We are pleased to announce the availability of Genomedata 1.4.4!
This is the first announced release with official Python 3 support!
Loading archives through AGP now merges adjacent entries. This will change the structure of your archives only a per-contig basis if you were previously loading your archives with AGP files that had adjacent entries. There's
no expectation that this will significantly impact any current workflow and will likely improve performance. If this behavior is undesirable for any reason, please let us know. All feedback is welcome.
There has been a significant delay in the Bioconda release of this particular version and is currently being debugged and investigated by us and the core Bioconda team. Version 1.4.1 is the latest version on Bioconda.
All environments, including conda environments, that have Python and HDF5 installed have the option of running "pip install genomedata" to install the latest version.
Along with Python 3 support, a number of bug fixes have been added. Dependency on the "forked-path" python module was dropped in favor of the more modern "path.py" module. Notably, this
package updates the name of the path object so this upgrade breaks compatibility with older Genomedata versions. Downgrading will likely not work and require manually uninstalling of the "path.py" module. However, manually installing specific versions should
Please let me know if you have any comments on Genomedata, its documentation, web site, installation, or anything else. (The preferred place to make these comments is on the genomedata-users mailing list or by reporting an issue on the issue tracker, both linked
from the main web site).
Here is a full list of changes made since the last announcement here
* added compatibilty for Python 3
* fixed genomedata script entry points for Python 3
* fixed pkg-config output encoding when finding HDF5 directories
* genomedata-load-seq: adjacent AGP entries are merged into a single supercontig
* Use pkg-config during setup to determine paths to HDF5 directories
* Removed forked-path dependency, added Path.py
* genomedata-hard-mask: fix verbosity line not outputting to stderr
* genomedata-load-data: fix hdf5 group leak
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