Version 4.6

• When passing an existing file (by name) to pyteomics.mgf.write or 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 behavior, or pass your own file objects.
• Add a special warning when trying to write a single spectrum with pyteomics.mgf.write. See also: #109.
• In pyteomics.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 and #101 by @mobiusklein).
• Fix issue #91 (#92 by @mobiusklein).
• Fix issue #96.
• Update the UniProt header pattern (fix rare parsing errors with pyteomics.fasta.UniProt and pyteomics.fasta.IndexedUniProt) in #93.
• Update the UniRef header pattern (fix parsing errors with pyteomics.fasta.UniRef and pyteomics.fasta.IndexedUniRef) in #102. Some keys are removed from the output.
• Fix pickling issues with pyteomics.mgf.IndexedMGF, pyteomics.ms1.IndexedMS1, 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).