Ruff

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,8 +10,7 @@ Include a summary of major changes in bullet points:
 * List all new dependencies needed and justify why. While adding dependencies that bring
   significantly useful functionality is perfectly fine, adding ones that add trivial
   functionality, e.g., to use one single easily implementable function, is frowned upon.
-  Provide a justification why that dependency is needed. Especially frowned upon are
-  circular dependencies.
+  Justify why that dependency is needed. Especially frowned upon are circular dependencies.
 
 ## TODO (if any)
 
@@ -26,20 +25,17 @@ title.
 
 Before a pull request can be merged, the following items must be checked:
 
-- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
+* [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
   The easiest way to handle this is to run the following in the **correct sequence** on
-  your local machine. Start with running [black](
-  https://black.readthedocs.io/en/stable/index.html) on your new code. This will
+  your local machine. Start with running [black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will
   automatically reformat your code to PEP8 conventions and removes most issues. Then run
-  [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by [flake8](
-  http://flake8.pycqa.org/en/latest/).
-- [ ] Docstrings have been added in the[Numpy docstring format](
-  https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html).
-  Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
-- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to
+  [ruff](https://ruff.rs).
+* [ ] Docstrings have been added in the [Numpy docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html).
+  Run [ruff](https://beta.ruff.rs/docs/rules/#pydocstyle-d) on your code.
+* [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org) to
   type check your code.
-- [ ] Tests have been added for any new functionality or bug fixes.
-- [ ] All linting and tests pass.
+* [ ] Tests have been added for any new functionality or bug fixes.
+* [ ] All linting and tests pass.
 
 Note that the CI system will run all the above checks. But it will be much more
 efficient if you already fix most errors prior to submitting the PR. It is highly

.pre-commit-config.yaml

@@ -2,6 +2,11 @@ default_language_version:
   python: python3
 exclude: '^src/atomate2/vasp/schemas/calc_types/'
 repos:
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.250
+  hooks:
+  - id: ruff
+    args: [--fix]
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.4.0
   hooks:
@@ -10,10 +15,6 @@ repos:
     args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/myint/autoflake
-  rev: v2.0.0
-  hooks:
-  - id: autoflake
 - repo: https://github.com/psf/black
   rev: 22.12.0
   hooks:
@@ -24,10 +25,6 @@ repos:
   - id: blacken-docs
     additional_dependencies: [black]
     exclude: README.md
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-  - id: isort
 - repo: https://github.com/pycqa/flake8
   rev: 6.0.0
   hooks:
@@ -63,8 +60,3 @@ repos:
   - id: codespell
     stages: [commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te']
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.3.1
-  hooks:
-    - id: pyupgrade
-      args: [--py38-plus]

docs/dev/dev_install.md

@@ -10,7 +10,7 @@ You can install the basic functionality of atomate2 using pip:
 pip install atomate2
 ```
 
-If you are planing to use atomate2 with fireworks, you can install the optional
+If you are planning to use atomate2 with fireworks, you can install the optional
 fireworks components:
 
 ```bash
@@ -39,7 +39,7 @@ You can also install fireworks dependencies:
 pip install .[fireworks]
 ```
 
-Or do a developer install by using the ``-e`` flag:
+Or do a developer install by using the `-e` flag:
 
 ```bash
 pip install -e .
@@ -50,13 +50,13 @@ pip install -e .
 If you're planning on contributing to the atomate2 source, you should also install
 the developer requirements with:
 
-```
+```bash
 pip install -e .[dev]
 pre-commit install
 ```
 
-The precommit command will ensure that changes to the source code match the
-atomate2 style guidelines by running code linters such as `black`, `isort`,
+The `pre-commit` command will ensure that changes to the source code match the
+atomate2 style guidelines by running code linters such as `black`, `ruff`,
 and `mypy` automatically with each commit.
 
 ## Running unit tests
@@ -76,8 +76,7 @@ pytest
 
 ## Building the documentation
 
-The atomate2 documentation can be built using the sphinx package. First, install the
-necessary requirement:
+The atomate2 documentation can be built using the sphinx package. First, install the requirements:
 
 ```bash
 pip install .[docs]

pyproject.toml

@@ -24,7 +24,7 @@ classifiers = [
     "Topic :: Scientific/Engineering",
 ]
 requires-python = ">=3.8"
-dependencies =[
+dependencies = [
     "pymatgen>=2022.8.23",
     "custodian>=2022.5.26",
     "pydantic",
@@ -47,7 +47,7 @@ docs = [
     "FireWorks==2.0.3",
     "autodoc_pydantic==1.8.0",
     "jupyter-book==0.13.1",
-    "jsonschema[format]"
+    "jsonschema[format]",
 ]
 dev = ["pre-commit>=2.12.1"]
 tests = ["pytest==7.2.1", "pytest-cov==4.0.0", "FireWorks==2.0.3"]
@@ -86,9 +86,6 @@ atomate2 = ["py.typed"]
 method = "git"
 default-tag = "0.0.1"
 
-[tool.isort]
-profile = "black"
-
 [tool.flake8]
 max-line-length = 88
 max-doc-length = 88
@@ -128,9 +125,47 @@ exclude_lines = [
     '^\s*@overload( |$)',
 ]
 
-[tool.autoflake]
-in-place = true
-remove-all-unused-imports = true
-remove-unused-variables = true
-ignore-init-module-imports = true
-expand-star-imports = true
+[tool.ruff]
+target-version = "py38"
+select = [
+    "B",   # flake8-bugbear
+    "C4",  # flake8-comprehensions
+    "D",   # pydocstyle
+    "E",   # pycodestyle
+    "F",   # pyflakes
+    "I",   # isort
+    "PLE", # pylint error
+    "PLW", # pylint warning
+    "Q",   # flake8-quotes
+    "RUF", # Ruff-specific rules
+    "SIM", # flake8-simplify
+    "TID", # tidy imports
+    "UP",  # pyupgrade
+    "W",   # pycodestyle
+    "YTT", # flake8-2020
+]
+ignore = [
+    "B019",    # functools.lru_cache on methods can lead to memory leaks
+    "B023",    # Function definition does not bind loop variable
+    "B904",    # Within an except clause, raise exceptions with ...
+    "D100",    # Missing docstring in public module
+    "D104",    # Missing docstring in public package
+    "D105",    # Missing docstring in magic method
+    "D107",    # Missing docstring in __init__
+    "D200",    # One-line docstring should fit on one line with quotes
+    "D205",    # 1 blank line required between summary line and description
+    "D212",    # Multi-line docstring summary should start at the first line
+    "D415",    # First line should end with a period, question mark, or exclamation point
+    "E741",    # tmp: we should fix all ambiguous variable names
+    "PLR2004", # Magic number
+    "PLW0120", # awaiting bug fix https://github.com/charliermarsh/ruff/issues/3019
+    "C408",    # Unnecessary dict call - rewrite as a literal
+    "D416",    # Section name should end with a colon
+    "SIM105",  # Use contextlib.suppress(socket.gaierror, socket.herror) instead of try-except-pass
+]
+pydocstyle.convention = "google"
+isort.known-first-party = ["atomate2"]
+
+[tool.ruff.per-file-ignores]
+"__init__.py" = ["F401"]
+"**/tests/*" = ["D"]

src/atomate2/amset/schemas.py

@@ -132,7 +132,7 @@ class AmsetTaskDocument(StructureMetadata):
     scattering_labels: List[str] = Field(
         None, description="The scattering types used in the calculation"
     )
-    soc: bool = Field(None, description="Whether spin–orbit coupling was included")
+    soc: bool = Field(None, description="Whether spin-orbit coupling was included")
     structure: Structure = Field(None, description="The structure used in this task")
     _schema: str = Field(
         __version__,

src/atomate2/cli/dev.py

@@ -115,7 +115,7 @@ def vasp_test_data(test_dir):
         [f"  {v}  ->  {k}" for k, v in original_mapping.items()]
     )
 
-    run_vasp_kwargs = {k: {"incar_settings": ["NSW", "ISMEAR"]} for k in mapping.keys()}
+    run_vasp_kwargs = {k: {"incar_settings": ["NSW", "ISMEAR"]} for k in mapping}
     run_vasp_kwargs_str = pformat(run_vasp_kwargs).replace("\n", "\n    ")
 
     test_function_str = f"""Test files generated in test_data.

src/atomate2/common/analysis/defects/schemas.py

@@ -291,11 +291,9 @@ def get_dQ(ref: Structure, distorted: Structure) -> float:
     """
     return np.sqrt(
         np.sum(
-            list(
-                map(
-                    lambda x: x[0].distance(x[1]) ** 2 * x[0].specie.atomic_mass,
-                    zip(ref, distorted),
-                )
-            )
+            [
+                x[0].distance(x[1]) ** 2 * x[0].specie.atomic_mass
+                for x in zip(ref, distorted)
+            ]
         )
     )

src/atomate2/common/files.py

@@ -357,11 +357,7 @@ def get_zfile(
         found, then ``None`` will be returned.
     """
     for file in directory_listing:
-        if base_name == file.name:
-            return file
-        elif base_name + ".gz" == file.name:
-            return file
-        elif base_name + ".GZ" == file.name:
+        if base_name in [file.name, file.name + ".gz", file.name + ".GZ"]:
             return file
 
     if allow_missing:

src/atomate2/common/jobs.py

@@ -106,7 +106,6 @@ def retrieve_structure_from_materials_project(
         and also the database version and specific task_id
         corresponding to that Structure object also stored
     """
-
     # inline import to avoid required dependency
     try:
         from mp_api.client import MPRester
@@ -132,14 +131,13 @@ def retrieve_structure_from_materials_project(
 
     structure = doc.structure
 
-    if reset_magnetic_moments:
+    if reset_magnetic_moments and "magmom" in structure.site_properties:
         # Materials Project stores magnetic moments via the `magmom` site property
         # and we can safely assume that here. In general, since magnetic order
         # can be represented in multiple ways such as Species.spin, the
         # following method would be better:
         # CollinearMagneticStructureAnalyzer.get_nonmagnetic_structure()
-        if "magmom" in structure.site_properties:
-            structure.remove_site_property("magmom")
+        structure.remove_site_property("magmom")
 
     return Response(
         output=structure,

src/atomate2/common/schemas/cclib.py

@@ -155,10 +155,9 @@ def from_logfile(
             metadata["cpu_time"] = [str(m) for m in metadata["cpu_time"]]
 
         # Get the final energy to store as its own key/value pair
-        if cclib_obj.scfenergies is not None:
-            energy = cclib_obj.scfenergies[-1]
-        else:
-            energy = None
+        energy = (
+            cclib_obj.scfenergies[-1] if cclib_obj.scfenergies is not None else None
+        )
 
         # Now we construct the input molecule. Note that this is not necessarily
         # the same as the initial molecule from the relaxation because the

src/atomate2/common/schemas/elastic.py

@@ -85,7 +85,7 @@ class FittingData(BaseModel):
         None, description="The strains used to fit the elastic tensor."
     )
     pk_stresses: List[Matrix3D] = Field(
-        None, description="The Piola–Kirchoff stresses used to fit the elastic tensor."
+        None, description="The Piola-Kirchoff stresses used to fit the elastic tensor."
     )
     deformations: List[Matrix3D] = Field(
         None, description="The deformations corresponding to each strain state."

src/atomate2/utils/file_client.py

@@ -488,7 +488,7 @@ def get_ssh_connection(
         # try reading ssh config file
         ssh_config = paramiko.SSHConfig().from_path(str(config_filename))
 
-        host_config = ssh_config.lookup(hostname)
+        host_config = ssh_config.lookup(hostname)  # type: ignore[attr-defined]
         for k in ("hostname", "user", "port"):
             if k in host_config:
                 config[k.replace("user", "username")] = host_config[k]

src/atomate2/vasp/files.py

@@ -61,7 +61,7 @@ def copy_vasp_outputs(
     directory_listing = file_client.listdir(src_dir, host=src_host)
 
     # find required files
-    files = ("INCAR", "OUTCAR", "CONTCAR", "vasprun.xml") + tuple(additional_vasp_files)
+    files = ("INCAR", "OUTCAR", "CONTCAR", "vasprun.xml", *additional_vasp_files)
     required_files = [get_zfile(directory_listing, r + relax_ext) for r in files]
 
     # find optional files; do not fail if KPOINTS is missing, this might be KSPACING

src/atomate2/vasp/flows/defect.py

@@ -43,6 +43,18 @@
 
 @dataclass
 class ConfigurationCoordinateMaker(BaseCCDMaker):
+    """Maker to calculate the configuration coordinate diagram.
+
+    Parameters
+    ----------
+    name: str
+        The name of the flow created by this maker.
+    relax_maker: BaseVaspMaker
+        A maker to perform the relaxation of the defect.
+    static_maker: BaseVaspMaker
+        A maker to perform the static calculation of the defect.
+    """
+
     relax_maker: BaseVaspMaker = field(
         default_factory=lambda: RelaxMaker(
             input_set_generator=DEFECT_RELAX_GENERATOR,

src/atomate2/vasp/jobs/phonons.py

@@ -93,10 +93,7 @@ def get_supercell_size(
         transformation.apply_transformation(structure=structure)
 
     else:
-        if "max_atoms" not in kwargs:
-            max_atoms = 1000
-        else:
-            max_atoms = kwargs["max_atoms"]
+        max_atoms = 1000 if "max_atoms" not in kwargs else kwargs["max_atoms"]
         if "angle_tolerance" not in kwargs:
             kwargs["angle_tolerance"] = 1e-2
         try:

src/atomate2/vasp/run.py

@@ -152,7 +152,7 @@ def run_vasp(
         raise ValueError(f"Unsupported job type: {job_type}")
 
     if wall_time is not None:
-        handlers = list(handlers) + [WalltimeHandler(wall_time=wall_time)]
+        handlers = [*handlers, WalltimeHandler(wall_time=wall_time)]
 
     c = Custodian(
         handlers,

src/atomate2/vasp/schemas/calc_types/utils.py

@@ -28,10 +28,7 @@ def run_type(vasp_parameters: Dict) -> RunType:
     RunType
         The run type.
     """
-    if vasp_parameters.get("LDAU", False):
-        is_hubbard = "+U"
-    else:
-        is_hubbard = ""
+    is_hubbard = "+U" if vasp_parameters.get("LDAU", False) else ""
 
     def _variant_equal(v1, v2) -> bool:
         """Check two strings equal."""

src/atomate2/vasp/schemas/calculation.py

@@ -55,7 +55,7 @@
 ]
 
 
-_BADER_EXE_EXISTS = True if (which("bader") or which("bader.exe")) else False
+_BADER_EXE_EXISTS = bool(which("bader") or which("bader.exe"))
 
 
 class Status(ValueEnum):