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@ewels ewels commented Jul 29, 2020

Now that tests are passing again and the cli tools match the updated template, I think that we can merge this to dev.

matthiasho and others added 30 commits July 22, 2020 16:55
update json-schema template to new structure
* Check that we have at least 1 parameter, fail if not
* Log number of parameters found
* Use 'pipeline schema' instead of 'JSON Schema' in logging
* Work with top-level schema and defintions sub-schema
* Strip out logic about object-type properties
* Test nf-core schema build with dummy pipeline
Also update all pytest.mark.xfail to use strict=True, so fails if an exception is not raised.
Check for presence and values of top-level $schema, $id, title and description
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ewels commented Jul 29, 2020

Assuming tests pass again, will self-merge as this PR is a combination of other smaller PRs that have already been reviewed.

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codecov bot commented Jul 29, 2020

Codecov Report

Merging #698 into dev will increase coverage by 1.07%.
The diff coverage is 72.07%.

Impacted file tree graph

@@            Coverage Diff             @@
##              dev     #698      +/-   ##
==========================================
+ Coverage   81.41%   82.49%   +1.07%     
==========================================
  Files          13       13              
  Lines        2696     2725      +29     
==========================================
+ Hits         2195     2248      +53     
+ Misses        501      477      -24     
Impacted Files Coverage Δ
nf_core/bump_version.py 94.36% <ø> (ø)
nf_core/create.py 94.44% <ø> (ø)
nf_core/sync.py 62.25% <0.00%> (ø)
nf_core/launch.py 70.94% <23.68%> (+0.91%) ⬆️
nf_core/__main__.py 63.63% <25.00%> (-1.23%) ⬇️
nf_core/schema.py 91.34% <93.75%> (+3.67%) ⬆️
nf_core/lint.py 91.93% <100.00%> (+0.31%) ⬆️
nf_core/utils.py 91.11% <100.00%> (+0.06%) ⬆️
nf_core/list.py 80.07% <0.00%> (+5.36%) ⬆️

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@ewels ewels merged commit ca77a53 into dev Jul 29, 2020
@ewels ewels deleted the new-new-schema branch July 29, 2020 08:43
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3 participants