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3.0.7

Update _version.py
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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.

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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.

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The validator was upgraded to conform to the 3.0.0 spec.

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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

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Minor release mainly with updated docs and tutorials for loompy fromfq command-line tool.

710c945
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What's new

  • 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
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Various bugfixes and improvements

  • Support importing cellranger 3.0.0 folders (#84)
  • Fixes bugs in sparse array support (#82)
  • Makes scan() faster (#90)
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Fixes #78 by not crashing when opening a file that has variable-length UTF8-encoded strings (in violation of the Loom specification).

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Bugfixes

  • Bug in slicing views using tuples #77
  • Fix: when attempting to connect to non-existing file, an empty file would be created