more descriptive variable names

src/atomate2/aims/jobs/convergence.py

@@ -102,8 +102,8 @@ def make(
         if prev_dir is not None:
             split_prev_dir = str(prev_dir).split(":")[-1]
             convergence_file = Path(split_prev_dir) / CONVERGENCE_FILE_NAME
-            with open(convergence_file, "w") as f:
-                json.dump(convergence_data, f)
+            with open(convergence_file, "w") as file:
+                json.dump(convergence_data, file)
 
         if idx < len(self.convergence_steps) and not converged:
             # finding next jobs

src/atomate2/aims/schemas/task.py

@@ -332,8 +332,8 @@ def from_aims_calc_doc(cls, calc_doc: Calculation) -> Self:
                 " in {calc_doc.dir_name}"
             )
 
-        with open(convergence_file) as f:
-            convergence_data = json.load(f)
+        with open(convergence_file) as file:
+            convergence_data = json.load(file)
 
         return cls(
             structure=calc_doc.output.structure,

src/atomate2/amset/schemas.py

@@ -191,8 +191,8 @@ def from_directory(
             }
             if include_mesh:
                 # remove duplicated data
-                for k in ("doping", "temperatures", "fermi_levels", "structure"):
-                    mesh.pop(k)
+                for key in ("doping", "temperatures", "fermi_levels", "structure"):
+                    mesh.pop(key)
 
                 mesh_kwargs["mesh"] = cast_dict_list(mesh)
 

src/atomate2/cli/dev.py

@@ -141,7 +141,7 @@ def vasp_test_data(test_dir: str | Path, additional_file: list[str]) -> None:
         [f"  {v}  ->  {k}" for k, v in original_mapping.items()]
     )
 
-    run_vasp_kwargs = {k: {"incar_settings": ["NSW", "ISMEAR"]} for k in mapping}
+    run_vasp_kwargs = {key: {"incar_settings": ["NSW", "ISMEAR"]} for key in mapping}
     run_vasp_kwargs_str = pformat(run_vasp_kwargs).replace("\n", "\n    ")
 
     test_function_str = f"""Test files generated in test_data.
@@ -221,8 +221,8 @@ def abinit_script_maker() -> None:
         "save_abinit_maker(maker)",
         "",
     ]
-    with open(script_fname, "w") as f:
-        f.write("\n".join(out))
+    with open(script_fname, "w") as file:
+        file.write("\n".join(out))
 
 
 @dev.command(context_settings={"help_option_names": ["-h", "--help"]})
@@ -593,8 +593,8 @@ def save_abinit_maker(maker: Maker) -> None:
 
     caller_frame = inspect.stack()[1]
     caller_filename_full = caller_frame.filename
-    with open(caller_filename_full) as f:
-        script_str = f.read()
+    with open(caller_filename_full) as file:
+        script_str = file.read()
     git = shutil.which("git")
     author = None
     author_mail = None
@@ -627,7 +627,7 @@ def save_abinit_maker(maker: Maker) -> None:
                 "You may want to manually set it in the 'maker.json' file.",
                 stacklevel=2,
             )
-    with open("maker.json", "w") as f:
+    with open("maker.json", "w") as file:
         json.dump(
             {
                 "author": author,
@@ -636,7 +636,7 @@ def save_abinit_maker(maker: Maker) -> None:
                 "maker": jsanitize(maker.as_dict()),
                 "script": script_str,
             },
-            f,
+            file,
         )
 
 

src/atomate2/cp2k/files.py

@@ -102,8 +102,10 @@ def copy_cp2k_outputs(
     # rename files to remove relax extension
     if relax_ext:
         files_to_rename = {
-            k.name.replace(".gz", ""): k.name.replace(relax_ext, "").replace(".gz", "")
-            for k in all_files
+            file.name.replace(".gz", ""): file.name.replace(relax_ext, "").replace(
+                ".gz", ""
+            )
+            for file in all_files
         }
         rename_files(files_to_rename, allow_missing=True, file_client=file_client)
 

src/atomate2/cp2k/schemas/calculation.py

@@ -87,9 +87,9 @@ class CalculationInput(BaseModel):
     @classmethod
     def remove_unnecessary(cls, atomic_kind_info: dict) -> dict:
         """Remove unnecessary entry from atomic_kind_info."""
-        for k in atomic_kind_info:
-            if "total_pseudopotential_energy" in atomic_kind_info[k]:
-                del atomic_kind_info[k]["total_pseudopotential_energy"]
+        for key in atomic_kind_info:
+            if "total_pseudopotential_energy" in atomic_kind_info[key]:
+                del atomic_kind_info[key]["total_pseudopotential_energy"]
         return atomic_kind_info
 
     @field_validator("dft", mode="before")

src/atomate2/qchem/files.py

@@ -75,8 +75,10 @@ def copy_qchem_outputs(
     if opt_ext:
         all_files = required_files
         files_to_rename = {
-            k.name.replace(".gz", ""): k.name.replace(opt_ext, "").replace(".gz", "")
-            for k in all_files
+            file.name.replace(".gz", ""): file.name.replace(opt_ext, "").replace(
+                ".gz", ""
+            )
+            for file in all_files
         }
         rename_files(files_to_rename, allow_missing=True, file_client=file_client)
 

src/atomate2/utils/file_client.py

@@ -273,8 +273,8 @@ def link(
         """
         try:
             os.symlink(src_filename, dest_filename)
-        except OSError as e:
-            if e.errno == errno.EEXIST:
+        except OSError as exc:
+            if exc.errno == errno.EEXIST:
                 os.remove(dest_filename)
                 os.symlink(src_filename, dest_filename)
             else:
@@ -546,9 +546,9 @@ def get_ssh_connection(
         ssh_config = paramiko.SSHConfig().from_path(str(config_filename))
 
         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]
+        for key in ("hostname", "user", "port"):
+            if key in host_config:
+                config[key.replace("user", "username")] = host_config[key]
 
         if "proxycommand" in host_config:
             config["sock"] = paramiko.ProxyCommand(host_config["proxycommand"])

src/atomate2/vasp/files.py

@@ -104,8 +104,10 @@ def copy_vasp_outputs(
     if relax_ext:
         all_files = optional_files + required_files
         files_to_rename = {
-            k.name.replace(".gz", ""): k.name.replace(relax_ext, "").replace(".gz", "")
-            for k in all_files
+            file.name.replace(".gz", ""): file.name.replace(relax_ext, "").replace(
+                ".gz", ""
+            )
+            for file in all_files
         }
         rename_files(files_to_rename, allow_missing=True, file_client=file_client)
 

tests/abinit/conftest.py

@@ -126,8 +126,8 @@ def check_run_abi(ref_path: str | Path):
 
     user = AbinitInputFile.from_file("run.abi")
     assert user.ndtset == 1, f"'run.abi' has multiple datasets (ndtset={user.ndtset})."
-    with zopen(ref_path / "inputs" / "run.abi.gz") as f:
-        ref_str = f.read()
+    with zopen(ref_path / "inputs" / "run.abi.gz") as file:
+        ref_str = file.read()
     ref = AbinitInputFile.from_string(ref_str.decode("utf-8"))
     # Ignore the pseudos as the directory depends on the pseudo root directory
     diffs = user.get_differences(ref, ignore_vars=["pseudos"])

tests/abinit/sets/test_base.py

@@ -87,11 +87,11 @@ def test_abinit_input_set_write_input(abinit_test_dir):
         assert os.path.isdir("testdir/tmpdata")
         assert "run.abi" in dirlist
         assert "abinit_input.json" in dirlist
-        with open("testdir/run.abi") as f:
-            abistr = f.read()
+        with open("testdir/run.abi") as file:
+            abistr = file.read()
             assert "ecut" in abistr
-        with open("testdir/abinit_input.json") as f:
-            abijsonstr = f.read()
+        with open("testdir/abinit_input.json") as file:
+            abijsonstr = file.read()
             assert "@module" in abijsonstr
         with pytest.raises(FileExistsError):
             ais.write_input("testdir", overwrite=False)
@@ -132,8 +132,8 @@ def test_abinit_input_set_write_input(abinit_test_dir):
         assert os.path.exists(in_den)
         assert os.path.isfile(in_den)
         assert not os.path.islink(in_den)
-        with open("testdir/run.abi") as f:
-            abistr = f.read()
+        with open("testdir/run.abi") as file:
+            abistr = file.read()
             assert "irdden 1" in abistr
         del ais.abinit_input["irdden"]
 

tests/abinit/sets/test_core.py

@@ -48,8 +48,8 @@ def test_static_generator_get_input_set(si_structure):
 #         assert len(dirlist) == 6
 #         assert "abinit_input_set_generator.json" in dirlist
 #         assert "abinit_input.json" in dirlist
-#         with open("first_run/run.abi", "r") as f:
-#             runabi1_str = f.read()
+#         with open("first_run/run.abi") as file:
+#             runabi1_str = file.read()
 #         assert "ecut 8.5" in runabi1_str
 #         assert "nband 13" in runabi1_str
 #         assert "occopt 5" in runabi1_str
@@ -76,8 +76,8 @@ def test_static_generator_get_input_set(si_structure):
 #         )
 #         assert os.path.islink(indenpath)
 #         assert os.readlink(indenpath) == outdenpath
-#         with open("second_run/run.abi", "r") as f:
-#             runabi2_str = f.read()
+#         with open("second_run/run.abi") as file:
+#             runabi2_str = file.read()
 #         assert "ecut 8.5" in runabi2_str
 #         assert "nband 8" in runabi2_str
 #         assert "occopt" not in runabi2_str
@@ -101,8 +101,8 @@ def test_static_generator_get_input_set(si_structure):
 #         )
 #         assert os.path.islink(inwfkpath)
 #         assert os.readlink(inwfkpath) == outwfkpath
-#         with open("second_run_bis/run.abi", "r") as f:
-#             runabi3_str = f.read()
+#         with open("second_run_bis/run.abi") as file:
+#             runabi3_str = file.read()
 #         assert "ecut 8.5" in runabi3_str
 #         assert "nband 13" in runabi3_str
 #         assert "occopt 5" in runabi3_str

tests/forcefields/test_md.py

@@ -166,10 +166,10 @@ def test_nve_and_dynamics_obj(si_structure: Structure, test_dir: Path):
     #    vs. as an ase.md.md.MolecularDynamics object
 
     output = {}
-    for k in ["from_str", "from_dyn"]:
-        if k == "from_str":
+    for attr in ("from_str", "from_dyn"):
+        if attr == "from_str":
             dyn = "velocityverlet"
-        elif k == "from_dyn":
+        elif attr == "from_dyn":
             dyn = VelocityVerlet
 
         job = CHGNetMDMaker(
@@ -180,7 +180,7 @@ def test_nve_and_dynamics_obj(si_structure: Structure, test_dir: Path):
         ).make(si_structure)
 
         response = run_locally(job, ensure_success=True)
-        output[k] = response[next(iter(response))][1].output
+        output[attr] = response[next(iter(response))][1].output
 
     # check that energy and volume are constants
     assert output["from_str"].output.energy == pytest.approx(-10.6, abs=0.1)
@@ -195,7 +195,10 @@ def test_nve_and_dynamics_obj(si_structure: Structure, test_dir: Path):
     # ensure that output is consistent if molecular dynamics object is specified
     # as str or as MolecularDynamics object
     for attr in ("energy", "forces", "stress", "structure"):
-        vals = {k: getattr(output[k].output, attr) for k in ("from_str", "from_dyn")}
+        vals = {
+            attr: getattr(output[attr].output, attr)
+            for attr in ("from_str", "from_dyn")
+        }
         if isinstance(vals["from_str"], float):
             assert vals["from_str"] == pytest.approx(vals["from_dyn"])
         elif isinstance(vals["from_str"], Structure):

tests/vasp/flows/test_defect.py

@@ -37,7 +37,7 @@ def test_ccd_maker(mock_vasp, clean_dir, test_dir):
         "finite diff q1": "Si_config_coord/finite_diff_q1",
         "finite diff q2": "Si_config_coord/finite_diff_q2",
     }
-    fake_run_vasp_kwargs = {k: {"incar_settings": ["ISIF"]} for k in ref_paths}
+    fake_run_vasp_kwargs = {path: {"incar_settings": ["ISIF"]} for path in ref_paths}
 
     # automatically use fake VASP and write POTCAR.spec during the test
     mock_vasp(ref_paths, fake_run_vasp_kwargs)
@@ -82,7 +82,7 @@ def test_nonrad_maker(mock_vasp, clean_dir, test_dir, monkeypatch):
         "finite diff q1": "Si_config_coord/finite_diff_q1",
         "finite diff q2": "Si_config_coord/finite_diff_q2",
     }
-    fake_run_vasp_kwargs = {k: {"incar_settings": ["ISIF"]} for k in ref_paths}
+    fake_run_vasp_kwargs = {path: {"incar_settings": ["ISIF"]} for path in ref_paths}
 
     # automatically use fake VASP and write POTCAR.spec during the test
     mock_vasp(ref_paths, fake_run_vasp_kwargs)
@@ -140,7 +140,8 @@ def test_formation_energy_maker(mock_vasp, clean_dir, test_dir, monkeypatch):
     }
 
     fake_run_vasp_kwargs = {
-        k: {"incar_settings": ["ISIF"], "check_inputs": ["incar"]} for k in ref_paths
+        path: {"incar_settings": ["ISIF"], "check_inputs": ["incar"]}
+        for path in ref_paths
     }
 
     # automatically use fake VASP and write POTCAR.spec during the test
@@ -177,18 +178,10 @@ def _check_plnr_locpot(name):
         plnr_locpot = job["output"]["calcs_reversed"][0]["output"]["locpot"]
         assert set(plnr_locpot) == {"0", "1", "2"}
 
-    for k in ref_paths:
-        _check_plnr_locpot(k)
+    for path in ref_paths:
+        _check_plnr_locpot(path)
 
     # make sure the the you can restart the calculation from prv
     prv_dir = test_dir / "vasp/GaN_Mg_defect/bulk_relax/outputs"
-    flow2 = maker.make(
-        defects[0],
-        bulk_supercell_dir=prv_dir,
-        defect_index=0,
-    )
-    _ = run_locally(
-        flow2,
-        create_folders=True,
-        ensure_success=True,
-    )
+    flow2 = maker.make(defects[0], bulk_supercell_dir=prv_dir, defect_index=0)
+    _ = run_locally(flow2, create_folders=True, ensure_success=True)

tests/vasp/jobs/test_core.py

@@ -16,7 +16,7 @@
 
 
 def test_static_maker(mock_vasp, clean_dir, si_structure):
-    jstore = jobflow.SETTINGS.JOB_STORE
+    job_store = jobflow.SETTINGS.JOB_STORE
 
     # mapping from job name to directory containing test files
     ref_paths = {"static": "Si_band_structure/static"}
@@ -42,10 +42,9 @@ def test_static_maker(mock_vasp, clean_dir, si_structure):
     assert isinstance(output1, TaskDoc)
     assert output1.output.energy == approx(-10.85037078)
 
-    with jstore.additional_stores["data"] as s:
-        doc = s.query_one({"job_uuid": job.uuid})
-        dd = doc["data"]
-        assert dd["@class"] == "Chgcar"
+    with job_store.additional_stores["data"] as store:
+        doc = store.query_one({"job_uuid": job.uuid})
+    assert doc["data"]["@class"] == "Chgcar"
 
 
 def test_relax_maker(mock_vasp, clean_dir, si_structure):