Update workflow installs with schematic 24.7.1

[anngvu]

https://github.com/Sage-Bionetworks/schematic/releases/tag/v24.7.1

Looking at release notes, workaround with ipython was removed successfully.

Update:

Just FYI, there are two submission failures that are a little confusing and might have to do with the test setup that I need to fix (concurrency issues with other tests running given multiple PRs at the same time ?) / doesn't seem to be schematic issue, since the other submissions pass. Overall, this update should be OK.

✓ Set up NF.jsonld for test
Using '../validate' as the scope containing all possible manifests for submission tests.
Using '../validate/logs' to filter for valid/qualifying manifests.
This manifest qualifies for and will undergo test submission: ../validate/GenomicsAssayTemplate_0.csv
Creating mock dataset folder...
Creating mock entities...

SynapseHTTPError: 403 Client Error: 
Lack of READ permission on the parent entity.


SynapseHTTPError: 403 Client Error: 
Lack of READ permission on the parent entity.

[github-actions]

Test Suite Report 24.7.1

Template Generation

template	result	link
ClinicalAssayTemplate	😄	template link
EpigeneticsAssayTemplate	😄	template link
FlowCytometryTemplate	😄	template link
GenomicsAssayTemplate	😄	template link
GenomicsAssayTemplateExtended	😄	template link
HumanCohortTemplate	😄	template link
ImagingAssayTemplate	😄	template link
LightScatteringAssayTemplate	😄	template link
MethylationArrayTemplate	😄	template link
MRIAssayTemplate	😄	template link
PharmacokineticsAssayTemplate	😄	template link
PlateBasedReporterAssayTemplate	😄	template link
ProcessedAlignedReadsTemplate	😄	template link
ProcessedExpressionTemplate	😄	template link
ProcessedVariantCallsTemplate	😄	template link
ProteomicsAssayTemplate	😄	template link
ProtocolTemplate	😄	template link
RNASeqTemplate	😄	template link
ScRNASeqTemplate	😄	template link
UpdateMilestoneReport	😄	template link
WESTemplate	😄	template link
WGSTemplate	😄	template link

Manifest Validation

manifest	result	expectation
GenomicsAssayTemplate_0.csv	😄	Lists can be blank if attr not required using ‘list like’ rule
GenomicsAssayTemplate_1.csv	😄	Mixing blanks and regular list values works
GenomicsAssayTemplate_2.csv	😄	Conditional validation for attributes is currently not supported
GenomicsAssayTemplate_control.csv	😄	There should be no issue with this template.
ScRNASeqTemplate_0.csv	😄	Single list val works by using ‘list like’ rule
ScRNASeqTemplate_1.csv	😄	Fail because of missing data in required field libraryStrand

Manifest Submission

manifest	pass
GenomicsAssayTemplate_0.csv	❌
GenomicsAssayTemplate_1.csv	😄
GenomicsAssayTemplate_2.csv	😄
GenomicsAssayTemplate_control.csv	❌
ScRNASeqTemplate_0.csv	😄

[allaway]

Glad this bug with ipython is fixed!