2 1 * *'
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+    steps:
+    - name: Get dates for last month
+      shell: bash
+      run: |
+        # Calculate the first day of the previous month
+        first_day=$(date -d "last month" +%Y-%m-01)
+
+        # Calculate the last day of the previous month
+        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+
+        #Set an environment variable with the date range
+        echo "$first_day..$last_day"
+        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+
+    - name: Run issue-metrics tool
+      uses: github/issue-metrics@v3
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SEARCH_QUERY: 'repo:materialsproject/pymatgen is:issue created:${{ env.last_month }} -reason:"not planned"'
+
+    - name: Create issue
+      uses: peter-evans/create-issue-from-file@v5
+      with:
+        title: Monthly issue metrics report
+        token: ${{ secrets.GITHUB_TOKEN }}
+        content-filepath: ./issue_metrics.md

.github/workflows/jekyll-gh-pages.yml

@@ -1,15 +1,11 @@
-# Sample workflow for building and deploying a Jekyll site to GitHub Pages
 name: Deploy Jekyll with GitHub Pages dependencies preinstalled
 
 on:
-  # Runs on pushes targeting the default branch
   push:
     branches: ["master"]
+  workflow_dispatch: # enable manual workflow execution
 
-  # Allows you to run this workflow manually from the Actions tab
-  workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+# Set permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: read
   pages: write
@@ -22,23 +18,26 @@ concurrency:
   cancel-in-progress: false
 
 jobs:
-  # Build job
   build:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+
       - name: Setup Pages
         uses: actions/configure-pages@v3
+
       - name: Build with Jekyll
         uses: actions/jekyll-build-pages@v1
         with:
           source: ./docs
           destination: ./_site
+
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v2
 
-  # Deployment job
   deploy:
     environment:
       name: github-pages

.github/workflows/lint.yml

@@ -27,7 +27,7 @@ jobs:
       - name: ruff
         run: |
           ruff --version
-          ruff .
+          ruff check .
           ruff format --check .
 
       - name: mypy

.github/workflows/test.yml

@@ -19,6 +19,9 @@ jobs:
   test:
     # prevent this action from running on forks
     if: github.repository == 'materialsproject/pymatgen'
+    defaults:
+      run:
+        shell: bash -l {0} # enables conda/mamba env activation by reading bash profile
     strategy:
       fail-fast: false
       matrix:
@@ -48,65 +51,41 @@ jobs:
       - name: Check out repo
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: setup.py
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@main
+
+      - name: Create mamba environment
+        run: |
+          micromamba create -n pmg python=${{ matrix.python-version }} --yes
 
       - name: Install uv
-        run: pip install uv
+        run: micromamba run -n pmg pip install uv
 
       - name: Copy GULP to bin
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo cp cmd_line/gulp/Linux_64bit/* /usr/local/bin/
 
-      - name: Install Bader
+      - name: Install ubuntu-only conda dependencies
         if: matrix.os == 'ubuntu-latest'
         run: |
-          wget https://theory.cm.utexas.edu/henkelman/code/bader/download/bader_lnx_64.tar.gz
-          tar xvzf bader_lnx_64.tar.gz
-          sudo mv bader /usr/local/bin/
-        continue-on-error: true # This is not critical to succeed.
+          micromamba install -n pmg -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
 
-      - name: Install Enumlib
-        if: matrix.os == 'ubuntu-latest'
+      - name: Install pymatgen and dependencies
         run: |
-          git clone --recursive https://github.com/msg-byu/enumlib.git
-          cd enumlib/symlib/src
-          export F90=gfortran
-          make
-          cd ../../src
-          make enum.x
-          sudo mv enum.x /usr/local/bin/
-          cd ..
-          sudo cp aux_src/makeStr.py /usr/local/bin/
-        continue-on-error: true # This is not critical to succeed.
-
-      - name: Install Packmol
-        if: matrix.os == 'ubuntu-latest'
-        run: |
-          wget -O packmol.tar.gz https://github.com/m3g/packmol/archive/refs/tags/v20.14.2.tar.gz
-          tar xvzf packmol.tar.gz
-          export F90=gfortran
-          cd packmol-20.14.2
-          ./configure
-          make
-          sudo mv packmol /usr/local/bin/
-          cd ..
-        continue-on-error: true # This is not critical to succeed.
-
-      - name: Install dependencies
-        run: |
-          uv pip install numpy cython --system
+          micromamba activate pmg
+          # TODO remove temporary fix. added since uv install torch is flaky.
+          # track https://github.com/astral-sh/uv/issues/1921 for resolution
+          pip install torch
+
+          uv pip install numpy cython
 
-          uv pip install -e '.[dev,optional]' --system
+          uv pip install --editable '.[dev,optional]'
 
           # 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
+          uv pip install --upgrade 'git+https://gitlab.com/ase/ase'
 
       - name: pytest split ${{ matrix.split }}
         run: |
+          micromamba activate pmg
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests

.pre-commit-config.yaml

@@ -8,14 +8,14 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.3.7
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer

dev_scripts/chemenv/equivalent_indices.py

@@ -99,9 +99,9 @@
         # 0. any point
         for i0 in range(8):
             # 1. point opposite to point 0. in the square face
-            if i0 in [0, 2]:
+            if i0 in {0, 2}:
                 i1 = i0 + 1
-            elif i0 in [1, 3]:
+            elif i0 in {1, 3}:
                 i1 = i0 - 1
             elif i0 == 4:
                 i1 = 7
@@ -111,10 +111,14 @@
                 i1 = 5
             elif i0 == 7:
                 i1 = 4
+            else:
+                raise RuntimeError("Cannot determine point.")
+
             # 2. one of the two last points in the square face
             sfleft = list(sf1) if i0 in sf1 else list(sf2)
             sfleft.remove(i0)
             sfleft.remove(i1)
+            i2 = 0
             for i2 in sfleft:
                 sfleft2 = list(sfleft)
                 sfleft2.remove(i2)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -279,7 +279,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 f"Get the explicit optimized permutations for geometry {cg.name!r} (symbol : "
                 f'{cg_symbol!r}) ? ("y" to confirm, "q" to quit)\n'
             )
-            if test not in ["y", "q"]:
+            if test not in ("y", "q"):
                 print("Wrong key, try again")
                 continue
             if test == "y":

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -151,17 +151,18 @@ def get_structure(self, morphing_factor):
 
         coords = copy.deepcopy(self.abstract_geometry.points_wcs_ctwcc())
         bare_points = self.abstract_geometry.bare_points_with_centre
+        origin = None
 
         for morphing in self.morphing_description:
-            if morphing["site_type"] == "neighbor":
-                i_site = morphing["ineighbor"] + 1
-                if morphing["expansion_origin"] == "central_site":
-                    origin = bare_points[0]
-                vector = bare_points[i_site] - origin
-                coords[i_site] += vector * (morphing_factor - 1.0)
-            else:
+            if morphing["site_type"] != "neighbor":
                 raise ValueError(f"Key \"site_type\" is {morphing['site_type']} while it can only be neighbor")
 
+            i_site = morphing["ineighbor"] + 1
+            if morphing["expansion_origin"] == "central_site":
+                origin = bare_points[0]
+            vector = bare_points[i_site] - origin
+            coords[i_site] += vector * (morphing_factor - 1.0)
+
         return Structure(lattice=lattice, species=species, coords=coords, coords_are_cartesian=True)
 
     def estimate_parameters(self, dist_factor_min, dist_factor_max, symmetry_measure_type="csm_wcs_ctwcc"):
@@ -269,7 +270,7 @@ def get_weights(self, weights_options):
         "+-------------------------------------------------------------+\n"
     )
 
-    with open("ce_pairs.json") as file:
+    with open("ce_pairs.json", encoding="utf-8") as file:
         ce_pairs = json.load(file)
     self_weight_max_csms: dict[str, list[float]] = {}
     self_weight_max_csms_per_cn: dict[str, list[float]] = {}

dev_scripts/chemenv/view_environment.py

@@ -52,6 +52,7 @@
             print()
         # Visualize the separation plane of a given algorithm
         sep_plane = False
+        algo = None
         if any(algo.algorithm_type == SEPARATION_PLANE for algo in cg.algorithms):
             test = input("Enter index of the algorithm for which you want to visualize the plane : ")
             if test != "":

dev_scripts/potcar_scrambler.py

@@ -4,6 +4,7 @@
 import shutil
 import warnings
 from glob import glob
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.os.path import zpath
@@ -14,6 +15,9 @@
 from pymatgen.io.vasp.sets import _load_yaml_config
 from pymatgen.util.testing import VASP_IN_DIR
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 
 class PotcarScrambler:
     """
@@ -34,26 +38,22 @@ class PotcarScrambler:
     from existing POTCAR `input_filename`
     """
 
-    def __init__(self, potcars: Potcar | PotcarSingle):
-        if isinstance(potcars, PotcarSingle):
-            self.PSP_list = [potcars]
-        else:
-            self.PSP_list = potcars
+    def __init__(self, potcars: Potcar | PotcarSingle) -> None:
+        self.PSP_list = [potcars] if isinstance(potcars, PotcarSingle) else potcars
         self.scrambled_potcars_str = ""
         for psp in self.PSP_list:
             scrambled_potcar_str = self.scramble_single_potcar(psp)
             self.scrambled_potcars_str += scrambled_potcar_str
-        return
 
-    def _rand_float_from_str_with_prec(self, input_str: str, bloat: float = 1.5):
+    def _rand_float_from_str_with_prec(self, input_str: str, bloat: float = 1.5) -> float:
         n_prec = len(input_str.split(".")[1])
         bd = max(1, bloat * abs(float(input_str)))
         return round(bd * np.random.rand(1)[0], n_prec)
 
     def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
         input_str = input_str.strip()
 
-        if input_str.lower() in ("t", "f", "true", "false"):
+        if input_str.lower() in {"t", "f", "true", "false"}:
             return bool(np.random.randint(2))
 
         if input_str.upper() == input_str.lower() and input_str[0].isnumeric():
@@ -68,7 +68,7 @@ def _read_fortran_str_and_scramble(self, input_str: str, bloat: float = 1.5):
         except ValueError:
             return input_str
 
-    def scramble_single_potcar(self, potcar: PotcarSingle):
+    def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         """
         Scramble the body of a POTCAR, retain the PSCTR header information.
 
@@ -124,20 +124,20 @@ def scramble_single_potcar(self, potcar: PotcarSingle):
             )
         return scrambled_potcar_str
 
-    def to_file(self, filename: str):
+    def to_file(self, filename: str) -> None:
         with zopen(filename, mode="wt") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod
-    def from_file(cls, input_filename: str, output_filename: str | None = None):
+    def from_file(cls, input_filename: str, output_filename: str | None = None) -> Self:
         psp = Potcar.from_file(input_filename)
         psp_scrambled = cls(psp)
         if output_filename:
             psp_scrambled.to_file(output_filename)
         return psp_scrambled
 
 
-def generate_fake_potcar_libraries():
+def generate_fake_potcar_libraries() -> None:
     """
     To test the `_gen_potcar_summary_stats` function in `pymatgen.io.vasp.inputs`,
     need a library of fake POTCARs which do not violate copyright
@@ -173,7 +173,7 @@ def generate_fake_potcar_libraries():
                     break
 
 
-def potcar_cleanser():
+def potcar_cleanser() -> None:
     """
     Function to replace copyrighted POTCARs used in io.vasp.sets testing
     with dummy POTCARs that have scrambled PSP and kinetic energy values