This commit creates two new packages - below a description of these packages and why they are being created.
galaxy-schema: This package contains the pydantic models that power the API. The purpose of packaging them is to ensure they can be reused by clients with minimal external dependencies. Reusing the schema in client code would very quickly provide rapid documentation and validation and static checking for Python clients using the Galaxy API.
galaxy-tool-shed: This package contains the tool shed server code. This has been a long term project to allow the tool shed to be spun out but maintain real galaxy dependencies and maintain testing. More discussions around this project can be found as part of https://github.com/galaxyproject/galaxy/pull/8830.
This reverts commit 353c08cbb9 .
pysam 0.20.0 doesn't build for Python 3.11 on macOS, so we need to
temporarily add the unnecessary Cython runtime dependency that
pysam 0.21 brings in.
- Update Python dependencies that didn't have a cp311 wheel: h5py and
psycopg2-binary.
- For packages for which there is no recent version that works on all
Python versions supported by Galaxy (numpy and scipy), replace old
requirement with multiple Python-version-specific requirements.
Fix `pysam.index()` calls which now use samtools 1.16 where
`samtools index input output` doesn't work any more if `output` is the path
of an already existing file, but `samtools index -o output input` works
fine.
Also:
- Pre-create the (empty) index file for mock test datasets as a unit test
reproducer of the above issue.
- Fix `test_cram` unit test that wasn't checking the return value of
`CRAM.set_index_file()`, which was in fact returning False because
`test-data/2.cram` was not sorted (updated now).
John Chilton