# tiledb_jupyter_bioimg
A jupyterlab extension to visualize bioimages in TileDB format
## Requirements
* JupyterLab >= 3.0
## Install
```bash
pip install tiledb_jupyter_bioimg
```
## Contributing
### Development install
Note: You will need NodeJS to build the extension package.
The `jlpm` command is JupyterLab's pinned version of
[yarn](https://yarnpkg.com/) 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 tiledb_jupyter_bioimg 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 run 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 run 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 run 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
```
### Uninstall
```bash
pip uninstall tiledb_jupyter_bioimg
```
### Usage
```python
from tiledb_jupyter_bioimg import Render
Render("<<NAMESPACE>>", "<<GROUP_ID>>", {"token": "<<TILEDB_API_TOKEN>>>"})
```
### Common issues
If you get error `Uncaught (in promise) Error: No provider for: jupyter.extensions.jupyterWidgetRegistry.` please make sure you are using correct version of `ipywidgets` (v8).
Raw data
{
"_id": null,
"home_page": "https://github.com/TileDB-Inc/TileDB-Jupyter-BioImage-Viewer",
"name": "tiledb-jupyter-bioimg",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "Jupyter,JupyterLab,JupyterLab3",
"author": "TileDB",
"author_email": "",
"download_url": "https://files.pythonhosted.org/packages/32/b2/b50983500fb3a70c943a5c065c083afa7a747bf98c8f2488b9aa2dff05f3/tiledb_jupyter_bioimg-0.2.1.tar.gz",
"platform": "Linux",
"description": "# tiledb_jupyter_bioimg\n\n\n\nA jupyterlab extension to visualize bioimages in TileDB format\n\n\n\n## Requirements\n\n* JupyterLab >= 3.0\n\n## Install\n\n```bash\npip install tiledb_jupyter_bioimg\n```\n\n\n## Contributing\n\n### Development install\n\nNote: You will need NodeJS to build the extension package.\n\nThe `jlpm` command is JupyterLab's pinned version of\n[yarn](https://yarnpkg.com/) that is installed with JupyterLab. You may use\n`yarn` or `npm` in lieu of `jlpm` below.\n\n```bash\n# Clone the repo to your local environment\n# Change directory to the tiledb_jupyter_bioimg directory\n# Install package in development mode\npip install -e .\n# Link your development version of the extension with JupyterLab\njupyter labextension develop . --overwrite\n# Rebuild extension Typescript source after making changes\njlpm run build\n```\n\nYou 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.\n\n```bash\n# Watch the source directory in one terminal, automatically rebuilding when needed\njlpm run watch\n# Run JupyterLab in another terminal\njupyter lab\n```\n\nWith 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).\n\nBy default, the `jlpm run 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:\n\n```bash\njupyter lab build --minimize=False\n```\n\n### Uninstall\n\n```bash\npip uninstall tiledb_jupyter_bioimg\n```\n\n### Usage\n\n```python\n\nfrom tiledb_jupyter_bioimg import Render\n\nRender(\"<<NAMESPACE>>\", \"<<GROUP_ID>>\", {\"token\": \"<<TILEDB_API_TOKEN>>>\"})\n\n```\n\n### Common issues\n\nIf you get error `Uncaught (in promise) Error: No provider for: jupyter.extensions.jupyterWidgetRegistry.` please make sure you are using correct version of `ipywidgets` (v8).\n",
"bugtrack_url": null,
"license": "BSD-3-Clause",
"summary": "A jupyterlab extension to visualize bioimages in TileDB format",
"version": "0.2.1",
"project_urls": {
"Homepage": "https://github.com/TileDB-Inc/TileDB-Jupyter-BioImage-Viewer"
},
"split_keywords": [
"jupyter",
"jupyterlab",
"jupyterlab3"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "1cf85b07e9b45f341c2badbe63bf07e40f7af5bb5602b56ab18bab063f918d87",
"md5": "c6837cab49c2e1d138b87d5293e365b3",
"sha256": "ec2b0b85ce792047c2e4a711cdd44bef16ebe9ab4164a0467501934275d8564e"
},
"downloads": -1,
"filename": "tiledb_jupyter_bioimg-0.2.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "c6837cab49c2e1d138b87d5293e365b3",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 905333,
"upload_time": "2023-08-11T11:01:34",
"upload_time_iso_8601": "2023-08-11T11:01:34.123373Z",
"url": "https://files.pythonhosted.org/packages/1c/f8/5b07e9b45f341c2badbe63bf07e40f7af5bb5602b56ab18bab063f918d87/tiledb_jupyter_bioimg-0.2.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "32b2b50983500fb3a70c943a5c065c083afa7a747bf98c8f2488b9aa2dff05f3",
"md5": "cf67fc67cf49bde156ab95f1f61927b7",
"sha256": "7ee5b2ff69edba70dae229748dc9b43794271676b0e354df74d8f70cf4b62959"
},
"downloads": -1,
"filename": "tiledb_jupyter_bioimg-0.2.1.tar.gz",
"has_sig": false,
"md5_digest": "cf67fc67cf49bde156ab95f1f61927b7",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 454927,
"upload_time": "2023-08-11T11:01:35",
"upload_time_iso_8601": "2023-08-11T11:01:35.640132Z",
"url": "https://files.pythonhosted.org/packages/32/b2/b50983500fb3a70c943a5c065c083afa7a747bf98c8f2488b9aa2dff05f3/tiledb_jupyter_bioimg-0.2.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-08-11 11:01:35",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "TileDB-Inc",
"github_project": "TileDB-Jupyter-BioImage-Viewer",
"github_not_found": true,
"lcname": "tiledb-jupyter-bioimg"
}
JSON
