Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
When we add a previously omitted class to api.rst, we suddenly find out whether its docstrings render well as reStructuredText or provide useful information at all. In this case, some of it's not great:
name
unicode
Type: name
These appear to be the default rendering for cdef public str from the .pxd file. (These are the only public str items in pysam.) “Unicode” is irrelevant as we're Python 3 only, and “Type” is just wrong.
Perhaps we can add some docstrings to the .pyx file to override this rendering and provide some meaningful information for these properties…
When we add a previously omitted class to api.rst, we suddenly find out whether its docstrings render well as reStructuredText or provide useful information at all. In this case, some of it's not great:
These appear to be the default rendering for
cdef public strfrom the .pxd file. (These are the onlypublic stritems in pysam.) “Unicode” is irrelevant as we're Python 3 only, and “Type” is just wrong.Perhaps we can add some docstrings to the .pyx file to override this rendering and provide some meaningful information for these properties…