MyBinder + JupyterLab: *JupyterLab build is suggested*

[thewtex]

I don't know if this is a JupyterLab or MyBinder or jupyter-matplotlib issue, but in this Binder link

https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKElastix/master?urlpath=lab/tree/examples%2F0_HelloRegistrationWorld.ipynb

for this repository:

https://github.com/InsightSoftwareConsortium/ITKElastix

The pop-up dialog is persistent:

Build Recommended
JupyterLab build is suggested:
jupyter-matplotlib changed from file:../extensions/jupyter-matplotlib-0.4.0.tgz to file:../extensions/jupyter-matplotlib-0.4.1.tgz

in spite of trying to fix the jupyter-matplotlib versions:

InsightSoftwareConsortium/ITKElastix@f26e70c

(the message before this references jupyter-matplotlib-0.5.0).

Any ideas how to resolve this?

[consideRatio]

My issue

jupyter-matplotlib changed from file:…/extensions/jupyter-matplotlib-0.5.0.tgz to file:…/extensions/jupyter-matplotlib-0.4.1.tgz

My guess

I figure something is set on using the NPM package with the jupyterlab extension of jupyter-matplotlib versioned 0.4.1 specifically. Looking at the NPM package list we see that there is also 0.4.2 available, so something is pinning 0.4.1 specifically somewhere.

Possibly relevant

• JupyterLab documentation about extensions and the build process
• The NPM package representing the labextension
• The conda feedstock publishing to conda-forge
• The PyPI pip package
• A comparison of the latest tag of this repo and the one before (0.3.3->0.4.0)

[consideRatio]

I wonder if JupyterLab has a dependency on jupyter-matplotlib by itself since JupyterLab 1.2 for example? I'm not sure how to interpret all this, but I've looked into this file for example.

# find the folder by using `jupyter lab paths`
cat /opt/conda/share/jupyter/lab/static/package.json

[consideRatio]

Haha... I removed the dedicated line to install jupyter-matplotlib as a jupyterlab extension. This is what it now shows.

(base) jovyan:~$ ls -alh /opt/conda/share/jupyter/lab/extensions/
total 22M
drwsrwsr-x 1 jovyan users 4.0K Jan 17 15:50 .
drwsrwsr-x 1 jovyan users 4.0K Jan 17 15:59 ..
-rw-rw-r-- 1 jovyan users 2.4M Jan 17 15:49 bqplot-0.5.2.tgz
-rw-rw-r-- 1 jovyan users 3.0K Jan 17 15:49 ijmbarr-jupyterlab_spellchecker-0.1.5.tgz
-rw-rw-r-- 1 jovyan users 1.6M Jan 17 15:49 ipyvolume-0.5.2.tgz
-rw-rw-r-- 1 jovyan users 1.1M Jan 17 15:49 itkwidgets-0.25.0.tgz
-rw-rw-r-- 1 jovyan users 5.0K Jan 17 15:50 jupyterlab_bokeh-1.0.0.tgz
-rw-rw-r-- 1 jovyan users 5.9K Jan 17 15:50 jupyterlab-chart-editor-0.2.0.tgz
-rw-rw-r-- 1 jovyan users 1.1K Jul  4  2019 jupyterlab-datawidgets-6.2.0.tgz
-rw-rw-r-- 1 jovyan users 8.2M Jan 17 15:50 jupyterlab-drawio-0.6.0.tgz
-rw-rw-r-- 1 jovyan users 6.0K Jan 17 15:49 jupyterlab-fasta-extension-1.0.0.tgz
-rw-rw-r-- 1 jovyan users 5.2K Jan 17 15:49 jupyterlab-geojson-extension-1.0.0.tgz
-rw-rw-r-- 1 jovyan users 9.0K Jan 17 15:50 jupyterlab_iframe-0.2.1.tgz
-rw-rw-r-- 1 jovyan users  11K Jan 17 15:50 jupyterlab-kernelspy-1.1.0.tgz
-rw-rw-r-- 1 jovyan users  15K Jan 17 15:49 jupyterlab-latex-1.0.0.tgz
-rw-rw-r-- 1 jovyan users 3.1K Jan 17 15:50 jupyterlab-plotly-1.4.0.tgz
-rw-rw-r-- 1 jovyan users 1.6K Jan 17 15:49 jupyterlab-server-proxy-2.0.0.tgz
-rw-rw-r-- 1 jovyan users  20K Jan 17 15:49 jupyterlab-shortcutui-0.4.0.tgz
-rw-rw-r-- 1 jovyan users  14K Jan 17 15:50 jupyterlab_tensorboard-0.1.6.tgz
-rw-rw-r-- 1 jovyan users  25K Jan 17 15:49 jupyterlab-toc-1.0.1.tgz
-rw-rw-r-- 1 jovyan users 229K Dec 17 15:38 jupyter-matplotlib-0.4.0.tgz
-rw-rw-r-- 1 jovyan users 229K Dec 17 15:38 jupyter-matplotlib-0.4.1.tgz
-rw-rw-r-- 1 jovyan users 232K Dec 17 15:38 jupyter-matplotlib-0.5.0.tgz
-rw-rw-r-- 1 jovyan users 3.2M Jan 17 15:50 jupyter-threejs-2.1.1.tgz
-rw-rw-r-- 1 jovyan users  12K Jan 17 15:49 jupyter-widgets-jupyterlab-manager-1.1.0.tgz
-rw-rw-r-- 1 jovyan users 3.1M Jan 17 15:49 jupyter-widgets-jupyterlab-sidecar-0.4.0.tgz
-rw-rw-r-- 1 jovyan users  12K Jan 17 15:49 lckr-jupyterlab_variableinspector-0.3.0.tgz
-rw-rw-r-- 1 jovyan users  12K Jan 17 15:50 nbdime-jupyterlab-1.0.0.tgz
-rw-rw-r-- 1 jovyan users 1.2M Jan 17 15:50 plotlywidget-1.4.0.tgz

I think I only saw 0.4.1 and 0.5.0 before, now I see 0.4.0 also. This made the rebuild suggestion show up at least. Hmmm... The extension stopped working also, by now showing me this:

Where is the logic that makes the install of a conda package also install a jupyterlab extension?

---

Not even installing ipyml or the npm labextension jupyter-matplotlib still gives me ipyml installed... This is because I do conda install itkwidgets and/or jupyter labextension install itkwidgets perhaps!

Aha.. Hmmm...

[thewtex]

@consideRatio thanks for the investigations! Yes, it is quite perplexing 😕

I figure something is set on using the NPM package with the jupyterlab extension of jupyter-matplotlib versioned 0.4.1 specifically.

Yes.

Or, there may be something pre-installed in the MyBinder image? I found that I needed to explicitly specify the version of jupyterlab in binder/requirements.txt because pip was finding an existing version, which was too old.

find the folder by using jupyter lab paths

Good to know about...

(base) jovyan:~$ ls -alh /opt/conda/share/jupyter/lab/extensions/

Checking this on the MyBinder image:

jovyan@jupyter-insightsoftware-2dtium-2ditkelastix-2dpws9jwom:~$ ls /srv/conda/envs/notebook/share/jupyter/lab/extensions/ -l
total 1584
-rw-r--r-- 1 jovyan jovyan 1126444 Jan 15 18:45 itkwidgets-0.24.2.tgz
-rw-r--r-- 1 jovyan jovyan    2151 Jan 15 18:45 jupyterlab-datawidgets-6.2.0.tgz
-rw-r--r-- 1 jovyan jovyan  233576 Jan 15 17:47 jupyter-matplotlib-0.4.0.tgz
-rw-r--r-- 1 jovyan jovyan  233523 Jan 15 18:45 jupyter-matplotlib-0.4.1.tgz
-rw-r--r-- 1 jovyan jovyan   12224 Jan 15 18:45 jupyter-widgets-jupyterlab-manager-1.1.0.tgz

Not even installing ipyml or the npm labextension jupyter-matplotlib still gives me ipyml installed... This is because I do conda install itkwidgets

itkwidgets has a Python dependency on ipympl, which would explain why it is installed. There is not dependency on the jupyter-matplotlib NPM package, though.

@SylvainCorlay @blink1073

[thewtex]

This worked around the issue:

InsightSoftwareConsortium/ITKElastix@8931df6

but it is a hack.

Two different sources are pulling in jupyter-matplotlib, which seems to be one issue.

It also seems that the duplicate packages could be better detected and handled by JupyterLab.

[thewtex]

Checking the contents of the ipympl-0.4.0 wheel, it contains multiple versions of jupyter-matplotlib-*.tgz It should only contain jupyter-matplotlib-0.5.0.tgz.

❯ find ipympl-0.4.0-py2.py3-none-any/*
─╯
ipympl-0.4.0-py2.py3-none-any/ipympl
ipympl-0.4.0-py2.py3-none-any/ipympl/jupyter-matplotlib-0.5.0.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl/__init__.py
ipympl-0.4.0-py2.py3-none-any/ipympl/static
ipympl-0.4.0-py2.py3-none-any/ipympl/static/index.js
ipympl-0.4.0-py2.py3-none-any/ipympl/static/index.js.map
ipympl-0.4.0-py2.py3-none-any/ipympl/static/package.json
ipympl-0.4.0-py2.py3-none-any/ipympl/static/extension.js
ipympl-0.4.0-py2.py3-none-any/ipympl/jupyter-matplotlib-0.3.0.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl/jupyter-matplotlib-0.4.1.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl/jupyter-matplotlib-0.4.0.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl/backend_nbagg.py
ipympl-0.4.0-py2.py3-none-any/ipympl/_version.py
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/etc
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/etc/jupyter
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/etc/jupyter/nbconfig
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/etc/jupyter/nbconfig/notebook.d
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/etc/jupyter/nbconfig/notebook.d/jupyter-matplotlib.json
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/lab
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/lab/extensions
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/lab/extensions/jupyter-matplotlib-0.5.0.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/lab/extensions/jupyter-matplotlib-0.4.1.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/lab/extensions/jupyter-matplotlib-0.4.0.tgz
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/nbextensions
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/nbextensions/jupyter-matplotlib
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/nbextensions/jupyter-matplotlib/index.js
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/nbextensions/jupyter-matplotlib/index.js.map
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/nbextensions/jupyter-matplotlib/package.json
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.data/data/share/jupyter/nbextensions/jupyter-matplotlib/extension.js
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.dist-info
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.dist-info/RECORD
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.dist-info/LICENSE
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.dist-info/METADATA
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.dist-info/WHEEL
ipympl-0.4.0-py2.py3-none-any/ipympl-0.4.0.dist-info/top_level.txt

[thewtex]

Building the wheel locally:

❯ find ipympl-0.4.1-py2.py3-none-any
─╯
ipympl-0.4.1-py2.py3-none-any
ipympl-0.4.1-py2.py3-none-any/ipympl
ipympl-0.4.1-py2.py3-none-any/ipympl/jupyter-matplotlib-0.5.0.tgz
ipympl-0.4.1-py2.py3-none-any/ipympl/__init__.py
ipympl-0.4.1-py2.py3-none-any/ipympl/static
ipympl-0.4.1-py2.py3-none-any/ipympl/static/index.js
ipympl-0.4.1-py2.py3-none-any/ipympl/static/index.js.map
ipympl-0.4.1-py2.py3-none-any/ipympl/static/package.json
ipympl-0.4.1-py2.py3-none-any/ipympl/static/extension.js
ipympl-0.4.1-py2.py3-none-any/ipympl/backend_nbagg.py
ipympl-0.4.1-py2.py3-none-any/ipympl/_version.py
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.dist-info
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.dist-info/RECORD
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.dist-info/LICENSE
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.dist-info/METADATA
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.dist-info/WHEEL
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.dist-info/top_level.txt
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/etc
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/etc/jupyter
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/etc/jupyter/nbconfig
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/etc/jupyter/nbconfig/notebook.d
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/etc/jupyter/nbconfig/notebook.d/jupyter-matplotlib.json
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/lab
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/lab/extensions
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/lab/extensions/jupyter-matplotlib-0.5.0.tgz
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/nbextensions
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/nbextensions/jupyter-matplotlib
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/nbextensions/jupyter-matplotlib/index.js
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/nbextensions/jupyter-matplotlib/index.js.map
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/nbextensions/jupyter-matplotlib/package.json
ipympl-0.4.1-py2.py3-none-any/ipympl-0.4.1.data/data/share/jupyter/nbextensions/jupyter-matplotlib/extension.js

#167 proposes cleaning before building the package and releasing a new version on PyPI.