M Bernt

**Describe the bug** I have a tool (metawrap) that creates output collections which I map over a collection. That is the output are a collections of collections. Some of the...

Replace `imghdr` by `puremagic`

6

`imghdr` allowed to detect a few image types and has been [deprecated in python 3.13](https://docs.python.org/3.12/library/imghdr.html) from the release notes: > The filetype, puremagic, or python-magic libraries should be used as...

All jobs fail if vault encryption keys are replaced.

2

**Describe the bug** I accidentally deleted vault encrytion keys in my dev instance. I expected that just the secrets are not decryptable. Instead job submission broke completely: ``` galaxy.jobs.runners ERROR...

(Re)move `job_conf.xml.sample_advanced`

1

The sample config is one of the main sources of docs for job configuration. Unfortunately docs are sometimes still added to the good old xml sample config (eg https://github.com/galaxyproject/galaxy/pull/18628). Here...

Check for ``format="input"`` as well as ``format="auto"`` in datatype linter

2

better consideration of `auto` and `input` ## How to test the changes? (Select all options that apply) - [ ] I've included appropriate [automated tests](https://docs.galaxyproject.org/en/latest/dev/writing_tests.html). - [x] This is a...

**Describe the bug** Data managers apparently write to the first loc file listed in `config/shed_tool_data_table_conf.xml`. In my config I find `grep busco_database ../config/shed_tool_data_table_conf.xml` ``` ... ... ``` running `data_manager_fetch_busco` in...

We could need a collection operation that extracts the 1st level elements of a collection (maybe subject to filters). > We might want to write a collection operation tool that...

Tool test runs despite not giving input datasets to mandatory data parameter

1

**Describe the bug** The following test should fail in my opinion, since the dataset `tab` is not given. ```xml '$out' ]]> ``` Instead the tool test auto-converts the fasta to...

Describe your pull request here ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions * If this PR adds or updates a...

**Are you using the latest release?** Yes **Describe the bug** `funannotate setup` leaves the downloaded `tar.gz` files ([e.g.](https://github.com/nextgenusfs/funannotate/blob/8cc40728fee61566fdf736c1f2292e14cc117660/funannotate/setupDB.py#L554)). Would be nice of there would be automatic cleanup.