Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Started with implementing unittests for lint #1

Merged
merged 3 commits into from
Feb 15, 2018

Conversation

sven1103
Copy link
Member

...and fixed one little thing.

@ewels
Copy link
Member

ewels commented Feb 14, 2018

Great! Yes I noticed the same config thing but forgot to submit a PR it seems.

Test code for the tests - very meta! ;)

@sven1103
Copy link
Member Author

Test code for the tests - very meta! ;)

Yes, I hope it is ok ... But I think code coverage is important and not a big deal if one does it right from the beginning.

@ewels
Copy link
Member

ewels commented Feb 15, 2018

Yeah I’m only joking :) I am terrible at writing tests so it’ll be great to learn how to do it properly..

@ewels ewels merged commit 9de60a9 into nf-core:master Feb 15, 2018
@sven1103
Copy link
Member Author

I think this project is going to be fun!

ewels pushed a commit that referenced this pull request Feb 23, 2020
ewels pushed a commit that referenced this pull request Jun 17, 2020
Made group containing required param required
ewels added a commit that referenced this pull request Mar 19, 2021
ewels pushed a commit that referenced this pull request Mar 26, 2021
njspix added a commit that referenced this pull request Apr 30, 2022
mashehu added a commit that referenced this pull request Jan 5, 2024
* 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]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants