pre-commit: fix stages

.github/workflows/tests.yml

@@ -43,9 +43,9 @@ jobs:
     - name: Lint with black
       run: pre-commit run black --show-diff-on-failure
     - name: Lint with flake8
-      run: pre-commit run flake8
+      run: pre-commit run flake8 --hook-stage manual
     - name: Check types with mypy
-      run:  pre-commit run mypy
+      run:  pre-commit run mypy --hook-stage manual
 
   rule_linter:
     runs-on: ubuntu-20.04
@@ -98,7 +98,7 @@ jobs:
     - name: Run tests (fast)
       # this set of tests runs about 80% of the cases in 20% of the time,
       # and should catch most errors quickly.
-      run:  pre-commit run pytest-fast --all-files
+      run:  pre-commit run pytest-fast --all-files --hook-stage manual
     - name: Run tests
       run: pytest -v tests/
 

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
     hooks:
     -   id: isort
         name: isort
-        stages: [commit, push]
+        stages: [commit, push, manual]
         language: system
         entry: isort
         args: 
@@ -45,7 +45,7 @@ repos:
     hooks:
     -   id: black
         name: black
-        stages: [commit, push]
+        stages: [commit, push, manual]
         language: system
         entry: black
         args: 
@@ -62,7 +62,7 @@ repos:
     hooks:
     -   id: ruff
         name: ruff
-        stages: [commit, push]
+        stages: [commit, push, manual]
         language: system
         entry: ruff
         args: 
@@ -79,7 +79,7 @@ repos:
     hooks:
     -   id: flake8
         name: flake8
-        stages: [push]
+        stages: [push, manual]
         language: system
         entry: flake8
         args: 
@@ -97,7 +97,7 @@ repos:
     hooks:
     -   id: mypy
         name: mypy
-        stages: [push]
+        stages: [push, manual]
         language: system
         entry: mypy
         args: 

doc/installation.md

@@ -107,16 +107,17 @@ We use [pre-commit](https://pre-commit.com/) so that its trivial to run the same
 
 Run all linters liks:
 
-    ❯ pre-commit run --all-files
+    ❯ pre-commit run --hook-stage manual
     isort....................................................................Passed
     black....................................................................Passed
     ruff.....................................................................Passed
     flake8...................................................................Passed
     mypy.....................................................................Passed
+    pytest (fast)............................................................Passed
 
 Or run a single linter like:
 
-    ❯ pre-commit run --all-files isort
+    ❯ pre-commit run --hook-stage manual isort
     isort....................................................................Passed