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Simon Bray simonbray Freiburg, Germany

bgruening/galaxytools 95

:microscope::books: Galaxy Tool wrappers

galaxycomputationalchemistry/galaxy-tools-compchem 9

:mega: Galaxy Tools for Computational Chemistry

BioContainers/singularity-build-bot 2

Nightly build of Singularity containers

abduskhazi/PL-Binding-Affinity-Prediction-using-ML 1

This repository is maintained for the documentation and coding of the MSc project @ Bioinformatics Lab Uni-Freiburg.

computational-metabolomics/dimspy-galaxy 1

Galaxy tools for Python package DIMSpy: data processing of Direct-Infusion Mass Spectrometry-based metabolomics and lipidomics data

galaxycomputationalchemistry/duck 1

Fork of open-source DUck (Dynamic Undocking) used by Galaxy

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Supplementary material for the paper 'Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial'

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check assertion arguments with inspect.Signature.bind()

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check assertion arguments with inspect.Signature.bind()

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Pull request review commentgalaxyproject/planemo

Adding best practices and assertion checks to workflow_lint

 def _lint_case(path, test_case, lint_context):             found_valid_expectation = True         # TODO: validate structure of test expectations +        assertion_definitions = test_case.output_expectations[test_output_id].get("asserts")+        if not _check_test_assertions(lint_context, assertion_definitions):+            test_valid = False+     if not found_valid_expectation:         lint_context.warn("Found no valid test expectations for workflow test")         test_valid = False      return test_valid  +def _check_test_assertions(lint_context, assertion_definitions):+    # we are already in Python, not XML, so it is simpler to lint assertions by checking against the+    # Python functions directly, rather than checking against galaxy.xsd as for tool linting+    assertions_valid = True+    if assertion_definitions:+        for module in asserts.assertion_modules:+            for function_name in dir(module):+                if function_name.split('assert_')[-1] in assertion_definitions:+                    f = module.__dict__[function_name]

run https://docs.python.org/3/library/inspect.html#inspect.Signature.bind, so we don't have to execute the test function.

That is cool, thanks!

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add best practices and assertion checks to workflow_lint

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Simon Bray

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tests for workflow_lint

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Simon Bray

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docs for workflow_lint + best practices

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add best practices and assertion checks to workflow_lint

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tests for workflow_lint

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Simon Bray

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docs for workflow_lint + best practices

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commit sha 741ded88b7133ea95564b6671c32f96cc3ba147c

add best practices and assertion checks to workflow_lint

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tests for workflow_lint

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docs for workflow_lint + best practices

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Pull request review commentgalaxyproject/planemo

Adding best practices and assertion checks to workflow_lint

 def _lint_tsts(path, lint_context):             lint_context.valid(f"Tests appear structurally correct for {runnable.path}")  +def _lint_best_practices(path, lint_context):  # noqa: C901+    """+    This function duplicates the checks made by Galaxy's best practices panel:+    https://github.com/galaxyproject/galaxy/blob/5396bb15fe8cfcf2e89d46c1d061c49b60e2f0b1/client/src/components/Workflow/Editor/Lint.vue+    """

It's not ideal for this to duplicate the best practices code in the Galaxy frontend but it's not too much work to maintain, I hope. It seems from #1211 like there is no obvious solution

simonbray

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Pull request review commentgalaxyproject/planemo

Adding best practices and assertion checks to workflow_lint

 def _lint_case(path, test_case, lint_context):             found_valid_expectation = True         # TODO: validate structure of test expectations +        assertion_definitions = test_case.output_expectations[test_output_id].get("asserts")+        if not _check_test_assertions(lint_context, assertion_definitions):+            test_valid = False+     if not found_valid_expectation:         lint_context.warn("Found no valid test expectations for workflow test")         test_valid = False      return test_valid  +def _check_test_assertions(lint_context, assertion_definitions):

maybe this can be improved, if someone knows more about importing Python functions than me?

simonbray

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PR opened galaxyproject/planemo

Adding best practices and assertion checks to workflow_lint

Fixes #1178, #1181, #1211

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pull request commentconda-forge/deepchem-feedstock

deepchem v2.6.0

@conda-forge-admin, please rerender

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update python pins

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pull request commentconda-forge/deepchem-feedstock

deepchem v2.6.0

Hi @arunppsg, can we just make the change in this PR? The CF infrastructure creates and uploads new builds every time a PR is merged.

Also, does deepchem support python 3.9? The readme says it only supports python 3.7 and 3.8.

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pull request commentconda-forge/deepchem-feedstock

deepchem v2.6.0

Hey @simonbray , the python pin should be updated in meta.yaml right? I am new to updating feedstock and I thank you very much for your help.

Hey @arunppsg, yes, exactly.

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issue closedgalaxyproject/galaxy

[feature request] allow users to relax the workflow connection restrictions

When connecting workflow nodes in the editor some connections are forbidden:

image

Obviously there should be some restraints on connections but I sometimes needed to override this behaviour. Probably the most common case was after designing a workflow with dataset inputs, to scale up the workflow to use collection inputs instead. Galaxy does not allow you to simply swap the dataset input for a collection input.

In the past, I've downloaded the workflow and used this commit (https://github.com/simonbray/galaxy/commit/036a13139220cdad43c86508c9681950d65d0bbc) on a local Galaxy to force the connection. I was wondering if it might be possible to allow users to temporarily relax workflow connection restrictions (e.g. with an option in the workflow editor)?

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simonbray

issue commentgalaxyproject/galaxy

[feature request] allow users to relax the workflow connection restrictions

This doesn't make sense, instead the bugs which are causing these problems should be resolved (e.g. #12825), so I will close.

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issue openedgalaxyproject/galaxy

Improve documentation of tool test assertions in galaxy.xsd

The documentation of the assertion functions in galaxy.xsd should be improved. Currently only 4 (has_h5_keys, has_h5_attribute, has_archive_member, has_size) specify the accepted attributes: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tool_util/xsd/galaxy.xsd#L2117.

This is important for tool / workflow linting. For example, running linting on the following XML returns no errors:

<assert_contents>
    <has_n_lines non_existent_parameter1="41"/>
    <has_line_matching non_existent_parameter2="123"/>
</assert_contents>

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pull request commentbioconda/bioconda-recipes

rebuild smudgeplot

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pull request commentbioconda/bioconda-recipes

Update gembs to 3.5.0

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