research-docker issueshttps://gitlab.kwant-project.org/qt/research-docker/-/issues2022-12-25T18:55:43Zhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/37fix system-wide git config2022-12-25T18:55:43ZAnton Akhmerovfix system-wide git configthe default git config provided by conda overwrites ours; we should postpone the creation of ours until after the conda installation is done.the default git config provided by conda overwrites ours; we should postpone the creation of ours until after the conda installation is done.https://gitlab.kwant-project.org/qt/research-docker/-/issues/36Create a testing notebook2022-12-25T00:00:43ZAnton AkhmerovCreate a testing notebookWe should start minimally, checking e.g. that dask connects correctly, `%matplotlib widget` works, and `Poisson` imports. Then we could add bits that break to testing protocols.
About making the code available, we could either instruct ...We should start minimally, checking e.g. that dask connects correctly, `%matplotlib widget` works, and `Poisson` imports. Then we could add bits that break to testing protocols.
About making the code available, we could either instruct the users to do `ln -s /usr/share/testing.ipynb ~/testing.ipynb` or symlink it on startup.https://gitlab.kwant-project.org/qt/research-docker/-/issues/34Incompatibility of python 3.10 with adaptive(asyncio)2022-12-24T22:30:51ZJuan TorresIncompatibility of python 3.10 with adaptive(asyncio)When executing an adaptive example, the runner fails due to a keyword error.
This error [has been found](https://github.com/jupyter/jupyter_console/issues/245) before. It requires to remove the `loop` keyword since it is not anymore supp...When executing an adaptive example, the runner fails due to a keyword error.
This error [has been found](https://github.com/jupyter/jupyter_console/issues/245) before. It requires to remove the `loop` keyword since it is not anymore supported by python 3.10.
The minimal code that produces the problem is:
```python
import adaptive
import numpy as np
adaptive.notebook_extension()
def ring(xy):
x, y = xy
a = 0.2
return x + np.exp(-(x**2 + y**2 - 0.75**2)**2/a**4)
learner = adaptive.Learner2D(ring, bounds=[(-1, 1), (-1, 1)])
runner = adaptive.Runner(learner, goal=lambda l: l.loss() < 0.01)
runner.task.result()
```
The error is:
```
TypeError Traceback (most recent call last)
Input In [27], in <cell line: 1>()
----> 1 runner.task.result()
File /opt/conda/lib/python3.10/site-packages/adaptive/runner.py:584, in AsyncRunner.status(self)
579 """Return the runner status as a string.
580
581 The possible statuses are: running, cancelled, failed, and finished.
582 """
583 try:
--> 584 self.task.result()
585 except asyncio.CancelledError:
586 return "cancelled"
File /opt/conda/lib/python3.10/site-packages/adaptive/runner.py:584, in AsyncRunner.status(self)
579 """Return the runner status as a string.
580
581 The possible statuses are: running, cancelled, failed, and finished.
582 """
583 try:
--> 584 self.task.result()
585 except asyncio.CancelledError:
586 return "cancelled"
File /opt/conda/lib/python3.10/site-packages/adaptive/runner.py:645, in AsyncRunner._run(self)
643 while not self.goal(self.learner):
644 futures = self._get_futures()
--> 645 done, _ = await asyncio.wait(
646 futures, return_when=first_completed, loop=self.ioloop
647 )
648 self._process_futures(done)
649 finally:
TypeError: wait() got an unexpected keyword argument 'loop'
```https://gitlab.kwant-project.org/qt/research-docker/-/issues/31Update ipyparallel2021-12-18T11:29:08ZAnton AkhmerovUpdate ipyparallelSee https://github.com/ipython/ipyparallel/issues/301 for detailsSee https://github.com/ipython/ipyparallel/issues/301 for detailshttps://gitlab.kwant-project.org/qt/research-docker/-/issues/20permissions in CI2021-06-21T21:50:07ZAnton Akhmerovpermissions in CIrecently CI in our image lost sudo: https://gitlab.kwant-project.org/pulkin/miniff/-/jobs/116097recently CI in our image lost sudo: https://gitlab.kwant-project.org/pulkin/miniff/-/jobs/116097https://gitlab.kwant-project.org/qt/research-docker/-/issues/30Update jupyterlab to v32021-06-21T21:48:57ZAnton AkhmerovUpdate jupyterlab to v3v3 should improve our installation time dramatically because labextensions don't require recompiling anymore. There are also all-around UI improvements.
Unfortunately most extension are slow to update, so we should wait for some time.
...v3 should improve our installation time dramatically because labextensions don't require recompiling anymore. There are also all-around UI improvements.
Unfortunately most extension are slow to update, so we should wait for some time.
Together with that update we should probably also:
- ~~[ ] Install mamba_gator https://github.com/mamba-org/gator for easy overview of the installed packages.~~https://gitlab.kwant-project.org/qt/research-docker/-/issues/29Use micromamba instead of miniconda2021-01-26T15:04:20ZAnton AkhmerovUse micromamba instead of minicondaFor greater speed https://github.com/thesnakepit/mamba#micromambaFor greater speed https://github.com/thesnakepit/mamba#micromambahttps://gitlab.kwant-project.org/qt/research-docker/-/issues/23vscode broken2020-08-11T08:49:28ZAnton Akhmerovvscode brokenSeems to work upstream, so the problem is likely configurationSeems to work upstream, so the problem is likely configurationhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/27Mirror repositoriy as normal people do2020-07-16T21:49:49ZViacheslav OstroukhMirror repositoriy as normal people dohttps://docs.gitlab.com/ee/user/project/repository/repository_mirroring.htmlhttps://docs.gitlab.com/ee/user/project/repository/repository_mirroring.htmlhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/10Install nbdime notebook extension2020-07-15T10:11:36ZAnton AkhmerovInstall nbdime notebook extensionnbdime [offers](https://nbdime.readthedocs.io/en/stable/extensions.html) a tool for showing a diff between a currently saved notebook and the last commit, we can enable it in the image.nbdime [offers](https://nbdime.readthedocs.io/en/stable/extensions.html) a tool for showing a diff between a currently saved notebook and the last commit, we can enable it in the image.Anton AkhmerovAnton Akhmerovhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/26%matplotlib widget not installed properly2020-07-03T19:07:42ZAnton Akhmerov%matplotlib widget not installed properlyto reproduce run
```python
%matplotlib widget
from matplotlib import pyplot
pyplot.plot([0, 1])
```to reproduce run
```python
%matplotlib widget
from matplotlib import pyplot
pyplot.plot([0, 1])
```https://gitlab.kwant-project.org/qt/research-docker/-/issues/25base image build fails2020-06-20T12:21:49ZAnton Akhmerovbase image build failsthis happens because jupyter/base-notebook migrated to ubuntu focal, where some packages were moved to universethis happens because jupyter/base-notebook migrated to ubuntu focal, where some packages were moved to universeAnton AkhmerovAnton Akhmerovhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/12split docker image into two2020-06-20T10:25:16ZRafal Skolasinskisplit docker image into twoI would like to suggest splitting our image into two:
1. ``jupyter/base-notebook`` + apt-packages + python environment
2. other modification that adjust image to our infrastructure.
This would allow to use ``1.`` exactly the same manne...I would like to suggest splitting our image into two:
1. ``jupyter/base-notebook`` + apt-packages + python environment
2. other modification that adjust image to our infrastructure.
This would allow to use ``1.`` exactly the same manner that like jupyter ``docker-stacks`` images. Especially we could just refer to their documentation about the usage.
Our image for example changes details like the entry point, etc.https://gitlab.kwant-project.org/qt/research-docker/-/issues/16jupyterlab_code_formatter is not working2020-06-20T10:24:02ZJoseph Westonjupyterlab_code_formatter is not workingupstream issue. Nothing we can do for now: https://github.com/ryantam626/jupyterlab_code_formatter/issues/59upstream issue. Nothing we can do for now: https://github.com/ryantam626/jupyterlab_code_formatter/issues/59https://gitlab.kwant-project.org/qt/research-docker/-/issues/13Image update2020-06-20T10:21:22ZAnton AkhmerovImage update- Remove anaconda and select the part that we need
- Make a separate environment for fenics + kwant (an environment file)
- Upgrade ipython
- remove git from apt
- bump versions
- remove everything `*dashboards*`
- Try to not override th...- Remove anaconda and select the part that we need
- Make a separate environment for fenics + kwant (an environment file)
- Upgrade ipython
- remove git from apt
- bump versions
- remove everything `*dashboards*`
- Try to not override the jupyter config (removing `jupyter_notebook_config.py`
- Update `profile.sh` (CC @basnijholt )
- Review and update lab extensions (@anton\-akhmerov )https://gitlab.kwant-project.org/qt/research-docker/-/issues/14repo is not being mirrored to github2020-06-20T10:20:46ZBas Nijholtrepo is not being mirrored to githubhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/17Plotly extension missing for jupyter lab2020-06-20T10:16:10ZMichael WimmerPlotly extension missing for jupyter labI noticed plotly doesn't work in our jupyterlab. Apparently, one needs to install a labextension for that.
In the internet I found two ways of doing it:
- `conda install -c conda-forge jupyterlab-plotly-extension`
- `jupyter labextensi...I noticed plotly doesn't work in our jupyterlab. Apparently, one needs to install a labextension for that.
In the internet I found two ways of doing it:
- `conda install -c conda-forge jupyterlab-plotly-extension`
- `jupyter labextension install @jupyterlab/plotly-extension` In that case, on my laptop I also had to do `conda install nodejs`.
Any ideas what's the better way?https://gitlab.kwant-project.org/qt/research-docker/-/issues/22nbdime shows outputs even when they are removed by git filters2020-05-21T20:56:13ZBas Nijholtnbdime shows outputs even when they are removed by git filtersWhen a git repository is configured to strip all the outputs from the notebooks, these still show up in the nbdime diffs.
---
## Original description:
Breaks
* https://github.com/kynan/nbstripout
* https://github.com/basnijholt/ipynb_...When a git repository is configured to strip all the outputs from the notebooks, these still show up in the nbdime diffs.
---
## Original description:
Breaks
* https://github.com/kynan/nbstripout
* https://github.com/basnijholt/ipynb_git_filters
I think the global gitconfig shouldn't have nbdime.https://gitlab.kwant-project.org/qt/research-docker/-/issues/21vim is the default git editor2020-05-20T12:29:35ZBas Nijholtvim is the default git editorhttps://gitlab.kwant-project.org/qt/research-docker/-/issues/18Broken cv22019-12-15T22:16:02ZAnton AkhmerovBroken cv2importing cv2 fails with `ImportError: libGL.so.1: cannot open shared object file: No such file or directory`
Installing `libgl1-mesa-glx` via apt would be a likely solution.importing cv2 fails with `ImportError: libGL.so.1: cannot open shared object file: No such file or directory`
Installing `libgl1-mesa-glx` via apt would be a likely solution.