Various improvements (Sourcery refactored)

.github/CODEOWNERS

@@ -28,18 +28,18 @@ LICENSE                             @glotaran/pyglotaran_creators
 # /docs/**/*.md                     @glotaran/maintainers @glotaran/pyglotaran_creators
 
 # analysis module:
-/glotaran/analysis/                 @jsnel @joernweissenborn
+# /glotaran/analysis/                 @jsnel @joernweissenborn
 
 # builtin module:
 /glotaran/builtin/io/*              @glotaran/admins
 /glotaran/builtin/io/ascii          @jsnel @glotaran/maintainers
 /glotaran/builtin/io/pandas         @glotaran/maintainers
 /glotaran/builtin/io/netCDF         @glotaran/maintainers
 /glotaran/builtin/io/sdt            @glotaran/maintainers
-/glotaran/builtin/megacomplexes/    @jsnel @joernweissenborn
+# /glotaran/builtin/megacomplexes/    @jsnel @joernweissenborn
 
-# cli
-/glotaran/cli/                      @jsnel @glotaran/admins
+# cli (deprecated)
+# /glotaran/cli/                      @jsnel @glotaran/admins
 
 # examples # Removed in PR #866
 # /glotaran/examples/                 @jsnel @glotaran/maintainers

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
 repos:
   # Formatters
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-ast
       - id: check-builtin-literals
@@ -19,7 +19,7 @@ repos:
         args: [--remove]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.0
     hooks:
       - id: pyupgrade
         types: [file]
@@ -36,7 +36,7 @@ repos:
         types_or: [python, pyi]
 
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
       - id: black
         types: [file]
@@ -52,7 +52,7 @@ repos:
         minimum_pre_commit_version: 2.9.0
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v2.4.0
+    rev: v2.5.0
     hooks:
       - id: setup-cfg-fmt
         args: [--include-version-classifiers]
@@ -103,24 +103,24 @@ repos:
         args:
           - "--count"
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
-    hooks:
-      - id: flake8
-        alias: flake8-docs
-        args:
-          - "--select=D,DAR"
-          - "--count"
-        name: "flake8 lint docstrings"
-        exclude: "docs|setup.py|tests?/|glotaran/builtin/megacomplexes|glotaran/cli|benchmark|glotaran/builtin/io/ascii"
-        additional_dependencies: [flake8-docstrings, darglint==1.8.0]
+  # - repo: https://github.com/PyCQA/flake8
+  #   rev: 6.0.0
+  #   hooks:
+  #     - id: flake8
+  #       alias: flake8-docs
+  #       args:
+  #         - "--select=D,DAR"
+  #         - "--count"
+  #       name: "flake8 lint docstrings"
+  #       exclude: "docs|setup.py|tests?/|glotaran/builtin/megacomplexes|glotaran/cli|benchmark|glotaran/builtin/io/ascii"
+  #       additional_dependencies: [flake8-docstrings, darglint==1.8.0]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.6.0
     hooks:
       - id: mypy
         exclude: "docs|benchmark/|.*/tests?/.*"
-        additional_dependencies: [types-all, types-attrs]
+        additional_dependencies: [types-all, types-attrs, pydantic]
 
   - repo: https://github.com/econchick/interrogate
     rev: 1.5.0
@@ -131,28 +131,29 @@ repos:
         additional_dependencies: [click<8]
 
   - repo: https://github.com/rstcheck/rstcheck
-    rev: "v6.1.2"
+    rev: "v6.2.0"
     hooks:
       - id: rstcheck
         additional_dependencies: [sphinx]
         exclude: "^docs/source/_templates"
 
-  - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.10.0
-    hooks:
-      - id: rst-backticks
-      - id: python-check-blanket-noqa
-        exclude: "docs|tests?"
-      - id: python-check-blanket-type-ignore
-        exclude: "docs|tests?"
-      - id: python-use-type-annotations
-      - id: rst-directive-colons
-      - id: rst-inline-touching-normal
+  # - repo: https://github.com/pre-commit/pygrep-hooks
+  #   rev: v1.10.0
+  #   hooks:
+  #     - id: rst-backticks
+  #     - id: python-check-blanket-noqa
+  #       exclude: "docs|tests?"
+  #     - id: python-check-blanket-type-ignore
+  #       exclude: "docs|tests?"
+  #     - id: python-use-type-annotations
+  #     - id: rst-directive-colons
+  #     - id: rst-inline-touching-normal
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - id: codespell
         types: [file]
         types_or: [python, pyi, markdown, rst, jupyter]
-        args: [-L doas]
+        args:
+          - --ignore-words-list=glotaran,doas,projectio