Harshil Patel
f34892c1af
Test PR for nf-core modules lint ( #414 )
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* 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 )
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* 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 )
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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 )
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* 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
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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
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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
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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"
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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"
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This reverts commit c63ba06777
2021-02-02 17:03:29 -06:00
Edmund Miller
c63ba06777
ci: Only test docker for now
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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
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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
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It's not necessary in if statements
2021-02-02 15:40:30 -06:00
Edmund Miller
654c6225f0
ci: Setup multiple profiles for testing
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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
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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
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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
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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
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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
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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
