Add autoupdate command #1065
Add autoupdate command #1065
Conversation
| from planemo.config import planemo_option | ||
|
|
||
|
|
||
| def dry_run_option(): |
There was a problem hiding this comment.
not sure if this should be moved to options.py or not
There was a problem hiding this comment.
It is totally fine here, especially if only one command is using it.
| def get_latest_versions(version_dict): | ||
| """ | ||
| Update a dict with current conda versions for tool requirements | ||
| """ |
There was a problem hiding this comment.
Thank you @jmchilton - I think this is ready for a review
There was a problem hiding this comment.
Actually, I take that back, there are still some things I can fix. Though any overall comments about the implementation would be welcome.
|
@simonbray some updated to the docs would be great. We can also use this in the IUC discussion then. Thanks. |
|
@bgruening where should these be added? It seems the docs are autogenerated from the code. |
|
@simonbray a similar page to this one maybe? https://github.com/galaxyproject/planemo/blob/master/docs/publishing.rst We can also wait until we have a CI setup ready and then add documentation for a potential CI setup as well? |
|
I ran it on the tools-iuc repository to test it out, have a look here: galaxyproject/tools-iuc@master...simonbray:autoupdate It looks mostly okay, but there are a few bugs (e.g. galaxyproject/tools-iuc@master...simonbray:autoupdate#diff-937fe802b3fe3877efcbd5e6a1f6e36eL2) which I'll take a look at. |
|
Testing of latest version on tools-iuc repo: galaxyproject/tools-iuc@master...simonbray:autoupdate8 |
|
Random idea that I want to write down before I forget it: this command should be able to update workflows as well as tools. |
|
@jmchilton what do you think about this? In particular in regards to your recent "update workflow" works? @simonbray it would be nice to have this in planemo soon so we can finally add this functionality into IUC and close the loop:
|
|
Seems like a very solid plan - it will be interesting to see what types of errors we can catch at each step. Let me know if there is anything I can do to help. |
I think this is probably quite close to merging - I will have another look at it. @lorrainealisha75 has also been working on implementing a CI bot here: https://github.com/planemo-autoupdate/autoupdate/blob/main/.github/workflows/update.yml Where is the code for workflow autoupdates, is this part of planemo or somewhere else? I had the idea this could be done using the same |
|
@simonbray please have a look at galaxyproject/galaxy#11032 and related PRs. There are new APIs that can upgrade workflows and can upgrade tools, report on changed params or dropped connections etc ... |
|
Nice! So if |
|
That is my understanding of the jmchilton mgic :) |
docs/autoupdate.rst
Outdated
| ``autoupdate`` assumes that XML tools are formatted in a certain way - in accordance with the `IUC best practices`_ | ||
|
|
||
| <https://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_xml.html/>`__. In particular: | ||
| ``autoupdate`` assumes that XML tools are formatted in a certain way - in accordance with the `IUC best practices`_. In particular: | ||
|
|
||
| - the tool ``version`` attribute must be set to ``@TOOL_VERSION@+galaxy0`` or ``@TOOL_VERSION@+galaxy@GALAXY_VERSION`` |
There was a problem hiding this comment.
| - the tool ``version`` attribute must be set to ``@TOOL_VERSION@+galaxy0`` or ``@TOOL_VERSION@+galaxy@GALAXY_VERSION`` | |
| - the tool ``version`` attribute must be set to ``@TOOL_VERSION@+galaxy0`` or ``@TOOL_VERSION@+galaxy@VERSION_SUFFIX@`` |
;)
By the way, should this be @VERSION_SUFFIX@ instead of @GALAXY_VERSION@? The latest documentation says it should be @VERSION_SUFFIX@ but it seems a significant amount of tools use @GALAXY_VERSION@
Update: I answer myself after reading galaxy-iuc/standards#59 :)
There was a problem hiding this comment.
Yes you are right - we decided on @VERSION_SUFFIX@ in the end but I didn't update here. Thanks!
There was a problem hiding this comment.
It's @VERSION_SUFFIX@ , @GALAXY_VERSION@ was the whole +galaxyN .
|
Not sure about the failing test - it doesn't seem related and I can't reproduce it locally: https://travis-ci.org/github/galaxyproject/planemo/jobs/763104995 |
|
@jmchilton maybe you could have a look at this when you have time? |
|
I don't love that you're custom parsing XML outside the abstractions established in Really awesome work, thanks so much! |
I definitely don't love it either but because of the need to rewrite the wrapper I'm not sure there's a good alternative. Either way, thanks a lot for the merge! |
A command for updating the requirements in XML tool files by checking for newer conda versions. Thanks to @lorrainealisha75 for working on this.
ping @mvdbeek, in this version a
@GALAXY_VERSION@token should no longer be necessary.ping @wm75, I added a
--dry-runflag as you suggested.