Prettier for markdown formatting

.gitignore

@@ -136,3 +136,4 @@ GRCh37_latest_genomic.sort.gff.gz.tbi
 bin
 lib64
 pyvenv.cfg
+node_modules

README.md

@@ -4,96 +4,38 @@
 
 # [JBrowse Jupyter](https://gmod.github.io/jbrowse-jupyter/)
 
-JBrowse Jupyter is a python package that let's you create JBrowse 2 views in Jupyter notebooks
-
-
-![demo-gif](https://user-images.githubusercontent.com/45598764/144863573-2bcd982b-1d18-4dc8-aa2f-fd8adf4985a2.gif)
-
-_You can open this browser.ipynb in colab_
-[here](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/browser.ipynb)
+JBrowse Jupyter is a python package that let's you create JBrowse 2 views in
+Jupyter notebooks
 
 ## Demos
 
-- Basic usage - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/browser.ipynb)
-- SKBR3 cancer cell line demo - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/skbr3.ipynb
+- Basic usage -
+  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/browser.ipynb)
+- SKBR3 cancer cell line demo -
+  [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/GMOD/jbrowse-jupyter/blob/main/skbr3.ipynb
 
 ## Documentation
 
-More documentation here https://gmod.github.io/jbrowse-jupyter/docs/html/index.html
+More documentation here
+https://gmod.github.io/jbrowse-jupyter/docs/html/index.html
 
 ## Installation
 
-
 ```
 $ pip install jbrowse-jupyter
 ```
 
-
-
-#### Using Jupyter URLS
-
-In this example, the notebook is configured to run in localhost in port 8888. It
-is assumed that you have Jupyter lab installed in your venv.
-
-File tree of the project:
-
-```
-- example_dir/
-    - example.ipynb
-    - data1.gff.gz
-    - data2.gff.gz.tbi
-```
-
-Running Jupyter
-
-```
-(venv)$ cd example_dir
-(venv)$ jupyter lab
-```
-
-This will be the url that you should see at the top of your browser if you
-opened the example.ipynb http://localhost:8888/lab/tree/example.ipynb
-
-Urls for file `data1.gff.gz` and `data2.gff.gz.tbi` would be in the form
-`http://localhost:8888/files/<your_file_name>`.
-
-- `http://localhost:8888/files/data1.gff.gz`
-- `http://localhost:8888/files/data2.gff.gz.tbi` Note that you do not need to
-  add lab or tree to this url.
-
-You can use these urls. For example, you could add a track with these urls like
-this:
-
-```python
-
-config.add_track(
-    "http://localhost:8888/files/data1.gff.gz", # track data
-    index="http://localhost:8888/files/data2.gff.gz.tbi", # track index
-    track_id="example-track", # track id
-    name="track-name" # track name
-)
-```
-
-Resources:
-
-- [Configuring the Jupyter Notebook server](https://jupyter-notebook.readthedocs.io/en/stable/config_overview.html#notebook-server)
-- [Getting started with Jupyter Lab](https://jupyterlab.readthedocs.io/en/stable/getting_started/starting.html)
-
 ## Resources
 
-- [JBrowse](https://jbrowse.org/jb2/) - the next generation genome browser
-- [JBrowse React Linear Genome View](https://www.npmjs.com/package/@jbrowse/react-linear-genome-view) -
-  interactive genome browser
-- [JBrowse React Linear Genome View Docs](https://jbrowse.org/storybook/lgv/main/?path=/story/getting-started--page) -
+- [JBrowse 2 homepage](https://jbrowse.org/jb2/)
+- [Linear Genome View docs](https://jbrowse.org/storybook/lgv/main/?path=/story/getting-started--page) -
   storybook docs of React LGV
 - [Dash Applications](https://dash.plotly.com/layout) how to get started to
   custumize Dash applications.
 - [Dash HTML components](https://dash.plotly.com/dash-html-components) Dash html
   components to build the Dash application layout.
-- [Dash Jupyter](https://github.com/plotly/jupyter-dash) library to enable
-  embedding Dash components in jupyter notebooks.
-- [Dash Jbrowse](https://github.com/GMOD/dash_jbrowse) suite of Dash components
-  for JBrowse views. (JBrowse Linear Genome View)
+- [Dash JBrowse](https://github.com/GMOD/dash_jbrowse) suite of Dash components
+  for JBrowse views
 
 ## Contributing
 
@@ -108,7 +50,6 @@ publish, please cite the most recent JBrowse paper, which will be linked from
 
 ## Contact us
 
-
 - Report a bug or request a feature at
   https://github.com/GMOD/jbrowse-jupyter/issues
 - Join our developers chat at https://gitter.im/GMOD/jbrowse2
@@ -145,15 +86,3 @@ notebook/lab server. Intended for those running their notebooks with jupyter lab
 or jupyter notebook. 2. Launch your own http server with CORS which will enable
 you to use local files. You can run our serve.py to launch our dev server.
 (Checkout our local_support.ipynb for tutorials on how to use your own data)
-
-
-### My data says it's is loading and never loads?
-
-If your view shows that it is loading and never loads, it could be a fetch error
-or CORS. - the JBrowse Dev Server has CORS enabled.
-
-- Make sure that your alias is correctly configured. Data that never loads could
-  also indicate that the format is correct, but will not display anything for it
-  if the assembly does not match.
-- Data that never loads could also indicate that the port and host do not match
-  where your data is hosted when using paths in jupyter envs

package.json

@@ -1,5 +1,6 @@
 {
   "devDependencies": {
+    "prettier": "^3.1.1",
     "react-docgen": "^7.0.1"
   }
 }

yarn.lock

@@ -427,6 +427,11 @@ picocolors@^1.0.0:
   resolved "https://registry.yarnpkg.com/picocolors/-/picocolors-1.0.0.tgz#cb5bdc74ff3f51892236eaf79d68bc44564ab81c"
   integrity sha512-1fygroTLlHu66zi26VoTDv8yRgm0Fccecssto+MhsZ0D/DGW2sm8E8AjW7NU5VVTRt5GxbeZ5qBuJr+HyLYkjQ==
 
+prettier@^3.1.1:
+  version "3.1.1"
+  resolved "https://registry.yarnpkg.com/prettier/-/prettier-3.1.1.tgz#6ba9f23165d690b6cbdaa88cb0807278f7019848"
+  integrity sha512-22UbSzg8luF4UuZtzgiUOfcGM8s4tjBv6dJRT7j275NXsy2jb4aJa4NNveul5x4eqlF1wuhuR2RElK71RvmVaw==
+
 react-docgen@^7.0.1:
   version "7.0.1"
   resolved "https://registry.yarnpkg.com/react-docgen/-/react-docgen-7.0.1.tgz#b6528fe45385908645ffbee1ec0d65709e1e047c"