pre-commit updates and code fixes

.pre-commit-config.yaml

@@ -2,23 +2,23 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 23.9.1
+    rev: 24.1.1
     hooks:
     -   id: black
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
     -   id: codespell
         additional_dependencies:
         - tomli
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8

docs/changes.rst

@@ -9,7 +9,7 @@ Release Notes
 * adding simple validators to input spec (using ``attr.validator``)
 * adding ``create_dotfile`` for workflows, that creates graphs as dotfiles (can convert to other formats if dot available)
 * adding a simple user guide with ``input_spec`` description
-* expanding docstrings for ``State``, ``audit`` and ``messanger``
+* expanding docstrings for ``State``, ``audit`` and ``messenger``
 * updating syntax to newer python
 
 0.7.0

docs/sphinxext/github_link.py

@@ -2,6 +2,7 @@
 This script comes from scikit-learn:
 https://github.com/scikit-learn/scikit-learn/blob/master/doc/sphinxext/github_link.py
 """
+
 import inspect
 import os
 import subprocess

pydra/__init__.py

@@ -5,6 +5,7 @@
 first-class operations. It forms the core of the Nipype 2.0 ecosystem.
 
 """
+
 # This call enables pydra.tasks to be used as a namespace package when installed
 # in editable mode. In normal installations it has no effect.
 __path__ = __import__("pkgutil").extend_path(__path__, __name__)

pydra/engine/__init__.py

@@ -1,4 +1,5 @@
 """The core of the workflow engine."""
+
 from .submitter import Submitter
 from .core import Workflow
 from .task import AuditFlag, ShellCommandTask

pydra/engine/audit.py

@@ -1,4 +1,5 @@
 """Module to keep track of provenance information."""
+
 import os
 import json
 import attr

pydra/engine/core.py

@@ -1,4 +1,5 @@
 """Basic processing graph elements."""
+
 import abc
 import json
 import logging
@@ -59,7 +60,7 @@ class TaskBase:
     """
     A base structure for the nodes in the processing graph.
 
-    Tasks are a generic compute step from which both elemntary tasks and
+    Tasks are a generic compute step from which both elementary tasks and
     :class:`Workflow` instances inherit.
 
     """
@@ -545,7 +546,7 @@ def _run(self, rerun=False, environment=None, **kwargs):
                 self.hooks.post_run_task(self, result)
                 self.audit.finalize_audit(result)
                 save(output_dir, result=result, task=self)
-                # removing the additional file with the chcksum
+                # removing the additional file with the checksum
                 (self.cache_dir / f"{self.uid}_info.json").unlink()
                 # # function etc. shouldn't change anyway, so removing
                 orig_inputs = {
@@ -1251,7 +1252,7 @@ async def _run(self, submitter=None, rerun=False, **kwargs):
                 self.hooks.post_run_task(self, result)
                 self.audit.finalize_audit(result=result)
                 save(output_dir, result=result, task=self)
-                # removing the additional file with the chcksum
+                # removing the additional file with the checksum
                 (self.cache_dir / f"{self.uid}_info.json").unlink()
                 os.chdir(cwd)
         self.hooks.post_run(self, result)

pydra/engine/environments.py

@@ -6,7 +6,7 @@
 class Environment:
     """
     Base class for environments that are used to execute tasks.
-    Right now it is asssumed that the environment, including container images,
+    Right now it is assumed that the environment, including container images,
     are available and are not removed at the end
     TODO: add setup and teardown methods
     """

pydra/engine/graph.py

@@ -1,4 +1,5 @@
 """Data structure to support :class:`~pydra.engine.core.Workflow` tasks."""
+
 from copy import copy
 from pathlib import Path
 import subprocess as sp
@@ -498,7 +499,7 @@ def _create_dotfile_single_graph(self, nodes, edges):
         return dotstr
 
     def export_graph(self, dotfile, ext="png"):
-        """exporting dotfile to other format, equires the dot command"""
+        """exporting dotfile to other formats requires the dot command"""
         available_ext = [
             "bmp",
             "canon",

pydra/engine/helpers.py

@@ -1,4 +1,5 @@
 """Administrative support for the engine framework."""
+
 import asyncio
 import asyncio.subprocess as asp
 from pathlib import Path

pydra/engine/specs.py

@@ -1,4 +1,5 @@
 """Task I/O specifications."""
+
 from pathlib import Path
 import typing as ty
 import inspect

pydra/engine/state.py

@@ -1,4 +1,5 @@
 """Keeping track of mapping and reduce operations over tasks."""
+
 from copy import deepcopy
 import itertools
 from functools import reduce

pydra/engine/submitter.py

@@ -1,4 +1,5 @@
 """Handle execution backends."""
+
 import asyncio
 import pickle
 from uuid import uuid4

pydra/engine/task.py

@@ -38,6 +38,7 @@
       <https://colab.research.google.com/drive/1RRV1gHbGJs49qQB1q1d5tQEycVRtuhw6>`__
 
 """
+
 from __future__ import annotations
 
 import platform

pydra/engine/tests/test_shelltask.py

@@ -4323,7 +4323,7 @@ def change_name(file):
                         "help_string": "bias field and neck cleanup",
                     },
                 ),
-            )
+            ),
             # ("number_classes", int, attr.ib(metadata={"help_string": 'number of tissue-type classes', "argstr": '-n',
             #                                            "allowed_values": {"min_val": 1, "max_val": 10}})),
             # ("output_biasfield", bool,
@@ -4815,7 +4815,7 @@ def formatter_3(in1, in3):
         == str(excinfo.value)
     )
 
-    # chcking if field value is accessible when None
+    # checking if field value is accessible when None
     def formatter_5(field):
         assert field == "-t test"
         # formatter must return a string
@@ -4832,7 +4832,7 @@ def formatter_5(field):
     )
     assert shelly.cmdline == "exec -t test"
 
-    # chcking if field value is accessible when None
+    # checking if field value is accessible when None
     def formatter_4(field):
         assert field is None
         # formatter must return a string

pydra/engine/workers.py

@@ -1,4 +1,5 @@
 """Execution workers."""
+
 import asyncio
 import sys
 import json

pydra/mark/functions.py

@@ -1,4 +1,5 @@
 """ Decorators to apply to functions used in Pydra workflows """
+
 from functools import wraps
 
 

pydra/tasks/__init__.py

@@ -5,6 +5,7 @@
 To create a task package, please fork the `pydra-tasks-template
 <https://github.com/nipype/pydra-tasks-template>`__.
 """
+
 # This call enables pydra.tasks to be used as a namespace package when installed
 # in editable mode. In normal installations it has no effect.
 __path__ = __import__("pkgutil").extend_path(__path__, __name__)

pydra/utils/hash.py

@@ -1,4 +1,5 @@
 """Generic object hashing dispatch"""
+
 import os
 
 # import stat
@@ -99,7 +100,7 @@ def hash_single(obj: object, cache: Cache) -> Hash:
 @runtime_checkable
 class HasBytesRepr(Protocol):
     def __bytes_repr__(self, cache: Cache) -> Iterator[bytes]:
-        ...  # pragma: no cover
+        pass  # pragma: no cover
 
 
 @singledispatch

pydra/utils/messenger.py

@@ -1,4 +1,5 @@
 """Messaging of states."""
+
 import abc
 import datetime as dt
 import enum
@@ -129,9 +130,11 @@ def send(self, message, **kwargs):
         r = requests.post(
             kwargs["post_url"],
             json=message,
-            auth=kwargs["auth"]()
-            if getattr(kwargs["auth"], "__call__", None)
-            else kwargs["auth"],
+            auth=(
+                kwargs["auth"]()
+                if getattr(kwargs["auth"], "__call__", None)
+                else kwargs["auth"]
+            ),
         )
         return r.status_code
 

pydra/utils/profiler.py

@@ -1,4 +1,5 @@
 """Utilities to keep track of performance and resource utilization."""
+
 from pathlib import Path
 import psutil
 import threading