updated README to include install from pypi and NWB conversion, and l…

…ink to readme in setup.cfg (for PyPI description)

README.md

@@ -1,4 +1,4 @@
-# SNUB (Systems Neuro Browser)
+# Systems Neuro Browser (SNUB)
 
 ## [Read the documentation!](https://snub.readthedocs.io/en/latest/)
 
@@ -9,18 +9,17 @@ SNUB is a visual interface for systems neuroscience. Using a set of linked data-
 
 ## Installation
 
-Create and activate a new conda environment with python≥3.8, clone this repo, and install via pip
+Create and activate a new conda environment with python≥3.8 and install via pip
 ```
 conda create -n snub python=3.8
 conda activate snub
-git clone https://github.com/calebweinreb/SNUB.git
-pip install -e SNUB
+pip install systems-neuro-browser
 ```
-To speed up selections, `pip install ncls`. To use the 3D mesh viewer, install `pip install PyOpenGL PyOpenGL_accelerate`. The docs include more detailed [installation instructions](https://snub.readthedocs.io/en/latest/install.html).
+To speed up selections, `pip install ncls`. To use the 3D pose viewer, install `pip install PyOpenGL PyOpenGL_accelerate`. The docs include more detailed [installation instructions](https://snub.readthedocs.io/en/latest/install.html).
 
 ## Getting Started
 
-* Download the [example project](https://www.dropbox.com/sh/ujr3ttdc3gsxtqt/AAAKLL9iaF54cOwPKRPMTENIa?dl=0). 
+* Download the [example project](https://zenodo.org/records/10578025/files/miniscope_project.zip?download=1). 
 * Launch SNUB from the command line with the command `snub`.
 * Go to `File > Open Project`, navigate to the project directory, and hit `Choose` with the directory selected.
 * Alternatively, launch SNUB directly with the project path `snub /path/to/project/directory`.
@@ -38,3 +37,33 @@ snub.io.project.create_project(project_directory, duration=1800)
 snub.io.project.add_video(project_directory, 'path/to/my_video.avi', name='IR_camera')
 snub.io.project.add_splikeplot(project_directory, 'my_ephys_data', spike_times, spike_labels) 
 ```
+
+## Convert an NWB file
+
+We provide a rudimentary tool for automatically generating SNUB datasets from Neurodata Without Borders (NWB) files, which contain raw and processed data from neuroscience recordings. The data in NWB files are stored hierarchically, and each component of the hierarchy has a specific neurodata type that reflects the measurement modality (e.g, "Units" for spike trains, "ImageSeries" for video). Our conversion tool generates a SNUB display element for each supported neurodata type. Users can optionally restrict this process to a subset of the NWB hierarchy (e.g., include pose tracking while excluding electrophysiology, or include just a subset of electrophysiology measurements). Here's an example:
+
+```
+# Run from the command line
+
+# Download NWB file
+dandi download https://api.dandiarchive.org/api/dandisets/000540/versions/0.230515.0530/assets/94307bee-459c-424e-b3a0-1e86b23f04b2/download/
+
+# Download associated video and create directory for it
+dandi download https://api.dandiarchive.org/api/dandisets/000540/versions/0.230515.0530/assets/942b0806-2c8b-4289-a072-9e965884fcb6/download/
+mkdir sub-SLR087_ses-20180706_obj-14ua2bs_behavior+image
+mv 9557b48e-46f0-45f2-a700-a2e15318c5bc_external_file_0.avi sub-SLR087_ses-20180706_obj-14ua2bs_behavior+image/
+```
+
+```
+# Run in python
+
+import os, snub
+
+# Define paths
+nwb_file = "sub-SLR087_ses-20180706_obj-14ua2bs_behavior+image.nwb"
+name = os.path.splitext(os.path.basename(nwb_file))[0]
+project_directory = os.path.join(os.path.dirname(nwb_file), f"SNUB-{name}")
+
+# Make SNUB plot that includes video and torso tracking
+snub.io.create_project_from_nwb(project_directory, nwb_file, branches=['torso_dlc', 'ImageSeries'])
+```

setup.cfg

@@ -1,11 +1,16 @@
 [metadata]
 author = Caleb Weinreb
 author_email = [email protected]
-url = https://github.com/dattalab/SNUB
+url = https://github.com/calebweinreb/SNUB
+description = Systems Neuro Browser
+long_description = file:README.md
+long_description_content_type = text/markdown
 classifiers =
     Programming Language :: Python :: 3
     Operating System :: OS Independent
 
+
+
 [options]
 packages = find:
 include_package_data = True