Merge branch 'master' of github.com:materialsproject/pymatgen

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

@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Setup Pages
         uses: actions/configure-pages@v3
       - name: Build with Jekyll

.github/workflows/lint.yml

@@ -22,17 +22,13 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff black mypy
+          pip install --upgrade ruff mypy
 
       - name: ruff
         run: |
           ruff --version
           ruff .
-
-      - name: black
-        run: |
-          black --version
-          black --check --diff --color ${{ github.event.repository.name }}
+          ruff format --check .
 
       - name: mypy
         run: |

.gitignore

@@ -40,4 +40,4 @@ venv/
 ENV/
 env.bak/
 venv.bak/
-**/secrets*
+docs/tokens.py

.pre-commit-config.yaml

@@ -8,25 +8,21 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.292
+    rev: v0.1.3
     hooks:
       - id: ruff
         args: [--fix]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.6.1
     hooks:
       - id: mypy
 

README.md

@@ -87,10 +87,10 @@ If you use `pymatgen` in your research, please consider citing the following wor
 
 In addition, some of `pymatgen`'s functionality is based on scientific advances/principles developed by the computational materials scientists in our team. Please refer to the [`pymatgen` docs] on how to cite them.
 
-### Soliciting contributions to an updated pymatgen paper
+### Soliciting contributions to 2nd `pymatgen` paper
 
 If you are a long-standing `pymatgen` contributor and would like to be involved in working on an updated `pymatgen` publication,
-please contact the maintainers [@shyuep, @mkhorton and @janosh](mailto:ongsp@ucsd.edu,m.k.horton@gmail.com,janosh@lbl.gov?subject=Contributing%20to%20updated%20pymatgen%20paper).
+please fill out this [co-author registration form](https://docs.google.com/forms/d/e/1FAIpQLSecIhD2YjdPGldrRTM8Go3VxVg_vjKjZAOXtIKDG7qckHLYaQ/viewform) or contact [@shyuep, @mkhorton and @janosh](mailto:ongsp@ucsd.edu,m.k.horton@gmail.com,janosh@lbl.gov?subject=Contributing%20to%20updated%20pymatgen%20paper) with questions.
 
 ## License
 

dev_scripts/chemenv/explicit_permutations.py

@@ -91,8 +91,7 @@ class Algo:
         if len(cg.algorithms) != 1:
             raise ValueError("Multiple algorithms !")
         cg._algorithms = [ExplicitPermutationsAlgorithm(permutations=explicit_permutations)]
-        newgeom_dir = "new_geometry_files"
-        if not os.path.exists(newgeom_dir):
-            os.makedirs(newgeom_dir)
-        with open(f"{newgeom_dir}/{cg_symbol}.json", "w") as f:
+        new_geom_dir = "new_geometry_files"
+        os.makedirs(new_geom_dir, exist_ok=True)
+        with open(f"{new_geom_dir}/{cg_symbol}.json", "w") as f:
             json.dump(cg.as_dict(), f)

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -431,7 +431,6 @@ def random_permutations_iterator(initial_permutation, n_permutations):
         )
         if test == "y":
             new_geom_dir = "new_geometry_files"
-            if not os.path.exists(new_geom_dir):
-                os.makedirs(new_geom_dir)
+            os.makedirs(new_geom_dir, exist_ok=True)
             with open(f"{new_geom_dir}/{cg_symbol}.json", "w") as file:
                 json.dump(cg.as_dict(), file)

dev_scripts/potcar_scrambler.py

@@ -95,10 +95,10 @@ def to_file(self, filename: str):
         with zopen(filename, "wt") as f:
             f.write(self.scrambled_potcars_str)
 
-    @staticmethod
-    def from_file(input_filename: str, output_filename: str | None = None):
+    @classmethod
+    def from_file(cls, input_filename: str, output_filename: str | None = None):
         psp = Potcar.from_file(input_filename)
-        psp_scrambled = PotcarScrambler(psp)
+        psp_scrambled = cls(psp)
         if output_filename:
             psp_scrambled.to_file(output_filename)
         return psp_scrambled

pymatgen/analysis/diffraction/tem.py

@@ -195,7 +195,8 @@ def x_ray_factors(
             coeffs = np.array(ATOMIC_SCATTERING_PARAMS[atom.symbol])
             for plane in bragg_angles:
                 scattering_factor_curr = atom.Z - 41.78214 * s2[plane] * np.sum(
-                    coeffs[:, 0] * np.exp(-coeffs[:, 1] * s2[plane]), axis=None  # type: ignore
+                    coeffs[:, 0] * np.exp(-coeffs[:, 1] * s2[plane]),
+                    axis=None,  # type: ignore
                 )
                 scattering_factors_for_atom[plane] = scattering_factor_curr
             x_ray_factors[atom.symbol] = scattering_factors_for_atom

pymatgen/analysis/diffraction/xrd.py

@@ -223,7 +223,8 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90)
                 #      fs = el.Z - 41.78214 * s2 * sum(
                 #          [d[0] * exp(-d[1] * s2) for d in coeff])
                 fs = zs - 41.78214 * s2 * np.sum(
-                    coeffs[:, :, 0] * np.exp(-coeffs[:, :, 1] * s2), axis=1  # type: ignore
+                    coeffs[:, :, 0] * np.exp(-coeffs[:, :, 1] * s2),
+                    axis=1,  # type: ignore
                 )
 
                 dw_correction = np.exp(-dwfactors * s2)

pymatgen/analysis/eos.py

@@ -65,10 +65,10 @@ def _initial_guess(self):
         b0 = 2 * a * v0
         b1 = 4  # b1 is usually a small number like 4
 
-        vmin, vmax = min(self.volumes), max(self.volumes)
+        vol_min, vol_max = min(self.volumes), max(self.volumes)
 
-        if not vmin < v0 and v0 < vmax:
-            raise EOSError("The minimum volume of a fitted parabola is not in the input volumes\n.")
+        if not vol_min < v0 and v0 < vol_max:
+            raise EOSError("The minimum volume of a fitted parabola is not in the input volumes.")
 
         return e0, b0, b1, v0
 
@@ -77,8 +77,7 @@ def fit(self):
         Do the fitting. Does least square fitting. If you want to use custom
         fitting, must override this.
         """
-        # the objective function that will be minimized in the least square
-        # fitting
+        # the objective function that will be minimized in the least square fitting
         self._params = self._initial_guess()
         self.eos_params, ierr = leastsq(
             lambda pars, x, y: y - self._func(x, pars),
@@ -87,7 +86,7 @@ def fit(self):
         )
         # e0, b0, b1, v0
         self._params = self.eos_params
-        if ierr not in [1, 2, 3, 4]:
+        if ierr not in (1, 2, 3, 4):
             raise EOSError("Optimal parameters not found")
 
     @abstractmethod
@@ -97,8 +96,8 @@ def _func(self, volume, params):
         that derive from this abstract class.
 
         Args:
-            volume (float/numpy.array)
-             params (list/tuple): values for the parameters other than the
+            volume (float | list[float])
+            params (list | tuple): values for the parameters other than the
                 volume used by the eos.
         """
 
@@ -108,17 +107,17 @@ def func(self, volume):
         to the ones obtained from fitting.
 
         Args:
-            volume (list/numpy.array)
+            volume (float | list[float]): volumes in Ang^3
 
         Returns:
             numpy.array
         """
         return self._func(np.array(volume), self.eos_params)
 
-    def __call__(self, volume):
+    def __call__(self, volume: float) -> float:
         """
         Args:
-            volume (): Volume.
+            volume (float | list[float]): volume(s) in Ang^3
 
         Returns:
             Compute EOS with this volume.