jupyterlab-sos
Jupyterlab extension for SoS Polyglot Notebook and Workflow Engine, allows multiple kernels in one notebook
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 5 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.0%) to scientific vocabulary
Keywords
Repository
Jupyterlab extension for SoS Polyglot Notebook and Workflow Engine, allows multiple kernels in one notebook
Basic Info
- Host: GitHub
- Owner: vatlab
- License: bsd-3-clause
- Language: TypeScript
- Default Branch: master
- Homepage: http://vatlab.github.io/sos-docs
- Size: 1.39 MB
Statistics
- Stars: 75
- Watchers: 4
- Forks: 8
- Open Issues: 14
- Releases: 4
Topics
Metadata Files
README.md
jupyterlab_sos
JupyterLab extension for SoS workflow engine and polyglot notebook
Requirements
- JupyterLab >= 4.0.0
Install
To install the extension, execute:
bash
pip install jupyterlab_sos
Uninstall
To remove the extension, execute:
bash
pip uninstall jupyterlab_sos
Contributing
Development install
Note: You will need NodeJS to build the extension package.
The jlpm command is JupyterLab's pinned version of
yarn that is installed with JupyterLab. You may use
yarn or npm in lieu of jlpm below.
```bash
Clone the repo to your local environment
Change directory to the jupyterlab_sos directory
Install package in development mode
pip install -e "."
Link your development version of the extension with JupyterLab
jupyter labextension develop . --overwrite
Rebuild extension Typescript source after making changes
jlpm build ```
You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.
```bash
Watch the source directory in one terminal, automatically rebuilding when needed
jlpm watch
Run JupyterLab in another terminal
jupyter lab ```
With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).
By default, the jlpm build command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:
bash
jupyter lab build --minimize=False
Development uninstall
bash
pip uninstall jupyterlab_sos
In development mode, you will also need to remove the symlink created by jupyter labextension develop
command. To find its location, you can run jupyter labextension list to figure out where the labextensions
folder is located. Then you can remove the symlink named jupyterlab-sos within that folder.
Testing the extension
Frontend tests
This extension is using Jest for JavaScript code testing.
To execute them, execute:
sh
jlpm
jlpm test
Integration tests
This extension uses Playwright for the integration tests (aka user level tests). More precisely, the JupyterLab helper Galata is used to handle testing the extension in JupyterLab.
More information are provided within the ui-tests README.
Packaging the extension
See RELEASE
Owner
- Name: Laboratory of Variant Analysis Tools
- Login: vatlab
- Kind: organization
- Email: Bo.Peng@bcm.edu
- Location: Baylor College of Medicine
- Website: http://vatlab.github.io
- Repositories: 49
- Profile: https://github.com/vatlab
Dr. Bo Peng's Bioinformatic Tools for Variant Analysis
GitHub Events
Total
- Issues event: 3
- Watch event: 5
- Issue comment event: 6
- Push event: 4
- Pull request event: 2
- Fork event: 1
- Create event: 2
Last Year
- Issues event: 3
- Watch event: 5
- Issue comment event: 6
- Push event: 4
- Pull request event: 2
- Fork event: 1
- Create event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Bo Peng | b****g@g****m | 247 |
| Bo Peng | b****b@g****m | 31 |
| Bo Peng | b****g@b****u | 18 |
| Bo | B****g | 17 |
| Ma | j****7@m****g | 6 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 68
- Total pull requests: 8
- Average time to close issues: 4 months
- Average time to close pull requests: 4 months
- Total issue authors: 13
- Total pull request authors: 1
- Average comments per issue: 4.62
- Average comments per pull request: 0.5
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 2
- Average time to close issues: about 19 hours
- Average time to close pull requests: about 14 hours
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 2.5
- Average comments per pull request: 2.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- BoPeng (36)
- gaow (20)
- lucasiscovici (2)
- aolney (1)
- MRYingLEE (1)
- liu-genomics (1)
- avianinc (1)
- jma7 (1)
- drivenbyentropy (1)
- thompsonmj (1)
- whyjz (1)
- crcmt (1)
Pull Request Authors
- BoPeng (9)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 4
-
Total downloads:
- npm 23 last-month
- pypi 154 last-month
- Total docker downloads: 4,100
-
Total dependent packages: 2
(may contain duplicates) -
Total dependent repositories: 4
(may contain duplicates) - Total versions: 79
- Total maintainers: 2
npmjs.org: jupyterlab-sos
JupyterLab extension for SoS workflow engine and polyglot notebook
- Homepage: https://github.com/vatlab/jupyterlab-sos
- License: BSD-3-Clause
-
Latest release: 0.8.0
published over 5 years ago
Rankings
Maintainers (1)
pypi.org: jupyterlab-sos
JupyterLab extension for SoS workflow engine and polyglot notebook
- Homepage: https://github.com/vatlab/jupyterlab-sos
- Documentation: https://jupyterlab-sos.readthedocs.io/
- License: BSD 3-Clause License Copyright (c) 2022, Bo Peng All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
Latest release: 0.11.0
published over 1 year ago
Rankings
Maintainers (1)
conda-forge.org: jupyterlab_sos
- Homepage: https://github.com/vatlab/jupyterlab-sos
- License: BSD-3-Clause
-
Latest release: 0.8.8
published almost 4 years ago
Rankings
conda-forge.org: jupyterlab-sos
- Homepage: https://github.com/vatlab/jupyterlab-sos
- License: BSD-3-Clause
-
Latest release: 0.8.8
published almost 4 years ago
Rankings
Dependencies
- @jupyterlab/builder ^3.4.0 development
- @types/codemirror 0.0.97 development
- @types/react ^17.0.0 development
- @typescript-eslint/eslint-plugin ^4.8.1 development
- @typescript-eslint/parser ^4.8.1 development
- codemirror ^5.53.2 development
- eslint ^7.14.0 development
- eslint-config-prettier ^6.15.0 development
- eslint-plugin-prettier ^3.1.4 development
- npm-run-all ^4.1.5 development
- prettier ^2.1.1 development
- rimraf ^3.0.2 development
- stylelint ^14.3.0 development
- stylelint-config-prettier ^9.0.3 development
- stylelint-config-recommended ^6.0.0 development
- stylelint-config-standard ~24.0.0 development
- stylelint-prettier ^2.0.0 development
- typedoc ^0.15.4 development
- typescript ~4.1.3 development
- @jupyterlab/application ^3.4.0
- @jupyterlab/apputils ^3.4.0
- @jupyterlab/cells ^3.4.0
- @jupyterlab/codemirror ^3.4.0
- @jupyterlab/console ^3.4.0
- @jupyterlab/coreutils ^5.1.0
- @jupyterlab/docregistry ^3.4.0
- @jupyterlab/notebook ^3.4.0
- @jupyterlab/services ^6.1.12
- @jupyterlab/settingregistry ^3.4.0
- @jupyterlab/ui-components ^3.4.0
- @lumino/algorithm ^1.3.3
- @lumino/commands ^1.12.0
- @lumino/disposable ^1.4.3
- react ^17.0.0
- transient-display-data ^0.4.3
- jupyterlab >=3.4.0
- sos-notebook >=0.23.3
- transient-display-data >=0.4.3
- actions/checkout v2 composite
- actions/setup-node v1 composite
- actions/setup-python v2 composite