Removes deprecated package jupyter dash (#79)

* rm jupyter dash

* require ipython

README.md

@@ -104,17 +104,15 @@ $ pip install jupyter-dash
 ```
 
 ```python
-from jupyter_dash import JupyterDash
-
-from dash import html
+from dash import html, Dash, jupyter_dash
 from jbrowse_jupyter import create, create_component
 import jupyter_server_proxy
 
-JupyterDash.infer_jupyter_proxy_config()
-#JupyterDash()._server_proxy # true if the proxy works as expected
-#JupyterDash().config # gives the proxy config
+jupyter_dash.infer_jupyter_proxy_config()
+#jupyter_dash._server_proxy # true if the proxy works as expected
+#jupyter_dash.config # gives the proxy config
 
-app = JupyterDash(__name__)
+app = Dash(__name__)
 jbrowse_conf = create("LGV", genome="hg38")
 
 config = jbrowse_conf.get_config()
@@ -147,12 +145,12 @@ You can find examples in the root of this repo or in the examples folder,
 
 - `browser.py` - uses the Dash library to create a python application with the
   Dash JBrowse LinearGenomeView component
-- `browser.ipynb` - jupyter notebook using the JupyterDash library to embed a
-  Dash JBrowse LinearGenomeView component in a cell
+- `browser.ipynb` - jupyter notebook using the Dash library to embed a Dash
+  JBrowse LinearGenomeView component in a cell
 - `examples/cgv_examples.py` - uses the Dash library to create a python
   application with the Dash JBrowse CircularGenomeView component
-- `examples/cgv_examples.ipynb` - jupyter notebook using the JupyterDash library
-  to embed a Dash JBrowse CircularGenomeView component in a cell
+- `examples/cgv_examples.ipynb` - jupyter notebook using the Dash library to
+  embed a Dash JBrowse CircularGenomeView component in a cell
 - `local_support.ipynb` - jupyter notebook with tutorial on using your local
   data and passing it to JBrowse views
 

docs/requirements.txt

@@ -1,6 +1,5 @@
 dash==2.3.0
 dash-jbrowse>=1.0.2
-jupyter_dash>=0.4.2
 Werkzeug==2.0.3
 pandas>=1.1.5
 pytest>=6.2.5

docs/source/installation.md

@@ -28,11 +28,11 @@ You can find examples in the root of the directory.
 
 `browser.py` uses the Dash library to create a python application with the Dash
 JBrowse LinearGenomeView component and configured with the help of this package.
-`browser.ipynb` is jupyter notebook using the JupyterDash library to embed a
-Dash JBrowse LinearGenomeView component in a cell. `cgv_examples.py` a Dash
+`browser.ipynb` is jupyter notebook using the Dash library to embed a Dash
+JBrowse LinearGenomeView component in a cell. `cgv_examples.py` a Dash
 application using the Dash JBrowse CircularGenomeView component
-`cgv_examples.ipynb` is jupyter notebook using the JupyterDash library to embed
-a Dash JBrowse CircularGenomeView component in a cell.
+`cgv_examples.ipynb` is jupyter notebook using the Dash library to embed a Dash
+JBrowse CircularGenomeView component in a cell.
 
 To run the Python Dash application
 

examples/dash_callbacks.ipynb

@@ -13,10 +13,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from dash import html, Dash\n",
+    "from dash import dcc, html, Dash\n",
     "from dash.dependencies import Input, Output\n",
-    "from dash import dcc\n",
-    "from jupyter_dash import JupyterDash\n",
     "from jbrowse_jupyter import create, create_component"
    ]
   },
@@ -27,7 +25,7 @@
    "outputs": [],
    "source": [
     "# Create a Jupyter dash app\n",
-    "app = JupyterDash(__name__)\n",
+    "app = Dash(__name__)\n",
     "server = app.server\n",
     "\n",
     "# Docs: https://github.com/plotly/jupyter-dash"

jbrowse_jupyter/util.py

@@ -3,10 +3,8 @@
 import json
 import pkg_resources
 import dash_jbrowse as jb
-from dash import html
+from dash import html, Dash
 from urllib.parse import urlparse
-from jupyter_dash import JupyterDash
-
 
 def is_url(filePath):
     """
@@ -128,7 +126,7 @@ def create_component(conf, **kwargs):
 def launch(conf, **kwargs):
     """
     Launches a LinearGenomeView Dash JBrowse component in a
-    server with the help of JupyterDash.
+    server.
 
     e.g
     launch(conf, dash_comp="CGV",height=400, port=8002)
@@ -141,11 +139,11 @@ def launch(conf, **kwargs):
         launch. Currently supporting LGV and CGV.
         defaults to `LGV` when no dash_comp= is specified
     :param int port: (optional) port to utilize when running
-        the JupyterDash app
+        the Dash app
     :param int height: (optional) the height to utilize for
-        the JupyterDash app
+        the Dash app
     """
-    app = JupyterDash(__name__)
+    app = Dash(__name__)
     # could add other JBrowse view types e.g Circular, Dotplot
     supported = set({"LGV", "CGV"})
     dash_comp = kwargs.get("dash_comp", "LGV")

local_support.ipynb

@@ -127,7 +127,7 @@
    "outputs": [],
    "source": [
     "from jbrowse_jupyter import launch, create, serve\n",
-    "from jupyter_dash import JupyterDash\n",
+    "from dash import jupyter_dash\n",
     "import requests"
    ]
   },
@@ -210,8 +210,8 @@
    "source": [
     "# Uncomment and run the next line if you are running this in jupyterlab/jupyternotebook\n",
     "\n",
-    "import jupyter_server_proxy\n",
-    "JupyterDash.infer_jupyter_proxy_config() "
+    "from dash import jupyter_dash\n",
+    "jupyter_dash.infer_jupyter_proxy_config() "
    ]
   },
   {

requirements.txt

@@ -1,5 +1,5 @@
 dash>=2.11.1
 dash-jbrowse>=1.2.0
-jupyter_dash>=0.4.2
 Werkzeug==2.0.3
 pandas>=1.1.5
+IPython>=8.18.1