Update pr workflow #135

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]>

when in .tt_biocontainer_skip

currently we see: ``` Warning: The `set-env` command is deprecated and will be disabled soon. Please upgrade to using Environment Files. For more information see: https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/ ```

- simplifies the logic a bit since tools and data managers don't need to be treated separately. - check if every path in find_tools is in the output of find_repos, i.e. check for missing .shed.yml - all linters run now on the result of ci_find_repos - tool testing uses ci_find_tools as suggested here galaxyproject/tools-iuc#3248 (comment)

Co-authored-by: Nicola Soranzo <[email protected]>

by removing quotes

When a secret is added (Settings -> Secrets -> New repository secret) on GitHub, the secret name is changed to uppercase in the secrets list, even if it is actually lower/mixed case. I find this confusing. N.B.: THIS CHANGE REQUIRES REMOVING AND RE-ADDING THE 2 SECRETS USING THE NEW UPPERCASE NAME!

Co-authored-by: Nicola Soranzo <[email protected]>

* Update kraken2 wrapper and data manager to version 2.1.1 - PR workflow: Check if any changed repo is a substring of each changed tool - Added true and false values to booleans, simplifying cheetah - Made tool version a token in data manager - Added support for the --load-factor parameter - Use the argument only where possible without breaking tool rerun Co-authored-by: Nicola Soranzo <[email protected]>

Co-authored-by: Nicola Soranzo <[email protected]>

Otherwise the number of chunks won't take into account tools for which the XML was not modified but other files in the repo were.

…(#3348) * Don't skip tools in `.tt_biocontainer_skip` during weekly CI testing * Fix regression in check for tool that can't be tested in biocontainers Partially revert commits be43a25be5eead2d1a1ae8b5ee8c49a35b6579f8 and 2c9ea0cdc81b499ec07aa2f0b54b575586b01d42 . Add explanatory comments. * Refactor check

- unquote `$TOOL` (which is renamed to TOOL_GROUP) because its a space separated list of tools - restore `--group_tools` argument for ci_find_tools

as already done in devteam repo

added in galaxyproject/tools-iuc#3403 . The Planemo issue should be fixed in 0.74.1

* Sync ci and pr GitHub workflows * Update bowtie2 to 2.4.2

Co-authored-by: Marius van den Beek <[email protected]>

that occured while making the action workflow ready

Also quote version string (could be mistaken for floats by YAML).

that indicates success if no tools were changed

Also: - Skip `combine_outputs` if no repo was modified - Fix `combine_outputs` job name inside `determine-success` - Small reorderings - Quote if conditions

from master to main. xref. galaxyproject/tools-iuc#3691

Co-authored-by: Nicola Soranzo <[email protected]>

* let PR workflow check file sizes * rename step * Apply suggestions from code review Co-authored-by: Nicola Soranzo <[email protected]> * temp bump * Update .github/workflows/pr.yaml Co-authored-by: Nicola Soranzo <[email protected]> * add comment in case of size violation * use up-to-date version of the action * try * just use another action for comment * Apply suggestions from code review Co-authored-by: Nicola Soranzo <[email protected]> * use peter-evans/create-or-update-comment * try without * Revert "try without" This reverts commit 56409e01076f62382fbcdb1c39f565c1e63161de. * do not comment seems not possible * make final status independent of file size status Co-authored-by: Nicola Soranzo <[email protected]>

* check file sizes only for changed files as pointed out here: galaxyproject/tools-iuc#3973 (comment) reducing the size of test data does not decrease the repo size if the files are already in. so we should only check for the sizes of changed files and be strict with them * Update .github/workflows/pr.yaml Co-authored-by: Nicola Soranzo <[email protected]> Co-authored-by: Nicola Soranzo <[email protected]>

otherwise find fails for deleted files

To be in line with the IUC Standards recommendation: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/integration_checklist.html#testing-your-tool

relies on galaxyproject/planemo-ci-action#25

- fix function that emits a deprecation warning - also output line (can't hurt)

as in CI .. otherwise we will just have failing CI jobs for long running tools

Fix: ``` Error: Unable to resolve action `r-lib/actions@master`, unable to find version `master` ``` Also update R version to 'release'.

Co-authored-by: Nicola Soranzo <[email protected]>

* trigger deployment message on anything but success * test bump

This reverts commit 356f921c6fb6b9c68f5df46510b23038fe1058fa. merged on accident

... 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

xref galaxyproject/galaxy#15962 (comment)

* 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]>

xref galaxyproject/tools-devteam#618 (comment)

* 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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Update pr workflow #135

Update pr workflow #135

Commits on Sep 24, 2024