applies the new conventions for imaging tools agreed at BioHackEU23 #53

kostrykin · 2023-11-02T11:27:46Z

xref https://github.com/elixir-europe/biohackathon-projects-2023/blob/main/16/conventions.md

CameronFRWatson

Thank you for the PR! I suggested one change to the Squidpy tool name to reflect that these tools are for both analysis and visualization and are specific to spatial data

tools/squidpy/squidpy_spatial.xml

bgruening · 2023-11-08T11:15:29Z

We need to update the CI to the lastest version. The failing tests are due to an outdated CI definition.

kostrykin · 2023-11-16T11:06:39Z

In another repo, our solution was to temporarily skip xsd linting during deployment:
https://github.com/BMCV/galaxy-image-analysis/pull/84/files

This is due to biii annotations being not yet included in a Galaxy release

I could make the same changes for the CI in this repo, if you agree.

alliecreason · 2023-11-21T18:05:34Z

Thanks @bgruening, we have updated the CI, @kostrykin could you pull in those changes from main?

luke-c-sargent · 2023-11-21T18:35:55Z

I PR'd the requested changes for you to review/accept @kostrykin:

https://github.com/kostrykin/tools-mti/pull/1

kostrykin · 2023-11-21T20:07:08Z

I PR'd the requested changes for you to review/accept @kostrykin:

update CI definitions kostrykin/tools-mti#1

Thanks @luke-c-sargent, but as I mentioned before, xsd linting needs to be skipped during deployment for this to work.

luke-c-sargent · 2023-11-22T17:17:27Z

sorry, didn't mean to come off as disregarding your comment! the pr you linked to was merged into release_23.1, i had assumed updating the CI workflows to use that same branch would be enough to bring the definition in to the testing apparatus.

kostrykin · 2024-02-27T16:53:41Z

Looks like planemo lint is failing for reasons unrelated to this PR?

The reported linting issues are:

Help section appears to be empty.
Found no valid citations.
Missing shed metadata field [long_description] for repository
Missing shed metadata field [homepage_url] for repository
Conditional [do_phenotyping] first param of type="boolean" is discouraged, use a select

I do not really now how to fix these since I do not have the knowledge of these tools.

+Linting tool /home/runner/work/tools-mti/tools-mti/tools/mti-utils/rename_tiff_channels.xml
Failed linting
Applying linter tests... CHECK
.. CHECK: 1 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 2 input parameters.
Applying linter help... WARNING
.. WARNING: Help section appears to be empty.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.0.1+galaxy3].
.. CHECK: Tool defines a name [Rename OME-TIFF channels].
.. CHECK: Tool defines an id [rename_tiff_channels].
.. CHECK: Tool specifies profile version [19.01].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: Found no valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [long_description] for repository
.. WARNING: Missing shed metadata field [homepage_url] for repository

+Linting tool /home/runner/work/tools-mti/tools-mti/tools/mti-utils/process_intensities.xml
Failed linting
Applying linter tests... CHECK
.. CHECK: 1 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 7 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [0.0.1+galaxy3].
.. CHECK: Tool defines a name [Process single-cell intensities].
.. CHECK: Tool defines an id [cell_intensity_processing].
.. CHECK: Tool specifies profile version [19.01].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: Found no valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [long_description] for repository
.. WARNING: Missing shed metadata field [homepage_url] for repository

Linting repository /home/runner/work/tools-mti/tools-mti/tools/mti-utils
Failed linting
Applying linter expansion... CHECK
.. INFO: Included files all found.
Applying linter tool_dependencies_xsd... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_sha256sum... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_actions... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: No README found, skipping.
Applying linter urls... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [homepage_url] for repository

+Linting tool /home/runner/work/tools-mti/tools-mti/tools/squidpy/squidpy_spatial.xml
Failed linting
Applying linter tests... CHECK
.. CHECK: 6 test(s) found.
Applying linter output... CHECK
.. INFO: 2 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 105 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [1.1.2+galaxy2].
.. CHECK: Tool defines a name [Analyze and visualize spatial multi-omics data].
.. CHECK: Tool defines an id [squidpy_spatial].
.. CHECK: Tool specifies profile version [20.01].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: Found no valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [long_description] for repository

+Linting tool /home/runner/work/tools-mti/tools-mti/tools/vitessce/vitessce_spatial.xml
Failed linting
Applying linter tests... CHECK
.. CHECK: 3 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... WARNING
.. WARNING: Conditional [do_phenotyping] first param of type="boolean" is discouraged, use a select
.. INFO: Found 19 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [1.0.4+galaxy2].
.. CHECK: Tool defines a name [Run multi-modal single-cell visualization].
.. CHECK: Tool defines an id [vitessce_spatial].
.. CHECK: Tool specifies profile version [20.01].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [long_description] for repository

+Linting tool /home/runner/work/tools-mti/tools-mti/tools/vitessce/gate_finder.xml
Failed linting
Applying linter tests... CHECK
.. CHECK: 1 test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 11 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [1.0.4+galaxy2].
.. CHECK: Tool defines a name [Perform gating].
.. CHECK: Tool defines an id [gate_finder].
.. CHECK: Tool specifies profile version [20.01].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... CHECK
.. CHECK: Found 1 likely valid citations.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.
Applying linter tool_urls... CHECK
.. INFO: URL OK https://scimap.xyz/
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [long_description] for repository

Linting repository /home/runner/work/tools-mti/tools-mti/tools/vitessce
Failed linting
Applying linter expansion... CHECK
.. INFO: Included files all found.
Applying linter tool_dependencies_xsd... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_sha256sum... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter tool_dependencies_actions... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: No README found, skipping.
Applying linter urls... CHECK
.. INFO: No tool_dependencies.xml, skipping.
Applying linter shed_metadata... WARNING
.. WARNING: Missing shed metadata field [long_description] for repository

CameronFRWatson · 2024-02-27T17:24:56Z

Thanks for enumerating the linter errors @kostrykin, I'll start addressing them

…elect param

CameronFRWatson · 2024-02-28T20:20:26Z

I added a few commits to this PR to address the linter warnings. These changes are summarized below:

Help sections, citations, and/or shed metadata were added for:

mti-utils/rename_tiff_channels.xml
mti-utils/process_intensities.xml
squidpy_spatial.xml
vitessce/gate_finder.xml
vitessce/vitessce_spatial.xml

Additionally, to address the following linter warning

Conditional [do_phenotyping] first param of type="boolean" is discouraged, use a select

Wrapper changes were made to vitessce_spatial.xml, changing a boolean parameter to a select-type parameter
The gate_finder tool shares logic with vitessce_spatial via vitessce/main_macros.xml, so the default value for a parameter in the gate finder tool was changed as well
Vitessce VERSION_SUFFIX incremented from 2 —> 3

bgruening

Very nice. Thanks for working on this @CameronFRWatson!

updates tools

538aa10

kostrykin marked this pull request as ready for review November 2, 2023 11:28

alliecreason requested review from CameronFRWatson and luke-c-sargent November 2, 2023 16:37

CameronFRWatson approved these changes Nov 2, 2023

View reviewed changes

tools/squidpy/squidpy_spatial.xml Outdated Show resolved Hide resolved

updates name of tool

ed23a00

alliecreason added 2 commits November 21, 2023 20:09

update CI from IUC

a4b34df

fix repo owner

387be6e

kostrykin added 5 commits February 26, 2024 13:57

Trigger CI

26ec957

Merge branch 'main' of github.com:goeckslab/tools-mti into biohackeu23

345da05

Fix linting issues

e4c21de

Trigger CI

2cf2256

Fix linting issues

10008f4

CameronFRWatson added 4 commits February 27, 2024 11:00

Address linter warnings for mti-utils

e62f7e0

Address linter warnings for squidpy

a6717ab

Vitessce: Wrapper update to address linter warnings

7616ee1

update gate_finder.xml phenotype_choice param to match new vitessce s…

f1a88b2

…elect param

CameronFRWatson requested review from bgruening and removed request for luke-c-sargent February 28, 2024 20:22

bgruening approved these changes Feb 28, 2024

View reviewed changes

CameronFRWatson merged commit 130ef7e into goeckslab:main Feb 28, 2024
13 checks passed

kostrykin deleted the biohackeu23 branch February 28, 2024 20:48

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applies the new conventions for imaging tools agreed at BioHackEU23 #53

applies the new conventions for imaging tools agreed at BioHackEU23 #53

kostrykin commented Nov 2, 2023 •

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bgruening commented Nov 8, 2023

kostrykin commented Nov 16, 2023

alliecreason commented Nov 21, 2023

luke-c-sargent commented Nov 21, 2023 •

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kostrykin commented Feb 27, 2024

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applies the new conventions for imaging tools agreed at BioHackEU23 #53

applies the new conventions for imaging tools agreed at BioHackEU23 #53

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kostrykin commented Nov 2, 2023 •

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