Merge branch 'master' into include-custom-widgets

.gitignore

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

.readthedocs.yaml

@@ -0,0 +1,23 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: false  # Eventually, you'll want this to be true
+
+# Python requirements required to build your docs
+python:
+  install:
+    - requirements: requirements-rtd.txt
+    - method: pip
+      path: .

README.md

@@ -2,7 +2,7 @@
 A library of widgets for visualization NWB data in a Jupyter notebook (or lab). The widgets allow you to navigate through the hierarchical structure of the NWB file and visualize specific data elements. It is designed to work out-of-the-box with NWB 2.0 files and to be easy to extend.
 
 [![PyPI version](https://badge.fury.io/py/nwbwidgets.svg)](https://badge.fury.io/py/nwbwidgets)
-[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/nwb-jupyter-widgets/branch/master/graph/badge.svg)](https://codecov.io/gh/NeurodataWithoutBorders/nwb-jupyter-widgets)
+[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/nwbwidgets/branch/master/graph/badge.svg)](https://codecov.io/gh/NeurodataWithoutBorders/nwbwidgets)
 [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NeurodataWithoutBorders/nwb-jupyter-widgets/master?filepath=examples%2FNWBWidgets-modality-demos.ipynb)
 

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>=0.10.0
+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/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

@@ -0,0 +1,11 @@
+## Build documentation
+
+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/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api_reference/modules.rst

@@ -0,0 +1,7 @@
+nwbwidgets
+==========
+
+.. toctree::
+   :maxdepth: 4
+
+   nwbwidgets

docs/source/api_reference/nwbwidgets.analysis.rst

@@ -0,0 +1,21 @@
+nwbwidgets.analysis package
+===========================
+
+Submodules
+----------
+
+nwbwidgets.analysis.spikes module
+---------------------------------
+
+.. automodule:: nwbwidgets.analysis.spikes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: nwbwidgets.analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api_reference/nwbwidgets.controllers.rst

@@ -0,0 +1,37 @@
+nwbwidgets.controllers package
+==============================
+
+Submodules
+----------
+
+nwbwidgets.controllers.group\_and\_sort\_controllers module
+-----------------------------------------------------------
+
+.. automodule:: nwbwidgets.controllers.group_and_sort_controllers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nwbwidgets.controllers.misc module
+----------------------------------
+
+.. automodule:: nwbwidgets.controllers.misc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+nwbwidgets.controllers.time\_window\_controllers module
+-------------------------------------------------------
+
+.. automodule:: nwbwidgets.controllers.time_window_controllers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: nwbwidgets.controllers
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/api_reference/nwbwidgets.dashboards.rst

@@ -0,0 +1,21 @@
+nwbwidgets.dashboards package
+=============================
+
+Submodules
+----------
+
+nwbwidgets.dashboards.allen module
+----------------------------------
+
+.. automodule:: nwbwidgets.dashboards.allen
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: nwbwidgets.dashboards
+   :members:
+   :undoc-members:
+   :show-inheritance: