CI: Re-enable pre-commit, disable failing checks.

See issue AIM-Harvard#899

Author: JoostJM

.github/workflows/ci.yml

@@ -19,7 +19,6 @@ env:
 
 jobs:
   pre-commit:
-    if: ${{ github.ref_name != 'refactor-build-system' }}
     name: Format
     runs-on: ubuntu-latest
     steps:
@@ -38,7 +37,7 @@ jobs:
   checks:
     name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
     runs-on: ${{ matrix.runs-on }}
-    #needs: [pre-commit]
+    needs: [pre-commit]
     strategy:
       fail-fast: false
       matrix:

.pre-commit-config.yaml

@@ -18,73 +18,75 @@ repos:
       - id: check-case-conflict
       - id: check-merge-conflict
       - id: check-symlinks
-      - id: check-yaml
+      #- id: check-yaml  # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
-      - id: name-tests-test
-        args: ["--pytest-test-first"]
+      #- id: name-tests-test  # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
+      #  args: ["--pytest-test-first"]
       - id: requirements-txt-fixer
-      - id: trailing-whitespace
+      #- id: trailing-whitespace  # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
 
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: "v1.10.0"
     hooks:
-      - id: rst-backticks
+      #- id: rst-backticks  # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
 
-  - repo: https://github.com/rbubley/mirrors-prettier
-    rev: "v3.4.2"
-    hooks:
-      - id: prettier
-        types_or: [yaml, markdown, html, css, scss, javascript, json]
-        args: [--prose-wrap=always]
+  # See Issue #899 (https://github.com/AIM-Harvard/pyradiomics/issues/899)
 
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.9.2"
-    hooks:
-      - id: ruff
-        args: ["--fix", "--show-fixes"]
-      - id: ruff-format
+  #- repo: https://github.com/rbubley/mirrors-prettier
+  #  rev: "v3.4.2"
+  #  hooks:
+  #    - id: prettier
+  #      types_or: [yaml, markdown, html, css, scss, javascript, json]
+  #      args: [--prose-wrap=always]
 
-  - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v19.1.7"
-    hooks:
-      - id: clang-format
-        types_or: [c++, c, cuda]
+  #- repo: https://github.com/astral-sh/ruff-pre-commit
+  #  rev: "v0.9.2"
+  #  hooks:
+  #    - id: ruff
+  #      args: ["--fix", "--show-fixes"]
+  #    - id: ruff-format
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.14.1"
-    hooks:
-      - id: mypy
-        files: src|tests
-        args: []
-        additional_dependencies:
-          - pytest
+  #- repo: https://github.com/pre-commit/mirrors-clang-format
+  #  rev: "v19.1.7"
+  #  hooks:
+  #    - id: clang-format
+  #      types_or: [c++, c, cuda]
 
-  - repo: https://github.com/codespell-project/codespell
-    rev: "v2.3.0"
-    hooks:
-      - id: codespell
+  #- repo: https://github.com/pre-commit/mirrors-mypy
+  #  rev: "v1.14.1"
+  #  hooks:
+  #    - id: mypy
+  #      files: src|tests
+  #      args: []
+  #      additional_dependencies:
+  #        - pytest
 
-  - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.10.0.1"
-    hooks:
-      - id: shellcheck
+  #- repo: https://github.com/codespell-project/codespell
+  #  rev: "v2.3.0"
+  #  hooks:
+  #    - id: codespell
 
-  - repo: local
-    hooks:
-      - id: disallow-caps
-        name: Disallow improper capitalization
-        language: pygrep
-        entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
-        exclude: .pre-commit-config.yaml
+  #- repo: https://github.com/shellcheck-py/shellcheck-py
+  #  rev: "v0.10.0.1"
+  #  hooks:
+  #    - id: shellcheck
 
-  - repo: https://github.com/cheshirekow/cmake-format-precommit
-    rev: "v0.6.13"
-    hooks:
-      - id: cmake-format
+  #- repo: local
+  #  hooks:
+  #    - id: disallow-caps
+  #      name: Disallow improper capitalization
+  #      language: pygrep
+  #      entry: PyBind|Numpy|Cmake|CCache|Github|PyTest
+  #      exclude: .pre-commit-config.yaml
+
+  #- repo: https://github.com/cheshirekow/cmake-format-precommit
+  #  rev: "v0.6.13"
+  #  hooks:
+  #    - id: cmake-format
 
   - repo: https://github.com/abravalheri/validate-pyproject
     rev: "v0.23"