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General

  • Please follow pep8 to format Python code.

Install all required packages for testing

pip install -r pip-requirements-test.txt
sh conda-requirements-test.sh

Making a Release

We use Versioneer to automatically update the version string (of a release but also in development). This means for a release a new git tag should be created. The tag should be of the form vX.Y or vX.Y.Z and generally follow pep440 with a prefixed "v".

git tag  -a vX.Y -m "version X.Y"
git push
git push origin --tags

python setup.py sdist
# Upload with twine:
twine upload dist/nglview*gz

Install

Install developer mode so you don't need to re-install after chaning your code.

pip install -e .

Test

pytest -vs nglview/tests/

Sync versions

There is not yet an elegant way to sync version in nglview/widget.py; js/package.json and jslab/package.json So make sure to update those

nglview/wiget.py: __frontend_version__ = '0.5.4-dev.13'
js/package.json:              "version": "0.5.4-dev.13",
jslab/package.json: "@jupyter-widgets/jupyterlab-manager": "^0.25.11", # make sure this compat with ipywidgets
jslab/package.json: "nglview-js-widgets": "0.5.4-dev.13"

Update Javascript build

# install nodejs
# conda install -c javascript nodejs

cd js
npm install

# known working versions:
# node: v6.6.0
# npm: 4.4.4

# then python setup.py install or pip install -e . # development, you can edit the source code without re-installing

# Tips
# - After changing js code:
#     - Kernel --> Restart and Clear Output
#     - Refresh webpage (F5)

# run quick test in terminal
nglview demo

My (Hai) workflow

cd /nglview/root/folder

# install development version for Python code
# so we can update Python source code without reinstall
pip install -e .
# Now you can start changing Python source code.

# make symlink the js code (nglview/static/*js)
# to $PREFIX/share/jupyter/nbextensions
# Example of $PREFIX: $HOME/miniconda3/
# Double-check
# $ ll $HOME/miniconda3/share/jupyter/nbextensions/
# Will see something like
# nglview-js-widgets@ -> $HOME/3d/nglview/nglview/static

nglview install --symlink
nglview enable

# Now, you can update JS code in js/src folder
cd js
npm install

# If your notebook is openning and you did above step, you need to clear the web cache via two steps
- Restart your notebook (Kernel -> Restart and Clear Output)
- Refresh browser (F5)

Jupyterlab Development

Installation:

# Install deps
conda create -n ngl python>=3.5
conda activate ngl
conda env update -f environment.yml

# Install nglview Python package
python -m pip install --no-deps -e .

# Install ipywidgets JLab extension
jupyter labextension install @jupyter-widgets/jupyterlab-manager

For a development install (requires npm version 4 or later), do the following in the repository directory:

cd js/
jlpm
jlpm build
jupyter labextension link .

You can watch the source directory and run JupyterLab in watch mode to watch for changes in the extension's source and automatically rebuild the extension and application.

# Watch the source directory in another terminal tab
jlpm watch

# Run jupyterlab in watch mode in one terminal tab
cd ../
jupyter lab --watch --no-browser

Using NGL locally

  1. Change var NGL = require('ngl'); to var NGL = require('./ngl'); https://github.com/arose/nglview/blob/master/js/src/widget_ngl.js#L2

  2. Then, build NGL, then copy ngl.js (or ngl.dev.js) to nglview/js/src/

  3. Rebuild js code

cd js
npm install
nglview install # install updated js code
nglview enable # enable again, (not sure if needed)

You need to install nodejs (which includes npm). Tips: conda install nodejs -c conda-forge (and so on)

Test notebook

  • [edit to add more notebooks] and update notebook files
python ./devtools/make_test_js.py --api
npm install -g nightwatch
  • install notebook runner
source devtools/travis-ci/clone_nbtest.sh # only once
  • (may be): To avoid entering notebook token or password, you might want to update
# in $HOME/.jupyter/jupyter_notebook_config.py
c.NotebookApp.token = ''
  • Run notebook server
jupyter notebook --port=8889 &
  • Run all tests
nightwatch
  • Run a single test
# nightwatch /path/to/your/file.js
nightwatch nglview/tests/js/render_image.js

More stuff

wiki