Move scanpy tools to scanpy 1.9.3

[pcm32]

Description

This PR aims to move scanpy tools to scanpy 1.9.3.

Fixes # (issue)

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Checklist

• I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
• If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
• If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).
• If I changed the version, the @TOOL_VERSION@ part of the version does not contain any + symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only + should be the one preceding galaxy<build> (unless that all the versions from that tool previously followed a different pattern).

[pcm32]

Current failures to be fixed are available on the report file attached.
test_report.html.zip

Most of them tend to be different file sizes. I would suggest that we change file comparisons with hdf5 paths checks according to the operation executed, which will avoid this issue in the future (see some of the tests in the anndata_operations tools).

[pcm32]

I have fixed now the older use of anndata.read in the base package

/usr/local/lib/python3.9/site-packages/anndata/__init__.py:51: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024.

ebi-gene-expression-group/scanpy-scripts#128

[pcm32]

Made some progress @anilthanki but still 25/44 to go.

[pcm32]

This is great, thanks for dealing with all the tests! I guess this means that we can do now a release of scanpy scripts at the other side.

(I mean before merging this)

[pmb59]

Code changes LGTM @pcm32 @anilthanki

[pcm32]

Thanks for the review @pmb59 !