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Dev -> Master for v1.13.2 release #951

Merged
merged 58 commits into from
Mar 23, 2021
Merged

Dev -> Master for v1.13.2 release #951

merged 58 commits into from
Mar 23, 2021

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ewels
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@ewels ewels commented Mar 23, 2021

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ewels and others added 30 commits March 19, 2021 14:07
@ewels
Bump to 1.14dev
dd00cde
@drpatelh
Merge pull request #925 from ewels/master
9439b3c 
Bump to 1.14dev
Add nf-core colors to rtd sphinx theme
00307a3 
add sphinx to requirements file
fix for linting
e7dddec
dummy commit to run the tests one more time 🙂
d058b1a
@KevinMenden
fix bug for updated messages
a59f497
@KevinMenden
update pytests
d1a9fb7
@KevinMenden
black
153e5fa
@ewels
Merge pull request #930 from KevinMenden/dev
f002538 
fix bug for updated messages
@ewels
Merge pull request #926 from mashehu/add-nf-core-colors-to-docs
f67d063 
Add nf-core colors to rtd sphinx theme
@KevinMenden
started with more robust jinja2 templating
6536ed7
@KevinMenden
add pytest-workflow dep
0771195
@KevinMenden
added check for binary extensions
676cf8f
@rivera10
Merge pull request #938 from KevinMenden/add-pytest-workflow
4275b1e 
add pytest-workflow dep
@KevinMenden
remove containsKey()
54b0eb8
@KevinMenden
add 'params.name' to failing params in nextflow.config lint check
f15824e
@ewels
Merge pull request #939 from KevinMenden/add-name-to-lint
1c0291e 
remove containsKey() from validateParams()
@ewels
Split create-lint-wf commands into separate steps
45f0009
@ewels
Automated PR comments for Python and Markdownlint CI test failures
879c12d
@ewels
Changelog, bump v1.13.2dev
c9a3b11
@KevinMenden
better logging for directory
a316a3a
@KevinMenden
changelog
b3c1d93
@ewels
Merge pull request #941 from ewels/split-steps-create-lint-wf
c51f8f0 
Split steps create lint wf
@ewels
Refactor code for tidyness points
3261493
@ewels
Merge branch 'dev' into better-log-output
655a1cf
@ewels
Merge pull request #942 from KevinMenden/better-log-output
3dd6427
@ewels
Merge pull request #936 from KevinMenden/fix-create
e0f0d1b 
Fixing bugs in nf-core create
@ewels
Pipeline create - apply file permissions to new files
e6ccc10 
Fixes #923
@ewels
File perms on nf-core modules create too
2013dd1
@ewels
Changelog
dcec829
ewels added 18 commits March 23, 2021 13:31
@ewels
Copy file if any exception with jinja in pipeline create
7a1c333
@ewels
Make lint summary table coloured according to overall status
719d22d
@ewels
Proper {{}} escaping in workflow for new comments
217ecea
@ewels
Changelog
6084456
@ewels
Merge pull request #946 from ewels/code-lint-comments
e79602e 
Add code lint CI PR comments to pipeline template
@ewels
Merge branch 'dev' into bugfix-tweaks
b7bd4c4
@ewels
Use '21.03.0-edge' in bump-versions code
17fbcf8
@ewels
Merge pull request #947 from ewels/bugfix-tweaks
29e98d1 
Bugfix tweaks
@ewels
Find yml and yaml files for yaml linting
a14af2f
@ewels
Log API headers on fail - create PR
f714baa
@ewels
Sync - keep trying if we get 403 errors
01dcdf2
@ewels
Changelog
07c3978
@ewels
Merge pull request #948 from ewels/bugfix-tweaks
ad0cddb 
Find yml and yaml files for yaml linting
@ewels
Fix copypasta syntax error
d0633b2
@ewels
fix tests
3f15ce0
@ewels
Reduce diff - didn't need to indent that bit
fa00cde
@ewels
Merge pull request #949 from ewels/sync-headers-abuse
1f888a5 
Sync headers abuse
@ewels
Bump to v1.13.2
ba85e6c
@ewels ewels marked this pull request as draft March 23, 2021 13:32
ewels
ewels commented Mar 23, 2021
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.github/workflows/pytest.yml Outdated Show resolved Hide resolved
@ewels ewels marked this pull request as ready for review March 23, 2021 13:36
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codecov bot commented Mar 23, 2021 •
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Codecov Report

Merging #951 (8e31d7f) into master (e5f53bf) will decrease coverage by 0.02%.
The diff coverage is 76.36%.

❗ Current head 8e31d7f differs from pull request most recent head 54f7f18. Consider uploading reports for the commit 54f7f18 to get more accurate results
Impacted file tree graph

@@            Coverage Diff             @@
##           master     #951      +/-   ##
==========================================
- Coverage   69.58%   69.56%   -0.03%     
==========================================
  Files          34       34              
  Lines        4176     4196      +20     
==========================================
+ Hits         2906     2919      +13     
- Misses       1270     1277       +7
Impacted Files Coverage Δ
nf_core/bump_version.py 85.93% <ø> (ø)
nf_core/lint/nextflow_config.py 69.62% <ø> (ø)
nf_core/modules/create.py 60.91% <66.66%> (+0.45%) ⬆️
nf_core/sync.py 51.98% <66.66%> (+0.14%) ⬆️
nf_core/create.py 90.56% <81.81%> (-3.12%) ⬇️
nf_core/lint/__init__.py 77.29% <87.50%> (+0.09%) ⬆️
nf_core/modules/lint.py 62.55% <100.00%> (-0.03%) ⬇️

Continue to review full report at Codecov.

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KevinMenden
KevinMenden approved these changes Mar 23, 2021
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Alright, been through it, looks good!
Fixes quite a lot of bugs 👍

drpatelh
drpatelh approved these changes Mar 23, 2021
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DOOOOO ITTT!!!

@KevinMenden KevinMenden added this to Ready for review in hackathon-march-2021-framework Mar 23, 2021
ggabernet
ggabernet approved these changes Mar 23, 2021
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Looks good to me!

@ewels ewels merged commit cd067e5 into master Mar 23, 2021
hackathon-march-2021-framework automation moved this from Ready for review to Done Tuesday Mar 23, 2021
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@ggabernet ggabernet ggabernet approved these changes

@KevinMenden KevinMenden KevinMenden approved these changes

@drpatelh drpatelh drpatelh approved these changes

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@ewels @ggabernet @KevinMenden @drpatelh @rivera10