Update the development environment (#1156)

* pre-commit autoupdate
* Update the conda environments
* Update the development instructions
* Remove unused files

.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

.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"]

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.

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

jupyterlab/packages/jupyterlab-jupytext-extension/README.md

@@ -13,26 +13,25 @@ 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 [email protected]  # for JupyterLab 3.x
 jupyter labextension install [email protected]  # for JupyterLab 2.x
 jupyter labextension install [email protected]  # for JupyterLab 1.x
 ```
 
 # How to develop this extension
 
-We assume that you have activated the conda environment described in [CONTRIBUTING.md](https://github.com/mwouts/jupytext/blob/main/CONTRIBUTING.md).
-
-Then you can rebuild the Jupytext python package (with `python -m build`) and reinstall it (`pip install dist/jupytext-x.x.x-py3-none-any.whl`).
-
-Alternatively, if you prefer to develop iteratively, you could install a development version of the extension with
+Please follow the instructions at [developing.md](../../../docs/developing.md), i.e.
+create a Python environment with a recent version of `nodejs`, and install
+a development version of Jupytext by running
 
 ```bash
-jupyter labextension develop . --overwrite
+pip install -e '.[dev]'
 ```
 
-Read more on this on the [JupyterLab documentation](https://jupyterlab.readthedocs.io/en/latest/extension/extension_dev.html#developing-a-prebuilt-extension).
+at the root of the Jupytext repository.
 
 # How to publish a new version of the extension on npm