set up precommit hooks

.gitlab-ci.yml

@@ -53,3 +53,15 @@ pages:
     paths:
       - public
 
+run pre-commit:
+  variables:
+    PRE_COMMIT_HOME: $CI_PROJECT_DIR/.pre-commit-cache
+  script:
+    - micromamba install -c conda-forge -y mamba pip pre-commit git
+    - git config --global --add safe.directory $CI_PROJECT_DIR
+    - pre-commit run --all-files
+  cache:
+    key: "$CI_JOB_NAME"
+    paths:
+      - .pre-commit-cache
+      - micromamba

.hooks/pre-commit

-
-#!/bin/sh
-#
-# strip output of IPython Notebooks
-# add this as `.git/hooks/pre-commit`
-# to run every time you commit a notebook
-#
-# requires `jupyter nbconvert` to be available on your PATH
-
-if git rev-parse --verify HEAD >/dev/null 2>&1; then
-   against=HEAD
-else
-   # Initial commit: diff against an empty tree object
-   against=4b825dc642cb6eb9a060e54bf8d69288fbee4904
-fi
-
-# Find notebooks to be committed
-(
-IFS='
-'
-NBS=`git diff-index --cached $against --name-only | grep '.ipynb$' | uniq`
-
-for NB in $NBS ; do
-    echo "Removing outputs from $NB"
-    cp "$NB" "$NB"_backup
-    jupyter nbconvert --to notebook --ClearOutputPreprocessor.enabled=True --ClearOutputPreprocessor.remove_metadata_fields="['deletable', 'editable', 'collapsed', 'scrolled']" "$NB" --output "$NB" --output-dir='.'
-    git add "$NB"
-    mv "$NB"_backup "$NB"
-done
-)
-
-exec git diff-index --check --cached $against --

.pre-commit-config.yaml

+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+-   repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+    -   id: black
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell
+        additional_dependencies:
+        - tomli