Fix all ruff PT011 (not checking error message when testing exception…

…s) (#698)

* bump ruff pre-commit to v0.1.15

* ruff auto fixes

* fix all ruff PT011 and unignore that rule

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3
 repos:
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.1.13
+  rev: v0.1.15
   hooks:
   - id: ruff
     args: [--fix]

pyproject.toml

@@ -148,37 +148,35 @@ exclude_lines = [
 target-version = "py39"
 select = ["ALL"]
 ignore = [
-    "ARG002",  # unused method argument
-    "COM812",  # trailing comma missing
-    "PD011",   # pandas-use-of-dot-values
-    "PERF203", # try-except-in-loop
-    "PLR",     # pylint-refactor
-    "PT004",   # pytest-missing-fixture-name-underscore
-    "PT006",   # pytest-parametrize-names-wrong-type
-    "RUF013",  # implicit-optional
-    # TODO remove PT011, pytest.raises() should always check err msg
     "ANN002",
     "ANN003",
-    "ANN101", # missing self type annotation
+    "ANN101",  # missing self type annotation
     "ANN102",
     "ANN401",
+    "ARG002",  # unused method argument
     "BLE001",
-    "C408",   # Unnecessary (dict/list/tuple) call - remove call
-    "C901",   # function too complex
-    "DTZ",    # datetime-tz-now
-    "EM",     # exception message must not use f-string literal
-    "ERA001", # found commented out code
+    "C408",    # Unnecessary (dict/list/tuple) call - remove call
+    "C901",    # function too complex
+    "COM812",  # trailing comma missing
+    "DTZ",     # datetime-tz-now
+    "EM",      # exception message must not use f-string literal
+    "ERA001",  # found commented out code
     "FBT001",
     "FBT002",
     "FIX002",
-    "G004",   # logging uses fstring
-    "PT011",  # pytest-raises-too-broad
-    "PT013",  # pytest-incorrect-pytest-import
-    "PTH",    # prefer Pathlib to os.path
-    "S324",   # use of insecure hash function
-    "SLF",    # private member accessed outside class
-    "TD",     # TODOs
-    "TRY003", # long message outside exception class
+    "G004",    # logging uses fstring
+    "PD011",   # pandas-use-of-dot-values
+    "PERF203", # try-except-in-loop
+    "PLR",     # pylint-refactor
+    "PT004",   # pytest-missing-fixture-name-underscore
+    "PT006",   # pytest-parametrize-names-wrong-type
+    "PT013",   # pytest-incorrect-pytest-import
+    "PTH",     # prefer Pathlib to os.path
+    "RUF013",  # implicit-optional
+    "S324",    # use of insecure hash function
+    "SLF",     # private member accessed outside class
+    "TD",      # TODOs
+    "TRY003",  # long message outside exception class
 ]
 pydocstyle.convention = "numpy"
 isort.known-first-party = ["atomate2"]

src/atomate2/common/schemas/defects.py

@@ -2,6 +2,7 @@
 
 import logging
 from collections.abc import Sequence
+from itertools import starmap
 from typing import Any, Callable, Optional, Union
 
 import numpy as np
@@ -237,7 +238,7 @@ def from_task_outputs(
             UUID of relaxed calculation in charge state (q2).
         """
 
-        def get_ent(
+        def get_cs_entry(
             struct: Structure,
             energy: float,
             dir_name: str,
@@ -249,14 +250,16 @@ def get_ent(
                 data={"dir_name": dir_name, "uuid": uuid},
             )
 
-        entries1 = [
-            get_ent(s, e, d, u)
-            for s, e, d, u in zip(structures1, energies1, static_dirs1, static_uuids1)
-        ]
-        entries2 = [
-            get_ent(s, e, d, u)
-            for s, e, d, u in zip(structures2, energies2, static_dirs2, static_uuids2)
-        ]
+        entries1 = list(
+            starmap(
+                get_cs_entry, zip(structures1, energies1, static_dirs1, static_uuids1)
+            )
+        )
+        entries2 = list(
+            starmap(
+                get_cs_entry, zip(structures2, energies2, static_dirs2, static_uuids2)
+            )
+        )
 
         return cls.from_entries(entries1, entries2, relaxed_uuid1, relaxed_uuid2)
 

src/atomate2/cp2k/sets/base.py

@@ -106,14 +106,14 @@ def write_input(
         }
         inputs.update(self.optional_files)
 
-        for k, v in inputs.items():
-            fn = v.get("filename")
-            obj = v.get("object")
-            if v is not None and (overwrite or not (directory / k).exists()):
-                with zopen(directory / fn, "wt") as f:
-                    f.write(str(obj))
-            elif not overwrite and (directory / fn).exists():
-                raise FileExistsError(f"{directory / fn} already exists.")
+        for key, val in inputs.items():
+            filename = val.get("filename")
+            obj = val.get("object")
+            if val is not None and (overwrite or not (directory / key).exists()):
+                with zopen(directory / filename, "wt") as file:
+                    file.write(str(obj))
+            elif not overwrite and (directory / filename).exists():
+                raise FileExistsError(f"{directory / filename} already exists.")
 
     @staticmethod
     def from_directory(

src/atomate2/forcefields/utils.py

@@ -114,18 +114,16 @@ def save(self, filename: str | PathLike) -> None:
         -------
             None
         """
-        with open(filename, "wb") as f:
-            pickle.dump(
-                {
-                    "energy": self.energies,
-                    "forces": self.forces,
-                    "stresses": self.stresses,
-                    "atom_positions": self.atom_positions,
-                    "cell": self.cells,
-                    "atomic_number": self.atoms.get_atomic_numbers(),
-                },
-                f,
-            )
+        traj_dict = {
+            "energy": self.energies,
+            "forces": self.forces,
+            "stresses": self.stresses,
+            "atom_positions": self.atom_positions,
+            "cell": self.cells,
+            "atomic_number": self.atoms.get_atomic_numbers(),
+        }
+        with open(filename, "wb") as file:
+            pickle.dump(traj_dict, file)
 
 
 class Relaxer:

src/atomate2/lobster/schemas.py

@@ -766,10 +766,7 @@ def from_directory(
 
         # Do automatic bonding analysis with LobsterPy
         condensed_bonding_analysis = None
-        sb_icobi = None
-        sb_icohp = None
-        sb_icoop = None
-        describe = None
+        sb_icobi = sb_icohp = sb_icoop = describe = None
         struct = Structure.from_file(structure_path)
 
         # will perform two condensed bonding analysis computations
@@ -1066,7 +1063,7 @@ def from_directory(
                     are_coops=False,
                     are_cobis=False,
                 )
-                doc.__setattr__("cohp_data", cohp_obj)
+                doc.cohp_data = cohp_obj
 
             if coopcar_path.exists() and doc.coop_data is None:
                 coop_obj = CompleteCohp.from_file(
@@ -1076,7 +1073,7 @@ def from_directory(
                     are_coops=True,
                     are_cobis=False,
                 )
-                doc.__setattr__("coop_data", coop_obj)
+                doc.coop_data = coop_obj
 
             if cobicar_path.exists() and doc.cobi_data is None:
                 cobi_obj = CompleteCohp.from_file(
@@ -1086,7 +1083,7 @@ def from_directory(
                     are_coops=False,
                     are_cobis=True,
                 )
-                doc.__setattr__("cobi_data", cobi_obj)
+                doc.cobi_data = cobi_obj
             with gzip.open(
                 computational_data_json_save_dir, "wt", encoding="UTF-8"
             ) as file:
@@ -1099,7 +1096,7 @@ def from_directory(
                         # objects and other data json compatible dict format
                         data = {
                             attribute: jsanitize(
-                                doc.__getattribute__(attribute),
+                                getattr(doc, attribute),
                                 allow_bson=False,
                                 strict=True,
                                 enum_values=True,
@@ -1113,9 +1110,9 @@ def from_directory(
 
             # Again unset the cohp, cobi and coop data fields if not desired in the DB
             if not add_coxxcar_to_task_document:
-                doc.__setattr__("cohp_data", None)
-                doc.__setattr__("coop_data", None)
-                doc.__setattr__("cobi_data", None)
+                doc.cohp_data = None
+                doc.coop_data = None
+                doc.cobi_data = None
 
         return doc.model_copy(update=additional_fields)
 
@@ -1316,9 +1313,9 @@ def read_saved_json(
     dict
         Returns a dictionary with lobster task json data corresponding to query.
     """
-    with gzip.open(filename, "rb") as f:
+    with gzip.open(filename, "rb") as file:
         lobster_data = {}
-        objects = ijson.items(f, "item", use_float=True)
+        objects = ijson.items(file, "item", use_float=True)
         for obj in objects:
             if query is None:
                 for field, data in obj.items():
@@ -1339,11 +1336,9 @@ def read_saved_json(
                 lobster_data[query_key] = MontyDecoder().process_decoded(value)
             elif "lobsterpy_data" in query_key:
                 for field in lobster_data[query_key].__fields__:
-                    lobster_data[query_key].__setattr__(
-                        field,
-                        MontyDecoder().process_decoded(
-                            lobster_data[query_key].__getattribute__(field)
-                        ),
+                    val = MontyDecoder().process_decoded(
+                        getattr(lobster_data[query_key], field)
                     )
+                    setattr(lobster_data[query_key], field, val)
 
     return lobster_data

src/atomate2/utils/file_client.py

@@ -411,7 +411,7 @@ def gzip(
             path.unlink()
         else:
             ssh = self.get_ssh(host)
-            _, stdout, _ = ssh.exec_command(f"gzip -f {path!s}")
+            _, _stdout, _ = ssh.exec_command(f"gzip -f {path!s}")
 
     def gunzip(
         self,

src/atomate2/vasp/flows/mp.py

@@ -232,9 +232,7 @@ class MPVaspLobsterMaker(VaspLobsterMaker):
     """
 
     name: str = "lobster"
-    relax_maker: BaseVaspMaker | None = field(
-        default_factory=lambda: MPGGADoubleRelaxMaker()
-    )
+    relax_maker: BaseVaspMaker | None = field(default_factory=MPGGADoubleRelaxMaker)
     lobster_static_maker: BaseVaspMaker = field(
         default_factory=lambda: MPGGAStaticMaker(
             input_set_generator=MPGGAStaticSetGenerator(
@@ -254,7 +252,7 @@ class MPVaspLobsterMaker(VaspLobsterMaker):
             )
         )
     )
-    lobster_maker: LobsterMaker | None = field(default_factory=lambda: LobsterMaker())
+    lobster_maker: LobsterMaker | None = field(default_factory=LobsterMaker)
     delete_wavecars: bool = True
     address_min_basis: str | None = None
     address_max_basis: str | None = None

src/atomate2/vasp/sets/base.py

@@ -109,7 +109,7 @@ def write_input(
                         # write POSCAR with more significant figures
                         file.write(val.get_str(significant_figures=16))
                     else:
-                        file.write(val.__str__())
+                        file.write(str(val))
             elif not overwrite and (directory / key).exists():
                 raise FileExistsError(f"{directory / key} already exists.")
 

tests/common/schemas/test_cclib.py

@@ -48,12 +48,11 @@ def test_cclib_taskdoc(test_dir):
 
     # Now we will try two possible extensions, but we will make sure that
     # it fails because the newest log file (.txt) is not valid
-    with open(p / "test.txt", "w") as f:
-        f.write("I am a dummy log file")
-    with pytest.raises(Exception) as e:
+    with open(p / "test.txt", "w") as file:
+        file.write("I am a dummy log file")
+    with pytest.raises(ValueError, match="Could not parse"):
         doc = TaskDocument.from_logfile(p, [".log", ".txt"]).dict()
     os.remove(p / "test.txt")
-    assert "Could not parse" in str(e.value)
 
     # Test a population analysis
     doc = TaskDocument.from_logfile(p, "psi_test.out", analysis="MBO").dict()

tests/forcefields/test_utils.py

@@ -93,8 +93,7 @@ def test_relaxer(si_structure, test_dir, tmp_dir, optimizer, traj_file):
         ]
 
     if optimizer is None:
-        # None is invalid, should raise ValueError
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match="Optimizer cannot be None"):
             Relaxer(calculator=LennardJones(), optimizer=optimizer)
         return
 

tests/vasp/flows/test_phonons.py

@@ -755,7 +755,10 @@ def test_phonon_wf_only_displacements_kpath_raises_no_cell_change(
     # automatically use fake VASP and write POTCAR.spec during the test
     mock_vasp(ref_paths, fake_run_vasp_kwargs)
 
-    with pytest.raises(ValueError):
+    with pytest.raises(
+        ValueError,
+        match="can only use other kpath schemes with the primitive standard structure",
+    ):
         PhononMaker(
             min_length=3.0,
             bulk_relax_maker=None,
@@ -785,7 +788,7 @@ def test_phonon_wf_only_displacements_kpath_raises(mock_vasp, clean_dir, kpath_s
 
     # automatically use fake VASP and write POTCAR.spec during the test
     mock_vasp(ref_paths, fake_run_vasp_kwargs)
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match="can only use other kpath schemes with the"):
         PhononMaker(
             min_length=3.0,
             bulk_relax_maker=None,