Refactored igv-jupyter to wrap igv-notebook; work in progress

g2nb · Apr 27, 2022 · 571dd1e · 571dd1e
1 parent b57ea02
commit 571dd1e
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diff --git a/Dockerfile b/Dockerfile
@@ -1,42 +1,27 @@
 # Dockerfile for running igv-jupyter from a pip install
 
 # Pull the latest known good scipy notebook image from the official Jupyter stacks
-FROM jupyter/scipy-notebook:2021-08-16
+FROM jupyter/scipy-notebook:2022-02-17
 
 MAINTAINER Thorin Tabor <[email protected]>
 EXPOSE 8888
 
-#############################################
-##  ROOT                                   ##
-##      Install npm                        ##
-#############################################
-
-USER root
-
-RUN apt-get update && apt-get install -y npm
-
-#############################################
-##  $NB_USER                               ##
-##      Install python libraries           ##
-#############################################
-
-USER $NB_USER
-
-RUN conda install -c conda-forge jupyterlab=3.1
-
 #############################################
 ##  $NB_USER                               ##
-##      Install nbtools                    ##
+##      Install dependencies               ##
 #############################################
 
-RUN pip install nbtools==21.9.0b1
+RUN pip install nbtools==22.3.0b2 igv-notebook
 
 #############################################
 ##  $NB_USER                               ##
 ##      Install nbtools igv-jupyter        ##
 #############################################
 
-RUN pip install igv-jupyter && jupyter lab build
+RUN pip install igv-jupyter
+
+# RUN git clone https://github.com/g2nb/igv-jupyter.git
+# RUN cd igv-jupyter && pip install -e .
 
 #############################################
 ##  $NB_USER                               ##

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2016-2021 The Broad Institute and The Regents of the University of California
+Copyright (c) 2016-2022 The Broad Institute and The Regents of the University of California
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/igv/.gitignore b/igv/.gitignore
diff --git a/igv/__init__.py b/igv/__init__.py
@@ -1,15 +1,6 @@
-from .browser import Browser
-from .nbextension import _jupyter_nbextension_paths
-from .labextension import _jupyter_labextension_paths
+from .navbar import show_navbar
 from .tool import igv_tool
-from .version import __version__
+from igv_notebook import Browser, init
 
 
-def _jupyter_server_extension_paths():
-    return [{
-        "module": "igv"
-    }]
-
-
-def load_jupyter_server_extension(nbapp):
-    nbapp.log.info("igv enabled!")
+__version__ = '2.0.0'
diff --git a/igv/browser.py b/igv/browser.py
diff --git a/igv/labextension.py b/igv/labextension.py
diff --git a/igv/navbar.py b/igv/navbar.py
@@ -0,0 +1,19 @@
+import os
+from IPython.display import HTML, Javascript, display
+
+
+def show_navbar():
+    # Display the base HTML container for the menu
+    display(HTML('<div class="igv-navbar"></div>'))
+
+    # Import the menu styles
+    menu_path = os.path.join(os.path.dirname(__file__), 'static/menu.css')
+    menu_file = open(menu_path, 'r')
+    menu_css = menu_file.read()
+    display(HTML(f'<style>{menu_css}</style>'))
+
+    # Build the menu with Javascript
+    menu_path = os.path.join(os.path.dirname(__file__), 'static/menu.js')
+    menu_file = open(menu_path, 'r')
+    menu_js = menu_file.read()
+    display(Javascript(menu_js))
diff --git a/igv/nbextension/__init__.py b/igv/nbextension/__init__.py