.pre-commit add code spell args

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: "^LICENSES"
 
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
+- repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.3.0
   hooks:
   - id: check-merge-conflict
@@ -13,44 +13,41 @@ repos:
     args: ["--maxkb=2000"]
 
   # Sort package imports alphabetically
-  - repo: https://github.com/PyCQA/isort
+- repo: https://github.com/PyCQA/isort
   rev: 5.10.1
   hooks:
   - id: isort
     args: ["--profile", "black", "--filter-files"]
 
   # Convert relative imports to absolute imports
-  - repo: https://github.com/MarcoGorelli/absolufy-imports
+- repo: https://github.com/MarcoGorelli/absolufy-imports
   rev: v0.3.1
   hooks:
   - id: absolufy-imports
 
   # Find common spelling mistakes in comments and docstrings
-  - repo: https://github.com/codespell-project/codespell
+- repo: https://github.com/codespell-project/codespell
   rev: v2.2.1
   hooks:
   - id: codespell
-        args: [
+    args: ['--ignore-regex="(\b[A-Z]+\b)"', '--ignore-words-list=FOM'] # Ignore capital case words, e.g. country codes
-            '--ignore-regex="(\b[A-Z]+\b)"',
-          ] # Ignore capital case words, e.g. country codes
     types_or: [python, rst, markdown]
     files: ^(scripts|doc)/
 
   # Make docstrings PEP 257 compliant
-  - repo: https://github.com/myint/docformatter
+- repo: https://github.com/myint/docformatter
   rev: v1.5.0
   hooks:
   - id: docformatter
-        args:
+    args: ["--in-place", "--make-summary-multi-line", "--pre-summary-newline"]
-          ["--in-place", "--make-summary-multi-line", "--pre-summary-newline"]
 
-  - repo: https://github.com/keewis/blackdoc
+- repo: https://github.com/keewis/blackdoc
   rev: v0.3.5
   hooks:
   - id: blackdoc
 
   # Formatting with "black" coding style
-  - repo: https://github.com/psf/black
+- repo: https://github.com/psf/black
   rev: 22.8.0
   hooks:
       # Format Python files
@@ -59,27 +56,27 @@ repos:
   - id: black-jupyter
 
   # Remove output from Jupyter notebooks
-  - repo: https://github.com/aflc/pre-commit-jupyter
+- repo: https://github.com/aflc/pre-commit-jupyter
   rev: v1.2.1
   hooks:
   - id: jupyter-notebook-cleanup
     args: ["--remove-kernel-metadata"]
 
   # Do YAML formatting (before the linter checks it for misses)
-  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
+- repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
   rev: v2.4.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --indent, "2", --preserve-quotes]
 
   # Format Snakemake rule / workflow files
-  - repo: https://github.com/snakemake/snakefmt
+- repo: https://github.com/snakemake/snakefmt
   rev: 0.4.4
   hooks:
   - id: snakefmt
 
   # For cleaning jupyter notebooks
-  -   repo: https://github.com/aflc/pre-commit-jupyter
+- repo: https://github.com/aflc/pre-commit-jupyter
   rev: v1.2.1
   hooks:
   - id: jupyter-notebook-cleanup