Use 3 build stages for Travis by nsoranzo · Pull Request #1349 · galaxyproject/tools-iuc

nsoranzo · 2017-06-08T11:51:29Z

The 3 stages are:

lint (1 job) for flake8 and planemo shed_lint
test (3 jobs) for planemo test
deploy (1 job) for planemo shed_update to TTS and MTS

Also:

Cache pip files
Use --conda_auto_install option of planemo test instead of running
planemo conda_install beforehand. This will install only the tool
dependencies required by the tools tested in the job

xref. #1316 (comment)

Fix #1308.

peterjc · 2017-06-08T13:06:43Z

This is in the order test, lint, deploy whereas I would have used lint, test, deploy.

i.e. Lint first as it is fairly quick and should fail quickly avoiding often wasted CPU time on the main tests.

peterjc · 2017-06-08T13:10:22Z

Looking at the .travis.yml file, I would have expected lint first - there is something odd about the build numbers on https://travis-ci.org/galaxyproject/tools-iuc/builds/240756115 too - perhaps a Travis question?

Test

4537.1 CHUNK=0

4537.2 CHUNK=1

4537.3 CHUNK=2

4537.5 CHUNK=0

Lint

4537.4

Deploy

4537.6

Where does job 4537.5 come from? It looks like a duplicate of 4537.1 using CHUNK=0

peterjc · 2017-06-08T13:13:26Z

Is it worth trying putting the environment variable list only under the test stage?

env:
  - CHUNK=0
  - CHUNK=1
  - CHUNK=2

Also, given the relative length of the test's before_install, install and script would it be clearer to define them directly under the test stage?

The 3 stages are: - lint (1 job) for `flake8` and `planemo shed_lint` - test (3 jobs) for `planemo test` - deploy (1 job) for `planemo shed_update` to TTS and MTS Also: - Cache pip files - Use `--conda_auto_install` option of `planemo test` instead of running `planemo conda_install` beforehand. This will install only the tool dependencies required by the tools tested in the job xref. galaxyproject#1316 (comment)

nsoranzo · 2017-06-08T14:33:47Z

@peterjc

This is in the order test, lint, deploy whereas I would have used lint, test, deploy.

lint, test, deploy is what I'm trying to achieve as explained in the PR description.

there is something odd about the build numbers

The interaction between build stages and the build matrix is far from ideal at the moment, because test is considered a special build stage which always run first if you have a build matrix, see travis-ci/beta-features#11.
The only way I've found to have the lint stage first is to embed (and demultiplex, see next comment) the build matrix of the test stage inside the jobs: section. It seems to work in the rebased commit now.

Is it worth trying putting the environment variable list only under the test stage?

That's not possible yet, see travis-ci/beta-features#11.

Also, given the relative length of the test's before_install, install and script would it be clearer to define them directly under the test stage?

Since I had to demultiplex the build matrix, it's best to have before_install, install and script in the common part.

nsoranzo · 2017-06-08T14:41:42Z

 # 'sudo required' will give os 7,5 GB memory, but has slower startup times, as we start a VM instead of a Container
 sudo: required
 language: python
+cache: pip


Thanks to this line the following:

pip install flake8 flake8-import-order planemo

went from ~32s to ~11s.

This is very nice!

That's a good tip - I should try cache: pip on my TravisCI setups...

If multiple repos were changed, chunking using ci_find_tools may result in running `planemo test` on a mix of tools from different repos, which does not work because Planemo expects all test data in the same directory, see e.g. https://travis-ci.org/galaxyproject/tools-iuc/jobs/240466613 Also exclude data_managers and packages from the start for the `test` stage.

Also: - Remove deprecated `interpreter` attribute of `<command>` - Use `detect_errors="exit_code"` - Use single quotes in `<command>` - Add CDATA to `<command>` and `<help>` - Add citation - IUC code style fixes - Add Python3 compatibility

bgruening

Cool! Haven't played with that by myself. So if @peterjc is ok with it! I'm 💯

Very nice improvement!

bgruening · 2017-06-08T16:12:37Z

+      env: CHUNK=2
+
+    - stage: deploy
+      before_install: skip


is this skip needed?

Not really, it's just for a cleaner log.

Without this TravisCI will use the top level before_install instructions which we don't need or want to be run (although right now that would be quick and harmless).

bgruening · 2017-06-08T16:12:51Z

 # 'sudo required' will give os 7,5 GB memory, but has slower startup times, as we start a VM instead of a Container
 sudo: required
 language: python
+cache: pip


This is very nice!

peterjc · 2017-06-08T17:09:29Z

The reworked .travis.yml is doing the stages in the intended order, and only defines the CHUNK environment within the test stages - so I'm happy with those changes 👍

(Presumably the other changes are on this branch in part to ensure there is something to test?)

nsoranzo · 2017-06-08T17:15:47Z

Presumably the other changes are on this branch in part to ensure there is something to test?

Yes, in particular that there are more than 1 repo with several tools.

bgruening · 2017-06-08T17:34:57Z

Ah this is beauty! What would we do without Nicola!
Thanks a bunch!!!

…s where in subdirs E.g. in the Travis job: https://travis-ci.org/galaxyproject/tools-iuc/jobs/240866693 for the pull request: galaxyproject/tools-iuc#1349 changed_repositories.list should also have contained the repo `data_managers/data_manager_bowtie_index_builder`

nsoranzo · 2017-06-08T19:27:15Z

And also the deploy stage worked (apart from a Planemo bug which will be fixed by galaxyproject/planemo#688)

https://travis-ci.org/galaxyproject/tools-iuc/builds/240884130

nsoranzo · 2017-06-08T19:28:33Z

@bgruening Maybe that's something you can mention in the IUC talk at GCC2017 ;)

bgruening · 2017-06-08T19:38:24Z

Sure, this will be in the talk, but maybe you will give the talk :)

Thanks @nsoranzo!

nsoranzo · 2017-06-08T19:40:29Z

@bgruening I'm the session 3 chair!

jmchilton · 2017-06-08T20:06:27Z

Use --conda_auto_install option of planemo test instead of running
planemo conda_install beforehand.

This is the default in the latest versions of Conda I think - you shouldn't need to specify it.

nsoranzo requested review from bgruening and peterjc June 8, 2017 11:52

nsoranzo added bug enhancement labels Jun 8, 2017

nsoranzo force-pushed the travis branch from e22e6f3 to 8cc82e1 Compare June 8, 2017 13:22

nsoranzo force-pushed the travis branch from 8cc82e1 to 7cebe80 Compare June 8, 2017 13:56

nsoranzo commented Jun 8, 2017

View reviewed changes

nsoranzo changed the title ~~[WIP] Use 3 build stages for Travis~~ Use 3 build stages for Travis Jun 8, 2017

nsoranzo added 3 commits June 8, 2017 17:36

Remove unused exclude from .shed.yml

25edf29

nsoranzo force-pushed the travis branch from d3e8293 to 7e16ddc Compare June 8, 2017 16:43

bgruening reviewed Jun 8, 2017

View reviewed changes

bgruening merged commit e2075ca into galaxyproject:master Jun 8, 2017

nsoranzo mentioned this pull request Jun 8, 2017

Fix ci_find_repos command to not filter repos whose only modifications where in subdirs galaxyproject/planemo#688

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nsoranzo commented Jun 8, 2017 •

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