Bijan Varjavand

Note most of the code has already been written, mostly debugging remains.

lines to be changed are every single type-checking line after a method (for example, `upload.py` lines [48-51](https://github.com/neurodata/brainlit/blob/develop/brainlit/utils/upload.py#L48-L51)). Scripts with type hints and checking so far include: - methods in [upload.py](https://github.com/neurodata/brainlit/blob/continue_upload/brainlit/utils/upload.py)...

Our ground truth data is a list of coordinates tracing a neuron, with the first vertex always at the soma. You can visualize the [data](https://viz.neurodata.io/?json_url=https://json.neurodata.io/v1?NGStateID=al3JCguHCsexWg) with neuron ids 2 and...

@JacopoTeneggi @tathey1 @alishakodibagkar I had things setup using the username stored in the travis.yml file, like [here](https://github.com/neurodata/brainlit/blob/axon-radius/.travis.yml). The password was encrypted and only available as a travis CI environment variable,...

The python kernel that the notebooks are running do not have `brainlit` pip-installed. This is an issue with specifying the kernel of the notebook, see [conf.py](https://github.com/neurodata/brainlit/blob/develop/docs/conf.py#L46). I guess the "python3"...

Docker and singularity are both container runtimes, which just means that they package the code you give them with its own computer. When you run code via docker or singularity,...

Indeed, - You can shell into a Singularity-ized Docker image - You can run a Docker image instantly as a Singularity image - You can pull a Docker image (without...

@jovo I've built an image with the working `brainlit` release [here](https://hub.docker.com/repository/docker/bvarjavand/brainlit/general). Now to run via singularity

Ok, the image is released at `neurodata/brainlit`. The code to shell, run, and execute the image via Singularity is ``` singularity shell docker://neurodata/brainlit:latest singularity run docker://neurodata/brainlit:latest singularity exec docker://neurodata/brainlit:latest echo...

Incorporating Vikram's stuff into brainlit is definitely the plan. Will do.