BiaPy 3.6.7

[danifranco]

This PR builds on and supersedes #7427 (Updating tools/biapy from version 3.6.5 to 3.6.7).

Changes:

• Update BiaPy version
• Fix errors when running a tool multiple times: ln -s command now is forced as ln -sf.

I'm trying to introduce a nested conditional but I can't do it. I've tried several things but anyone worked. What I want is to control the visibility of the ground truth data related fields, e.g. train_gt_param and test_gt_param parameters defined in macros.xml, based on the workflow selected (workflow param defined in biapy.xml). For example, the denoising workflow does not require ground truth, as it is self-supervised, so I don't want even to show that field for the user so they don't get confused. My last attempt, and the one in this PR, is define those ground-truth parameters as follows (here the example of test_gt_param) :

<xml name="test_gt_param">
    <conditional name="test_gt_workflow_cond">
        <param name="workflow_check" type="select" value_from="mode_selection.workflow" label="Internal Workflow Check"/>
        <when value="semantic">
            <expand macro="test_gt_param_question"/>
        </when>
        <when value="instance">
            <expand macro="test_gt_param_question"/>
        </when>
        <when value="detection">
            <expand macro="test_gt_param_question"/>
        </when>
        <when value="sr">
            <expand macro="test_gt_param_question"/>
        </when>
        <when value="cls">
            <expand macro="test_gt_param_question"/>
        </when>
        <when value="sr2">
            <expand macro="test_gt_param_question"/>
        </when>
        <when value="i2i">
            <expand macro="test_gt_param_question"/>
        </when>
       <when value="denoising"/>
    </conditional>
</xml>

If you see, for the "denoising" case, i.e. mode_selection.workflow has the value "denoising", "test_gt_param_question" macro is not expanded. How can I do this? The resulting tool tested locally looks as follows:

On top of that, I'd like to remove that "Internal Workflow Check" frame if possible so it's transparent for the user and don't add extra unnecessary frames into the tool.

Thank you so much!!

@bernt-matthias @bgruening

[bernt-matthias]

On top of that, I'd like to remove that "Internal Workflow Check" frame if possible so it's transparent for the user and don't add extra unnecessary frames into the tool.

This is not possible at the moment. Please open a feature request at the galaxy repo.

[danifranco]

Hi, I can not understand why the newest version of biapy is not being installed properly. I can not see in the logs any error related to conda/mamba installation. Can you please help me?

[bernt-matthias]

Errors related to conda can always be found in the logs of the actual test job. https://github.com/galaxyproject/tools-iuc/actions/runs/20228591486/job/58066005201?pr=7499#step:9:1009

The problem looked like a temporary problem. I restarted the tests.

FYI: if we test multiple tools in a CI job we split them into up to 4 test jobs (in your case its only one). These jobs will allways be reported successful (even if the tool tests fail). This is done since all tests would be aborted if a single one fails (and we want to see the results for all tools). The tool tests errors are then reported when the separate test results are combined in the combine job.

[danifranco]

Thanks but there is still an error related to biapy package installation. I only changed the package version, which is available in conda. I have checked again the logs and I can not guess what's the problem... Can you please guide me a bit please?