pre-commit autoupdate (#332)

* pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.4.3](astral-sh/ruff-pre-commit@v0.3.5...v0.4.3) - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](pre-commit/mirrors-mypy@v1.9.0...v1.10.0) * ruff auto fixes * manual ruff fixes * fix typos and doc strings * fix AttributeError: 'list' object has no attribute 'astype' if self.half_kpts and os.path.isfile(os.path.join(directory, "KPOINTS")): kpts = Kpoints.from_file(os.path.join(directory, "KPOINTS")) kpts.kpts = np.maximum(np.array(kpts.kpts) / 2, 1) > kpts.kpts = kpts.kpts.astype(int).tolist() * fix more directory kwargs missing in doc strings --------- Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
materialsproject · May 6, 2024 · 8832873 · 8832873
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,22 +7,22 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [--fix, --ignore, D, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
         exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         additional_dependencies: [types-requests]

diff --git a/custodian/ansible/interpreter.py b/custodian/ansible/interpreter.py
@@ -41,6 +41,8 @@ def __init__(self, actions=None, strict=True, directory="./") -> None:
                 mode, unsupported actions are simply ignored without any
                 errors raised. In strict mode, if an unsupported action is
                 supplied, a ValueError is raised. Defaults to True.
+            directory (str): The directory containing the files to be modified.
+                Defaults to "./".
         """
         self.supported_actions = {}
         actions = actions if actions is not None else [DictActions]

diff --git a/custodian/cp2k/handlers.py b/custodian/cp2k/handlers.py
@@ -18,6 +18,7 @@
 import os
 import re
 import time
+from typing import ClassVar
 
 import numpy as np
 from monty.os.path import zpath
@@ -56,7 +57,11 @@ class StdErrHandler(ErrorHandler):
     is_monitor = True
     raises_runtime_error = False
 
-    error_msgs = {"seg_fault": ["SIGSEGV"], "out_of_memory": ["insufficient virtual memory"], "abort": ["SIGABRT"]}
+    error_msgs: ClassVar = {
+        "seg_fault": ["SIGSEGV"],
+        "out_of_memory": ["insufficient virtual memory"],
+        "abort": ["SIGABRT"],
+    }
 
     def __init__(self, std_err="std_err.txt") -> None:
         """Initialize the handler with the output file to check.

diff --git a/custodian/cp2k/interpreter.py b/custodian/cp2k/interpreter.py
@@ -35,7 +35,8 @@ def __init__(self, filename="cp2k.inp", actions=None, strict=True, ci=None, dire
                 supplied, a ValueError is raised. Defaults to True.
             ci (Cp2kInput): A Cp2kInput object from the current directory.
                 Initialized automatically if not passed (but passing it will
-                avoid having to reparse the directory).
+                avoid having to re-parse the directory).
+            directory (str): The directory containing the Cp2kInput set. Defaults to "./".
         """
         self.directory = directory
         self.ci = ci or Cp2kInput.from_file(os.path.join(self.directory, filename))

diff --git a/custodian/cp2k/jobs.py b/custodian/cp2k/jobs.py
@@ -77,7 +77,7 @@ def __init__(
         self.final = final
         self.backup = backup
         self.suffix = suffix
-        self.settings_override = settings_override if settings_override else []
+        self.settings_override = settings_override or []
         self.restart = restart
 
     def setup(self, directory="./") -> None:

diff --git a/custodian/custodian.py b/custodian/custodian.py
@@ -212,12 +212,12 @@ def __init__(
     def _load_checkpoint(directory):
         restart = 0
         run_log = []
-        chkpts = glob(os.path.join(directory, "custodian.chk.*.tar.gz"))
-        if chkpts:
-            chkpt = sorted(chkpts, key=lambda c: int(c.split(".")[-3]))[0]
-            restart = int(chkpt.split(".")[-3])
-            logger.info(f"Loading from checkpoint file {chkpt}...")
-            with tarfile.open(chkpt) as file:
+        chk_pts = glob(os.path.join(directory, "custodian.chk.*.tar.gz"))
+        if chk_pts:
+            chk_pt = min(chk_pts, key=lambda c: int(c.split(".")[-3]))
+            restart = int(chk_pt.split(".")[-3])
+            logger.info(f"Loading from checkpoint file {chk_pt}...")
+            with tarfile.open(chk_pt) as file:
 
                 def is_within_directory(directory, target):
                     abs_directory = os.path.abspath(directory)
@@ -381,7 +381,7 @@ def run(self):
 
             try:
                 # skip jobs until the restart
-                for job_n, job in islice(enumerate(self.jobs, 1), self.restart, None):
+                for job_n, job in islice(enumerate(self.jobs, start=1), self.restart, None):
                     self._run_job(job_n, job)
                     # We do a dump of the run log after each job.
                     dumpfn(self.run_log, os.path.join(self.directory, Custodian.LOG_FILE), cls=MontyEncoder, indent=4)

diff --git a/custodian/feff/interpreter.py b/custodian/feff/interpreter.py
@@ -25,8 +25,8 @@ def __init__(self, actions=None, strict=True, feffinp=None, directory="./") -> N
                 supplied, a ValueError is raised. Defaults to True.
             feffinp (FEFFInput): A FeffInput object from the current directory.
                 Initialized automatically if not passed (but passing it will
-                avoid having to reparse the directory).
-            directory (str): Directory to run in
+                avoid having to re-parse the directory).
+            directory (str): The directory containing the FeffInput set. Defaults to "./".
         """
         self.directory = directory
         self.feffinp = feffinp or FEFFDictSet.from_directory(self.directory)

diff --git a/custodian/gaussian/__init__.py b/custodian/gaussian/__init__.py
@@ -1,6 +1,4 @@
-"""
-This package implements various Gaussian Jobs and Error Handlers.
-"""
+"""This package implements various Gaussian Jobs and Error Handlers."""
 
 __author__ = "Rasha Atwi"
 __version__ = "0.1"

diff --git a/custodian/gaussian/handlers.py b/custodian/gaussian/handlers.py
@@ -9,7 +9,7 @@
 import os
 import re
 import shutil
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, ClassVar
 
 import numpy as np
 from monty.io import zopen
@@ -47,7 +47,7 @@ class GaussianErrorHandler(ErrorHandler):
     """
 
     # definition of job errors as they appear in Gaussian output file
-    error_defs = {
+    error_defs: ClassVar = {
         "Optimization stopped": "opt_steps",
         "Convergence failure": "scf_convergence",
         "FormBX had a problem": "linear_bend",
@@ -71,15 +71,15 @@ class GaussianErrorHandler(ErrorHandler):
     recom_mem_patt = re.compile(
         r"Use %mem=([0-9]+)MW to provide the minimum amount of memory required to complete this step."
     )
-    conv_critera = {
+    conv_criteria: ClassVar = {
         "max_force": re.compile(r"\s+(Maximum Force)\s+(-?\d+.?\d*|.*)\s+(-?\d+.?\d*)"),
         "rms_force": re.compile(r"\s+(RMS {5}Force)\s+(-?\d+.?\d*|.*)\s+(-?\d+.?\d*)"),
         "max_disp": re.compile(r"\s+(Maximum Displacement)\s+(-?\d+.?\d*|.*)\s+(-?\d+.?\d*)"),
         "rms_disp": re.compile(r"\s+(RMS {5}Displacement)\s+(-?\d+.?\d*|.*)\s+(-?\d+.?\d*)"),
     }
 
     grid_patt = re.compile(r"(-?\d{5})")
-    GRID_NAMES = [
+    GRID_NAMES = (
         "finegrid",
         "fine",
         "superfinegrid",
@@ -90,8 +90,8 @@ class GaussianErrorHandler(ErrorHandler):
         "sg1",
         "pass0grid",
         "pass0",
-    ]
-    MEM_UNITS = ["kb", "mb", "gb", "tb", "kw", "mw", "gw", "tw"]
+    )
+    MEM_UNITS = ("kb", "mb", "gb", "tb", "kw", "mw", "gw", "tw")
 
     activate_better_guess = False
 
@@ -504,7 +504,7 @@ def check(self, directory: str = "./") -> bool:
                     self.recom_mem = GaussianErrorHandler.convert_mem(float(mem), "mw")
 
                 if self.check_convergence and "opt" in self.gin.route_parameters:
-                    for k, v in GaussianErrorHandler.conv_critera.items():
+                    for k, v in GaussianErrorHandler.conv_criteria.items():
                         m = v.search(line)
                         if m:
                             if k not in self.conv_data["values"]:

diff --git a/custodian/utils.py b/custodian/utils.py
@@ -5,6 +5,7 @@
 import os
 import tarfile
 from glob import glob
+from typing import ClassVar
 
 
 def backup(filenames, prefix="error", directory="./") -> None:
@@ -60,7 +61,7 @@ class tracked_lru_cache:
     Allows Custodian to clear the cache after all the checks have been performed.
     """
 
-    cached_functions: set = set()
+    cached_functions: ClassVar = set()
 
     def __init__(self, func) -> None:
         """

diff --git a/custodian/vasp/handlers.py b/custodian/vasp/handlers.py
@@ -16,6 +16,7 @@
 import warnings
 from collections import Counter
 from math import prod
+from typing import ClassVar
 
 import numpy as np
 from monty.dev import deprecated
@@ -66,7 +67,7 @@ class VaspErrorHandler(ErrorHandler):
 
     is_monitor = True
 
-    error_msgs = {
+    error_msgs: ClassVar = {
         "tet": [
             "Tetrahedron method fails",
             "tetrahedron method fails",
@@ -135,20 +136,17 @@ def __init__(
                 is being redirected. The error messages that are checked are
                 present in the stdout. Defaults to "vasp.out", which is the
                 default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-            errors_subset_to_detect (list): A subset of errors to catch. The
+            errors_subset_to_catch (list): A subset of errors to catch. The
                 default is None, which means all supported errors are detected.
                 Use this to catch only a subset of supported errors.
                 E.g., ["eddrmm", "zheev"] will only catch the eddrmm and zheev
                 errors, and not others. If you wish to only exclude one or
-                two of the errors, you can create this list by the following
-                lines:
+                two of the errors, you can create this list by the following lines:
 
-                ```
-                subset = list(VaspErrorHandler().error_msgs)
-                subset.remove("eddrmm")
+                    subset = list(VaspErrorHandler().error_msgs)
+                    subset.remove("eddrmm")
+                    handler = VaspErrorHandler(errors_subset_to_catch=subset)
 
-                handler = VaspErrorHandler(errors_subset_to_catch=subset)
-                ```
             vtst_fixes (bool): Whether to consider VTST optimizers. Defaults to
                 False for compatibility purposes, but if you have VTST, you
                 would likely benefit from setting this to True.
@@ -691,7 +689,7 @@ class LrfCommutatorHandler(ErrorHandler):
 
     is_monitor = True
 
-    error_msgs = {"lrf_comm": ["LRF_COMMUTATOR internal error"]}
+    error_msgs: ClassVar = {"lrf_comm": ["LRF_COMMUTATOR internal error"]}
 
     def __init__(self, output_filename: str = "std_err.txt") -> None:
         """Initialize the handler with the output file to check.
@@ -744,7 +742,7 @@ class StdErrHandler(ErrorHandler):
 
     is_monitor = True
 
-    error_msgs = {
+    error_msgs: ClassVar = {
         "kpoints_trans": ["internal error in GENERATE_KPOINTS_TRANS: number of G-vector changed in star"],
         "out_of_memory": ["Allocation would exceed memory limit"],
     }
@@ -804,7 +802,7 @@ class AliasingErrorHandler(ErrorHandler):
 
     is_monitor = True
 
-    error_msgs = {
+    error_msgs: ClassVar = {
         "aliasing": ["WARNING: small aliasing (wrap around) errors must be expected"],
         "aliasing_incar": ["Your FFT grids (NGX,NGY,NGZ) are not sufficient for an accurate"],
     }

diff --git a/custodian/vasp/interpreter.py b/custodian/vasp/interpreter.py
@@ -24,7 +24,8 @@ def __init__(self, actions=None, strict=True, vi=None, directory="./") -> None:
                 supplied, a ValueError is raised. Defaults to True.
             vi (VaspInput): A VaspInput object from the current directory.
                 Initialized automatically if not passed (but passing it will
-                avoid having to reparse the directory).
+                avoid having to re-parse the directory).
+            directory (str): The directory containing the VaspInput set.
         """
         self.vi = vi or VaspInput.from_directory(directory)
         self.directory = directory

diff --git a/custodian/vasp/jobs.py b/custodian/vasp/jobs.py
@@ -315,6 +315,7 @@ def double_relaxation_run(
                 wall-time handler which will write a read-only STOPCAR to
                 prevent VASP from deleting it once it finishes. Defaults to
                 False.
+            directory (str): Directory where the job was run. Defaults to './'.
 
         Returns:
             List of two jobs corresponding to an AFLOW style run.
@@ -382,12 +383,8 @@ def metagga_opt_run(
         metaGGA = incar.get("METAGGA", "SCAN")
 
         # Pre optimize WAVECAR and structure using regular GGA
-        pre_opt_settings = [
-            {
-                "dict": "INCAR",
-                "action": {"_set": {"METAGGA": None, "LWAVE": True, "NSW": 0}},
-            }
-        ]
+        new_settings = {"METAGGA": None, "LWAVE": True, "NSW": 0}
+        pre_opt_settings = [{"dict": "INCAR", "action": {"_set": new_settings}}]
         jobs = [
             VaspJob(
                 vasp_cmd,
@@ -460,6 +457,7 @@ def full_opt_run(
             half_kpts_first_relax (bool): Whether to halve the kpoint grid
                 for the first relaxation. Speeds up difficult convergence
                 considerably. Defaults to False.
+            directory (str): Directory where the job was run. Defaults to './'.
             **vasp_job_kwargs: Passthrough kwargs to VaspJob. See
                 :class:`custodian.vasp.jobs.VaspJob`.
 
@@ -558,6 +556,7 @@ def constrained_opt_run(
                 which is more robust but can be a bit slow. The code does fall
                 back on the bisection when bfgs gives a nonsensical result,
                 e.g., negative lattice params.
+            directory (str): Directory where the job was run. Defaults to './'.
             **vasp_job_kwargs: Passthrough kwargs to VaspJob. See
                 :class:`custodian.vasp.jobs.VaspJob`.
 
@@ -807,8 +806,7 @@ def __init__(
         self.settings_override = settings_override
 
     def setup(self, directory="./") -> None:
-        """
-        Performs initial setup for VaspNEBJob, including overriding any settings
+        """Performs initial setup for VaspNEBJob, including overriding any settings
         and backing up.
         """
         neb_dirs, neb_sub = self._get_neb_dirs(directory)
@@ -825,7 +823,6 @@ def setup(self, directory="./") -> None:
         if self.half_kpts and os.path.isfile(os.path.join(directory, "KPOINTS")):
             kpts = Kpoints.from_file(os.path.join(directory, "KPOINTS"))
             kpts.kpts = np.maximum(np.array(kpts.kpts) / 2, 1)
-            kpts.kpts = kpts.kpts.astype(int).tolist()
             if tuple(kpts.kpts[0]) == (1, 1, 1):
                 kpt_dic = kpts.as_dict()
                 kpt_dic["generation_style"] = "Gamma"

diff --git a/docs/_themes/flask_theme_support.py b/docs/_themes/flask_theme_support.py
@@ -1,5 +1,7 @@
 """flasky extensions. flasky pygments style based on tango style."""
 
+from typing import ClassVar
+
 from pygments.style import Style
 from pygments.token import (
     Comment,
@@ -23,7 +25,7 @@ class FlaskyStyle(Style):
     background_color = "#f8f8f8"
     default_style = ""
 
-    styles = {
+    styles: ClassVar = {
         # No corresponding class for the following:
         # Text:                     "", # class:  ''
         Whitespace: "underline #f8f8f8",  # class: 'w'

diff --git a/tasks.py b/tasks.py
@@ -13,7 +13,7 @@
 
 from custodian import __version__ as CURRENT_VER
 
-NEW_VER = datetime.datetime.today().strftime("%Y.%-m.%-d")
+NEW_VER = datetime.datetime.now(tz=datetime.timezone.utc).strftime("%Y.%-m.%-d")
 
 
 @task

diff --git a/tests/gaussian/test_jobs.py b/tests/gaussian/test_jobs.py
@@ -67,8 +67,8 @@ def test_better_guess(self):
             self.output_file,
             self.stderr_file,
             self.backup,
-            True,
-            self.directory,
+            cart_coords=True,
+            directory=self.directory,
         )
         jobs = list(job_gen)
         assert len(jobs) == 1, "One job should be generated under normal conditions."