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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/krassowski/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.
Michał Krassowski krassowski University of Oxford Oxford, UK linkedin.com/in/michal-krassowski/ CS applied to biomedical research. Mike for short. Wrangling omics data, sometimes helping out with @jupyter.

jupyterlab/jupyterlab 11408

JupyterLab computational environment.

jupyterlab-contrib/spellchecker 127

Spellchecker for JupyterLab notebook markdown cells and file editor.

jupytercalpoly/jupyterlab-tabular-data-editor 107

Manipulate your tabular data responsively and effectively within JupyterLab.

krassowski/Anki-Night-Mode 72

Enabling studying at night with Anki - without eye strain

jupyterlab/language-packs 29

Language packs for JupyterLab ecosystem

krassowski/Anki-TouchScreen 17

Touchscreen functionality for Anki

krassowski/anki_testing 8

A small utility for testing Anki 2.1 addons

krassowski/Anki-Zoom 6

Zoom add-on for Anki 2.1, forked from ospalh/anki-addons

jupyterlab/jupyterlab-translate 5

JupyterLab Language pack helper

jupyterlab/language-pack-cookiecutter 2

Cookiecutter for Jupyterlab Language packs

issue commentjupyterlab/jupyterlab_app

Displaying available kernels

Good points. I think that it largely depends on configuration - if you have kernels installed on system level, any instance of JupyterLab will list those (whether in a virtual environment or not).

the JupyterLab-app and local JupyterLab server seem to be able to share state re: current directory and currently opened notebooks(?!); *this is quite scary and I suspect could lead to all sorts of mishaps depending on what is shared and which server last wrote whatever state is shared);

This happens with Jupyter(Lab) config and sessions in general; it is annoying because I get my workspace reset from time to time when I open a new session in a different environment. I think that this needs discussion in main JupyterLab repo (if there is not any).

psychemedia

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issue commentjupyterlab/jupyterlab_app

Signed electron app on Mac O/S

Duplicate of #202?

psychemedia

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issue commentjupyterlab/jupyterlab_app

jupyterlabb_app fails to start with JupyterServer Not Found

How are you starting JupyterLab-App? Are you using command line, or the icon in the Ubuntu launcher?

ghshephard

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commit sha 5cc9b7eb359b1228247a85efb73c6b16d491229c

Bump tmpl from 1.0.4 to 1.0.5 Bumps [tmpl](https://github.com/daaku/nodejs-tmpl) from 1.0.4 to 1.0.5. - [Release notes](https://github.com/daaku/nodejs-tmpl/releases) - [Commits](https://github.com/daaku/nodejs-tmpl/commits/v1.0.5) --- updated-dependencies: - dependency-name: tmpl dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com>

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commit sha 8ddcf058040aa0bad0d2b8d22582fd52ee7031ff

Merge pull request #682 from krassowski/dependabot/npm_and_yarn/tmpl-1.0.5 Bump tmpl from 1.0.4 to 1.0.5

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PR merged krassowski/jupyterlab-lsp

Bump tmpl from 1.0.4 to 1.0.5 dependencies

Bumps tmpl from 1.0.4 to 1.0.5. <details> <summary>Commits</summary> <ul> <li>See full diff in <a href="https://github.com/daaku/nodejs-tmpl/commits/v1.0.5">compare view</a></li> </ul> </details> <br />

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pull request commentpython-lsp/python-lsp-server

doc: fix CONFIGURATION pyls prefix

You may also have python-language-server installed. Opening an issue first is usually a good idea.

jamesob

comment created time in 21 hours

issue commentjupyterlab/jupyterlab

Jupyteran 3.1.7 Table of content of notebook seems to be broken

@Rchatru the latest release 3.1.12 is available on conda-forge: https://anaconda.org/conda-forge/jupyterlab

danieltomasz

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issue commentpython-lsp/python-lsp-server

python-lsp-server vs Pyright language server.

pyright also supports some undocumented behaviour of LSP like sending null to close signature requests, as it well comes from the creators of LSP.

hongyi-zhao

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issue commentpython-lsp/python-lsp-server

python-lsp-server vs Pyright language server.

For one python-lsp-server is written in Python but pyright is written in TypeScript. Depending on how well you know each of the languages you may find it easier to contribute to one project or the other (but presumably it would be easier for target audience to contribute to python-lsp-server). pyright is a more recent server and has a strong emphasis on typing support (but you need to configure it to do so as the actual typing are only distributed in the closed-source pylance). Also pyright requires you to install node.js and npm, which is something that many users prefer to avoid. Finally before contributing to pyright you would need to sign a CLA with Microsoft, whereas python-lsp-server is more of an open source community supported project.

hongyi-zhao

comment created time in 2 days

issue commentraphaelvallat/pingouin

Partial correlations out of range when variance = 0

Thanks for a quick reply!

raise ValueError("Invalid range, bla bla bla...")

maybe a warning is better in that case as 1.00000001 might happen due to float representation issues? I don't have an example, but it could be pretty annoying for the user if that happens and they are not to blame.

The former case (of input data containing NA/constant values) is where raising a ValueError makes more sense as it is up to the user to prepare the data.

krassowski

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issue commentpython-lsp/python-lsp-server

How to prevent `()` added during company completions

It does not work like that in other editors, so it would seem that either:

  • the company-mode uses label when it should be using insertText (most likely)
  • you have snippets enabled (which are disabled by default)
avatar-lavventura

comment created time in 2 days

issue openedraphaelvallat/pingouin

Partial correlations out of range when variance = 0

The following reproducer:

from pandas import DataFrame
from random import seed, sample

import pingouin as pg

seed(0, 1)
sample_size = 100
random_columns = 60

n = [0.0000001 for _ in range(sample_size)]
df = DataFrame(dict(
    n1b=n, n2b=n, n3b=n,
    **{
        f'x{i}': sample(range(2000), sample_size)
        for i in range(random_columns)
    }
))

pg.pcorr(df).max().max()

gives a value of 6.754645467173336 with pingouin 0.4.0. I encountered this behaviour (giving out of range coefficients) in the wild when I accidentally forgot to remove variables with no variance.

To ensure that incorrect results like that don't get published, I would:

  • add a check on the data verifying that var() != 0 prior to running computations; not sure if this should raise or warn
  • add a check on the results; if any of the coefficients are out of range it would warn and provide name of the column those come from and a helpful message like "your data may have close-to-zero variance variables or be otherwise ill-conditioned".

It might be also worth investigating if there is a way to workaround these numerical issues, but the two points above should address the most urgent worries.

created time in 2 days

issue commentjupyterlab/team-compass

Transfer jupyterlab-dynext to the JupyterLab org

The same question but a different angle: do we need it to be a separate extension, or could it get merged straight into the JupyterLab core repository? If the goal is to make the start simpler, to lower the entry barrier, maybe not having to install an extension would make a better UX?

jasongrout

comment created time in 3 days

issue commentkrassowski/jupyterlab-lsp

Issues configuring + switching between additional LSP servers

Sorry, I do not currently have bandwidth to support Kite - if you would like to use jupyterlab-lsp I would recommend uninstalling the Kite server. Maybe we could make it work in the future but last I checked they ceased the service for individual users, so I don't know how it would work.

mjnur

comment created time in 5 days

issue commentkrassowski/jupyterlab-lsp

lsp diagnostics not recongnize the `%pylab` magic function

Personally I would not use %pylab inline as it pollutes the global namespace (see https://stackoverflow.com/a/24338062/6646912 for explanation), but we are not an authority on good code, so indeed we could make an exception and include the additional imports. PRs welcome.

gaowutong

comment created time in 5 days

issue commentjupyterlab/jupyterlab

Tab completion used with multiple cursors only completes one instance

Did it work as you would expect in JupyterLab versions older that 3.1, e.g. 3.0?

robna

comment created time in 6 days

issue commentjupyterlab/jupyterlab

Save the notebook from command line or line magic

Thanks @kolibril13. Another approach is to use ipylab:

from ipylab import JupyterFrontEnd

app = JupyterFrontEnd()
app.commands.execute('docmanager:save')

And yet another way is to trigger <kbd>ctrl</kbd> + <kbd>s</kbd> from JavaScript as in https://stackoverflow.com/a/66911341/6646912 (but this is very hacky and will likely break at some point in the future, so I would not recommend this one).

PierreGuilmin

comment created time in 6 days

issue commentjupyterlab/jupyterlab

Add a configuration to avoid checkSync function

@jmari this is the same what I was suggesting on gitter: maybe it does not matter that the code is different and the only thing that matters is that the line endings and different.

jmari

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startedllrs/RGCCA

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created tagkrassowski/easy-entrez

tagv0.3.0

Retrieve PubMed articles, text-mining annotations, or molecular data from >35 Entrez databases via easy to use Python package - built on top of Entrez E-utilities API.

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v0.3.0

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Use content type instead of pandoc

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Allow to search by passing a dictionary

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