Lon Blauvelt

 ### Snyk has created this PR to fix 2 vulnerabilities in the pip dependencies of this project. #### Snyk changed the following file(s): - `requirements.txt` ⚠️ Warning ``` Flask...

`__init__.py` files are run at runtime, and with `[extras]` can develop conditional imports that break if you don't have a fully installed version of toil. Moving code from these into...

This is low priority, but at some point, we should make a small chart with rabbitmq, gunicorn, flask, and celery for the docs. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1716)...

``` =================================== FAILURES =================================== __________________________ UtilsTest.testGetPIDStatus __________________________ [gw2] linux -- Python 3.9.20 /builds/databiosphere/toil/venv/bin/python Traceback (most recent call last): File "/usr/lib/python3.9/unittest/case.py", line 59, in testPartExecutor yield File "/usr/lib/python3.9/unittest/case.py", line 592, in...

Warn users about disk usage prior to each run.

3

Wherever they set the jobstore, if it's local, we can have a user warning telling people how much disk space they have left. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-837)...

Currently a draft, but making this to support it in the future: https://github.com/common-workflow-language/cwl-v1.3 . ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1680) ┆Issue Number: TOIL-1680

We probably shouldn't let these build up infinitely. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-626) ┆Issue Number: TOIL-626

CWL: Too many bind mounts in Singularity.

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Discussion and original issue is here: https://cwl.discourse.group/t/too-many-arguments-on-the-command-line/248/2 Short summary: If I use as input to a step and I put a directory array (Directory[]) and I run the workflow with...