We currently use pyfits in multiple packages: afw, coadd_chisquared, obs_base, meas_astrom, meas_deblender, meas_extensions_psfex, meas_mosaic, obs_cfht, obs_lsstSim, obs_sdss, obs_subaru and obs_test.
Strangely, we only have explicit dependencies on pyfits listed for afw, obs_base, galsim, healpy and obs_subaru.
galsim can use astropy.io.fits or pyfits. healpy really does seem to not work with astropy.io.fits – is there a newer version that does?
Please replace pyfits with astropy.io.fits where appropriate and update the table files to correctly express the dependency (and removing pyfits where inappropriate).