Changelog¶
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project attempts to adhere to Semantic Versioning.
0.2.1 - 2020-05-03¶
Added¶
- A license (MIT).
- Utilty functions for APA plots in
hic3defdr.util.apa
with a corresponding demo indocs/apa.rst
. - Utility function for importing loop calls from HiCCUPS in
hic3defdr.util.clusters.hiccups_to_clusters()
.
Updates/maintenance¶
- Demos now run as tests within the readme tox environments.
- Release pipeline no longer creates any artifacts, see comments on this commit.
0.2.0 - 2020-03-13¶
This version adds Python 3 support!
Added¶
Changed¶
- numpy arrays containing strings now use a “U”-based dtype.
Updates/maintenance¶
- Bumped minimum lib5c dependency to 0.6.0.
- Version information is now provided by setuptools-scm instead of versioneer.
- Added Sphinx documentation and readthedocs configuration to build it.
- Linting, testing, running the README, and building docs are now all handled using tox.
- Reworked Docker image build, see creminslab/lib5c#57.
0.1.1 - 2020-02-27¶
Streamlined data loading, see #19.
Added¶
- A new convenience function
HiC3DeFDR.get_matrix()
which selects a dense matrix slice for any stage of the data in one line. - A new convenience kwarg
coo
onHiC3DeFDR.load_data()
which (when True) causes the function to return a COO-formatrow, col, data
tuple that’s guaranteed to be aligned for any stage of the data. - New convenience kwargs
rep
andcond
onHiC3DeFDR.load_data()
which allow selecting the right column of rectangular data stages by name automatically (i.e., without having to manually computerep_idx
). - The
stage
kwarg ofHiC3DeFDR.plot_heatmap()
can now be any stage, including ‘qvalues’. This allows easy plotting of heatmaps showing the significance of each pixel. An example showing how to do this has been added to the README.
Changed¶
- The signature of
HiC3DeFDR.plot_heatmap()
has been reworked so thatrep
is now a kwarg instead of the first positional arg. - The signature of
hic3defdr.plotting.heatmap.plot_heatmap()
has been reworked so that it accepts a dense matrixmatrix
as the first positional arg instead ofrow, col, data, row_slice, col_slice
. Clients are expected to usehic3defdr.util.matrix.select_matrix()
to get the dense matrix before callingplot_heatmap()
. HiC3DeFDR.load_data('loop_idx', ...)
now returns a vector of True ifloop_patterns
was not passed to the HiC3DeFDR constructor.
0.1.0 - 2020-02-12¶
Adds a first draft of TSV output tables.
Added¶
- This changelog!
- The pipeline now generates a final table of loop calls as requested by #23.
- Added a new pipeline step
HiC3DeFDR.collect()
- we now recommend running this instead ofHiC3DeFDR.classify()
. - Added a new utility module
hic3defdr.util.cluster_table
to support creating tabular files summarizing cluster information - Added a few new functions in
hic3defdr.util.clusters
as well as some better test coverage in this module. - The README has been updated to cover this new step and output format.
- Added a new pipeline step
Changed¶
- Renamed
hic3defdr.util.logging
tohic3defdr.util.printing
to avoid a rare name clash bug related to this issue, see #28
0.0.9 - 2019-11-26¶
First official release, corresponds to what was used in the second submission of the related manuscript.