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Sam3 add option (normalize and quality)#250

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bgruening merged 58 commits intogalaxyecology:masterfrom
TuturBaba:Sam3
Apr 10, 2026
Merged

Sam3 add option (normalize and quality)#250
bgruening merged 58 commits intogalaxyecology:masterfrom
TuturBaba:Sam3

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@TuturBaba
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TuturBaba and others added 30 commits March 23, 2026 11:20
Update sam3_semantic_segmentation.py
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
@TuturBaba TuturBaba marked this pull request as draft April 3, 2026 15:53
@TuturBaba TuturBaba marked this pull request as ready for review April 9, 2026 09:16
@TuturBaba TuturBaba requested review from bgruening and yvanlebras and removed request for yvanlebras April 9, 2026 09:36
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THANK You Arthur ! Seems to me ok ! This will enhance ++ the useability of the tool!

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Nice, very cool. Can you please add a test for the new functionality?

@TuturBaba
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TuturBaba commented Apr 10, 2026

Nice, very cool. Can you please add a test for the new functionality?

I'm not sure what kind of test you want. The only existing test checks for a failure case: <test expect_exit_code="1" expect_failure="true">
I can add a test that uses the new functionality, new inputs but it will still test a failure case. Is that what you mean?

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A test that is testing the different output filters for example. That we know the tool logic is working?

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TuturBaba commented Apr 10, 2026

A test that is testing the different output filters for example. That we know the tool logic is working?

I'm sorry, I'm not sure I understand what you mean. I can add this test

<test expect_exit_code="1" expect_failure="true">
    <param name="sam3_models" value="unknown"/>
    <conditional name="input">
        <param name="input_kind" value="video" />
        <param name="source" value="video-elephant.mp4"/>
        <param name="quality" value="copy"/>
        <param name="coco_video_mode" value="video"/>
        <param name="outputs_format" value="yolo_bbox"/>
    </conditional>
    <param name="text_prompt" value="elephant"/>
    <param name="conf" value="0.25"/>
    <param name="vid_stride" value="5"/>
    <assert_stdout>
        <has_text text="Invalid model!"/>
    </assert_stdout>
</test>

It has the same failure case as the other one, but with different inputs (new feature). However, I can't test a wrong input for the new options, because they are all select inputs, so Galaxy will not even run the test if the value is invalid.

@bgruening bgruening merged commit 8209fd3 into galaxyecology:master Apr 10, 2026
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Ok, thanks for trying!

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THANK YOU Arthur, Björn ! Have a nice end of week, and week-end !

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3 participants