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Diffstat (limited to 'CHANGELOG')
| -rw-r--r-- | CHANGELOG | 104 |
1 files changed, 101 insertions, 3 deletions
diff --git a/CHANGELOG b/CHANGELOG index 94f5eae040c7..15672ad90dd2 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,10 +1,106 @@ +3.4 +--- + + - New module :py:mod:`pyteomics.mzxml` for parsing of MzXML files. + + - New parameter `dtype` in :py:func:`pyteomics.mgf.read`, :py:func:`pyteomics.mzml.read` + and :py:func:`pyteomics.mzxml.read` + allows changing the dtype of arrays yielded by the parsers. + + - :py:mod:`pyteomics.featurexml` moved into a subpackage :py:mod:`pyteomics.openms`. + + - New module :py:mod:`pyteomics.openms.trafoxml` for OpenMS transformation files. + + - Bugfix in XML indexing code to make it work on Python 3.x versions prior to 3.5. + + - Bugfix in :py:func:`pyteomics.pylab_aux.scatter_trend` (support for lists and other non-ndarrays). + + - Performance improvements in :py:mod:`pyteomics.achrom` calibration functions. + +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 +--- + +New submodule :py:mod:`pyteomics.mass.unimod` contains rewritten machinery +for handling of Unimod relational databases (contributed by Joshua Klein). +This is a substitution and extension for the old :py:class:`mass.Unimod` class. +:py:mod:`pyteomics.mass.unimod` requires SQLAlchemy. + +Other changes: + + - New function :py:func:`pyteomics.auxiliary.linear_regression_perpendicular` + provides a linear fit minimizing distances from data points to the fit line + (as opposed to :py:func:`pyteomics.auxiliary.linear_regression`, which + minimizes vertical distances). + + - Both new and old linear regression functions now accept a single array of shape (N, 2). + + - :py:func:`pyteomics.pylab_aux.scatter_trend` now has an optional parameter + `regression` which can be a callable performing the regression. + Also, the regression equation is now the label of the regression line, not + the scatter plot. + + - Another two new parameters for :py:func:`pyteomics.pylab_aux.scatter_trend` + are `sigma_kwargs` and `sigma_values`. + + - :py:mod:`pyteomics.pylab_aux` functions :py:func:`plot_line` and + :py:func:`scatter_trend` now return the objects they create. + + - Writer functions (:py:func:`pyteomics.mgf.write`, :py:func:`pyteomics.fasta.write`, + :py:func:`pyteomics.fasta.write_decoy_db`) now accept a `file_mode` argument that + overrides the mode in which the file is opened. + + - In :py:func:`pyteomics.mgf.write` one can now override the format spec for fragment m/z, + intensity and charge values using the optinal `fragment_format` argument. Key order and + key-value parameter formatters are now also handled via optional arguments. + + - :py:func:`pyteomics.fasta.decoy_db` now supports `ignore_comments` and `parser` arguments. + + 3.1.1 ----- - Bugfix in :py:mod:`pyteomics.auxiliary`. - New parameter `show_legend` in :py:func:`pyteomics.pylab_aux.scatter_trend`. - + - Performance improvements in :py:mod:`pyteomics.parser`. 3.1 @@ -176,8 +272,10 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects ----- - Bugfixes in :py:func:`pyteomics.parser.isoforms`: - - handling of the `labels` argument is now in accordance with new policy - - solved memory problems when using `max_mods` + + - handling of the `labels` argument is now in accordance with new policy + - solved memory problems when using `max_mods` + - :py:func:`pyteomics.parser.cleave` does not require a valid *modX* sequence by default. |