[pre-commit.ci] pre-commit autoupdate (#884)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0](pre-commit/pre-commit-hooks@v4.3.0...v4.4.0)
- [github.com/asottile/pyupgrade: v2.38.2 → v3.3.1](asottile/pyupgrade@v2.38.2...v3.3.1)
- [github.com/PyCQA/isort: 5.10.1 → 5.11.4](PyCQA/isort@5.10.1...5.11.4)
- [github.com/psf/black: 22.8.0 → 22.12.0](psf/black@22.8.0...22.12.0)
- [github.com/PyCQA/flake8: 5.0.4 → 6.0.0](PyCQA/flake8@5.0.4...6.0.0)
- [github.com/pre-commit/mirrors-mypy: v0.981 → v0.991](pre-commit/mirrors-mypy@v0.981...v0.991)

* Fix flake8.

* Update mypy configuration.

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Bradley Dice <bdice@bradleydice.com>

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ exclude: ^signac/_vendor/.*
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 'v4.3.0'
+    rev: 'v4.4.0'
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -17,36 +17,36 @@ repos:
       - id: debug-statements
       - id: requirements-txt-fixer
   - repo: https://github.com/asottile/pyupgrade
-    rev: 'v2.38.2'
+    rev: 'v3.3.1'
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
   - repo: https://github.com/PyCQA/isort
-    rev: '5.10.1'
+    rev: '5.11.4'
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: '22.8.0'
+    rev: '22.12.0'
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
-    rev: '5.0.4'
+    rev: '6.0.0'
     hooks:
       - id: flake8
   - repo: https://github.com/PyCQA/pydocstyle
-    rev: '6.1.1'
+    rev: '6.3.0'
     hooks:
       - id: pydocstyle
         exclude: |
           (?x)^(
             ^doc/|
-            ^tests/|
+            ^tests/
           )
         additional_dependencies:
-          - toml
+          - tomli
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: 'v0.981'
+    rev: 'v0.991'
     hooks:
       - id: mypy
         additional_dependencies:

pyproject.toml

@@ -87,6 +87,15 @@ add-ignore = "D105, D107, D203, D204, D213"
 
 [tool.mypy]
 ignore_missing_imports = true
+scripts_are_modules = true
+exclude = [
+    'signac/_vendor/',
+    'tests/',
+]
+
+[[tool.mypy.overrides]]
+module = "signac._vendor.*"
+follow_imports = 'skip'
 
 [tool.pytest.ini_options]
 xfail_strict = true

signac/_config.py

@@ -68,7 +68,7 @@ def _locate_config_dir(search_path):
         Starting path to search.
 
     Returns
-    --------
+    -------
     str or None
         The directory containing the configuration file if one is found, otherwise None.
     """
@@ -132,7 +132,7 @@ def _load_config(path=None):
         The project path to pull project-local configuration data from.
 
     Returns
-    --------
+    -------
     :class:`_Config`
         The composite configuration including both project-local and global
         config data if requested. Note that because this config is a composite,

signac/_synced_collections/backends/__init__.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2020 The Regents of the University of Michigan
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
-"""This subpackage defines supported backends.
+"""Define supported backends.
 
 No backends are imported by default. Users should import desired backends as
 needed.

signac/_synced_collections/data_types/__init__.py

@@ -1,7 +1,7 @@
 # Copyright (c) 2020 The Regents of the University of Michigan
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
-"""This subpackage defines various synced data types."""
+"""Define various synced data types."""
 
 from .synced_collection import SyncedCollection
 from .synced_dict import SyncedDict

tests/test_project.py

@@ -1564,7 +1564,7 @@ def clean(filter=None):
         all_links = list(_find_all_links(view_prefix))
         dst = set(
             map(
-                lambda l: os.path.realpath(os.path.join(view_prefix, l, "job")),
+                lambda link: os.path.realpath(os.path.join(view_prefix, link, "job")),
                 all_links,
             )
         )
@@ -1575,7 +1575,7 @@ def clean(filter=None):
         assert len(all_links) == len(self.project)
         dst = set(
             map(
-                lambda l: os.path.realpath(os.path.join(view_prefix, l, "job")),
+                lambda link: os.path.realpath(os.path.join(view_prefix, link, "job")),
                 all_links,
             )
         )
@@ -1590,7 +1590,7 @@ def clean(filter=None):
         assert len(all_links) == len(id_subset)
         dst = set(
             map(
-                lambda l: os.path.realpath(os.path.join(view_prefix, l, "job")),
+                lambda link: os.path.realpath(os.path.join(view_prefix, link, "job")),
                 all_links,
             )
         )
@@ -1602,7 +1602,7 @@ def clean(filter=None):
         assert len(all_links) == len(self.project)
         dst = set(
             map(
-                lambda l: os.path.realpath(os.path.join(view_prefix, l, "job")),
+                lambda link: os.path.realpath(os.path.join(view_prefix, link, "job")),
                 all_links,
             )
         )
@@ -1614,7 +1614,7 @@ def clean(filter=None):
         assert len(all_links) == len(self.project)
         dst = set(
             map(
-                lambda l: os.path.realpath(os.path.join(view_prefix, l, "job")),
+                lambda link: os.path.realpath(os.path.join(view_prefix, link, "job")),
                 all_links,
             )
         )