set run-tests only if condition is true #1
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This reverts commit 83d6efe.
Run sync on self-hosted runners
don't warn about missing `meta` value in meta.yml
…refix Download: Add docker prefix for absolute container URIs as well.
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* Parallelize pytest (#1) * use PR to test aws runners * fix coverage step * try self-hosted again * smaller naming changes * try to use github runner when available * Revert "try to use github runner when available" This reverts commit 3b69094. * run all tests even if one fails * print nextflow config * use full path for nextflow.config * fix workflow * use different logic * revert * try more self-hosted * remove config options * switch to new profile * print config files, try fix for coverage creation * print configs with profiles * fix config command * simply list_tests * print more configs * don't print configs in this step * exclude some template settings to be able to use nf-core configs * try to fix coverage upload * debugging coverage step * ignore coverage errors for now * seems to work now? * add codecov token * try to fix name collisions * add github token to editorconfig step * debug changed directory * don't change path * more codecov debuggin * specify codecov file * test on github runners, to see speed differences * run also list_test in github * don't reverse for now * more reversion * remove debugging * cleanup work directory * switch to self-hosted again * don't need to install everything for coverage * always cleanup work directory * debug coverage * cleanup everything * debugging coverage * fail gracefully during cleanup * debug no cleaned up paths * install tools also in coverage job * add coverage report back in * coverage debugging... * change nextflow working dir * kick off tests * add debugger ssh * more debugging * try non-cached python * figure out differences in paths * trying to set the python directory manually * hopefully harmonizing python paths * fix coverage step * trying to fix the source error * specify full path for coverage * copy more settings from pytest-split * handle exit code better * didn't work * switch to new gitlab branch * remove coverage output specification * omit all template files in coverage * try different coverage_config path * fix coverage artifact upload * upgrade artifact download * run coverage step explicetly * change location of coverage config * add ssh debugger * use old version of artifact upload * debug artifact upload * use files codecov-action argument * debug coverage * update action versions * fix cleanup step * run small jobs still on github * switch to pre-commit for code linting * don't run pyupgrade for now * fix job name * debugging * keep coverage files * test better cleanup * fix parameter position * add cleanup step to nextflow steps * use nextflow clean * remove ssh step * test cirun.io * don't set AGENT_TOOLSDIRECTORY * add java setup step * use general gitlab branch * change image id back * debug cleanup step * use sudo rm * run everything on our own runners again * use correct gitlab branch * use java from runners * test coverage for one file * run individual test also parallel * add github token to setup-python * use same directory structure for coverage * don't ran everything parallel * move coveragerc * remove debugging code * run some template variations on github * remove more left over code * set correct runner * set profile depending on runner * set profile docker for github runners * use pre-commit for all linting jobs * fix editorconfig * fix .editorconfig and makefile * update changelog --------- Co-authored-by: Júlia Mir Pedrol <[email protected]>
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testing