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Diffstat (limited to 'CHANGELOG')
-rw-r--r-- | CHANGELOG | 29 |
1 files changed, 27 insertions, 2 deletions
diff --git a/CHANGELOG b/CHANGELOG index 15672ad90dd2..26e06e13a1cc 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,28 @@ +3.4.1 +----- + + - Add selenocysteine ("U") and pyrrolysine ("O") to :py:data:`pyteomics.mass.std_aa_mass` and + :py:data:`pyteomics.mass.std_aa_comp`. + + - An optional parameter `encoding` is now accepted by text file readers (:py:func:`pyteomics.mgf.read` + and :py:func:`pyteomics.fasta.read`). This can be useful for MGF files with non-ASCII spectrum + titles or comments. + + - New function :py:func:`pyteomics.mass.mass.isotopologues`. + + - Performance improvements in :py:func:`pyteomics.electrochem.pI`. + + - Fix the issue in :py:mod:`pyteomics.xml` which resulted in very long processing times for indexed XML files + with a byte ordering mark (BOM). + + - Support all standard and non-standard data array names in :py:mod:`pyteomics.mzml`. + + - Change default value of ``retrieve_refs`` in :py:func:`pyteomics.mzid.read` to :py:const:`True`. + + - Preserve unit information extracted from cvParam tags in PSI XML files. + + - Fix in :py:mod:`pyteomics.mzxml`, other minor fixes. + 3.4 --- @@ -188,8 +213,8 @@ API changes - All :py:func:`fdr`, :py:func:`qvalues`, and :py:func:`!filter` functions now accept a new parameter `correction`. It is used for more accurate - estimation of the number of false positives using TDA (paper with explanation - submitted to JPR). + estimation of the number of false positives using TDA (`paper with explanation + <http://dx.doi.org/10.1021/acs.jproteome.6b00144>`_). - :py:func:`!filter` functions now support both iterator protocol and context manager protocol. They now also accept the `full_output` parameter, which has |