All notable changes to this project will be documented in this file.
0.6.0 - 2020-03-11¶
This version finally brings Python 3 support to lib5c!
Currently all tests and all tutorials pass under both Python 2.7 and Python 3.6, but it’s possible that a few bugs exist in areas with low test coverage.
numpy arrays containing strings are now always created with a “U” dtype.
You can now pass a
(positions, labels)tuple to the
ytickskwargs of a function decorated with
@plotter, see #25.
When running in Python 3 environments where ConfigParser is not available, the default pipeline config will have all its “%” symbols escaped when it is dropped to disk, see #73.
Y-axis gene tracks now appear correctly on trans heatmaps, see #69.
Two-way thresholding now works even when there is only one region, see #71.
Quoting paths with wildcards when passing them to lib5c commands no longer prevents glob expansion in Windows, see #76.
matplotlibdependency, see #59.
Changed testing/linting to use tox. tox now serves as a centralized place to control maintenance-related actions like running the tutorials, building Docker images, testing the doc build, etc.
Since tox doesn’t support shell redirection/expansion, we moved the Docker one-liners into a new utility script
_docker.pyin the project root which is called by the new docker testenv (
tox -e docker).
Overhauled doc build process. We now use sphinxcontrib-apidoc to automatically run
sphinx-apidocon every doc build, avoiding the need to commit the per-module apidoc-generated .rst files to git. We also use the readthedocs config file to configure the doc build on readthedocs. Both the local (
tox -e docs) and readthedocs builds are now configured to exit when they encounter a warning.
Reduced the fragility of many doctest cases that relied on the ordering of dictionary keys.
We now use setuptools-scm to manage version information instead of versioneer. We repurposed the existing
lib5c._versionmodule to provide setuptools-scm specific functionality.
Added dependency on configparser to make config file parsing more consistent across Python versions.
Relaxed maximum version constraint on python-daemon, since luigi seems to be handling this now.
Replaced references to pandas’s deprecated
get_matrix()bound method with the now-recommended
0.5.5 - 2020-02-04¶
Enforce maximum supported version of
statsmodelssince they are no longer building Python 2 wheels.
0.5.4 - 2019-06-07¶
First wave of major heatmap plotting upgrades plus streamlining of the release process via Bitbucket Pipelines.
ExtendableHeatmap ChIP-seq track and gene track plotting are now faster thanks to the use of PolyCollection and LineCollection, see #28.
flake8configuration (to match previous behavior when using latest version of
Tests are now performed by Bitbucket Pipelines on every push.
Reworked documentation to use Read the Docs.
Moved tutorials to new
tutorials/directory under project root.
Tutorials are now built and published as an independent step in Bitbucket Pipelines, separate from the documentation build process.
Deployment to PyPI and Docker Hub is now performed on tag push by Bitbucket Pipelines.
0.5.3 - 2018-10-15¶
First official release, corresponds to what was used in the final version of this paper.