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We had acquired a dependency on
h5py>=2.10.0 when we introduced variable-length UTF8 string attributes (specifically, we used
h5py.string_dtype). This was sad, because scanpy has a dependency
h5py!=2.10.0 which makes loompy and scanpy strictly incompatible. However, it turns out there's a way to describe the same thing that works in older versions of h5py (specifically, using
special_dtype(vlen=str)). This release uses the old way, and removes the dependency on h5py 2.10.0.
Validator now automatically validates against the spec version that the file itself declares (rather than a spec version requested by the caller). This can be overridden by specifying a specific version for validation.
Fixes a couple of minor bugs
- Missing dependency added: numpy_groupies
- Accidental Python 3.7 dependency removed
Updates the Loom v3.0.0 file format specification
- Improved performance
- Full sparse matrix support
- Unlimited size of global attributes
- Variable-length Unicode string attributes
- New command-line tool to create .loom directly from fastq using kallisto
Various bugfixes and improvements
Fixes #78 by not crashing when opening a file that has variable-length UTF8-encoded strings (in violation of the Loom specification).