Glob

[pjotrp]

Globbing multiple documents.

• Fixed test that allowed 2 schemas to be passed in
• Multiple documents on command line
• Solve RDF compression because of shared placeholder ID (PubSeq style) or emit warning
• Add real filename globbing

Later we may need to add chunking when these documents take all RAM.

[codecov]

Codecov Report

Merging #392 (b8d9433) into main (012c5a7) will decrease coverage by 9.38%.
The diff coverage is 60.00%.

❗ Current head b8d9433 differs from pull request most recent head 1869e96. Consider uploading reports for the commit 1869e96 to get more accurate results

@@            Coverage Diff             @@
##             main     #392      +/-   ##
==========================================
- Coverage   79.29%   69.90%   -9.39%     
==========================================
  Files          18       16       -2     
  Lines        3260     2911     -349     
  Branches      879      766     -113     
==========================================
- Hits         2585     2035     -550     
- Misses        442      677     +235     
+ Partials      233      199      -34     

Impacted Files	Coverage Δ
schema_salad/main.py	59.67% <60.00%> (-15.61%)	⬇️
schema_salad/makedoc.py	10.22% <0.00%> (-72.78%)	⬇️
schema_salad/jsonld_context.py	74.09% <0.00%> (-5.43%)	⬇️
schema_salad/utils.py	80.35% <0.00%> (-2.98%)	⬇️
schema_salad/avro/schema.py	61.14% <0.00%> (-1.60%)	⬇️
schema_salad/validate.py	70.50% <0.00%> (-0.62%)	⬇️
schema_salad/python_codegen.py	95.20% <0.00%> (-0.07%)	⬇️
schema_salad/__init__.py
schema_salad/schema.py
... and 3 more

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[pjotrp]

Added multiple document support and globbing. Also added a PubSeq test. Ready for review!

[mr-c]

Thank you @pjotrp !

Re: https://github.com/common-workflow-language/schema_salad/pull/392/checks?check_run_id=2708947782#step:7:16

Can you run make format and then check the output of make flake8?

Re: https://github.com/common-workflow-language/schema_salad/pull/392/checks?check_run_id=2708947654#step:7:25

Please run make diff_pydocstyle_report as shown above and fix the complaint :-)

Re: https://github.com/common-workflow-language/schema_salad/pull/392/checks?check_run_id=2708948393#step:6:1173

Looks like the MANIFEST.in needs updating..

Feel free to run tox as the CI tests stopped once the first error was reached.

[pjotrp]

Will fix. Are you OK with the test data hosted in test/data/pubseq?

[mr-c]

Will fix. Are you OK with the test data hosted in test/data/pubseq?

I can't think of a reason not to be. What's the total size? We install our tests so users can verify post installation - (via pip, apt, whatever)

[mr-c]

Ping :-)

[pjotrp]

On my todo list. Probably end of July because of holiday and other things.