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Diffstat (limited to 'CHANGELOG')
-rw-r--r-- | CHANGELOG | 29 |
1 files changed, 29 insertions, 0 deletions
diff --git a/CHANGELOG b/CHANGELOG index b9483672c03b..bdb0730ab1b2 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,32 @@ +4.6 +--- + + - When passing an existing file (by name) to :py:func:`pyteomics.mgf.write` or :py:func:`pyteomics.fasta.write` and + other writing functions, **the file will be opened for writing by default**. Previously, it would be opened for + appending with a warning about the upcoming change. Please be aware that existing files will be overwritten + if passed by name. The rationale for this is better reproducibility if the same code is run multiple + times. You can use the `file_mode` argument of the writing functions to override this behaviour, or pass your own + file objects. + - Add a special warning when trying to write a single spectrum with :py:func:`pyteomics.mgf.write`. + See also: `Writing one or more MGF spectra to a file <https://github.com/levitsky/pyteomics/discussions/109>`_. + - In :py:func:`pyteomics.mass.mass.calculate_mass`, the `absolute` parameter is now `True` by default. + When calculating *m/z* for negative charges, the returned value will be positive by default. + - Fix issue #98 (`#99 <https://github.com/levitsky/pyteomics/pull/99>`_ and + `#101 <https://github.com/levitsky/pyteomics/pull/101>`_ by Joshua Klein). + - Fix issue #91 (`#92 <https://github.com/levitsky/pyteomics/pull/92>`_ by Joshua Klein). + - Fix issue #96. + - Update the UniProt header pattern (fix rare parsing errors with + :py:class:`pyteomics.fasta.UniProt` and :py:class:`pyteomics.fasta.IndexedUniProt`) in + `#93 <https://github.com/levitsky/pyteomics/pull/93>`_. + - Update the UniRef header pattern (fix parsing errors with + :py:class:`pyteomics.fasta.UniRef` and :py:class:`pyteomics.fasta.IndexedUniRef`) in + `#102 <https://github.com/levitsky/pyteomics/pull/102>`_. Some keys are removed from the output. + - Fix pickling issues with :py:class:`pyteomics.mgf.IndexedMGF`, :py:class:`pyteomics.ms1.IndexedMS1`, + :py:class:`pyteomics.ms2.IndexedMS2` (#108). + - Add "charge array" and "resolution array" to the output of MS2 parsers (#108). Add new arguments `read_charges` + and `read_resolutions` to disable parsing, and `convert_arrays` to govern the creation of NumPy arrays + (and masked arrays). + 4.5.6 ----- |