Update CI to work with pre-commit

Check stage tries to find the commit hash being merged into

Uses that hash to get  a list of changed files

Passes this list of files to pre-commit so that checks only run on
modified files

.gitlab-ci.yml

-isort:
-  stage: test
+stages:
+  - check
+  - test
+
+checks:
+  stage: check
+  only: [merge_requests]
   script:
-    - python3 -m pip install --user isort==5.6.4
-    - isort --diff **/*.py && isort -c **/*.py
+    - export PATH=/home/gitlab-runner/.local/bin:$PATH
+    - export CI_MERGE_REQUEST_TARGET_BRANCH_SHA=$(git ls-remote origin $CI_MERGE_REQUEST_TARGET_BRANCH_NAME | cut -d$'\t' -f1)
+    - export FILES=$(git diff $CI_COMMIT_SHA  $CI_MERGE_REQUEST_TARGET_BRANCH_SHA --name-only | tr '\n' ' ')
+    - echo "Running pre-commit on diff from  $CI_COMMIT_SHA to $CI_MERGE_REQUEST_TARGET_BRANCH_SHA ($CI_MERGE_REQUEST_TARGET_BRANCH_NAME)"
+    - python3 -m pip install --user -r requirements.txt
+    - echo $FILES | xargs pre-commit run --color=always --files
 
 pytest:
   stage: test
+  only: [merge_requests]
   script:
     - python3 -m pip install --user -r requirements.txt
     - python3 -m pip install --user pytest