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48 commits

Author SHA1 Message Date
Edmund Miller
f8f9155b45
ci: Fix pip skip 2021-04-12 14:22:38 -05:00
Edmund Miller
ec3a2172a6
ci: Remove duplicate python setups 2021-04-12 14:20:21 -05:00
Harshil Patel
f34892c1af
Test PR for nf-core modules lint (#414) 
* Update functions.nf for publish_by_id

* Pass a list of publish_by_id instead of a string

* Remove NF version

* Rename code linting file

* Run separate workflow for nf-core modules lint

* Adjust nf-core update comment

* Comment out linting from pytest-workflow.yml

* Remove commented out linting code from pytest-workflow.yml

* Adjust spacing

* Adjust spacing again

* Move NF version to job level for linting

* Add CAPSULE_LOG none env when installing NF

* Remove NXF_ANSI_LOG env for linting

* Revert changes
 2021-04-09 07:58:43 +01:00
Edmund Miller
a3684d9594
Lint modules ci (#389) 
* ci: Add modules lint step

Moved it ahead of the nextflow install so ideally it'll fail before we
bother doing any more setup

* ci: _ => /

* Update tests/config/pytest_software.yml

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-04-08 09:10:52 +01:00
Edmund Miller
6e4b23a1ca
ci: Upload work directory on failure (#388) 
Closes #374
 2021-03-25 09:34:19 +00:00
Edmund Miller
1fc4aa260d
ci: Add 21.03.0 version to matrix (#317) 2021-03-22 22:57:59 +00:00
Harshil Patel
9b99b33401
Rename .github/filters.yml -> tests/config/pytest_software.yml (#271) 
* Rename pytest filters.yml

* Change filters.yml name

* Update resoures for ivar trim
 2021-03-15 12:51:30 +00:00
Gregor Sturm
38349417ad
Update .github/workflows/pytest-workflow.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2021-02-23 14:14:29 +01:00
Gregor Sturm
94bdc62123 Only use one thread for pytest-workflow 
This avoids a race condition on the conda cache.
 2021-02-23 14:06:52 +01:00
drpatelh
418bd64e80 Test module with Conda 2021-02-07 21:33:42 +00:00
Edmund Miller
05c09429a3
ci: Fix artifact path 
Had to change it for singularity
 2021-02-04 08:45:34 -06:00
Edmund Miller
6fe7b48b5b
Revert "Run alllll the testsgit add .github/workflows/pytest-workflow.yml" 
This reverts commit ffc218e51b.
 2021-02-03 20:08:11 -06:00
drpatelh
ffc218e51b
Run alllll the testsgit add .github/workflows/pytest-workflow.yml 2021-02-03 20:03:45 -06:00
drpatelh
0c88ff7458
Upgrade Singularity and change TMPDIR for pytest output 2021-02-03 20:03:43 -06:00
drpatelh
3968c18fd7 Only run Docker tests 2021-02-03 14:04:58 +00:00
drpatelh
9e44b0f4f2 Add conda clean step to action 2021-02-03 12:57:55 +00:00
drpatelh
49fecaa4f0 Switch channel order 2021-02-03 12:07:39 +00:00
drpatelh
d783e2d535 Only test Docker and Conda 2021-02-03 09:02:12 +00:00
Edmund Miller
54bb0ae7a1
ci: Name logs 2021-02-02 17:51:20 -06:00
Edmund Miller
42b8962320
ci: Add bioconda channels 2021-02-02 17:13:35 -06:00
Edmund Miller
0813e61c01
ci: Kick off all container types 2021-02-02 17:08:10 -06:00
Edmund Miller
725de25ce4
Revert "ci: Only test docker for now" 
This reverts commit c63ba06777.
 2021-02-02 17:03:29 -06:00
Edmund Miller
c63ba06777
ci: Only test docker for now 
I can't access the artifacts.
 2021-02-02 16:49:03 -06:00
Edmund Miller
bb3196ddeb
ci: Update name to use matrix 2021-02-02 16:49:03 -06:00
Edmund Miller
dcfd1089e5
ci: Add --keep-workflow-wd-on-fail 2021-02-02 16:49:03 -06:00
Edmund Miller
983b024010
ci: Use ubuntu-20.04 for singularity 2021-02-02 16:49:02 -06:00
Edmund Miller
8cd6e41df9
ci: Change singularity version 3.6.4 => 3.5.3 
Per @grst having issues after 3.6
 2021-02-02 16:49:02 -06:00
Edmund Miller
bf2e027fdf
ci: Remove conda to kickoff CI 2021-02-02 16:48:58 -06:00
Edmund Miller
1e9aad430d
ci: Remove ${{}} for style points 
It's not necessary in if statements
 2021-02-02 15:40:30 -06:00
Edmund Miller
654c6225f0
ci: Setup multiple profiles for testing 
Added conda and singularity
 2021-02-02 15:38:51 -06:00
Edmund Miller
341fa43ae3
ci: Add PROFILE ahead of pytest run 2021-02-02 13:07:58 -06:00
Edmund Miller
ce2a5b32f5
refactor: Move away from composite-action 2021-02-02 12:21:36 -06:00
Edmund Miller
6da00a8a1b
ci: Put python setup before cache 
34cf8a3e0f
 2021-01-24 11:38:29 -06:00
Edmund Miller
c7262e27d8
ci: Cache nextflow 2021-01-24 11:35:24 -06:00
Edmund Miller
73b572eede
ci: Cache pip 2021-01-24 11:25:13 -06:00
Edmund Miller
b048bf33e0
ci: Check to see if it's an example array 2021-01-24 11:14:48 -06:00
Edmund Miller
7a89902657
ci: Fix check for no checks 
https://github.community/t/needs-job-outputs-issue/149156
https://github.community/t/jobs-being-skipped-while-using-both-needs-and-if-unclear-why/18480
 2021-01-24 10:34:40 -06:00
Edmund Miller
b008afe2e6
ci(#119): Upload logs on failure 2021-01-24 10:33:45 -06:00
Edmund Miller
13539e1c1a
ci: Change name of pytest step 2021-01-24 10:33:45 -06:00
Edmund Miller
860a49d456
ci: Need to wrap matrix's in [] 2021-01-24 10:33:45 -06:00
Edmund Miller
0f1016e4a3
ci: Remove any filter 2021-01-24 10:33:45 -06:00
Edmund Miller
9577f5dd64
ci: Reference output rather than a step 
The step wasn't there
 2021-01-24 10:33:45 -06:00
Edmund Miller
939b1490b7
ci: Check if there's a change to anything 2021-01-24 10:33:45 -06:00
Edmund Miller
3aaacdde09
ci: Checkout code before looking for changes 2021-01-24 10:33:44 -06:00
Edmund Miller
f4316480c5
ci: Use paths-filter to make one CI test 2021-01-24 10:33:44 -06:00
Edmund Miller
474a6fad64
ci: Add python setup 
Cause apparently you can use an action inside of an action. Yet.
 2021-01-24 10:33:44 -06:00
Edmund Miller
d00bd5f6b1
ci: v0.1 => master 
Living life on the edge
 2021-01-24 10:33:44 -06:00
Edmund Miller
95270092b0
ci: Add universal CI Test 2021-01-24 10:33:44 -06:00