Releases: linnarsson-lab/loompy
Release recent changes
3.0.7 Update _version.py
Remove dependency on h5py 2.10.0
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.
Backwards compatibility of validator
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.
Upgraded the validator
The validator was upgraded to conform to the 3.0.0 spec.
Bugfixes and spec update
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
Loompy 3.0.1
Minor release mainly with updated docs and tutorials for loompy fromfq command-line tool.
Loompy 3.0
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
Bugfixes and cellranger V3 compatibility
Handle non-standard files with UTF8 strings
Fixes #78 by not crashing when opening a file that has variable-length UTF8-encoded strings (in violation of the Loom specification).
Minor bugfixes
Bugfixes
- Bug in slicing views using tuples #77
- Fix: when attempting to connect to non-existing file, an empty file would be created