Version 0.9.10

This long-awaited release includes major plotting enhancements in the heatmap, scatter, and diagram commands, as well as a new export gistic command, thanks to joint work by @tetedange13 and @tskir (see below).

There are also significant infrastructure improvements including bug fixes, modernized packaging, and build/test automation.

New features

diagram:

• New options --no-gene-labels to not display gene labels on the plot, and -c / --chromosome to plot a single chromosome (#628, #629, #634; thanks @tetedange13)

heatmap:

New CLI options (#35, #625, #632, #652; thanks @tetedange13 and @tskir):

• --vertical: Transpose the plot, displaying the genome axis vertically instead of horizontally
• --delimit-samples: Add an delimitation line between each sample row (or column, with --vertical)
• --title: Set the plot title

scatter:

• New option --fig-size: Set the output image dimensions (#600, #641; thanks @tetedange13 and @tskir)
• Show triangles at the bottom of the plot to indicate where segments are hidden below the plotted region by automatic pruning at 'ymin=-5'. Also log a warning when this happens. (#385, #643, #645; thanks @tetedange13, @tskir, and @micknudsen)

export gistic:

• New export command to generate an unsegmented "markers" file for use with GISTIC. GISTIC also takes a second input file with corresponding segments in SEG format, which CNVkit can generate with export seg. (#622, #623, #776; thanks @tetedange13, @tskir, @BioComSoftware)

API and CLI changes

• Running cnvkit.py without any arguments will now display the full help text instead of an error message.
• Supporting scripts (aside from cnvkit.py) are no longer installed automatically. They are still available in the source tree.

Documentation

• Clarified bintest usage, provided an example, and explained outputs. (#646; thanks @tetedange13 and @tskir)

Bugfixes

• Fixed several errors and warnings due to outdated usage of dependencies, e.g. pandas, pysam.
• Fixed the Dockerfile and Docker image to install R packages properly for CNVkit to use internally. (#765; thanks @28rietd)
• Made the Makefile example/test workflow more portable across environments. (#661, #666, #695, #699; thanks @tetedange13)
• batch: Apply --drop-low-coverage option in the segmetrics step. (#694)
• bintest: Include 'probes' column in .cns output so that it is valid .cns (closes #693)
• fix: Condense the error message when coordinate set contains duplicate values. (#637, #638; thanks @tskir)
• fix: Choose a smoothing window fraction based on the data size to help correct biases better at the extremes of the GC range, where previously some residual GC bias could still be present after correction. (#379)
• BED inputs: Handle UCSC BED 'browser' header line, as used in Agilent BED files with a 2-line header. (closes #696, #618)

Internal

• Modernized the packaging configuration with pyproject.toml, leaving a stub setup.py for legacy setuptools compatibility. (#790)
• Set up automated testing through GitHub Actions (GHA) to verify Python versions 3.7 through 3.10 using pytest and tox. The latter make local testing with multiple Python versions more reliable, too. (#792, #793, #794)
• Updated minimum dependency versions to roughly match Ubuntu 22.04 LTS packages; these are used in CI, too.
• Applied black and pylint to reformat the codebase consistently and replace deprecated calls to libraries. (#795)
• Remove joblib pinning (#589, #770; thanks @DavidCain and @risicle)
• Remove networkx pinning (#606, #771; thanks @DavidCain)
• Make the extreme-GC filters more easily configurable via params.py (#738, #752, #753, #764; thanks @tetedange13 and @tsivaarumugam)