New-new schema #695
Merged
New-new schema #695
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Use fnmatch to properly apply glob expressions found in the .gitignore file
Use new Rich syntax for markup logs.
* 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.
Codecov Report
@@ Coverage Diff @@
## new-new-schema #695 +/- ##
==================================================
+ Coverage 81.41% 82.49% +1.07%
==================================================
Files 13 13
Lines 2696 2725 +29
==================================================
+ Hits 2195 2248 +53
+ Misses 501 477 -24
Continue to review full report at Codecov.
|
Lint TODO - ignore editor files
ewels
added a commit
to ewels/nf-core-website
that referenced
this pull request
Jul 28, 2020
See change in nf-core/tools at nf-core/tools#695
Check for presence and values of top-level $schema, $id, title and description
3 tasks
…b/workflows/push_dockerhub.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Dockerhub ci actions
apeltzer
approved these changes
Jul 28, 2020
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Updated nf-core/tools for the newer style of pipeline schema, using sub-schema in
definitionsfor grouping. See #687x-ref #688 and note that the PR is to the
new-new-schemabranch (we want to merge all of this in one go if possible).Quite a bit in this PR, but some key points:
params.key.other_key), but no longer explicitly disallowedPR checklist
docsis updatedCHANGELOG.mdis updatedREADME.mdis updated