Docker voila

.gitignore

@@ -139,4 +139,7 @@ dmypy.json
 *.code-workspace
 
 # Local History for Visual Studio Code
-.history/
+.history/
+
+# NWB streaming cache
+*/nwb-cache

docker/Dockerfile

@@ -0,0 +1,16 @@
+FROM python:3.10
+
+RUN cd ..
+COPY requirements.txt .
+RUN pip install --upgrade pip \
+    && pip install -r requirements.txt \
+    && pip install git+https://github.com/NeurodataWithoutBorders/nwbwidgets.git
+
+COPY notebook.ipynb .
+RUN mkdir nwb-cache
+
+EXPOSE 8866
+CMD ["voila", "notebook.ipynb", "--port=8866", "--Voila.ip=0.0.0.0", "--enable_nbextensions=True", "--autoreload=True", "--no-browser"]
+
+# EXPOSE 8888
+# CMD ["jupyter", "notebook", "notebook.ipynb", "--port=8888", "--ip=0.0.0.0", "--no-browser", "--allow-root", "--NotebookApp.token=''"]

docker/README.md

@@ -0,0 +1,23 @@
+## Build Docker Image
+
+From `/docker` directory, run:
+```bash
+$ docker build -t nwbwidgets-voila .
+```
+
+## Run Docker Image
+
+To run with `Panel`:
+```bash
+$ docker run -p 8866:8866 nwbwidgets-voila
+```
+
+By default, the Panel will run with `enable_local_source=False` (see [Panel](https://nwb-widgets.readthedocs.io/en/latest/contents/quickstart.html#basic-usage-with-panel)). To allow for local files browsering, run the container with:
+```bash
+$ docker run -p 8866:8866 -e ENABLE_LOCAL_SOURCE=True nwbwidgets-voila 
+```
+
+To run for a specific NWB file, pass the s3 url as an ENV variable to the container:
+```bash
+$ docker run -p 8866:8866 -e S3_URL_NWBFILE=<s3_url_to_nwb_file> nwbwidgets-voila 
+```

docker/notebook.ipynb

@@ -0,0 +1,74 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "\n",
+    "\n",
+    "s3_url = os.getenv(\"S3_URL_NWBFILE\", None)\n",
+    "enable_local_source  = bool(os.getenv(\"ENABLE_LOCAL_SOURCE\", False))\n",
+    "\n",
+    "if s3_url:\n",
+    "    from pynwb import NWBHDF5IO\n",
+    "    from nwbwidgets import nwb2widget\n",
+    "    from dandi.dandiapi import DandiAPIClient\n",
+    "    import h5py\n",
+    "    import fsspec\n",
+    "    from fsspec.implementations.cached import CachingFileSystem\n",
+    "    \n",
+    "    # Create a virtual filesystem based on the http protocol and use caching to save accessed data to RAM.\n",
+    "    fs = CachingFileSystem(\n",
+    "        fs=fsspec.filesystem(\"http\"),\n",
+    "        cache_storage=\"nwb-cache\",  # Local folder for the cache\n",
+    "    )\n",
+    "    f = fs.open(s3_url, \"rb\")\n",
+    "    file = h5py.File(f)\n",
+    "    io = NWBHDF5IO(file=file, load_namespaces=True)\n",
+    "    nwbfile = io.read()\n",
+    "    w = nwb2widget(nwbfile)\n",
+    "else:\n",
+    "    from nwbwidgets import Panel\n",
+    "    w = Panel(enable_local_source=enable_local_source)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "w"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3.8.5 ('base')",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  },
+  "vscode": {
+   "interpreter": {
+    "hash": "698d109e506a444d1bfd677c8f66adf4920b11c19b28ee52fae9b02c95d46a98"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

docker/requirements.txt

@@ -0,0 +1,35 @@
+pynwb>=2.2.0
+dandi>=0.46.6
+# nwbwidgets>=0.9.2
+ndx-grayscalevolume==0.0.2
+ndx-icephys-meta==0.1.0
+ndx-spectrum==0.2.2
+voila==0.3.6
+numpy==1.23.3
+matplotlib==3.6.1
+scikit-image==0.19.3
+plotly==5.10.0
+ipydatagrid==1.1.13
+ipydatawidgets==4.3.2
+ipytree==0.2.2
+ipyvolume==0.6.0a10
+ipyvue==1.8.0
+ipyvuetify==1.8.4
+ipywebrtc==0.6.0
+ipywidgets==7.7.2
+ipykernel==6.16.0
+ipympl==0.9.2
+jupyter_client==7.4.2
+jupyter_core==4.11.1
+jupyter-server==1.21.0
+jupyterlab==3.4.8
+jupyterlab-pygments==0.2.2
+jupyterlab_server==2.15.2
+jupyterlab-widgets==1.1.1
+tqdm>=4.36.0
+zarr==2.13.3
+aiohttp==3.8.3
+tifffile==2022.10.10
+trimesh==3.15.4
+importlib-metadata<5.0
+fsspec==2022.8.2

docs/README.md

@@ -1,6 +1,11 @@
 ## Build documentation
 
-From `/docs` run:
+To run auto-doc for the API, from `/docs` run:
+```bash
+$ sphinx-apidoc -f -o ./source/api_reference ../nwbwidgets
+```
+
+To build the HTML, from `/docs` run:
 ```bash
 $ sphinx-build -b html ./source ./build
 ```

docs/source/api_reference/nwbwidgets.rst

@@ -111,6 +111,14 @@ nwbwidgets.ophys module
    :undoc-members:
    :show-inheritance:
 
+nwbwidgets.panel module
+-----------------------
+
+.. automodule:: nwbwidgets.panel
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 nwbwidgets.spectrum module
 --------------------------
 

docs/source/api_reference/nwbwidgets.utils.rst

@@ -12,6 +12,14 @@ nwbwidgets.utils.cmaps module
    :undoc-members:
    :show-inheritance:
 
+nwbwidgets.utils.dandi module
+-----------------------------
+
+.. automodule:: nwbwidgets.utils.dandi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 nwbwidgets.utils.dynamictable module
 ------------------------------------
 

docs/source/conf.py

@@ -26,7 +26,7 @@
 # Insert the project root dir as the first element in the PYTHONPATH.
 # This lets us ensure that the source package is imported, and that its
 # version is used.
-sys.path.insert(0, os.path.join(project_root, 'src'))
+sys.path.insert(0, os.path.join(project_root, '../../nwbwidgets'))
 
 
 
@@ -61,4 +61,11 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_static_path = ['_static']
+
+
+# TODO - not working- Include arguments with typehints from classes
+# ref: https://stackoverflow.com/questions/5599254/how-to-use-sphinxs-autodoc-to-document-a-classs-init-self-method
+# ref: https://stackoverflow.com/questions/63957326/sphinx-does-not-show-class-instantiation-arguments-for-generic-classes-i-e-par
+autoclass_content = 'both'
+autodoc_typehints = 'signature'

docs/source/contents/quickstart.md → docs/source/contents/running_on_jupyter.md

@@ -1,7 +1,7 @@
 
-# Quickstart
+# Running NWB widgets on Jupyter
 
-## Basic usage with `Panel`
+## Using `Panel`
 
 The easiest way to use NWB widgets is with the interactive `Panel`:
 ```python
@@ -10,13 +10,25 @@ from nwbwidgets.panel import Panel
 Panel()
 ```
 
-![panel](../_static/quickstart/panel_fsspec.gif)
+![panel](../_static/panel.gif)
 
 With `Panel` you can easily browser through local files as well as stream remote datasets from DANDI archive.
-For data streaming the default mode is [fsspec](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html#streaming-method-2-fsspec). If you would like to use [ROS3](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html#streaming-method-1-ros3) instead, you can do so with `Panel(stream_mode='ros3')`.
+For data streaming the default mode is [fsspec](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html#streaming-method-2-fsspec). If you would like to use [ROS3](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/streaming.html#streaming-method-1-ros3) instead, you can do so with: 
+```python
+Panel(stream_mode='ros3')
+```
 
+If you intend to you `Panel` only for local storage (no streaming), you can instantiate it as:
+```python
+Panel(enable_dandi_source=False, enable_s3_source=False)
+```
+
+If you intend to you `Panel` only for streaming data (no local storage), you can instantiate it as:
+```python
+Panel(enable_local_source=False)
+```
 
-## Basic usage with `nwb2widget`
+## Using `nwb2widget`
 
 If you're working with a nwb file object in your Jupyter notebook, you can also explore it with NWB Widgets using `nwb2widget`:
 ```python

docs/source/contents/running_remotely.md

@@ -0,0 +1,32 @@
+# Running NWB widgets remotely
+
+## Using Docker
+You can easily deploy a webapp for visualizing NWB files using NWB widgets, [Voila](https://voila.readthedocs.io/en/stable/using.html) and Docker. Start by cloning the repository:
+```bash
+$ git clone https://github.com/NeurodataWithoutBorders/nwbwidgets.git
+$ cd nwbwidgets/docker
+```
+
+Build a Docker image:
+```bash
+$ docker build -t nwbwidgets-voila .
+```
+
+Finally, run a container:
+```bash
+$ docker run -p 8866:8866 nwbwidgets-voila
+```
+
+By default, the Panel will run with `enable_local_source=False` (see [Panel](https://nwb-widgets.readthedocs.io/en/latest/contents/quickstart.html#basic-usage-with-panel)). To allow for local files browsering, run the container with:
+```bash
+$ docker run -p 8866:8866 -e ENABLE_LOCAL_SOURCE=True nwbwidgets-voila
+```
+
+If you want to skip the default Panel and instead run it for a specific NWB file, pass the s3 url as an ENV variable to the container:
+```bash
+$ docker run -p 8866:8866 -e S3_URL_NWBFILE=<s3_url_to_nwb_file> nwbwidgets-voila
+```
+
+
+## Using Binder
+

docs/source/index.rst

@@ -28,7 +28,8 @@ NWB Widgets is a library of widgets for visualization NWB data in a Jupyter note
    :caption: Contents:
 
    contents/installation
-   contents/quickstart
+   contents/running_on_jupyter
+   contents/running_remotely
    contents/developer_guide
 
 .. toctree::