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.
0.6.1 2020-05-16¶
Added¶
A license (MIT).
Changed¶
Reduced the usage of shortcut imports to improve compatibility with clctools, see clctools#4.
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.
Added¶
Changed¶
numpy arrays containing strings are now always created with a “U” dtype.
Fixed¶
You can now pass a
(positions, labels)
tuple to thexticks
andyticks
kwargs 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.
Updates/maintenance¶
Bumped minimum
matplotlib
dependency, 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.py
in 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-apidoc
on 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.
Streamlined Docker image build so that building the wheel beforehand is no longer necessary, see #67. This also fixes #68.
We now use setuptools-scm to manage version information instead of versioneer. We repurposed the existing
lib5c._version
module 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-recommendedvalues
property.Thanks to #75 and #76, tutorials have been updated to use
lib5c.util.demo_data
and now run on Windows (tox -e tutorials
). Tutorials now run on Python 3.6.
0.5.5 - 2020-02-04¶
Updates/maintenance¶
Enforce maximum supported version of
statsmodels
since 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.
Changed¶
ExtendableHeatmap ChIP-seq track and gene track plotting are now faster thanks to the use of PolyCollection and LineCollection, see #28.
Updates/maintenance¶
Updated
flake8
configuration (to match previous behavior when using latest version offlake8
).Simplified
.gitignore
.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.