Merge pull request #464 from materialsproject/match-atomate2-ruff-config

Match `atomate2` `ruff` config

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 exclude: "^src/atomate2/vasp/schemas/calc_types/"
 repos:
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.1.0
+    rev: v0.1.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -46,7 +46,7 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.0
+    rev: v1.6.1
     hooks:
       - id: mypy
         files: ^src/

examples/data_store.py

@@ -17,8 +17,7 @@ def generate_big_data():
     The data=True in the job decorator tells jobflow to store all outputs in the "data"
     additional store.
     """
-    mydata = list(range(1000))
-    return mydata
+    return list(range(1000))
 
 
 big_data_job = generate_big_data()

pyproject.toml

@@ -121,26 +121,56 @@ exclude_lines = [
 target-version = "py39"
 ignore-init-module-imports = true
 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
+    "B",      # flake8-bugbear
+    "C4",     # flake8-comprehensions
+    "D",      # pydocstyle
+    "E",      # pycodestyle error
+    "EXE",    # flake8-executable
+    "F",      # pyflakes
+    "FA",     # flake8-future-annotations
+    "FBT003", # boolean-positional-value-in-call
+    "FLY",    # flynt
+    "I",      # isort
+    "ICN",    # flake8-import-conventions
+    "ISC",    # flake8-implicit-str-concat
+    "PD",     # pandas-vet
+    "PERF",   # perflint
+    "PIE",    # flake8-pie
+    "PL",     # pylint
+    "PT",     # flake8-pytest-style
+    "PYI",    # flakes8-pyi
+    "Q",      # flake8-quotes
+    "RET",    # flake8-return
+    "RSE",    # flake8-raise
+    "RUF",    # Ruff-specific rules
+    "SIM",    # flake8-simplify
+    "SLOT",   # flake8-slots
+    "TCH",    # flake8-type-checking
+    "TID",    # flake8-tidy-imports
+    "UP",     # pyupgrade
+    "W",      # pycodestyle warning
+    "YTT",    # flake8-2020
+]
+# PLR0911: too-many-return-statements
+# PLR0912: too-many-branches
+# PLR0913: too-many-arguments
+# PLR0915: too-many-statements
+ignore = [
+    "B028",
+    "PLR0911",
+    "PLR0912",
+    "PLR0913",
+    "PLR0915",
+    "PLW0603",
+    "RUF013",
 ]
-ignore = ["B028", "PLW0603", "RUF013"]
 pydocstyle.convention = "numpy"
 isort.known-first-party = ["jobflow"]
 
 [tool.ruff.per-file-ignores]
 "__init__.py" = ["F401"]
-"**/tests/*" = ["B018", "D"]
+# PLR2004: magic-value-comparison
+# PT004: pytest-missing-fixture-name-underscore
+# PLR0915: too-many-statements
+# PT011: pytest-raises-too-broad TODO fix these, should not be ignored
+"**/tests/*" = ["B018", "D", "PLR0915", "PLR2004", "PT004", "PT011"]

src/jobflow/core/flow.py

@@ -4,7 +4,6 @@
 
 import logging
 import warnings
-from collections.abc import Sequence
 from copy import deepcopy
 from typing import TYPE_CHECKING
 
@@ -15,7 +14,7 @@
 from jobflow.utils import ValueEnum, contains_flow_or_job, suuid
 
 if TYPE_CHECKING:
-    from collections.abc import Iterator
+    from collections.abc import Iterator, Sequence
     from typing import Any, Callable
 
     from networkx import DiGraph

src/jobflow/core/reference.py

@@ -4,7 +4,6 @@
 
 import contextlib
 import typing
-from collections.abc import Sequence
 from typing import Any
 
 from monty.json import MontyDecoder, MontyEncoder, MSONable, jsanitize
@@ -14,6 +13,8 @@
 from jobflow.utils.enum import ValueEnum
 
 if typing.TYPE_CHECKING:
+    from collections.abc import Sequence
+
     import jobflow
 
 
@@ -88,14 +89,14 @@ def __init__(
         uuid: str,
         attributes: tuple[tuple[str, Any], ...] = (),
         output_schema: type[BaseModel] = None,
-    ):
+    ) -> None:
         super().__init__()
         self.uuid = uuid
         self.attributes = attributes
         self.output_schema = output_schema
 
         for attr_type, attr in attributes:
-            if attr_type not in ("a", "i"):
+            if attr_type not in {"a", "i"}:
                 raise ValueError(
                     f"Unrecognised attribute type '{attr_type}' for attribute '{attr}'"
                 )
@@ -161,9 +162,9 @@ def resolve(
                 f"Could not resolve reference - {self.uuid}{istr} not in store or "
                 f"{index=}, {cache=}"
             )
-        elif on_missing == OnMissing.NONE and index not in cache[self.uuid]:
+        if on_missing == OnMissing.NONE and index not in cache[self.uuid]:
             return None
-        elif on_missing == OnMissing.PASS and index not in cache[self.uuid]:
+        if on_missing == OnMissing.PASS and index not in cache[self.uuid]:
             return self
 
         data = cache[self.uuid][index]
@@ -200,12 +201,11 @@ def set_uuid(self, uuid: str, inplace=True) -> OutputReference:
         if inplace:
             self.uuid = uuid
             return self
-        else:
-            from copy import deepcopy
+        from copy import deepcopy
 
-            new_reference = deepcopy(self)
-            new_reference.uuid = uuid
-            return new_reference
+        new_reference = deepcopy(self)
+        new_reference.uuid = uuid
+        return new_reference
 
     def __getitem__(self, item) -> OutputReference:
         """Index the reference."""
@@ -263,7 +263,7 @@ def __hash__(self) -> int:
         """Return a hash of the reference."""
         return hash(str(self))
 
-    def __eq__(self, other: Any) -> bool:
+    def __eq__(self, other: object) -> bool:
         """Test for equality against another reference."""
         if isinstance(other, OutputReference):
             return (
@@ -285,15 +285,14 @@ def as_dict(self):
         """Serialize the reference as a dict."""
         schema = self.output_schema
         schema_dict = MontyEncoder().default(schema) if schema is not None else None
-        data = {
+        return {
             "@module": self.__class__.__module__,
             "@class": type(self).__name__,
             "@version": None,
             "uuid": self.uuid,
             "attributes": self.attributes,
             "output_schema": schema_dict,
         }
-        return data
 
 
 def resolve_references(
@@ -376,7 +375,7 @@ def find_and_get_references(arg: Any) -> tuple[OutputReference, ...]:
         # if the argument is a reference then stop there
         return (arg,)
 
-    elif isinstance(arg, (float, int, str, bool)):
+    if isinstance(arg, (float, int, str, bool)):
         # argument is a primitive, we won't find a reference here
         return ()
 
@@ -432,7 +431,7 @@ def find_and_resolve_references(
         # if the argument is a reference then stop there
         return arg.resolve(store, cache=cache, on_missing=on_missing)
 
-    elif isinstance(arg, (float, int, str, bool)):
+    if isinstance(arg, (float, int, str, bool)):
         # argument is a primitive, we won't find a reference here
         return arg
 

src/jobflow/core/state.py

@@ -15,8 +15,6 @@
 from monty.design_patterns import singleton
 
 if typing.TYPE_CHECKING:
-    pass
-
     import jobflow
 
 

src/jobflow/core/store.py

@@ -8,7 +8,6 @@
 from monty.json import MSONable
 
 from jobflow.core.reference import OnMissing
-from jobflow.schemas.job_output_schema import JobStoreDocument
 from jobflow.utils.find import get_root_locations
 
 if typing.TYPE_CHECKING:
@@ -19,6 +18,8 @@
 
     from maggma.core import Sort
 
+    from jobflow.schemas.job_output_schema import JobStoreDocument
+
     obj_type = Union[str, Enum, type[MSONable], list[Union[Enum, str, type[MSONable]]]]
     save_type = Optional[dict[str, obj_type]]
     load_type = Union[bool, dict[str, Union[bool, obj_type]]]
@@ -250,8 +251,7 @@ def query_one(
         docs = self.query(
             criteria=criteria, properties=properties, load=load, sort=sort, limit=1
         )
-        d = next(docs, None)
-        return d
+        return next(docs, None)
 
     def update(
         self,
@@ -496,7 +496,7 @@ def get_output(
         #       this could be fixed but will require more complicated logic just to
         #       catch a very unlikely event.
 
-        if isinstance(which, int) or which in ("last", "first"):
+        if isinstance(which, int) or which in {"last", "first"}:
             sort = -1 if which == "last" else 1
 
             criteria: dict[str, Any] = {"uuid": uuid}
@@ -522,28 +522,27 @@ def get_output(
             return find_and_resolve_references(
                 result["output"], self, cache=cache, on_missing=on_missing
             )
-        else:
-            results = list(
-                self.query(
-                    criteria={"uuid": uuid},
-                    properties=["output"],
-                    sort={"index": 1},
-                    load=load,
-                )
+        results = list(
+            self.query(
+                criteria={"uuid": uuid},
+                properties=["output"],
+                sort={"index": 1},
+                load=load,
             )
+        )
 
-            if len(results) == 0:
-                raise ValueError(f"UUID: {uuid} has no outputs.")
+        if len(results) == 0:
+            raise ValueError(f"UUID: {uuid} has no outputs.")
 
-            results = [r["output"] for r in results]
+        results = [r["output"] for r in results]
 
-            refs = find_and_get_references(results)
-            if any(ref.uuid == uuid for ref in refs):
-                raise RuntimeError("Reference cycle detected - aborting.")
+        refs = find_and_get_references(results)
+        if any(ref.uuid == uuid for ref in refs):
+            raise RuntimeError("Reference cycle detected - aborting.")
 
-            return find_and_resolve_references(
-                results, self, cache=cache, on_missing=on_missing
-            )
+        return find_and_resolve_references(
+            results, self, cache=cache, on_missing=on_missing
+        )
 
     @classmethod
     def from_file(cls: type[T], db_file: str | Path, **kwargs) -> T:
@@ -761,7 +760,7 @@ def _group_blobs(infos, locs):
 
     new_blobs = []
     new_locations = []
-    for _store_name, store_load in load.items():
+    for store_load in load.values():
         for blob, location in zip(blob_infos, locations):
             if store_load is True:
                 new_blobs.append(blob)

src/jobflow/managers/fireworks.py

@@ -10,6 +10,7 @@
     from collections.abc import Sequence
 
     import jobflow
+    from jobflow.core.job import Job
 
 
 def flow_to_workflow(
@@ -146,7 +147,6 @@ class JobFiretask(FiretaskBase):
     def run_task(self, fw_spec):
         """Run the job and handle any dynamic firework submissions."""
         from jobflow import SETTINGS, initialize_logger
-        from jobflow.core.job import Job
 
         job: Job = self.get("job")
         store = self.get("store")
@@ -190,11 +190,10 @@ def run_task(self, fw_spec):
             else:
                 detours = [detour_wf]
 
-        fwa = FWAction(
+        return FWAction(
             stored_data=response.stored_data,
             detours=detours,
             additions=additions,
             defuse_workflow=response.stop_jobflow,
             defuse_children=response.stop_children,
         )
-        return fwa

src/jobflow/managers/local.py

@@ -6,8 +6,6 @@
 import typing
 
 if typing.TYPE_CHECKING:
-    pass
-
     import jobflow
 
 
@@ -133,17 +131,15 @@ def _run_job(job: jobflow.Job, parents):
 
         if not all(diversion_responses):
             return None, False
-        else:
-            return response, False
+        return response, False
 
     def _get_job_dir():
         if create_folders:
             time_now = datetime.utcnow().strftime(SETTINGS.DIRECTORY_FORMAT)
             job_dir = root_dir / f"job_{time_now}-{randint(10000, 99999)}"
             job_dir.mkdir()
             return job_dir
-        else:
-            return root_dir
+        return root_dir
 
     def _run(root_flow):
         encountered_bad_response = False

src/jobflow/utils/enum.py

@@ -14,8 +14,7 @@ def __eq__(self, other):
         """Compare to another enum for equality."""
         if type(self) == type(other) and self.value == other.value:
             return True
-        else:
-            return str(self.value) == str(other)
+        return str(self.value) == str(other)
 
     def __hash__(self):
         """Get a hash of the enum."""