CSS and JS fixes to get the menubar to work with igv-notebook

g2nb · Apr 28, 2022 · be5233b · be5233b
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diff --git a/README.md b/README.md
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 # igv Jupyter Extension
 
-[![Binder](https://beta.mybinder.org/badge.svg)](https://mybinder.org/v2/gh/igvteam/igv-jupyter/master?filepath=examples/BamFiles.ipynb)
+[![Binder](https://beta.mybinder.org/badge.svg)](https://mybinder.org/v2/gh/g2nb/igv-jupyter/master)
 =======
 
 
-igv-jupyter is an extension for [Jupyter Notebook](http://jupyter.org/) which
-wraps [igv.js](https://github.com/igvteam/igv.js). With this
-extension you can render igv.js in a cell and call its API from
-the notebook. The extension exposes a python API that mimics the igv.js 
-Browser creation and control APIs. Dictionaries are used for browser and track 
-configuration objects. Track data can be loaded from local or remote 
-URLs, or supplied directly as lists of objects.
+igv-jupyter is tool for [JupyterLab](http://jupyter.org/) which wraps [igv.js](https://github.com/igvteam/igv.js) and
+integrates with [g2nb](https://github.com/g2nb/g2nb). With this tool you can render igv.js in a cell and call its API
+from a user-friendly web form in the notebook. Track data can be loaded from local or remote URLs, or supplied directly.
+
+For programmatic access to igv.js in a Jupyter notebook, see [igv-notebook](https://github.com/igvteam/igv-notebook).
 
 ## Installation
 
 Requirements:
+
 * python >= 3.6.4
 * jupyterlab >= 3.0
 
-
 ```bash
 pip install igv-jupyter
-
-# To install to configuration in your home directory
-jupyter serverextension enable --py igv
-jupyter labextension enable igv
-jupyter nbextension install --py igv
-jupyter nbextension enable --py igv
-
-
-# If using a virtual environment
-jupyter serverextension enable --py igv --sys-prefix
-jupyter labextension enable igv --level sys_prefix
-jupyter nbextension install --py igv --sys-prefix
-jupyter nbextension enable --py igv --sys-prefix
-
-```
-
-## Usage
-
-### Examples
-
-Example notebooks are available in the github repository. To download without cloning the repository use 
-this [link](https://github.com/igvteam/igv.js-jupyter/archive/master.zip). Notebooks are available in the
-"examples" directory.
-
-
-
-### Initialization
-
-To insert an IGV instance into a cell:
-
-(1) create an igv.Browser object,and (2) call showBrowser on the instance.
-
-Example:
-
-```python
-import igv
-
-b = igv.Browser({"genome": "hg19"})
-```
-
-The igv.Browser initializer takes a configuration object which is converted to JSON and passed to the igv.js
-createBrowser function. The configuration object is described in the
-[igv.js documentation](https://github.com/igvteam/igv.js/wiki/Browser-Configuration-2.0).
-
-
-To instantiate the client side IGV instance in a cell call show()
-
-
-```python
-b.show()
-```
-
-### Tracks
-
-To load a track pass a track configuration object to load_track(). Track configuration
-objects are described in the [igv.js documentation](https://github.com/igvteam/igv.js/wiki/Tracks-2.0).
-The configuration object will be converted to JSON and passed to the igv.js browser
-instance.
-
-Data for the track can be loaded by URL or passed directly as an array of JSON objects.
-
-
-#### Remote URL
-
-```python
-b.load_track(
-    {
-        "name": "Segmented CN",
-        "url": "https://data.broadinstitute.org/igvdata/test/igv-web/segmented_data_080520.seg.gz",
-        "format": "seg",
-        "indexed": False
-    })
-
-```
-
-#### Local File
-
-```python
-b.load_track(
-    {
-        "name": "Local VCF",
-        "url": "data/example.vcf",
-        "format": "vcf",
-        "type": "variant",
-        "indexed": False
-    })
-```
-
-#### Embedded Features
-
-Features can also be passed directly to tracks.
-
-```python
-b.load_track({
-    "name": "Copy number",
-    "type": "seg",
-    "displayMode": "EXPANDED",
-    "height": 100,
-    "isLog": True,
-    "features": [
-        {
-            "chr": "chr20",
-            "start": 1233820,
-            "end": 1235000,
-            "value": 0.8239,
-            "sample": "TCGA-OR-A5J2-01"
-        },
-        {
-            "chr": "chr20",
-            "start": 1234500,
-            "end": 1235180,
-            "value": -0.8391,
-            "sample": "TCGA-OR-A5J3-01"
-        }
-    ]
-})
-```
-
-### Navigation
-
-Zoom in by a factor of 2
-
-```python
-b.zoom_in()
-```
-
-Zoom out by a factor of 2
-
-```python
-b.zoom_out()
-```
-
-Jump to a specific locus
-
-```python
-b.search('chr1:3000-4000')
-
-```
-
-Jump to a specific gene. This uses the IGV search web service, which currently supports a limited number of genomes:  hg38, hg19, and mm10.
-To configure a custom search service see the [igv.js documentation](https://github.com/igvteam/igv.js/wiki/Browser-Configuration-2.0#search-object-details)
-
-```python
-b.search('myc')
-
-```
-
-### SVG output
-
-Saving the current IGV view as an SVG image requires two calls.
-
-```python
-b.get_svg()
-
-b.display_svg()
-
-```
-
-
-### Events
-
-**_Note: This is an experimental feature._**
-
-```python
-
-def locuschange(data):
-    b.locus = data
-
-    b.on("locuschange", locuschange)
-
-    b.zoom_in()
-
-    return b.locus
-
-```
-
-#### Development
-
-To build and install from source:
-
-```bash
-python setup.py build
-pip install -e .
-jupyter labextension develop . --overwrite
-jupyter nbextension install --py igv --symlink
-jupyter nbextension enable --py igv
-```
-
-After source changes, the extension can be rebuilt using:
-
-```bash
-jupyter labextension build .
-```
-
-Creating a conda environment
-```bash
-conda create -n test python=3.7.1
-conda activate test
-conda install pip
-conda install jupyter
-
 ```
diff --git a/igv/__init__.py b/igv/__init__.py
@@ -1,6 +1,5 @@
 from .navbar import show_navbar
 from .tool import igv_tool
-from igv_notebook import Browser, init
 
 
 __version__ = '2.0.0'