Clean up pre-commit

.github/workflows/tests.yml

@@ -75,3 +75,24 @@ jobs:
 
       - name: Code coverage
         run: codecov
+
+  # Run "pre-commit run --all-files --hook-stage=manual"
+  pre-commit:
+    runs-on: ubuntu-20.04
+    timeout-minutes: 5
+    steps:
+      - uses: actions/checkout@v2
+      - uses: jupyterlab/maintainer-tools/.github/actions/base-setup@v1
+      - uses: pre-commit/action@v2.0.0
+        with:
+          extra_args: --all-files --hook-stage=manual
+      - name: Help message if pre-commit fail
+        if: ${{ failure() }}
+        run: |
+          echo "You can install pre-commit hooks to automatically run formatting"
+          echo "on each commit with:"
+          echo "    pre-commit install"
+          echo "or you can run by hand on staged files with"
+          echo "    pre-commit run"
+          echo "or after-the-fact on already committed files with"
+          echo "    pre-commit run --all-files --hook-stage=manual"

.pre-commit-config.yaml

@@ -1,6 +1,3 @@
-ci:
-  skip: [check-jsonschema]
-
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.1.0
@@ -30,6 +27,7 @@ repos:
       - id: isort
         files: \.py$
         args: [--profile=black]
+        stages: [manual]
 
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v2.6.1
@@ -47,6 +45,7 @@ repos:
     hooks:
       - id: doc8
         args: [--max-line-length=200]
+        stages: [manual]
 
   - repo: https://github.com/pycqa/flake8
     rev: 4.0.1
@@ -58,6 +57,7 @@ repos:
             "flake8-logging-format==0.6.0",
             "flake8-implicit-str-concat==0.2.0",
           ]
+        stages: [manual]
 
   - repo: https://github.com/sirosen/check-jsonschema
     rev: 0.14.1
@@ -67,3 +67,4 @@ repos:
         files: ^\.github/workflows/
         types: [yaml]
         args: ["--schemafile", "https://json.schemastore.org/github-workflow"]
+        stages: [manual]

CONTRIBUTING.md

@@ -62,6 +62,9 @@ hook with `pre-commit install`, you can fix everything up using
 `pre-commit run --all-files`. You need to make the fixing commit
 yourself after that.
 
+Some of the hooks only run on CI by default, but you can invoke them by
+running with the `--hook-stage manual` argument.
+
 # Releasing
 
 If you are going to release a version of `nbconvert` you should also be capable