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Release notes

DISCOVER packages are made available for both Python and R. The packages for both languages expose the same set of features and a similar programming interface, where differences in the latter only serve to conform to language-specific conventions. Increments of the major or minor version number (e.g. 0.9 -> 1.0, or 1.0 -> 1.1) will be made upon the introduction of substantial new features. Bug fixes or smaller new features are introduced in the patch releases (e.g. 0.9.1). Whereas the major and minor release series will always be kept in sync between Python and R, patch releases may be published independently. In other words, version 0.9.3 of the Python package would not have more functionality than version 0.9.1 of the R package; it would simply have required more bug fixes. However, version 1.0.0 of the Python package would have features that do not exist in version 0.9.1 of the R package.

0.9 series

Latest Python version:0.9.5 (May 11, 2023)
Latest R version:0.9.4 (July 28, 2021)

Python package

0.9.5 (May 11, 2023)

Fixed:

  • If pandas >= 2.0 was installed, constructing a DiscoverMatrix object gave rise to "AttributeError: 'DataFrame' object has no attribute '__array_wrap__'".

0.9.4 (July 28, 2021)

Added:

  • The new fdr_method argument of the pairwise_discover_test function selects the false discovery rate estimation method used for multiple testing correction. Its default value selects a Benjamini-Hochberg procedure adapted for discrete test statistics. As an alternative, the standard Benjamini-Hochberg procedure can be selected. While the latter is much faster, it is also more conservative than the discrete version. The discrete method was always used in previous versions and is still the recommended choice.

Changed:

  • Speed improvements in DiscoverMatrix and pairwise_discover_test. DiscoverMatrix finishes instantaneously for small to medium-sized data sets and takes only a few seconds for very large data sets. pairwise_discover_test (with discrete Benjamini-Hochberg) is about twice as fast as in previous versions.
  • Python 2.7 is no longer supported.

Fixed:

  • If pandas >= 1.0 was installed, subsetting a DiscoverMatrix object gave rise to "AttributeError: 'DataFrame' object has no attribute 'ix'".
  • Fixed the underlying Fortran code to make it compile with GNU Fortran >= 10. Due to these changes the minimum supported GNU Fortran version is now version 5.

0.9.3 (June 18, 2019)

Fixed:

  • Applied a small fix to the Fortran code to make it compile with GNU Fortran >= 8.2.

0.9.2 (April 20, 2018)

Added:

  • Added a new conda recipe, which takes advantage of features introduced by conda build 3.

Fixed:

  • The RuntimeWarning fix added in version 0.9.1 did not work when the pairwise_discover_test function was given a grouping factor.

0.9.1 (October 11, 2017)

Fixed:

  • Removed the "RuntimeWarning: invalid value encountered in less" warnings generated by the PairwiseDiscoverResult class' __repr__ and significant_pairs methods

0.9 (September 23, 2016)

First public release

R package

0.9.4 (July 28, 2021)

Added:

  • The new fdr.method argument of the pairwise.discover.test function selects the false discovery rate estimation method used for multiple testing correction. Its default value selects a Benjamini-Hochberg procedure adapted for discrete test statistics. As an alternative, the standard Benjamini-Hochberg procedure can be selected. While the latter is much faster, it is also more conservative than the discrete version. The discrete method was always used in previous versions and is still the recommended choice.

Changed:

  • Speed improvements in discover.matrix and pairwise.discover.test. discover.matrix finishes instantaneously for small to medium-sized data sets and takes only a few seconds for very large data sets. pairwise.discover.test (with discrete Benjamini-Hochberg) is about twice as fast as in previous versions.
  • The matrixStats package is no longer a dependency.

Fixed:

  • Re-enabled OpenMP, which distributes the computations in pairwise.discover.test across multiple CPUs. OpenMP was disabled since R 4.0.
  • Fixed the underlying Fortran code to make it compile with GNU Fortran >= 10. Due to these changes the minimum supported GNU Fortran version is now version 5.

0.9.3 (June 18, 2019)

Fixed:

  • Applied a small fix to the Fortran code to make it compile with GNU Fortran >= 8.2.

0.9.2 (October 11, 2017)

Added:

  • Added citation info to the R package, use with citation("discover")

Fixed:

  • Fixed a bug in pairwise.discover.out's print method that caused the value of the fdr.threshold argument to be ignored

0.9.1 (September 23, 2016)

First public release