Travis Wrightsman

Add a few new things to manuscript stats

2

I think it would be useful to flesh out [get_manuscript_stats](https://github.com/manubot/manubot/blob/71fbbf71bb4b7804bc132d78b85f73be76425ef8/manubot/process/manuscript.py#L21-L28) a bit. I was thinking of two main improvements: 1. Add paragraph and character counts 2. Break down the stats...

Hello, I've noticed an issue with Jupyter Lab finding kernels inside Conda environments using `nb_conda_kernels` on the managed notebooks on Google Cloud. Here is the start of the server logs,...

Handling cache on Mac

5

I'm exploring the cache on Mac OSX, located in ~/Jagex/Runescape, and I believe the file format has changed. They have switched over to sqlite3 databases, is this the NXT format...

Use releases

5

Dear Jasper, Would you consider using versions and tagging releases with REVEAL? It would help the package managers, like `conda`, organize things a little better. Cheers, Travis

Cell execution interrupted when browser closed

3

### Description I couldn't find any issue already raised about this, but it would be great if cells could continue execution on the server when the browser is closed or...

Allow specifying language server priority per notebook

2

## Elevator Pitch Language server priorities or at least the preferred language server should be specifiable per notebook. ## Motivation I use Jupyter Lab with [`nb_conda_kernels`](https://github.com/Anaconda-Platform/nb_conda_kernels), which allows one to...

Speed RagTag up a few orders of magnitude on fragmented assemblies with caching

1

I noticed computing the line numbers of AGP files and objects was ~99% (!) of the runtime on our very fragmented contig assemblies. This patch pre-computes the line numbers and...

Add hal

1

Add the `hal` recipe and bump its `sonlib` dependency as well as add `run_exports`. ---- ### Bot commands for PR management Please use the following BiocondaBot commands: Everyone has access...

Basset-style training failing due to shape mismatch

6

I'm attempting to train a Basset-style model using a single dataset of peak calls but I'm getting the following error after running `basenji_train.py -k -o tmp/train_basset basenji/manuscripts/basset/params_basset.json tmp/data_basset` ``` Traceback...

Payees do not autocomplete

1

As far as I can tell there is no completion for payees. I think this is a useful feature because it helps keep consistent naming with payees, which in turn...