Fix docs (materialsproject#1109)

* pre-commit autoupdate && pre-commit run --all-files

bump ruff to v0.9.3, mypy to v1.14.1, and codespell to v2.4.0 plus auto-fixes

* fix .github/workflows/docs.yml by bumping actions/upload-pages-artifact@v2 to v3, actions/deploy-pages@v2 to v4

prior actions/upload-pages-artifact versions started failing, see
https://github.blog/changelog/2024-04-16-deprecation-notice-v3-of-the-artifact-actions
and https://github.com/actions/upload-pages-artifact/releases/tag/v3.0.0

.github/workflows/docs.yml

@@ -39,7 +39,7 @@ jobs:
         run: sphinx-build docs docs_build
 
       - name: Upload build artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: ./docs_build
 
@@ -52,4 +52,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: ^(.github/|tests/test_data/abinit/)
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.8.0
+  rev: v0.9.3
   hooks:
   - id: ruff
     args: [--fix]
@@ -30,15 +30,15 @@ repos:
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v1.13.0
+  rev: v1.14.1
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.3.0
+  rev: v2.4.0
   hooks:
   - id: codespell
     stages: [pre-commit, commit-msg]

src/atomate2/abinit/jobs/base.py

@@ -54,8 +54,7 @@ def setup_job(
 
     if structure is None and prev_outputs is None and restart_from is None:
         raise RuntimeError(
-            "At least one of structure, prev_outputs or "
-            "restart_from should be defined."
+            "At least one of structure, prev_outputs or restart_from should be defined."
         )
 
     if history is None:

src/atomate2/aims/flows/phonons.py

@@ -77,8 +77,8 @@ class PhononMaker(BasePhononMaker):
           High-throughput electronic band structure calculations:
           Challenges and tools. Computational Materials Science,
           49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.
-          We will however use seekpath and primitive structures
-          as determined by from phonopy to compute the phonon band structure
+          We will, however, use seekpath and primitive structures
+          as determined by phonopy to compute the phonon band structure
     bulk_relax_maker : .BaseAimsMaker or None
         A maker to perform a tight relaxation on the bulk.
         Set to ``None`` to skip the
@@ -106,7 +106,7 @@ class PhononMaker(BasePhononMaker):
         it relies on phonopy to handle the relationship
         to the primitive cell and not pymatgen
     code: str
-        determines the dft or forcefield code.
+        determines the DFT or forcefield code.
     store_force_constants: bool
         if True, force constants will be stored
     socket: bool

src/atomate2/ase/schemas.py

@@ -51,8 +51,7 @@ class AseResult(BaseModel):
     is_force_converged: Optional[bool] = Field(
         None,
         description=(
-            "Whether the calculation is converged with respect "
-            "to interatomic forces."
+            "Whether the calculation is converged with respect to interatomic forces."
         ),
     )
 
@@ -220,8 +219,7 @@ class AseStructureTaskDoc(StructureMetadata):
     is_force_converged: Optional[bool] = Field(
         None,
         description=(
-            "Whether the calculation is converged with respect "
-            "to interatomic forces."
+            "Whether the calculation is converged with respect to interatomic forces."
         ),
     )
 
@@ -285,8 +283,7 @@ class AseMoleculeTaskDoc(MoleculeMetadata):
     is_force_converged: Optional[bool] = Field(
         None,
         description=(
-            "Whether the calculation is converged with respect "
-            "to interatomic forces."
+            "Whether the calculation is converged with respect to interatomic forces."
         ),
     )
 
@@ -329,8 +326,7 @@ class AseTaskDoc(AseBaseModel):
     is_force_converged: Optional[bool] = Field(
         None,
         description=(
-            "Whether the calculation is converged with respect "
-            "to interatomic forces."
+            "Whether the calculation is converged with respect to interatomic forces."
         ),
     )
 

src/atomate2/cli/dev.py

@@ -561,9 +561,9 @@ def test_run_{test_name}(self, mock_abinit, abinit_test_dir, clean_dir):
         from atomate2.abinit.schemas.core import AbinitTaskDocument
 
         # load the initial structure, the maker and the ref_paths from the test_dir
-        test_dir = abinit_test_dir / {" / ".join(
-        [f'"{part}"' for part in test_dir.parts[index_part:]]
-    )}
+        test_dir = abinit_test_dir / {
+        " / ".join([f'"{part}"' for part in test_dir.parts[index_part:]])
+    }
         structure = Structure.from_file(test_dir / "initial_structure.json.gz")
         maker_info = loadfn(test_dir / "maker.json.gz")
         maker = maker_info["maker"]

src/atomate2/common/flows/anharmonicity.py

@@ -95,7 +95,7 @@ def make(
             It has to be given per formula unit (as a result in corresponding Doc).
             Instead of recomputing the energy of the bulk structure every time, this
             value can also be provided in eV. If it is provided, the static run will be
-            skipped. This energy is the typical output dft energy of the dft workflow.
+            skipped. This energy is the typical output DFT energy of the DFT workflow.
             No conversion needed. It is set to 0 by default.
         supercell_matrix: Optional[Matrix3D]
             Instead of min_length, also a supercell_matrix can be given, e.g.

src/atomate2/common/flows/gruneisen.py

@@ -52,7 +52,7 @@ class BaseGruneisenMaker(Maker, ABC):
     bulk_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker, .BaseVaspMaker, or None
         A maker to perform an initial tight relaxation on the bulk.
     code: str
-        determines the dft or force field code.
+        determines the DFT or force field code.
     const_vol_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker,
         .BaseVaspMaker, or None. A maker to perform a tight relaxation
         on the expanded and shrunk structures at constant volume.

src/atomate2/common/flows/mpmorph.py

@@ -165,9 +165,8 @@ def make(
                 structure=deformed_structures[index].final_structure,
                 prev_dir=None,
             )
-            md_job.name = (
-                f"{self.name} {md_job.name} {len(working_outputs['relax']['volume'])+1}"
-            )
+            relaxed_vol = len(working_outputs["relax"]["volume"])
+            md_job.name = f"{self.name} {md_job.name} {relaxed_vol + 1}"
 
             working_outputs["relax"]["energies"].append(md_job.output.output.energy)
             working_outputs["relax"]["volume"].append(md_job.output.structure.volume)

src/atomate2/common/flows/phonons.py

@@ -93,8 +93,8 @@ class BasePhononMaker(Maker, ABC):
           High-throughput electronic band structure calculations:
           Challenges and tools. Computational Materials Science,
           49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.
-          We will however use seekpath and primitive structures
-          as determined by from phonopy to compute the phonon band structure
+          We will, however, use seekpath and primitive structures
+          as determined by phonopy to compute the phonon band structure
     bulk_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker, .BaseVaspMaker, or None
         A maker to perform a tight relaxation on the bulk.
         Set to ``None`` to skip the
@@ -128,7 +128,7 @@ class BasePhononMaker(Maker, ABC):
         it relies on phonopy to handle the relationship
         to the primitive cell and not pymatgen
     code: str
-        determines the dft or force field code.
+        determines the DFT or force field code.
     store_force_constants: bool
         if True, force constants will be stored
     socket: bool
@@ -200,7 +200,7 @@ def make(
             It has to be given per formula unit (as a result in corresponding Doc).
             Instead of recomputing the energy of the bulk structure every time, this
             value can also be provided in eV. If it is provided, the static run will be
-            skipped. This energy is the typical output dft energy of the dft workflow.
+            skipped. This energy is the typical output dft energy of the DFT workflow.
             No conversion needed.
         supercell_matrix: list
             Instead of min_length, also a supercell_matrix can be given, e.g.

src/atomate2/common/schemas/elastic.py

@@ -125,7 +125,7 @@ class ElasticTensorDocument(BaseModel):
 class ElasticWarnings(Enum):
     """Warnings for elastic document."""
 
-    FAILED_PERTURBATIONS: str = "failed_perturbations"
+    FAILED_PERTURBATIONS = "failed_perturbations"
 
 
 class ElasticDocument(StructureMetadata):

src/atomate2/common/schemas/qha.py

@@ -23,8 +23,7 @@ class PhononQHADoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
 
     temperatures: Optional[list[float]] = Field(
         None,
-        description="temperatures at which the vibrational"
-        " part of the free energies"
+        description="temperatures at which the vibrational part of the free energies"
         " and other properties have been computed",
     )
 
@@ -33,8 +32,8 @@ class PhononQHADoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     )
     thermal_expansion: Optional[list[float]] = Field(
         None,
-        description="Thermal expansion coefficients at temperatures."
-        "Shape=(temperatures, ). ",
+        description="Thermal expansion coefficients at temperatures. "
+        "Shape=(temperatures,).",
     )
     helmholtz_volume: Optional[list[list[float]]] = Field(
         None,
@@ -43,25 +42,24 @@ class PhononQHADoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     )
     volume_temperature: Optional[list[float]] = Field(
         None,
-        description="Volumes in Angstrom^3 at temperatures.Shape: (temperatures, )",
+        description="Volumes in Angstrom^3 at temperatures.Shape: (temperatures,)",
     )
     gibbs_temperature: Optional[list[float]] = Field(
         None,
-        description="Gibbs free energies in eV at temperatures."
-        "Shape: (temperatures, )",
+        description="Gibbs free energies in eV at temperatures. Shape: (temperatures,)",
     )
     bulk_modulus_temperature: Optional[list[float]] = Field(
         None,
-        description="Bulk modulus in GPa  at temperature.Shape: (temperatures, )",
+        description="Bulk modulus in GPa  at temperature.Shape: (temperatures,)",
     )
     heat_capacity_p_numerical: Optional[list[float]] = Field(
         None,
         description="Heat capacities in J/K/mol at constant pressure at temperatures."
-        "Shape: (temperatures, )",
+        "Shape: (temperatures,)",
     )
     gruneisen_temperature: Optional[list[float]] = Field(
         None,
-        description="Gruneisen parameters at temperatures.Shape: (temperatures, )",
+        description="Gruneisen parameters at temperatures.Shape: (temperatures,)",
     )
     pressure: Optional[float] = Field(
         None, description="Pressure in GPA at which Gibb's energy was computed"
@@ -75,17 +73,17 @@ class PhononQHADoc(StructureMetadata, extra="allow"):  # type: ignore[call-arg]
     free_energies: Optional[list[list[float]]] = Field(
         None,
         description="List of free energies in J/mol for per formula unit. "
-        "Shape: (temperatuers, volumes)",
+        "Shape: (temperatures, volumes)",
     )
     heat_capacities: Optional[list[list[float]]] = Field(
         None,
         description="List of heat capacities in J/K/mol  per formula unit. "
-        "Shape: (temperatuers, volumes)",
+        "Shape: (temperatures, volumes)",
     )
     entropies: Optional[list[list[float]]] = Field(
         None,
         description="List of entropies in J/(K*mol) per formula unit. "
-        "Shape: (temperatuers, volumes) ",
+        "Shape: (temperatures, volumes) ",
     )
     formula_units: Optional[int] = Field(None, description="Formula units")
 

src/atomate2/forcefields/flows/gruneisen.py

@@ -34,7 +34,7 @@ class GruneisenMaker(BaseGruneisenMaker):
     bulk_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker, .BaseVaspMaker, or None
         A maker to perform an initial tight relaxation on the bulk.
     code: str
-        determines the dft or force field code.
+        determines the DFT or force field code.
     const_vol_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker,
         .BaseVaspMaker, or None. A maker to perform a tight relaxation
         on the expanded and shrunk structures at constant volume.

src/atomate2/forcefields/flows/phonons.py

@@ -72,8 +72,8 @@ class PhononMaker(BasePhononMaker):
           High-throughput electronic band structure calculations:
           Challenges and tools. Computational Materials Science,
           49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.
-          We will however use seekpath and primitive structures
-          as determined by from phonopy to compute the phonon band structure
+          We will, however, use seekpath and primitive structures
+          as determined by phonopy to compute the phonon band structure
     bulk_relax_maker : .ForceFieldRelaxMaker or None
         A maker to perform a tight relaxation on the bulk.
         Set to ``None`` to skip the
@@ -101,7 +101,7 @@ class PhononMaker(BasePhononMaker):
         it relies on phonopy to handle the relationship
         to the primitive cell and not pymatgen
     code: str
-        determines the dft or force field code.
+        determines the DFT or force field code.
     store_force_constants: bool
         if True, force constants will be stored
     socket: bool

src/atomate2/forcefields/schemas.py

@@ -63,8 +63,7 @@ class ForceFieldTaskDocument(AseStructureTaskDoc):
     is_force_converged: Optional[bool] = Field(
         None,
         description=(
-            "Whether the calculation is converged with respect "
-            "to interatomic forces."
+            "Whether the calculation is converged with respect to interatomic forces."
         ),
     )
 

src/atomate2/openmm/jobs/generate.py

@@ -31,8 +31,7 @@
     from openff.units import unit
 except ImportError as e:
     raise ImportError(
-        "Using the atomate2.openmm.generate "
-        "module requires the openff-toolkit package."
+        "Using the atomate2.openmm.generate module requires the openff-toolkit package."
     ) from e
 
 

src/atomate2/utils/datetime.py

@@ -1,4 +1,4 @@
-"""Helper functions for datetime objects."""
+"""Helper functions for datetime objects."""  # noqa: A005
 
 from __future__ import annotations
 

src/atomate2/vasp/flows/gruneisen.py

@@ -38,7 +38,7 @@ class GruneisenMaker(BaseGruneisenMaker):
     bulk_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker, .BaseVaspMaker, or None
         A maker to perform an initial tight relaxation on the bulk.
     code: str
-        determines the dft or force field code.
+        determines the DFT or force field code.
     const_vol_relax_maker: .ForceFieldRelaxMaker, .BaseAimsMaker,
         .BaseVaspMaker, or None. A maker to perform a tight relaxation
         on the expanded and shrunk structures at constant volume.

src/atomate2/vasp/flows/phonons.py

@@ -79,8 +79,8 @@ class PhononMaker(BasePhononMaker):
           High-throughput electronic band structure calculations:
           Challenges and tools. Computational Materials Science,
           49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.
-          We will however use seekpath and primitive structures
-          as determined by from phonopy to compute the phonon band structure
+          We will, however, use seekpath and primitive structures
+          as determined by phonopy to compute the phonon band structure
     bulk_relax_maker : .BaseVaspMaker or None
         A maker to perform a tight relaxation on the bulk.
         Set to ``None`` to skip the

tests/abinit/conftest.py

@@ -158,8 +158,10 @@ def check_equivalent_frac_coords(
         len(find_in_coord_list_pbc(ref_frac_coords, coord, atol=atol)) > 0
         for coord in user_frac_coords
     ]
-    assert all(coord_match), f"The two structures have different frac. coords: \
+    assert all(coord_match), (
+        f"The two structures have different frac. coords: \
         {user_frac_coords} vs. {ref_frac_coords}."
+    )
 
 
 def check_equivalent_znucl_typat(
@@ -172,20 +174,20 @@ def check_equivalent_znucl_typat(
 
     sorted_znucl_a = sorted(znucl_a, reverse=True)
     sorted_znucl_b = sorted(znucl_b, reverse=True)
-    assert (
-        sorted_znucl_a == sorted_znucl_b
-    ), f"The elements are different: {znucl_a} vs. {znucl_b}"
+    assert sorted_znucl_a == sorted_znucl_b, (
+        f"The elements are different: {znucl_a} vs. {znucl_b}"
+    )
 
     count_sorted_znucl_a = [
         list(typat_a).count(list(znucl_a).index(s) + 1) for s in sorted_znucl_a
     ]
     count_sorted_znucl_b = [
         list(typat_b).count(list(znucl_b).index(s) + 1) for s in sorted_znucl_b
     ]
-    assert (
-        count_sorted_znucl_a == count_sorted_znucl_b
-    ), f"The number of same elements is different: \
+    assert count_sorted_znucl_a == count_sorted_znucl_b, (
+        f"The number of same elements is different: \
         {count_sorted_znucl_a} vs. {count_sorted_znucl_b}"
+    )
 
 
 def check_abinit_input_json(ref_path: str | Path):