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Fix "planemo conda_search". #826

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merged 2 commits into from May 16, 2018

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jmchilton commented May 16, 2018

There was a change in the galaxy-lib interface it used that broke it, and the underlying CLI seems to require * to do a more SQL-like search now so I've updated that as well.

Fixes #824.

Fix "planemo conda_search".
There was a change in the galaxy-lib interface it used that broke it, and the underlying CLI seems to require * to do a more SQL-like search now so I've updated that as well.

Fixes #824.
@@ -23,4 +23,5 @@ def cli(ctx, term, **kwds):
Implicitly adds channels Planemo is configured with.
"""
conda_context = build_conda_context(ctx, handle_auto_init=True, **kwds)
conda_context.exec_command("search", [term])
args = conda_context._override_channels_args + ["*%s*" % term]

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nsoranzo May 16, 2018

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This is not going to work on older Conda:

$ ~/miniconda3/bin/conda --version
conda 4.3.33
$ ~/miniconda3/bin/conda search '*samt*'

CommandArgumentError: Failed to compile regex pattern for search: *samt*
regex error: error('nothing to repeat at position 0',)

Workaround Conda search behavior changes in Conda 4.4.
Last released version of Planemo would work only with Conda 4.3.* or older but my previous fix would only work with 4.4 or newer (thanks to @nsoranzo for the catch). This should now work with any Conda 3 or 4 version I assume - at least the couple I have tried.

@jmchilton jmchilton merged commit bbb60f9 into galaxyproject:master May 16, 2018

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jmchilton commented May 16, 2018

Thanks for the review and the catch @nsoranzo.

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