Merge branch 'master' into dependabot/pip/pymatgen-2024.10.3

Author: shyuep

.github/workflows/linting.yml

@@ -11,7 +11,7 @@ jobs:
         python-version: [3.11]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
@@ -21,11 +21,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements-ci.txt --quiet
+          pip install --upgrade -r requirements-ci.txt --quiet
       - name: mypy
         run: |
-          mypy --namespace-packages --explicit-package-bases pymatgen
+          mypy --namespace-packages --explicit-package-bases src
       - name: ruff
         run: |
-          ruff check pymatgen
-          ruff format pymatgen
+          ruff check .
+          ruff format .

.github/workflows/testing.yml

@@ -17,7 +17,7 @@ jobs:
       MPLBACKEND: "Agg"
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -30,8 +30,8 @@ jobs:
         pip install -e '.[ci]'
     - name: pytest
       run: |
-        python -m pytest --cov=pymatgen.analysis.diffusion --durations=30 pymatgen
+        python -m pytest --cov=pymatgen.analysis.diffusion --durations=30 tests
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -8,46 +8,46 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.9.9
     hooks:
       - id: ruff
         args: [ --fix, --unsafe-fixes ]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.15.0
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
       - id: codespell
-        stages: [ commit, commit-msg ]
+        stages: [ pre-commit, commit-msg ]
         exclude_types: [ html ]
         additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.2
+    rev: v0.16.6
     hooks:
       - id: cython-lint
         args: [ --no-pycodestyle ]
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.16.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.41.0
+    rev: v0.44.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -58,12 +58,12 @@ repos:
         args: [ --disable, MD013, MD024, MD025, MD033, MD041, "--" ]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.8.1
     hooks:
       - id: nbstripout
         args: [ --drop-empty-cells, --keep-output ]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.369
+    rev: v1.1.396
     hooks:
       - id: pyright

MANIFEST.in

@@ -1,6 +1,2 @@
 include LICENSE COPYRIGHT *.md *.in requirements.txt
 recursive-include pymatgen *.py
-recursive-include scripts *.py
-prune */tests
-prune */*/tests
-prune */*/*/tests

examples/neb_idpp_solver.ipynb

@@ -6,18 +6,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from pymatgen.core import Structure\n",
-    "from pymatgen.analysis.diffusion.neb.pathfinder import IDPPSolver\n",
-    "import numpy as np\n",
+    "from __future__ import annotations\n",
+    "\n",
     "import os\n",
     "\n",
+    "from pymatgen.analysis.diffusion.neb.pathfinder import IDPPSolver\n",
+    "from pymatgen.core import Structure\n",
+    "\n",
     "dirname = \"../pymatgen/analysis/diffusion/neb/tests/pathfinder_files/\"\n",
     "\n",
     "init_struct = Structure.from_file(os.path.join(dirname, \"CONTCAR-0\"), False)\n",
     "final_struct = Structure.from_file(os.path.join(dirname, \"CONTCAR-1\"), False)\n",
     "\n",
-    "obj = IDPPSolver.from_endpoints(endpoints=[init_struct, final_struct], nimages=3, \n",
-    "                                sort_tol=1.0)\n",
+    "obj = IDPPSolver.from_endpoints(endpoints=[init_struct, final_struct], nimages=3, sort_tol=1.0)\n",
     "new_path = obj.run(maxiter=5000, tol=1e-5, gtol=1e-3, species=[\"Li\"])"
    ]
   }

examples/neb_path_mapping.ipynb

@@ -14,7 +14,10 @@
    "outputs": [],
    "source": [
     "# Start with a lithiated structure\n",
+    "from __future__ import annotations\n",
+    "\n",
     "from pymatgen.core import Structure\n",
+    "\n",
     "struct = Structure.from_file(\"../pymatgen/analysis/diffusion/neb/tests/full_path_files/Li6MnO4.cif\")"
    ]
   },
@@ -25,7 +28,8 @@
    "outputs": [],
    "source": [
     "from pymatgen.analysis.diffusion.neb.full_path_mapper import MigrationGraph\n",
-    "# Instantiate MigrationGraph and consider all hops within 4 Angstroms \n",
+    "\n",
+    "# Instantiate MigrationGraph and consider all hops within 4 Angstroms\n",
     "mg = MigrationGraph.with_distance(structure=struct, migrating_specie=\"Li\", max_distance=4)"
    ]
   },
@@ -316,7 +320,7 @@
    "source": [
     "# Get migration paths through the material of interest using the MigrationGraph hop data\n",
     "paths = []\n",
-    "for u, path in mg.get_path():\n",
+    "for _u, path in mg.get_path():\n",
     "    paths.append(path)"
    ]
   },
@@ -389,14 +393,14 @@
     }
    ],
    "source": [
-    "print(\"Number of paths =\", len(paths), \"\\n\\nA example of a path of length\", len(paths[0]))\n",
+    "print(f\"Number of paths = {len(paths)} \\n\\nA example of a path of length {len(paths[0])}\")\n",
     "paths[0]"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -410,7 +414,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,

examples/probability_analysis.ipynb

@@ -29,22 +29,25 @@
     }
    ],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
+    "import numpy as np\n",
+    "\n",
     "from pymatgen.analysis.diffusion.aimd.pathway import ProbabilityDensityAnalysis\n",
     "from pymatgen.core import Structure\n",
-    "import numpy as np\n",
     "\n",
-    "#First prepare the structure and ionic trajectories files\n",
+    "# First prepare the structure and ionic trajectories files\n",
     "trajectories = np.load(\"../pymatgen/analysis/diffusion/aimd/tests/cNa3PS4_trajectories.npy\")\n",
     "structure = Structure.from_file(\"../pymatgen/analysis/diffusion/aimd/tests/cNa3PS4.cif\", False)\n",
     "\n",
-    "#ProbabilityDensityAnalysis object\n",
+    "# ProbabilityDensityAnalysis object\n",
     "pda = ProbabilityDensityAnalysis(structure, trajectories, interval=0.5)\n",
-    "#Save probability distribution to a CHGCAR-like file\n",
+    "# Save probability distribution to a CHGCAR-like file\n",
     "pda.to_chgcar(filename=\"CHGCAR_new.vasp\")\n",
     "\n",
-    "print(\"Maximum: %s, Minimum: %s\" % (pda.Pr.max(), pda.Pr.min()))\n",
+    "print(f\"Maximum: {pda.Pr.max()}, Minimum: {pda.Pr.min()}\")\n",
     "# \\int P(r)d^3r = 1\n",
-    "print(\"Total probability: %s\" % np.sum(pda.Pr * pda.structure.lattice.volume / pda.lens[0]/pda.lens[1]/pda.lens[2]))\n"
+    "print(f\"Total probability: {np.sum(pda.Pr * pda.structure.lattice.volume / pda.lens[0] / pda.lens[1] / pda.lens[2])}\")"
    ]
   },
   {
@@ -69,29 +72,29 @@
     }
    ],
    "source": [
-    "from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer\n",
     "import json\n",
     "\n",
-    "#ProbabilityDensityAnalysis object\n",
-    "filename=\"../pymatgen/analysis/diffusion/aimd/tests/cNa3PS4_pda.json\"\n",
+    "from pymatgen.analysis.diffusion.analyzer import DiffusionAnalyzer\n",
+    "\n",
+    "# ProbabilityDensityAnalysis object\n",
+    "filename = \"../pymatgen/analysis/diffusion/aimd/tests/cNa3PS4_pda.json\"\n",
     "\n",
-    "data = json.load(open(\"../pymatgen/analysis/diffusion/aimd/tests/cNa3PS4_pda.json\", \"r\"))\n",
+    "data = json.load(open(\"../pymatgen/analysis/diffusion/aimd/tests/cNa3PS4_pda.json\"))\n",
     "diff_analyzer = DiffusionAnalyzer.from_dict(data)\n",
     "\n",
-    "pda = ProbabilityDensityAnalysis.from_diffusion_analyzer(diff_analyzer, interval=0.5,\n",
-    "                                                         species=(\"Na\", \"Li\"))\n",
-    "#Save probability distribution to a CHGCAR-like file\n",
+    "pda = ProbabilityDensityAnalysis.from_diffusion_analyzer(diff_analyzer, interval=0.5, species=(\"Na\", \"Li\"))\n",
+    "# Save probability distribution to a CHGCAR-like file\n",
     "pda.to_chgcar(filename=\"CHGCAR_new2.vasp\")\n",
     "\n",
-    "print(\"Maximum: %s, Minimum: %s\" % (pda.Pr.max(), pda.Pr.min()))\n",
+    "print(f\"Maximum: {pda.Pr.max()}, Minimum: {pda.Pr.min()}\")\n",
     "# \\int P(r)d^3r = 1\n",
-    "print(\"Total probability: %s\" % np.sum(pda.Pr * pda.structure.lattice.volume / pda.lens[0]/pda.lens[1]/pda.lens[2]))\n"
+    "print(f\"Total probability: {np.sum(pda.Pr * pda.structure.lattice.volume / pda.lens[0] / pda.lens[1] / pda.lens[2])}\")"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -105,9 +108,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.8"
+   "version": "3.11.10"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 1
+ "nbformat_minor": 4
 }