M Bernt

velveth results depending on `OMP_NUM_THREADS` and stalling if `OMP_THREAD_LIMIT=1`

3

I'm currently working on the velvet Galaxy wrappers: https://github.com/galaxyproject/tools-iuc/pull/4641 We recently changed our CI to use 2 instead of 1 core. So far we only used `OMP_NUM_THREADS` which produced different...

is there a way to determine the number of used slots from the return value of `wait()`?

get_origin gives inconsistent results for differently defined Unions

3

If I got it right, `Union[X, Y]` should be equivalent to `X | Y` . But I get inconsistent results for `get_origin`: ``` import typing from types import UnionType import...

Better display of estimated line numbers and add number of columns for tabular

9

- Show estimated line number as a power of 10: showing all these zeros for an estimated number seems like a waste of space - Show number of columns for...

Make columns types an empty list for empty tabular data

1

- show number of columns https://github.com/galaxyproject/galaxy/issues/13258 - [ ] could also be `rows x cols` (I.e. drop the words lines and columns) for compacter display - [x] empty files currently...

Consider Null inputs

4

as a possibility to allow the pick value tool to create an empty file. Allows to connect an optional dataset to the pick value tool .. ## How to test...

fixes https://github.com/galaxyproject/galaxy/issues/17189 ## How to test the changes? (Select all options that apply) - [x] I've included appropriate [automated tests](https://docs.galaxyproject.org/en/latest/dev/writing_tests.html). - [ ] This is a refactoring of components with...

makes `data_column` work for all data types setting `column_names` and still fallback to try to take the first line (tab separated). The later is necessary for `tabular` which does not...

tabular: get column names from header

1

- if it starts # - and has the same number of columns may be better than https://github.com/galaxyproject/galaxy/issues/2611 TODO - [ ] TODO put into separate PR (did some manual...

tool verification: move no output assertion

1

from `planemo` the `verify_tool` function is called from [within an try-except block](https://github.com/galaxyproject/planemo/blob/1aa3eb05a97ad20c0be6f6560ab5cec090e76612/planemo/engine/galaxy.py#L109) which silently catches any exception. Thus any exception raised from within verify_tool will not be detected, i.e. the...