Merge remote-tracking branch 'origin/add_adsorption' into add_adsorption

Author: itsduowang

.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: v0.4.4
+  rev: v0.4.10
   hooks:
   - id: ruff
     args: [--fix]
@@ -38,7 +38,7 @@ repos:
     - tokenize-rt==4.1.0
     - types-paramiko
 - repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
+  rev: v2.3.0
   hooks:
   - id: codespell
     stages: [commit, commit-msg]

docs/dev/abinit_tests.md

@@ -17,7 +17,6 @@ be added to this pseudopotential table.
 Note that information from the real pseudopotential files is used in the creation
 of the jobs and flows, hence fake pseudopotentials are not an option here.
 
-
 ### File sizes
 
 The files produced by ABINIT are generally large and would overwhelm the size of the
@@ -121,7 +120,7 @@ atm dev abinit-test-data TEST_NAME
 
 You should change `TEST_NAME` to be a name for the workflow test. Note, `TEST_NAME` should not
 contain spaces or punctuation. For example, the band structure workflow test data was
-genenerated using `atm dev vasp-test-data Si_band_structure`.
+generated using `atm dev vasp-test-data Si_band_structure`.
 
 This will automatically detect whether the Maker is a Job Maker or a Flow Maker and
 copy files in the corresponding `tests/test_data/abinit/jobs/NameOfMaker/TEST_NAME`
@@ -145,6 +144,7 @@ a unique name. For example, there cannot be two calculations called "relax".
 Instead you should ensure they are named something like "relax 1" and "relax 2".
 
 Each `REF_RUN_FOLDER` contains:
+
 - A folder called "inputs" with the run.abi and abinit_input.json, as well as with the
   indata, outdata and tmpdata directories. The indata directory potentially contains
   the reference fake input files needed for the job to be executed (e.g. a fake link to a

pyproject.toml

@@ -95,12 +95,12 @@ strict = [
     "monty==2024.5.24",
     "mp-api==0.41.2",
     "numpy",
-    "phonopy==2.24.2",
-    "pydantic-settings==2.3.1",
-    "pydantic==2.7.3",
+    "phonopy==2.24.3",
+    "pydantic-settings==2.3.3",
+    "pydantic==2.7.4",
     "pymatgen-analysis-defects==2024.5.11",
-    "pymatgen==2024.5.31",
-    "python-ulid==2.6.0",
+    "pymatgen==2024.6.10",
+    "python-ulid==2.7.0",
     "quippy-ase==0.9.14",
     "seekpath==2.1.0",
     "torch==2.2.1",
@@ -165,15 +165,14 @@ select = ["ALL"]
 ignore = [
     "ANN002",
     "ANN003",
-    "ANN101",  # missing self type annotation
-    "ANN102",
+    "ANN101", # missing self type annotation
+    "ANN102", # missing cls annotation
     "ANN401",
-    "ARG002",  # unused method argument
-    "BLE001",
+    "ARG002", # unused method argument
+    # "BLE001",
     "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",
@@ -183,15 +182,18 @@ ignore = [
     "ISC001",
     "PD011",   # pandas-use-of-dot-values
     "PERF203", # try-except-in-loop
-    "PLR",     # pylint-refactor
+    "PLR0911", # too many returns
+    "PLR0912", # too many branches
+    "PLR0913", # too many arguments
+    "PLR0915", # too many local statements
+    "PLR2004",
     "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
     "S507",    # paramiko auto trust
-    "SLF",     # private member accessed outside class
     "TD",      # TODOs
     "TRY003",  # long message outside exception class
 ]
@@ -204,7 +206,7 @@ docstring-code-format = true
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
-"**/tests/*" = ["ANN", "ARG001", "D", "INP001", "S101"]
+"**/tests/*" = ["ANN", "ARG001", "D", "INP001", "PLR2004", "S101"]
 # flake8-type-checking (TCH): things inside TYPE_CHECKING aren't available
 #     at runtime and so can't be used by pydantic models
 # flake8-future-annotations (FA): pipe operator for type unions only work in pydantic models in python 3.10+

src/atomate2/abinit/run.py

@@ -62,4 +62,3 @@ def run_abinit(
                     process.terminate()
 
         process.wait()
-    return

src/atomate2/abinit/schemas/calculation.py

@@ -4,7 +4,7 @@
 
 import logging
 import os
-from datetime import datetime
+from datetime import datetime, timezone
 from pathlib import Path
 from typing import Optional, Union
 
@@ -236,7 +236,9 @@ def from_abinit_files(
 
         abinit_gsr = GsrFile.from_file(abinit_gsr_file)
 
-        completed_at = str(datetime.fromtimestamp(os.stat(abinit_log_file).st_mtime))
+        completed_at = str(
+            datetime.fromtimestamp(os.stat(abinit_log_file).st_mtime, tz=timezone.utc)
+        )
 
         output_doc = CalculationOutput.from_abinit_gsr(abinit_gsr)
 
@@ -255,7 +257,7 @@ def from_abinit_files(
             if report.run_completed:
                 has_abinit_completed = TaskState.SUCCESS
 
-        except Exception as exc:
+        except (ValueError, RuntimeError, Exception) as exc:
             msg = f"{cls} exception while parsing event_report:\n{exc}"
             logger.critical(msg)
 

src/atomate2/abinit/sets/base.py

@@ -356,7 +356,7 @@ def get_input_set(
         else:
             if prev_outputs is not None and not self.prev_outputs_deps:
                 raise RuntimeError(
-                    f"Previous outputs not allowed for {self.__class__.__name__}."
+                    f"Previous outputs not allowed for {type(self).__name__}."
                 )
             abinit_input = self.get_abinit_input(
                 structure=structure,
@@ -573,7 +573,7 @@ def get_abinit_input(
         if self.factory_prev_inputs_kwargs:
             if not prev_outputs:
                 raise RuntimeError(
-                    f"No previous_outputs. Required for {self.__class__.__name__}."
+                    f"No previous_outputs. Required for {type(self).__name__}."
                 )
 
             # TODO consider cases where structure might be defined even if
@@ -588,18 +588,16 @@ def get_abinit_input(
             )
             total_factory_kwargs.update(abinit_inputs)
 
-        else:
-            # TODO check if this should be removed or the check be improved
-            if structure is None:
-                msg = (
-                    f"Structure is mandatory for {self.__class__.__name__} "
-                    f"generation since no previous output is used."
-                )
-                raise RuntimeError(msg)
+        elif structure is None:
+            msg = (
+                f"Structure is mandatory for {type(self).__name__} "
+                f"generation since no previous output is used."
+            )
+            raise RuntimeError(msg)
 
         if not self.prev_outputs_deps and prev_outputs:
             msg = (
-                f"Previous outputs not allowed for {self.__class__.__name__} "
+                f"Previous outputs not allowed for {type(self).__name__} "
                 "Consider if restart_from argument of get_input_set method "
                 "can fit your needs instead."
             )

src/atomate2/abinit/utils/common.py

@@ -425,7 +425,7 @@ def get_event_report(ofile: File, mpiabort_file: File) -> EventReport | None:
                     report.append(last_abort_event)
                 else:
                     report.append(last_abort_event)
-    except Exception as exc:
+    except (ValueError, RuntimeError, Exception) as exc:
         # Return a report with an error entry with info on the exception.
         logger.critical(f"{ofile}: Exception while parsing ABINIT events:\n {exc!s}")
         return parser.report_exception(ofile.path, exc)

src/atomate2/aims/jobs/convergence.py

@@ -97,7 +97,7 @@ def make(
                 "convergence_field_values": [],
                 "epsilon": self.epsilon,
             }
-        convergence_data.update({"idx": idx, "converged": converged})
+        convergence_data.update(idx=idx, converged=converged)
 
         if prev_dir is not None:
             split_prev_dir = str(prev_dir).split(":")[-1]

src/atomate2/aims/schemas/calculation.py

@@ -4,7 +4,7 @@
 
 import os
 from collections.abc import Sequence
-from datetime import datetime
+from datetime import datetime, timezone
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Optional, Union
 
@@ -291,7 +291,9 @@ def from_aims_files(
         volumetric_files = [] if volumetric_files is None else volumetric_files
         aims_output = AimsOutput.from_outfile(aims_output_file)
 
-        completed_at = str(datetime.fromtimestamp(os.stat(aims_output_file).st_mtime))
+        completed_at = str(
+            datetime.fromtimestamp(os.stat(aims_output_file).st_mtime, tz=timezone.utc)
+        )
 
         output_file_paths = _get_output_file_paths(volumetric_files)
         aims_objects: dict[AimsObject, Any] = _get_volumetric_data(

src/atomate2/aims/utils/__init__.py

@@ -1,6 +1,6 @@
 """A collection of helper utils found in atomate2 package."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 
 
 def datetime_str() -> str:
@@ -12,4 +12,4 @@ def datetime_str() -> str:
     str
         The current time.
     """
-    return str(datetime.utcnow())
+    return str(datetime.now(tz=timezone.utc))