fix: Get CI running again

.github/workflows/continuous-integration.yml

@@ -23,12 +23,37 @@ jobs:
     if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
-      - uses: pre-commit/[email protected]
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]
+
+  lint:
+    name: Lint
+    needs: skip_duplicate
+    if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # all Python files should follow PEP8 (except some notebooks, see setup.cfg)
+          flake8 jupytext tests
+          # exit-zero treats all errors as warnings.  The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --statistics
 
   analyse:
     name: Analyse
@@ -38,7 +63,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           # We must fetch at least the immediate parents so that if this is
           # a pull request then we can check out the head.
@@ -60,41 +85,29 @@ jobs:
         uses: github/codeql-action/analyze@v1
 
   test-pip:
-    needs: skip_duplicate
+    needs: lint
     if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
     strategy:
       matrix:
         python-version: [ 3.7, 3.8, 3.9, "3.10", "3.11"]
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
-          # install black, isort, and autopep8 for testing the pipe mode
-          pip install black
-          pip install isort>=5.3.0
-          pip install autopep8
+          python -m pip install -r requirements.txt
+          python -m pip install -r requirements-dev.txt
           # install sphinx_gallery and matplotlib if available (may not work on pypy)
-          pip install sphinx_gallery~=0.7.0 || true
-          pip install jupyter-fs || true
-      - name: Lint with flake8
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # all Python files should follow PEP8 (except some notebooks, see setup.cfg)
-          flake8 jupytext tests
-          # exit-zero treats all errors as warnings.  The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --statistics
+          python -m pip install sphinx_gallery~=0.7.0 || true
+          python -m pip install jupyter-fs || true
       - name: Install from source (required for the pre-commit tests)
-        run: pip install .
+        run: python -m pip install .
       - name: Install a Jupyter Kernel
         run: python -m ipykernel install --name python_kernel --user
       - name: Install Quarto
@@ -111,7 +124,7 @@ jobs:
         uses: codecov/codecov-action@v1
 
   test-conda:
-    needs: skip_duplicate
+    needs: lint
     if: ${{ needs.skip_duplicate.outputs.should_skip == 'false' }}
     strategy:
       matrix:
@@ -120,9 +133,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Cache conda
-        uses: actions/cache@v1
+        uses: actions/cache@v3
         with:
           path: ~/conda_pkgs_dir
           key: conda-${{ matrix.os }}-python-${{ matrix.python-version }}-${{ hashFiles('environment-ci.yml') }}
@@ -136,19 +149,10 @@ jobs:
           channels: defaults,conda-forge
           environment-file: environment-ci.yml
           use-only-tar-bz2: true
-      - name: Lint with flake8
-        shell: pwsh
-        run: |
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # all Python files should follow PEP8 (except some notebooks, see setup.cfg)
-          flake8 jupytext tests
-          # exit-zero treats all errors as warnings.  The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --statistics
       - name: Install from source
         # This is required for the pre-commit tests
         shell: pwsh
-        run: pip install .
+        run: python -m pip install .
       - name: Create kernel
         shell: pwsh
         run: |
@@ -177,17 +181,17 @@ jobs:
       runs-on: ubuntu-latest
       steps:
         - name: Checkout
-          uses: actions/checkout@v2
+          uses: actions/checkout@v3
         - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v2
+          uses: actions/setup-python@v4
           with:
             python-version: ${{ matrix.python-version }}
         - name: Install dependencies, except markdown-it-py
           run: |
             python -m pip install --upgrade pip
             # All dependencies but markdown-it-py
-            pip install nbformat pyyaml toml
-            pip install -r requirements-dev.txt
+            python -m pip install nbformat pyyaml toml
+            python -m pip install -r requirements-dev.txt
         - name: Install a Jupyter Kernel
           run: python -m ipykernel install --name python_kernel --user
         - name: Test with pytest
@@ -204,16 +208,16 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
+          python -m pip install -r requirements.txt
+          python -m pip install -r requirements-dev.txt
       - name: Test with pytest
         run: pytest --cov=./ --cov-report=xml
       - name: Upload coverage
@@ -228,19 +232,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           # All dependencies but markdown-it-py
-          pip install -r requirements.txt
-          pip install -r requirements-dev.txt
+          python -m pip install -r requirements.txt
+          python -m pip install -r requirements-dev.txt
           # Notebook pre-release version #933
-          pip install --pre -U notebook
+          python -m pip install --pre -U notebook
       - name: Install a Jupyter Kernel
         run: python -m ipykernel install --name python_kernel --user
       - name: Test with pytest
@@ -253,14 +257,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python 3.9
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       - name: Build package
         run: |
-          pip install wheel jupyter-packaging jupyterlab>=3
+          python -m pip install wheel jupyter-packaging jupyterlab>=3
           BUILD_JUPYTERLAB_EXTENSION=1 python setup.py sdist bdist_wheel
           # Don't publish a tar.gz file over 1MB  (Issue #730)
           if (($(wc -c < dist/*.tar.gz) > 1000000)); then exit 1; fi
@@ -270,7 +274,7 @@ jobs:
           if (($(tar -tf dist/*.tar.gz | grep packages/labextension/package.json$ | wc -l)==0)); then echo "Missing lab extension" && exit 1; fi
           if (($(tar -tf dist/*.tar.gz | grep jupytext/nbextension/index.js$ | wc -l)==0)); then echo "Missing notebook extension" && exit 1; fi
           # Install
-          pip install dist/*.tar.gz
+          python -m pip install dist/*.tar.gz
           echo "Install went OK"
   publish:
     name: Publish to PyPi
@@ -279,14 +283,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up Python 3.9
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       - name: Build package
         run: |
-          pip install wheel jupyter-packaging jupyterlab>=3
+          python -m pip install wheel jupyter-packaging jupyterlab>=3
           BUILD_JUPYTERLAB_EXTENSION=1 python setup.py sdist bdist_wheel
       - name: Publish
         uses: pypa/[email protected]

.pre-commit-config.yaml

@@ -18,39 +18,39 @@ exclude: >
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.4.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.31.1
+    rev: v3.3.1
     hooks:
     - id: pyupgrade
       args: ["--py36-plus"]
 
   - repo: https://github.com/myint/autoflake
-    rev: v1.4
+    rev: v2.0.1
     hooks:
     - id: autoflake
       args: ['--in-place', '--remove-all-unused-imports', '--remove-unused-variable']
 
   - repo: https://github.com/pycqa/flake8
-    rev: 3.9.2
+    rev: 6.0.0
     hooks:
     - id: flake8
 
   - repo: https://github.com/PyCQA/isort
-    rev: 5.10.1
+    rev: 5.12.0
     hooks:
       # isort needs the 'black' profile when used in combination with black
       # See https://github.com/PyCQA/isort/issues/1518
     - id: isort
       args: ["--profile", "black"]
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
     - id: black

jupytext/cell_reader.py

@@ -770,7 +770,6 @@ def find_region_end(self, lines):
                     self.cell_marker_start or i == 0 or _BLANK_LINE.match(lines[i - 1])
                 )
             ):
-
                 if self.explicit_end_marker_required:
                     # Metadata here was conditioned on finding an explicit end marker
                     # before the next start marker. So we dismiss it.

jupytext/compare.py

@@ -246,7 +246,6 @@ def compare_cells(
         if (ref_cell.cell_type == "code" and not allow_missing_code_cell_metadata) or (
             ref_cell.cell_type != "code" and not allow_missing_markdown_cell_metadata
         ):
-
             ref_metadata = ref_cell.metadata
             test_metadata = test_cell.metadata
             if allow_filtered_cell_metadata:

jupytext/myst.py

@@ -311,7 +311,6 @@ def _flush_markdown(start_line, token, md_metadata):
     md_metadata = {}
 
     for token in tokens:
-
         nesting_level += token.nesting
 
         if nesting_level != 0:
@@ -381,7 +380,6 @@ def notebook_to_myst(
 
     last_cell_md = False
     for i, cell in enumerate(nb.cells):
-
         if cell.cell_type == "markdown":
             metadata = from_nbnode(cell.metadata)
             if metadata or last_cell_md:

tests/test_combine.py

@@ -46,7 +46,7 @@ def test_read_text_and_combine_with_outputs(tmpdir):
     tmp_ipynb = "notebook.ipynb"
     tmp_script = "notebook.py"
 
-    with (open(str(tmpdir.join(tmp_script)), "w")) as fp:
+    with open(str(tmpdir.join(tmp_script)), "w") as fp:
         fp.write(
             """# ---
 # jupyter:
@@ -61,7 +61,7 @@ def test_read_text_and_combine_with_outputs(tmpdir):
 """
         )
 
-    with (open(str(tmpdir.join(tmp_ipynb)), "w")) as fp:
+    with open(str(tmpdir.join(tmp_ipynb)), "w") as fp:
         fp.write(
             """{
  "cells": [

tests/test_hide_remove_input_outputs_rmarkdown.py

@@ -56,7 +56,8 @@ def test_jupyter_book_options_to_rmarkdown(md, rmd):
 )
 def test_runtools_options_to_rmarkdown(md, rmd):
     """Options set by the runtools extension are mapped to the corresponding R Markdown options
-    https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/nbextensions/runtools/readme.html"""
+    https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/nbextensions/runtools/readme.html
+    """
     md = (
         "```python "
         + md

tests/test_read_simple_python.py

@@ -1209,7 +1209,6 @@ def test_arg(arg):
     ],
 )
 def test_indented_magic_commands(script, cell):
-
     nb = jupytext.reads(script, "py")
     assert len(nb.cells) == 1
     assert nb.cells[0].cell_type == "code"