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CHANGELOG.rst

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Version History and Changes

Version 0.6.5 (2022-07-01)

  • Always use the Agg matplotlib backend (to avoid problems with systems where DISPLAY environment variable is set but no graphical display is available.
  • Update documentation for mk_pegs_intervals to clarify how to obtain suitable input files.

Version 0.6.4 (2021-11-08)

Version 0.6.3 (2021-10-25)

  • Patches to improve handling of input files: fix problems with sorting filenames, and perform explicit checks on peaks and cluster files to ensure that they exist and are not actually directories.
  • Update the Conda installation instructions in the README and documentation.

Version 0.6.2 (2021-09-28)

  • Update the README and "getting started" documentation to include installation from Conda.

Version 0.6.1 (2021-09-14)

  • Patches to update the README and glucocorticoid examples to reflect the new command line format introduced in version 0.6.0.

Version 0.6.0 (2021-09-14)

This version includes updates that are not backwards compatible with older versions of PEGS

  • Substantial update to how input files and distances are specified: - New compulsory --peaks and --genes

    arguments must now be used to specify one or more peakset and gene cluster files respectively.

    • Distance intervals must be specified with new --distances option.

  • New options added to customise the output heatmaps: - --x-label and --y-label options allow custom

    axis labels to be specified.

    • Documentation on setting custom colours for heatmap has been expanded (along with examples).
    • Heatmap image format can be specified on the command line either implicitly (via output file name extension) or explicitly (using --format option). Supports PNG, SVG, PDF etc.

  • Added information on how to cite PEGS.

Version 0.5.1 (2021-05-12)

  • Patches to fix display of README landing page on PyPI and include the changelog in the documentation.

Version 0.5.0 (2021-05-12)

  • Added support for Python 3.9.
  • Dropped support for Python 2.7.
  • Fixed bug with automatic installation of bedtools (was failing on some systems).
  • Updated versions of dependencies: numpy (1.19.5), scipy (1.5.4), matplotlib (3.3.4) and seaborn (0.11.1).
  • Update to installation information to indicate that PEGS can be installed directly from PyPI.

Version 0.4.2 (2021-05-12)

  • Updates to setup.py to enable distributions to be built for upload to the Python Package Index (PyPI).

Version 0.4.1 (2021-05-10)

  • Fixes to the 'quick start' and 'licensing' sections of the README
  • Add worked example using mouse glucocorticoidal data to the README and the documentation.
  • Update requirement for Pillow library to 8.1.1.
  • Fix unit tests and add continuous integration testing workflow in Github Actions.

Version 0.4.0 (2020-08-18)

  • Drop the requirement that cluster files must be named cluster_*.txt; all files in the clusters directory will now be included in the analysis. The file names (without the file extension) will be used as x-axis labels in the plots.

Version 0.3.0 (2020-05-13)

  • Automatically install a local version of bedtools if one is not found on the user's PATH.

Version 0.2.0 (2020-03-20)

  • Use bedtools intersect instead of intersectBed to calculate overlaps.
  • Cosmetic updates to reporting program progress.
  • Add initial Sphinx documentation.

Version 0.1.0 (2020-01-30)

  • Initial version of PEGS.