Update pr workflow #135
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Update pr workflow #135
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Co-Authored-By: Marius van den Beek <[email protected]>
reformatting and reformulations Co-Authored-By: Nicola Soranzo <[email protected]>
Co-Authored-By: Nicola Soranzo <[email protected]>
and pass as artifact to subsequent jobs also store flake8 and its dependencies in the cache
Co-Authored-By: Marius van den Beek <[email protected]>
only test needs it also remove one seemingly unnecessary step
- move output of changed repos to setup job - switch to checkout@v2 - unlimited checkout in setup step (depth: 0) - check for cache hit needs to be disjunction - fetch all branches - add missing checkout step to deploy - added a few comments docs - triple dot instead of double dots - get diff range for merge from github context Co-Authored-By: Nicola Soranzo <[email protected]>
- make galaxy sha persistent as artifacts - place changed_repos.list and galaxy.sha in a single folder in order to have only one artifact for both - use the galaxy sha also for caching pip - store workflow artifacts in HOME - add comments remove debug
and stylistic changes
Co-Authored-By: Nicola Soranzo <[email protected]>
latest galaxy commit sha was not saved in artifacts file (workflow_artifacts/galaxy.sha) since the environment variable seems to be available only after the step where it is set. pip cache name was inconsistent: - pip_cache_py - pip_cache_python_
Co-Authored-By: Nicola Soranzo <[email protected]>
fix bug introduced in galaxyproject/tools-iuc#3002 where checkout was moved to top because upload@v2 can act on `../`. result: fake planemo run takes whole IUC tree -> time out solution: `cd ..` before upload
ci: - check final success - use pip to install planemo - rename workflow to differentiate it more clearly from the PR workflow - small changes as done in galaxyproject/tools-iuc#2939 - sync with pr workflow - switch to 20.05 ci+pr: - use [email protected] - upload-artifacti v2 -> v2.0.1 Co-authored-by: Marius van den Beek <[email protected]>
And switch PR testing to Galaxy 20.05 too.
Restore flake8-import-order linting, lost when moving from Travis to GitHub workflows.
Co-authored-by: Nicola Soranzo <[email protected]>
... but keep testing PR commits as before.
* add test 3 * try to fix galaxyproject/tools-iuc#5240 * try always * add weekly CI job checking for missing containers * circos: test for a resolvable environment * circos: fix test by sorting output * circos: remove python and gawk requirements python restrictions should come via conda, removing it seems to allow to resolve the environment. also gawk seems not to be used in the tools, so it should come via conda. Co-authored-by: Nicola Soranzo <[email protected]> * circos: bump --------- Co-authored-by: Helena Rasche <[email protected]> Co-authored-by: Nicola Soranzo <[email protected]>
- do not count tool linting artifact - and move test to the end such that the combined tool test output artifact is uploaded in any case
* Do not initiate tool tests if no tool folder was changed * Provide fallback workflow with required job for PRs * Fix indentation of comment lines * Add closing single quote
and clean dornet folder for consistency with weekly CI
* merge: skip python and R linting and use fail level error * test bump * Revert bump
styler the R code linter/styler from the tidyverse. in contrast to lintr it can also fix the found problems (added a script that can be used for checking and fixing)
that is do not deploy if failing
Co-authored-by: Nicola Soranzo <[email protected]>
* update ci.yaml * update pr.yaml * forget -
This reverts commit 30843d2e3fd504a29c09e8b28229572810c9db25.
styler the R code linter/styler from the tidyverse. in contrast to lintr it can also fix the found problems (added a script that can be used for checking and fixing)
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