WIP: Adding support for reading vaspwave.h5 in Wavecar and Chgcar class

.editorconfig

@@ -0,0 +1,16 @@
+# https://editorconfig.org/
+root = true
+
+# Default settings for all files.
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+max_line_length = 120
+
+# Set indent size for json and YAML files.
+[*.{json,yml,yaml}]
+indent_size = 2

.gitattributes

@@ -1,5 +1,4 @@
 # declare HTML, rST and test files as vendored/docs to exclude them when calculating repo languages on GitHub
 tests/files/**/* linguist-vendored
-cmd_line/* linguist-vendored
 docs/**/* linguist-generated
 dev_scripts/**/* linguist-vendored

.github/code_of_conduct.md

@@ -6,7 +6,7 @@ In the interest of fostering an open and welcoming environment, we as
 contributors and maintainers pledge to make participation in our project and
 our community a harassment-free experience for everyone, regardless of age, body
 size, disability, ethnicity, sex characteristics, gender identity and expression,
-level of experience, education, socio-economic status, nationality, personal
+level of experience, education, socioeconomic status, nationality, personal
 appearance, race, religion, or sexual identity and orientation.
 
 ## Our Standards

.github/release.yml

@@ -2,6 +2,8 @@ changelog:
   exclude:
     authors: [dependabot, github-actions, pre-commit-ci]
   categories:
+    - title: 💥 Breaking Changes
+      labels: [breaking]
     - title: 🎉 New Features
       labels: [feature]
     - title: 🐛 Bug Fixes
@@ -20,8 +22,6 @@ changelog:
       labels: [refactor]
     - title: 🧪 Tests
       labels: [tests]
-    - title: 💥 Breaking Changes
-      labels: [breaking]
     - title: 🔒 Security Fixes
       labels: [security]
     - title: 🏥 Package Health

.github/workflows/lint.yml

@@ -18,11 +18,11 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: '3.x'
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff mypy
+          pip install --upgrade ruff mypy pyright
 
       - name: ruff
         run: |
@@ -31,7 +31,7 @@ jobs:
           ruff format --check .
 
       - name: mypy
-        run: |
-          mypy --version
-          rm -rf .mypy_cache
-          mypy ${{ github.event.repository.name }}
+        run: mypy src
+
+      - name: pyright
+        run: pyright

.github/workflows/release.yml

@@ -29,7 +29,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Build sdist
         run: |
@@ -45,7 +45,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-14, windows-latest]
-        python-version: ["39", "310", "311"]
+        python-version: ["39", "310", "311", "312"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
@@ -68,10 +68,10 @@ jobs:
       # For pypi trusted publishing
       id-token: write
     steps:
-      - name: Set up Python 3.11
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Get build artifacts
         uses: actions/download-artifact@v3

.github/workflows/test.yml

@@ -25,26 +25,32 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # pytest-split automatically distributes work load so parallel jobs finish in similar time
-        os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.11"]
-        split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
-        # include/exclude is meant to maximize CI coverage of different platforms and python
-        # versions while minimizing the total number of jobs. We run all pytest splits with the
-        # oldest supported python version (currently 3.9) on windows (seems most likely to surface
-        # errors) and with newest version (currently 3.11) on ubuntu (to get complete and speedy
-        # coverage on unix). We ignore mac-os, which is assumed to be similar to ubuntu.
-        exclude:
+        # maximize CI coverage of different platforms and python versions while minimizing the
+        # total number of jobs. We run all pytest splits with the oldest supported python
+        # version (currently 3.9) on windows (seems most likely to surface errors) and with
+        # newest version (currently 3.12) on ubuntu (to get complete coverage on unix).
+        config:
           - os: windows-latest
-            python-version: "3.11"
+            python: "3.9"
+            resolution: highest
+            extras: ci,optional
           - os: ubuntu-latest
-            python-version: "3.9"
+            python: '>3.9'
+            resolution: lowest-direct
+            extras: ci,optional
+          - os: macos-latest
+            python: '3.10'
+            resolution: lowest-direct
+            extras: ci # test with only required dependencies installed
+
+        # pytest-split automatically distributes work load so parallel jobs finish in similar time
+        # update durations file with `pytest --store-durations --durations-path tests/files/.pytest-split-durations`
+        split: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
 
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{ matrix.config.os }}
 
     env:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-      GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries
       PMG_VASP_PSP_DIR: ${{ github.workspace }}/tests/files
 
     steps:
@@ -56,18 +62,13 @@ jobs:
 
       - name: Create mamba environment
         run: |
-          micromamba create -n pmg python=${{ matrix.python-version }} --yes
+          micromamba create -n pmg python=${{ matrix.config.python }} --yes
 
       - name: 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 ubuntu-only conda dependencies
-        if: matrix.os == 'ubuntu-latest'
+        if: matrix.config.os == 'ubuntu-latest'
         run: |
           micromamba install -n pmg -c conda-forge enumlib packmol bader openbabel openff-toolkit --yes
 
@@ -76,16 +77,30 @@ jobs:
           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
+          pip install torch --upgrade
 
           uv pip install numpy cython
-
-          uv pip install --editable '.[dev,optional]'
-
-          # TODO remove next line installing ase from main branch when FrechetCellFilter is released
-          uv pip install --upgrade 'git+https://gitlab.com/ase/ase'
+          uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 
       - name: pytest split ${{ matrix.split }}
         run: |
           micromamba activate pmg
           pytest --splits 10 --group ${{ matrix.split }} --durations-path tests/files/.pytest-split-durations tests
+
+  trigger_atomate2_ci:
+    needs: test
+    runs-on: ubuntu-latest
+    # only run if changes were pushed to master
+    if: github.ref == 'refs/heads/master'
+    steps:
+      - name: Trigger Atomate2 CI
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          curl -L \
+            -X POST \
+            -H "Accept: application/vnd.github+json" \
+            -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            -H "X-GitHub-Api-Version: 2022-11-28" \
+            https://api.github.com/repos/materialsproject/atomate2/dispatches \
+            -d '{"event_type": "pymatgen-ci-trigger", "client_payload": {"pymatgen_ref": "${{ github.sha }}"}}'

.gitignore

@@ -1,9 +1,6 @@
 __pycache__/
 .DS_Store
 pymatgen.egg-info
-dependencies/PyCifRW-3.3/PyCifRW.egg-info
-dependencies/spglib*/pyspglib.egg-info
-dependencies/spglib*/build
 *.o
 *.so
 *.pyc
@@ -26,7 +23,6 @@ setuptools*
 .cache
 .tox
 .eggs/
-gulptmp_4_1
 .coverage
 .*_cache
 # VS Code
@@ -40,3 +36,4 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+.pdm-python

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
-exclude: ^(docs|tests/files|cmd_line|tasks.py)
+exclude: ^(docs|tests/files|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [mypy]
+  skip: [ mypy, pyright ]
   autofix_commit_msg: pre-commit auto-fixes
   autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.7
+    rev: v0.5.4
     hooks:
       - id: ruff
-        args: [--fix, --unsafe-fixes]
+        args: [ --fix, --unsafe-fixes ]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -22,43 +22,49 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.11.0
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
-        exclude_types: [html]
-        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
+        stages: [ commit, commit-msg ]
+        exclude_types: [ html ]
+        additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11
+        exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.0
+    rev: v0.16.2
     hooks:
       - id: cython-lint
-        args: [--no-pycodestyle]
+        args: [ --no-pycodestyle ]
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.16.0
+    rev: 1.18.0
     hooks:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.39.0
+    rev: v0.41.0
     hooks:
       - id: markdownlint
         # MD013: line too long
         # MD024: Multiple headings with the same content
         # MD033: no inline HTML
         # MD041: first line in a file should be a top-level heading
         # MD025: single title
-        args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
+        args: [ --disable, MD013, MD024, MD025, MD033, MD041, "--" ]
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1
     hooks:
       - id: nbstripout
-        args: [--drop-empty-cells, --keep-output]
+        args: [ --drop-empty-cells, --keep-output ]
+
+  - repo: https://github.com/RobertCraigie/pyright-python
+    rev: v1.1.373
+    hooks:
+      - id: pyright

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -44,16 +44,14 @@
             raise ValueError("Should all be separation plane")
 
         perms_on_file = f"Permutations on file in this algorithm ({len(sep_plane_algo._permutations)}) "
-        print(perms_on_file)
-        print(sep_plane_algo._permutations)
+        print(f"{perms_on_file}\n{sep_plane_algo._permutations}")
         permutations = sep_plane_algo.safe_separation_permutations(
             ordered_plane=sep_plane_algo.ordered_plane, ordered_point_groups=sep_plane_algo.ordered_point_groups
         )
 
         sep_plane_algo._permutations = permutations
 
-        print(f"Test permutations ({len(permutations)}) :")
-        print(permutations)
+        print(f"Test permutations ({len(permutations)}):\n{permutations}")
 
         lgf = LocalGeometryFinder()
         lgf.setup_parameters(structure_refinement=lgf.STRUCTURE_REFINEMENT_NONE)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -209,7 +209,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
             # Definition of the facets
             all_planes_point_indices = [algo.plane_points]
             if algo.other_plane_points is not None:
-                all_planes_point_indices.extend(algo.other_plane_points)
+                all_planes_point_indices += algo.other_plane_points
 
             # Loop on the facets
             explicit_permutations_per_plane = []
@@ -236,7 +236,7 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                 sym_measures = [c["symmetry_measure"] for c in csms]
                 prt1(string="Continuous symmetry measures", printing_volume=printing_volume)
                 prt1(string=sym_measures, printing_volume=printing_volume)
-                csms_with_recorded_permutation = []  # type: ignore
+                csms_with_recorded_permutation: list = []
                 explicit_permutations = []
                 for icsm, csm in enumerate(csms):
                     found = False
@@ -305,10 +305,9 @@ def random_permutations_iterator(initial_permutation, n_permutations):
             # Definition of the facets
             all_planes_point_indices = [algo.plane_points]
             if algo.other_plane_points is not None:
-                all_planes_point_indices.extend(algo.other_plane_points)
+                all_planes_point_indices += algo.other_plane_points
 
             # Setup of the permutations to be used for this algorithm
-
             indices = list(range(cg.coordination_number))
             if permutations_setup_type == "all":
                 perms_iterator = itertools.permutations(indices)
@@ -399,8 +398,10 @@ def random_permutations_iterator(initial_permutation, n_permutations):
                         perms_used[some_perm] += 1
                     else:
                         perms_used[some_perm] = 1
-                tcurrent = time.process_time()
-                time_left = (n_permutations - idx_perm) * (tcurrent - t0) / idx_perm  # type: ignore
+                t_now = time.process_time()
+                if n_permutations is None:
+                    raise ValueError(f"{n_permutations=}")
+                time_left = (n_permutations - idx_perm) * (t_now - t0) / idx_perm
                 time_left = f"{time_left:.1f}"
                 idx_perm += 1
             print(