Merge branch 'main' into jlab_frontend_extension

mwouts · Nov 12, 2023 · ef304e9 · ef304e9
2 parents 3612e89 + 865a242
commit ef304e9
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diff --git a/.ci/environment-ci.yml b/.ci/environment-ci.yml
@@ -15,7 +15,7 @@ dependencies:
   - nbformat>=5.1.2
   - pyyaml
   - toml
-  - markdown-it-py~=1.0
+  - markdown-it-py
   - mdit-py-plugins
   - pip
   - pytest
@@ -25,7 +25,7 @@ dependencies:
   - flake8
   - autopep8
   - black
-  - isort>=5.3.0
+  - isort
   - pandoc==2.16.2
   - sphinx-gallery<0.8
   - pre-commit

diff --git a/.lgtm.yml b/.lgtm.yml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,31 +18,19 @@ exclude: >
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-json
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.9.0
+    rev: v3.15.0
     hooks:
     - id: pyupgrade
       args: ["--py38-plus"]
 
-  - repo: https://github.com/myint/autoflake
-    rev: v2.2.0
-    hooks:
-    - id: autoflake
-      args: ['--in-place', '--remove-all-unused-imports', '--remove-unused-variable']
-
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.0
-    hooks:
-      - id: ruff
-        args: ["--fix", "--show-fixes"]
-
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
@@ -52,6 +40,12 @@ repos:
       args: ["--profile", "black"]
 
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.11.0
     hooks:
     - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.5
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
diff --git a/Makefile b/Makefile
diff --git a/docs/advanced-options.md b/docs/advanced-options.md
@@ -39,4 +39,4 @@ You might want to make some cell active only when the notebook is run in Jupyter
 
 ## More options
 
-There are a couple more options available - please have a look at the `JupytextConfiguration` class in [config.py](https://github.com/mwouts/jupytext/blob/main/jupytext/config.py).
+There are a couple more options available - please have a look at the `JupytextConfiguration` class in [config.py](https://github.com/mwouts/jupytext/blob/main/src/jupytext/config.py).
diff --git a/docs/developing.md b/docs/developing.md
@@ -22,11 +22,14 @@ Most of Jupytext's code is written in Python. To develop the Python part of Jupy
 ```
 conda env create --file environment.yml  # or conda env update --file ...
 conda activate jupytext-dev
-python -m ipykernel install --name jupytext-dev --user
-pip install -e .
 ```
 
-We use the [pre-commit](https://pre-commit.com) package to run pre-commit scripts like `black` and `flake8` on the code.
+Install the `jupytext` package in development mode with
+```
+pip install -e '.[dev]'
+```
+
+We use the [pre-commit](https://pre-commit.com) package to run pre-commit scripts like `black` and `ruff` on the code.
 Install it with
 ```
 pre-commit install
@@ -37,20 +40,11 @@ Tests are executed with `pytest`. You can run them in parallel with for instance
 pytest -n 5
 ```
 
-Build the `jupytext` package and install it with
-```
-pip install -U build wheel
-python -m build
-pip install dist/jupytext-x.x.x-py3-none-any.whl
+Some tests require a Jupyter kernel pointing to the current environment:
 ```
-
-or with
-```
-pip install .
+python -m ipykernel install --name jupytext-dev --user
 ```
 
-Finally, note that you can use `HATCH_BUILD_HOOKS_ENABLE=false` if you don't need the lab extension - the build time will be slightly shorter.
-
 ## Jupytext's extension for JupyterLab
 
 Our extension for JupyterLab adds a series of Jupytext commands to JupyterLab. The code is in `packages/labextension`. See the `README.md` there for instructions on how to develop that extension.

diff --git a/docs/formats-scripts.md b/docs/formats-scripts.md
@@ -2,7 +2,7 @@
 
 ## The `percent` format
 
-The `percent` format is a representation of Jupyter notebooks as scripts, in which all cells are explicitly delimited with a commented double percent sign `# %%`. The `percent` format is currently available for these [languages](https://github.com/mwouts/jupytext/blob/main/jupytext/languages.py).
+The `percent` format is a representation of Jupyter notebooks as scripts, in which all cells are explicitly delimited with a commented double percent sign `# %%`. The `percent` format is currently available for these [languages](https://github.com/mwouts/jupytext/blob/main/src/jupytext/languages.py).
 
 The format was introduced by Spyder in 2013, and is now supported by many editors, including
 - [Spyder IDE](https://docs.spyder-ide.org/editor.html#defining-code-cells),
@@ -70,7 +70,7 @@ By default, [Jupyter magics](advanced-options.md#magic-commands) are commented i
 
 ## The `light` format
 
-The `light` format was introduced by Jupytext. That format can represent any script in one of these [languages](https://github.com/mwouts/jupytext/blob/main/jupytext/languages.py) as a Jupyter notebook.
+The `light` format was introduced by Jupytext. That format can represent any script in one of these [languages](https://github.com/mwouts/jupytext/blob/main/src/jupytext/languages.py) as a Jupyter notebook.
 
 When a script in the `light` format is converted to a notebook, Jupytext code paragraphs are turned into code cells, and comments that are not adjacent to code are converted to Markdown cells. Cell breaks occurs on blank lines outside of functions, classes or multiline comments.
 

diff --git a/environment.yml b/environment.yml
@@ -12,25 +12,17 @@ dependencies:
   - mdit-py-plugins
   - nbconvert
   - ipykernel
-  - jupyter_contrib_nbextensions
   - pytest
   - pytest-xdist
   - pytest-randomly
   - pytest-cov
   - pre-commit
   - gitpython
   - pylint
-  - flake8==3.9.1
-  - black==21.4b2
-  - isort==5.8.0
+  - flake8
+  - black==23.11.0
+  - isort==5.12.0
   - autopep8
   - sphinx-gallery<0.8
-  - pip
-  - setuptools
-  - twine
   - pandoc==2.16.2
-  # make html in docs folder
-  - sphinx
-  - tox-conda
-  - pip:
-    - sphinx_copybutton
+  - nodejs>=20
diff --git a/jupyterlab/packages/jupyterlab-jupytext-extension/README.md b/jupyterlab/packages/jupyterlab-jupytext-extension/README.md
@@ -13,9 +13,10 @@ Most users do not need to install this extension, since it is already included i
 
 Please install [Jupytext](https://github.com/mwouts/jupytext/blob/main/README.md#Install) first. As mentioned above, both the `pip` and `conda` packages do include the latest version of the JupyterLab extension, so in most cases you don't need to specifically install this `npm` package.
 
-In case you're not using JupyterLab 3.x, you will have to install an older version of the extension that is compatible with your version. Please first install `jupytext` using `pip` or `conda`, and then downgrade the extension to a version compatible with your version of Jupyter Lab with:
+In case you're not using JupyterLab 4.x, you will have to install an older version of the extension that is compatible with your version. Please first install `jupytext` using `pip` or `conda`, and then downgrade the extension to a version compatible with your version of Jupyter Lab with:
 
 ```bash
+jupyter labextension install jupyterlab-jupytext@1.3.11  # for JupyterLab 3.x
 jupyter labextension install jupyterlab-jupytext@1.2.2  # for JupyterLab 2.x
 jupyter labextension install jupyterlab-jupytext@1.1.1  # for JupyterLab 1.x
 ```
@@ -31,6 +32,8 @@ jlpm
 jlpm install:extension     # Symlink into `{sys.prefix}/share/jupyter/labextensions`
 ```
 
+(see also the instructions at [developing.md](../../../docs/developing.md) on how to create a Python environment with a recent version of `nodejs`)
+
 Watch the source directory and automatically rebuild the `lib` folder:
 
 ```bash

diff --git a/make.bat b/make.bat