Bijan Varjavand

Don't use local s3 data for tests, use open-neurodata with `use_https=True`

9

There is around 500mb of s3-formatted data in our data folder which isn't strictly necessary for testing. Specifically, the change requested is that tests for the neuron trace class use...

Change all napari notebooks to use nbscreenshot

1

The current notebooks are a sad shadow of when they are running, mostly because none of the napari interactivity is there. I suggest everyone with a notebook using napari to...

We forward the netlify documentation website to neurodata.io and somewhere along the way it becomes insecure. Everything looks good on the netlify end.

Downloading multiple chunks of data from s3 takes a long time, and is often the slowest step in a pipeline by far. For example, ``` from brainlit.utils.session import NeuroglancerSession sess...

Reformat the code in [base.py](https://github.com/neurodata/brainlit/blob/feature_rename/brainlit/feature_extraction/base.py), [neighborhood.py](https://github.com/neurodata/brainlit/blob/feature_rename/brainlit/feature_extraction/neighborhood.py), and [linear_features.py](https://github.com/neurodata/brainlit/blob/feature_rename/brainlit/feature_extraction/linear_features.py). Additionally, refactor and overhaul [test_subneighborhood.py](https://github.com/neurodata/brainlit/blob/feature_rename/tests/archive/test_subneighborhood.py) according to the standards mentioned in the [Refactor](https://github.com/neurodata/brainlit/projects) project. This means: - typing hints on every method...

Improve type checking via typeguard

2

As the repo is refactored (see the [Reformatting project](https://github.com/neurodata/brainlit/projects/1)), pep484 type hints are being added (example [here](https://github.com/neurodata/brainlit/blob/continue_upload/brainlit/utils/upload.py#L97)). [Typeguard](https://github.com/agronholm/typeguard ) allows for type checking via pep484 type hints, and using them...

Allow upload_volumes to start from a specfic mip/chunk_idx

1

CloudVolume will sometimes hang randomly, interrupting large uploads. Currently, if an error happens, we only print a short error message, and the upload must be restarted from scratch. It would...

Reformat the [code](https://github.com/neurodata/brainlit/blob/develop/brainlit/utils/swc.py) and [tests](https://github.com/neurodata/brainlit/blob/develop/tests/test_swc.py) to be similar to [upload.py]() and [session.py](). This means: - [ ] typing hints on every method and class - [ ] google-formatted docstrings on...

Reformat the code in [preprocess.py](https://github.com/neurodata/brainlit/tree/develop/brainlit/preprocessing/preprocess.py) and [image_process.py](https://github.com/neurodata/brainlit/tree/develop/brainlit/preprocessing/image_process.py), along with tests in [test_preprocess.py](https://github.com/neurodata/brainlit/tree/develop/tests/archive/test_preprocess.py) and [test_image_processs.py](https://github.com/neurodata/brainlit/tree/develop/tests/archive/test_image_process.py). This means: - [ ] typing hints on every method and class - [ ] google-formatted...