diff options
Diffstat (limited to 'CHANGELOG')
| -rw-r--r-- | CHANGELOG | 70 |
1 files changed, 70 insertions, 0 deletions
diff --git a/CHANGELOG b/CHANGELOG index 651d67e47056..74f952a62177 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,12 @@ +4.6.2 +----- + + - :py:func:`pyteomics.fasta.write` can now write entries with parsed sequences + (`#120 <https://github.com/levitsky/pyteomics/pull/120>`_ by Vladimir Gorshkov, Joshua Klein and Lev Levitsky). + - Fix `#119 <https://github.com/levitsky/pyteomics/issues/119>`_. + - Fix import issue with :py:mod:`pyteomics.pylab_aux`. + + 4.6.1 ----- @@ -8,6 +17,7 @@ - Remove :py:class:`auxiliary.Version`. :py:class:`pyteomics.version.VersionInfo` can be used instead. - For target-decoy calculations, :py:mod:`pandas` is assumed to be 0.17 or newer. + 4.6 --- @@ -37,6 +47,7 @@ and `read_resolutions` to disable parsing, and `convert_arrays` to govern the creation of NumPy arrays (and masked arrays). + 4.5.6 ----- @@ -50,11 +61,13 @@ - Update :py:func:`pyteomics.pylab_aux.annotate_spectrum` for compatibility with latest :py:mod:`spectrum_utils`. Pyteomics is now compatible with :py:mod:`spectrum_utils` 0.4.0 and newer. + 4.5.5 ----- - Fix issue #77. + 4.5.4 ----- @@ -64,6 +77,7 @@ - Provide more accurate amino acid masses in :py:data:`mass.std_aa_mass`. - Fix SyntaxError in :py:mod:`pyteomics.pylab_aux` on Python 2.7. + 4.5.3 ----- @@ -76,11 +90,13 @@ Charge is now only handled in :py:meth:`Composition.mass` and not :py:meth:`Composition.__init__`. - Bugfix in :py:mod:`pyteomics.tandem` (`#71 <https://github.com/levitsky/pyteomics/pull/71>`_ by @superrino130). + 4.5.2 ----- - Support Python 3.10. + 4.5.1 ----- @@ -92,6 +108,7 @@ - Bugfixes (`#63 <https://github.com/levitsky/pyteomics/pull/63>`_ and `#64 <https://github.com/levitsky/pyteomics/pull/64>`_ by Joshua Klein). + 4.5 --- @@ -156,6 +173,7 @@ - Fix compatibility with :py:mod:`SQLAlchemy` 1.4 (`#32 <https://github.com/levitsky/pyteomics/pull/32>`_ by Joshua Klein). + 4.4.1 ----- @@ -170,6 +188,7 @@ - Also, check out the `Pyteomics Discussions page <https://github.com/levitsky/pyteomics/discussions>`_! You can use it to share your thoughts, ask questions, discuss coding practices, etc. + 4.4 --- @@ -208,16 +227,19 @@ To avoid all of this, you are encouraged to instantiate parser classes directly, or explicitly specify `use_index` to :py:func:`read` in all corner cases. + 4.3.2 ----- Fix `#7 <https://github.com/levitsky/pyteomics/issues/7>`_. + 4.3.1 ----- Technical release. + 4.3 --- @@ -232,6 +254,7 @@ Changes in this release: - Fix `#3 <https://github.com/levitsky/pyteomics/issues/3>`_, `#5 <https://github.com/levitsky/pyteomics/issues/5>`_, and some issues in :py:mod:`tandem`. + 4.2 --- @@ -275,6 +298,7 @@ Changes in this release: Bugfix: fix the standard mass value for pyrrolysine (issue #42). + 4.1.1 ----- @@ -290,6 +314,7 @@ API changes - In :py:func:`ms1.read` and :py:func:`ms2.read`, the default value for `use_index` is now :py:const:`False`. Using the indexed parsers may result in incorrect behavior if the "first" scan number in S-lines is not unique. + 4.1 --- @@ -313,6 +338,7 @@ API changes Fix issue `#35 <hhttps://levitsky.github.io/bitbucket_backup/#!/levitsky/pyteomics/issues/35/page/1>`_ (incorrect order of deserialized offset indexes on older Python versions). + 4.0 --- @@ -399,6 +425,7 @@ Fix issue `#35 <hhttps://levitsky.github.io/bitbucket_backup/#!/levitsky/pyteomi - Multiple fixes and improvements. + 3.5.1 ----- @@ -406,6 +433,7 @@ Technical release to update the package metadata on PyPI. Project documentation on pythonhosted.org has been deleted. Latest documentation is available at: https://pyteomics.readthedocs.io/. + 3.5 --- @@ -464,6 +492,7 @@ Latest documentation is available at: https://pyteomics.readthedocs.io/. - Bugfixes. + 3.4.2 ----- @@ -485,6 +514,7 @@ Latest documentation is available at: https://pyteomics.readthedocs.io/. - Performance optimizations in XML parsing code. + 3.4.1 ----- @@ -510,6 +540,7 @@ Latest documentation is available at: https://pyteomics.readthedocs.io/. - Fix in :py:mod:`pyteomics.mzxml`, other minor fixes. + 3.4 --- @@ -529,11 +560,13 @@ Latest documentation is available at: https://pyteomics.readthedocs.io/. - 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 --- @@ -568,6 +601,7 @@ API changes - 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 --- @@ -616,6 +650,7 @@ Other changes: - Performance improvements in :py:mod:`pyteomics.parser`. + 3.1 --- @@ -658,6 +693,7 @@ API changes - Default value of `remove_decoy` in :py:func:`qvalues` is now :py:const:`False`. + 3.0.1 ----- @@ -666,6 +702,7 @@ API changes - Minor fixes. + 3.0.0 ----- @@ -739,12 +776,14 @@ API changes default. To keep using them as iterators / context managers, specify ``full_output=False`` (see above for details). + 2.5.5 ----- Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects :py:func:`pyteomics.mzid.read` with ``retrieve_refs=True``. + 2.5.4 ----- @@ -756,6 +795,7 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects modules. Parsing of mzIdentML files with ``retrieve_refs=True`` got significantly faster. + 2.5.3 ----- @@ -773,6 +813,7 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects - Performance improvements. + 2.5.2 ----- @@ -788,6 +829,7 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects - Unknown labels now allowed in :py:mod:`pyteomics.electrochem` and :py:mod:`pyteomics.achrom` functions in accordance with new general policy. + 2.5.1 ----- @@ -799,6 +841,7 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects - :py:func:`pyteomics.parser.cleave` does not require a valid *modX* sequence by default. + 2.5.0 ----- @@ -839,6 +882,7 @@ API changes Sequences with one terminal group specified will be supported where possible, but be advised that sequences such as "H-OH" are intrinsically ambiguous. + 2.4.3 ----- @@ -851,6 +895,7 @@ API changes - Removed non-functional parameter ``read_schema`` for :py:func:`pyteomics.tandem.read`. + 2.4.2 ----- @@ -859,6 +904,7 @@ API changes :py:data:`pyteomics.mass.nist_mass` was expanded. Also, the format of the returned value is now in accordance with the documentation. + 2.4.1 ----- @@ -867,6 +913,7 @@ API changes - Also, a format-agnostic helper function :py:func:`pyteomics.auxiliary.fdr`. + 2.4.0 ----- @@ -897,6 +944,7 @@ API changes .. note:: Rounding errors may be significant in this case. + 2.3.0 ----- @@ -928,12 +976,14 @@ API change - In :py:func:`pyteomics.mgf.read` the precursor charge is now always represented by a list of ints (a :py:class:`ChargeList` object). + 2.2.2 ----- - Bugfix in :py:mod:`pyteomics.tandem`. The info about all proteins is now extracted. + 2.2.1 ----- @@ -942,12 +992,14 @@ API change - NamedTuple for FASTA entries is now defined globally, which should solve pickling problems. + 2.2.0 ----- - New module :py:mod:`pyteomics.tandem` for reading output files of X!Tandem search engine. + 2.1.6 ----- @@ -964,6 +1016,7 @@ API change - Improved arithmetics for :py:class:`Composition` objects. + 2.1.4 ----- @@ -982,6 +1035,7 @@ Bugfixes: - Other minor corrections. + 2.1.3 ----- @@ -991,12 +1045,14 @@ Bugfixes: - Add support for overlapping matches in :py:func:`parser.cleave`. + 2.1.2 ----- - Bugfix in XML parsers. The bug caused the mzML parser to break on some files. The fix can slightly change the format of the output. + 2.1.1 ----- @@ -1006,6 +1062,7 @@ Bugfixes: - The items yielded by :py:func:`fasta.read` now have attributes `description` and `sequence`. + 2.1.0 ----- @@ -1037,6 +1094,7 @@ API changes function. If a file path is given, the file object will be created and closed inside the corresponding function. + 2.0.3 ----- @@ -1050,12 +1108,14 @@ API changes - Bugfix in :py:func:`auxiliary.linear_regression`. + 2.0.2 ----- - Added new function :py:func:`iterfind` in :py:mod:`pyteomics.mzid`, :py:mod:`pyteomics.pepxml` and :py:mod:`pyteomics.mzml`. + 2.0.1 ----- @@ -1065,6 +1125,7 @@ API changes - :py:func:`pyteomics.parser.peptide_length` is renamed to :py:func:`pyteomics.parser.length`. + 2.0.0 ----- @@ -1086,6 +1147,7 @@ API changes - the output format of all :py:func:`read` functions has changed. + 1.2.5 ----- @@ -1094,6 +1156,7 @@ API changes - Minor bugfix in :py:mod:`pyteomics.fasta`. + 1.2.4 ----- @@ -1124,6 +1187,7 @@ API changes :py:class:`collections.defaultdict` so one can safely retrieve values without checking if a key exists. + 1.2.3 ----- @@ -1141,6 +1205,7 @@ API changes - :py:func:`pyteomics.parser.isoforms` now returns a generator object + 1.2.2 ----- @@ -1159,11 +1224,13 @@ API changes - Memory usage **significantly** decreased when parsing large mzML and pepXML files. + 1.2.0 ----- - Added support for Python 3. Python 2.7 is still supported, Python 2.6 is not. + 1.1.1 ----- @@ -1172,12 +1239,14 @@ API changes - Also, :py:func:`pyteomics.parser.isoforms` is a new function to get all possible modified sequences of a peptide. + 1.1.0 ----- - New module added - :py:mod:`pyteomics.mgf`. It is intended for reading and writing files in Mascot Generic Format. + 1.0.2 ----- @@ -1197,6 +1266,7 @@ API changes: - Fix compatibility issues in :py:mod:`pyteomics.pepxml` module. + 1.0.0 ----- |