Update linting tools and and workflows

.github/workflows/python-publish.yml

@@ -6,6 +6,7 @@ on:
 
 permissions:
   contents: read
+  id-token: write
 
 jobs:
   deploy:
@@ -26,5 +27,3 @@ jobs:
       run: python -m build
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/testing.yml

@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
@@ -58,8 +58,8 @@ jobs:
       - name: Test Notebooks
         run: pytest --nbmake ./docs/source/content
 
-      - uses: codecov/codecov-action@v1
-        if: matrix.python-version == 3.10
+      - uses: codecov/codecov-action@v4
+        if: matrix.python-version == '3.10'
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
@@ -92,7 +92,7 @@ jobs:
         # Develop branch only
       - name: Deploy
         if: github.ref == 'refs/heads/main'
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           deploy_key: ${{ secrets.ACTIONS_DEPLOY_KEY }}
           publish_dir: ./docs/_build/html

.github/workflows/update-precommit.yml

@@ -9,12 +9,12 @@ jobs:
   auto-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
-      - uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version:  ${{ 3.10 }}
+          python-version: "3.11"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -25,7 +25,7 @@ jobs:
         run: pre-commit autoupdate
 
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v6
         with:
           branch: update/pre-commit-autoupdate
           title: Auto-update pre-commit hooks

.gitignore

@@ -145,3 +145,4 @@ docs.old/_build/
 docs.old/
 
 docs/source/api_ref/pymatgen.*.rst
+.envrc

.pre-commit-config.yaml

@@ -1,15 +1,15 @@
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.4.4
+  rev: v0.12.4
   hooks:
     # Run the linter.
     - id: ruff
       args: [ --fix, --unsafe-fixes]
     # Run the formatter.
     - id: ruff-format
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.10.0
+  rev: v1.17.0
   hooks:
   - id: mypy
     files: ^pymatgen/
@@ -20,20 +20,20 @@ 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
     description: Checks for common misspellings in text files.
     entry: codespell
     language: python
-    types: [text]
+    files: \.(md|py)$
     args: [
       --ignore-words-list, 'titel,statics,ba,nd,te,mater,commun,vise,dscribe',
       --skip, "*.ipynb,./tests,*paper*",
       ]
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.7.1
+  rev: 0.8.1
   hooks:
     - id: nbstripout
       args: [

docs/source/content/defect-finder.ipynb

@@ -25,10 +25,8 @@
     "from pathlib import Path\n",
     "\n",
     "import numpy as np\n",
-    "from pymatgen.io.vasp import Locpot\n",
     "\n",
     "TEST_FILES = Path(\"../../../tests/test_files\")\n",
-    "import glob\n",
     "\n",
     "from pymatgen.analysis.defects.finder import DefectSiteFinder\n",
     "from pymatgen.core.structure import Structure\n",
@@ -37,7 +35,7 @@
     "finder = DefectSiteFinder()\n",
     "\n",
     "for q in range(-1, 3):\n",
-    "    fname = f\"{str(TEST_FILES)}/v_N_GaN/q={q}/CONTCAR.gz\"\n",
+    "    fname = f\"{TEST_FILES!s}/v_N_GaN/q={q}/CONTCAR.gz\"\n",
     "    struct = Structure.from_file(fname)\n",
     "    fpos = finder.get_defect_fpos(defect_structure=struct, base_structure=base_struct)\n",
     "    fpos -= np.round(fpos)\n",

docs/source/content/formation-energy.ipynb

@@ -59,9 +59,9 @@
    "outputs": [],
    "source": [
     "import warnings\n",
+    "\n",
     "from monty.serialization import loadfn\n",
     "from pymatgen.analysis.defects.thermo import FormationEnergyDiagram\n",
-    "from pymatgen.io.vasp import Vasprun\n",
     "\n",
     "warnings.filterwarnings(\"ignore\")\n",
     "\n",
@@ -131,7 +131,7 @@
    "source": [
     "for i, p in enumerate(fed.chempot_limits):\n",
     "    print(f\"Limits for the chemical potential changes for point {i}\")\n",
-    "    for k,v in p.items():\n",
+    "    for k, v in p.items():\n",
     "        print(f\"Δμ_{k} = {v:.2f} eV\")"
    ]
   },
@@ -164,10 +164,11 @@
    "outputs": [],
    "source": [
     "from pymatgen.analysis.defects.corrections.freysoldt import plot_plnr_avg\n",
+    "\n",
     "plot_data = fed.defect_entries[1].corrections_metadata[\"freysoldt\"][\"plot_data\"]\n",
     "plot_plnr_avg(plot_data[0], title=\"Lattice Direction 1\")\n",
     "plot_plnr_avg(plot_data[1], title=\"Lattice Direction 2\")\n",
-    "plot_plnr_avg(plot_data[2], title=\"Lattice Direction 3\")\n"
+    "plot_plnr_avg(plot_data[2], title=\"Lattice Direction 3\")"
    ]
   }
  ],

docs/source/content/freysoldt-correction.ipynb

@@ -81,7 +81,7 @@
     "        defect_frac_coords=center,\n",
     "    )\n",
     "    align = np.mean(list(freysoldt_results[q].metadata[\"alignments\"].values()))\n",
-    "    print(f\"alignment correction: {align}\")\n"
+    "    print(f\"alignment correction: {align}\")"
    ]
   },
   {
@@ -114,7 +114,7 @@
     "    \"\"\"\n",
     "    v_line_file = DEFECT_DIR / f\"q={q}/vline-eV-a{direction}.dat\"\n",
     "    # split the file into blocks based on the location of the string \"&\"\n",
-    "    with open(v_line_file, \"r\") as f:\n",
+    "    with open(v_line_file) as f:\n",
     "        blocks = f.read().split(\"&\")\n",
     "\n",
     "    # convert each block into a list of lines and convert to a numpy array\n",
@@ -210,7 +210,7 @@
    "outputs": [],
    "source": [
     "def get_sxd_result(q):\n",
-    "    \"\"\"Read the output of sxdefectalign\"\"\"\n",
+    "    \"\"\"Read the output of sxdefectalign.\"\"\"\n",
     "    fname = str(DEFECT_DIR / f\"q={q}/corr_align.out\")\n",
     "    gen = reverse_readfile(fname)\n",
     "    line = next(gen)\n",

docs/source/content/nonradiative.ipynb

@@ -21,8 +21,10 @@
    "source": [
     "# disable warnings\n",
     "import warnings\n",
+    "\n",
     "warnings.filterwarnings(\"ignore\", category=UserWarning)\n",
     "from pathlib import Path\n",
+    "\n",
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
     "from pymatgen.analysis.defects.ccd import HarmonicDefect, get_SRH_coefficient"
@@ -186,7 +188,7 @@
     "wswq_dir = TEST_FILES / \"ccd_0_-1\" / \"wswqs\"\n",
     "print(f\"The parsed WSWQ files are: {[f.name for f in wswq_dir.glob('WSWQ*')]}\")\n",
     "hd0.read_wswqs(TEST_FILES / \"ccd_0_-1\" / \"wswqs\")\n",
-    "print(f\"Parsed {len(hd0.wswqs)} WSWQ files.\")\n"
+    "print(f\"Parsed {len(hd0.wswqs)} WSWQ files.\")"
    ]
   },
   {
@@ -205,11 +207,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(f\"The automatically determined defect electronic states are: {hd0.defect_band} \"\n",
-    "    \"(with [band, k-point, spin] indexing).\")\n",
+    "print(\n",
+    "    f\"The automatically determined defect electronic states are: {hd0.defect_band} \"\n",
+    "    \"(with [band, k-point, spin] indexing).\"\n",
+    ")\n",
     "epME = hd0.get_elph_me(defect_state=(138, 1, 1))\n",
-    "print(f\"The resulting array of shape {epME.shape} contains the matrix elements from the \"\n",
-    "    \"defect state to all other states at the same k-point.\")\n"
+    "print(\n",
+    "    f\"The resulting array of shape {epME.shape} contains the matrix elements from the \"\n",
+    "    \"defect state to all other states at the same k-point.\"\n",
+    ")"
    ]
   },
   {
@@ -233,7 +239,7 @@
     "hd1 = HarmonicDefect.from_directories(\n",
     "    directories=dirs10,\n",
     "    store_bandstructure=True,\n",
-    ")\n"
+    ")"
    ]
   },
   {
@@ -252,7 +258,9 @@
    "outputs": [],
    "source": [
     "T = np.linspace(100, 1000, 20)\n",
-    "srh_c = get_SRH_coefficient(initial_state=hd0, final_state=hd1, defect_state=(138, 1, 1), T=T, dE=0.3)\n",
+    "srh_c = get_SRH_coefficient(\n",
+    "    initial_state=hd0, final_state=hd1, defect_state=(138, 1, 1), T=T, dE=0.3\n",
+    ")\n",
     "plt.plot(T, srh_c)\n",
     "plt.xlabel(\"Temperature [K]\")\n",
     "plt.ylabel(\"SRH coefficient [cm$^{-3}$s$^{-1}$]\");"

docs/source/content/photo-conduct.ipynb

@@ -25,11 +25,14 @@
    "outputs": [],
    "source": [
     "# disable tqdm progress bar\n",
-    "from tqdm import tqdm\n",
     "from functools import partialmethod\n",
+    "\n",
+    "from tqdm import tqdm\n",
+    "\n",
     "tqdm.__init__ = partialmethod(tqdm.__init__, disable=True)\n",
     "# disable warnings\n",
     "import warnings\n",
+    "\n",
     "warnings.filterwarnings(\"ignore\", category=UserWarning)"
    ]
   },
@@ -40,13 +43,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import bisect\n",
+    "import collections\n",
     "from pathlib import Path\n",
-    "from pymatgen.analysis.defects.ccd import HarmonicDefect, get_SRH_coefficient\n",
-    "from pymatgen.io.vasp.optics import DielectricFunctionCalculator, Spin, Vasprun, Waveder\n",
+    "\n",
     "import numpy as np\n",
     "from matplotlib import pyplot as plt\n",
-    "import bisect\n",
-    "import collections\n",
+    "from pymatgen.analysis.defects.ccd import HarmonicDefect\n",
+    "from pymatgen.io.vasp.optics import Spin, Waveder\n",
+    "\n",
     "TEST_FILES = Path(\"../../../tests/test_files/v_Ga/\")"
    ]
   },
@@ -96,37 +101,36 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
-    "def print_eigs(vr, bwind=5, defect_bands = ()):\n",
+    "def print_eigs(vr, bwind=5, defect_bands=()):\n",
     "    \"\"\"Print the eigenvalues in a small band window around the Fermi level.\n",
     "\n",
     "    Args:\n",
     "        vr (Vasprun): The Vasprun object.\n",
     "        bwind (int): The number of bands above and below the Fermi level to print.\n",
     "        defect_bands (list): A list of tuples of the form (band index, kpt index, spin index)\n",
     "    \"\"\"\n",
-    "    def _get_spin_idx(spin):\n",
+    "\n",
+    "    def _get_spin_idx(spin) -> int:\n",
     "        if spin == Spin.up:\n",
     "            return 0\n",
     "        return 1\n",
+    "\n",
     "    occ = vr.eigenvalues[Spin.up][0, :, 1] * -1\n",
-    "    fermi_idx = bisect.bisect_left(occ, -0.5) \n",
+    "    fermi_idx = bisect.bisect_left(occ, -0.5)\n",
     "    output = collections.defaultdict(list)\n",
     "    for k, spin_eigs in vr.eigenvalues.items():\n",
     "        spin_idx = _get_spin_idx(k)\n",
     "        for kpt in range(spin_eigs.shape[0]):\n",
     "            for ib in range(fermi_idx - bwind, fermi_idx + bwind):\n",
     "                e, o = spin_eigs[kpt, ib, :]\n",
     "                idx = (ib, kpt, spin_idx)\n",
-    "                if idx in defect_bands:\n",
-    "                    e_out = f\"{e:7.4f}*\"\n",
-    "                else:\n",
-    "                    e_out = f\"{e:8.5f}\"\n",
+    "                e_out = f\"{e:7.4f}*\" if idx in defect_bands else f\"{e:8.5f}\"\n",
     "                output[(ib)].append(e_out)\n",
     "    print(\"band s=0,k=0  s=0,k=1  s=1,k=0  s=1,k=1\")\n",
     "    for ib, eigs in output.items():\n",
     "        print(f\"{ib:3d} {' '.join(eigs)}\")\n",
     "\n",
+    "\n",
     "print_eigs(vr=hd0.vrun, defect_bands=hd0.defect_band)"
    ]
   },
@@ -177,7 +181,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "energy, eps_vbm, eps_cbm = hd0.get_dielectric_function(idir=0,jdir=0)\n",
+    "energy, eps_vbm, eps_cbm = hd0.get_dielectric_function(idir=0, jdir=0)\n",
     "# plotting\n",
     "plt.plot(energy, np.imag(eps_vbm), label=\"VBM\")\n",
     "plt.plot(energy, np.imag(eps_cbm), label=\"CBM\")\n",
@@ -216,15 +220,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pymatgen.analysis.defects.plotting.optics import plot_optical_transitions\n",
     "import matplotlib as mpl\n",
+    "from pymatgen.analysis.defects.plotting.optics import plot_optical_transitions\n",
+    "\n",
     "fig, ax = plt.subplots()\n",
-    "cm_ax  = fig.add_axes([0.8,0.1,0.02,0.8])\n",
-    "df_k0, cmap, norm = plot_optical_transitions(hd0, kpt_index=1, band_window=5, x0=3, ax=ax)\n",
-    "df_k1, _, _ = plot_optical_transitions(hd0, kpt_index=0, band_window=5, x0=0, ax=ax, cmap=cmap, norm=norm)\n",
-    "mpl.colorbar.ColorbarBase(cm_ax,cmap=cmap,norm=norm,orientation='vertical')\n",
-    "ax.set_ylabel(\"Energy (eV)\");\n",
-    "ax.set_xticks([0,3])\n",
+    "cm_ax = fig.add_axes([0.8, 0.1, 0.02, 0.8])\n",
+    "df_k0, cmap, norm = plot_optical_transitions(\n",
+    "    hd0, kpt_index=1, band_window=5, x0=3, ax=ax\n",
+    ")\n",
+    "df_k1, _, _ = plot_optical_transitions(\n",
+    "    hd0, kpt_index=0, band_window=5, x0=0, ax=ax, cmap=cmap, norm=norm\n",
+    ")\n",
+    "mpl.colorbar.ColorbarBase(cm_ax, cmap=cmap, norm=norm, orientation=\"vertical\")\n",
+    "ax.set_ylabel(\"Energy (eV)\")\n",
+    "ax.set_xticks([0, 3])\n",
     "ax.set_xticklabels([\"Kpoint-0\", \"Kpoint-1\"])"
    ]
   },

docs/source/content/quickstart.ipynb

@@ -21,15 +21,6 @@
     "To ensure that the namespace is installed properly run"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "from pymatgen.analysis.defects.core import __file__"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -127,7 +118,6 @@
     "\n",
     "from monty.serialization import loadfn\n",
     "from pymatgen.analysis.defects.thermo import FormationEnergyDiagram\n",
-    "from pymatgen.io.vasp import Vasprun\n",
     "\n",
     "warnings.filterwarnings(\"ignore\")\n",
     "\n",