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Implement ``shed_update`` to upload & update repo metadata. #216

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merged 2 commits into from May 21, 2015

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jmchilton commented May 20, 2015

This should replace shed_upload in many potential workflows - but this does require a .shed.yml file with all metadata populated so shed_upload is still useful for directly uploading custom tar files for instance. I have filled out the documentation on shed_upload and shed_update to reflect this.

Additionally, for consistency with the new shed_update operation - shed_create now also performs an upload in addition to simply populating the metadata for a new remote repository. The old behavior of shed_create can be obtained by supplying a new --skip_upload flag. shed_create can also take in a -m/--message option now as well to reflect this new behavior.

Updated publish.rst to reflect these simplifications (instructions now easier).

Closes #199.

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erasche commented May 20, 2015

+1!

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erasche commented May 20, 2015

@jmchilton what's the timeline for the next planemo release? You've added a LOT of great shed interactivity lately

"--check_diff",
is_flag=True,
help="Skip uploading if the shed_diff detects there would be no "
"'difference' (only attributes populated by the shed would would "

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peterjc May 20, 2015

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Typo: double would

important because the tool shed will automatically populate certain
attributes in tool shed artifact files (such as ``tool_dependencies.xml``)
and this may cause unwanted installable revisions to be created when
there are no important changes.

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peterjc May 20, 2015

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This could be a little clearer: Does the diff happen after the meta-data update, but before the tar-ball upload?

e.g. Given a previously up to date tool (in sync with the tool shed), I fix a typo in the .shed.yml description, and run planemo shed_update .... What happens (with or without --check-diff)?

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jmchilton May 21, 2015

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--check_diff would only affect the upload - so the metadata would be updated and the tar ball would not be uploaded. I will try to clarify this in the text. There is a problem with exit codes also though - I think in this case the exit code would be non-zero but probably shouldn't be. That is a smaller bug though - so I will just create an issue for this.

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bgruening commented May 20, 2015

Wonderful!

Implement ``shed_update`` to upload and update repository metadata.
This should replace ``shed_upload`` in many potential workflows - but this does require a ``.shed.yml`` file with all metadata populated so ``shed_upload`` is still useful for directly uploading custom tar files for instance. I have filled out the documentation on ``shed_upload`` and ``shed_update`` to reflect this.

Additionally, for consistency with the new ``shed_update`` operation - ``shed_create`` now also performs an upload in addition to simply populating the metadata for a new remote repository. The old behavior of ``shed_create`` can be obtained by supplying a new ``--skip_upload`` flag. ``shed_create`` can also take in a ``-m/--message`` option now as well to reflect this new behavior.

Updated ``publish.rst`` to reflect these simplifications (the instructions are now easier).

@jmchilton jmchilton force-pushed the jmchilton:update_metadata branch from 8b49c71 to 0aaae9a May 21, 2015

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jmchilton commented May 21, 2015

@erasche new planemo release should happen today or tomorrow.

jmchilton added a commit that referenced this pull request May 21, 2015

Merge pull request #216 from jmchilton/update_metadata
Implement ``shed_update`` to upload & update repo metadata.

@jmchilton jmchilton merged commit 4cdc641 into galaxyproject:master May 21, 2015

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@jmchilton jmchilton deleted the jmchilton:update_metadata branch May 21, 2015

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