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Diffstat (limited to 'CHANGELOG')
| -rw-r--r-- | CHANGELOG | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/CHANGELOG b/CHANGELOG index 985854c56860..f6c6d142edfc 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,41 @@ +3.3.1 +----- + +New submodule :py:mod:`pyteomics.featurexml` with a parser for OpenMS **featureXML** files. + +3.3 +--- + + - mzML and mzIdentML parsers can now create an index of element offsets. + This allows quick random access to elements by unique ID. + + - mzML parsers now come in two flavors: :py:class:`pyteomics.mzml.MzML` and + :py:class:`pyteomics.mzml.PreIndexedMzML`. The latter uses the byte offsets + listed at the end of the file. + + - New parameters `convert_arrays` and `read_charges` in :py:func:`mgf.read` + allow using it without :py:mod:`numpy` and possibly improve performance. + The default behavior is retained. + + - Performance optimizations in :py:func:`mgf.read` and :py:func:`parser.cleave`. + + - New decoy generation mode called "fused decoy", described in the paper accepted to JASMS. + +API changes +........... + + - :py:func:`pyteomics.parser.cleave` no longer accepts the `labels` argument. + It is emphasized that the input sequences are expected to be in plain one-letter + notation, but no checks are performed. + + - :py:func:`DataFrame` functions in :py:mod:`pepxml` and :py:mod:`tandem` now + extract more protein-related information. The list-like protein-related values + can be reported as lists or packed into strings, depending on the optional + paramter `sep`. Some column names have changed as a result. + + - Call signatures of :py:func:`pyteomics.fasta.decoy_sequence` and the functions using it + are slightly changed. Standard modes are now also exposed as individual functions. + 3.2 --- |