William Stein's Status Report for Sage Days 12

I fixed the following bugs:

Math

• #1234 -- analytic_rank crashes: fix use mwrank

• #1867 -- factoring multivariate polynomials over finite fields is broken in Singular: wrote code to reduce to GF(p) case, then found that even that is buggy in Singular, much to my surprise.

• #2020 -- change an error message when running a certain command and the elliptic curve database is too small: make a clean workaround.
• #2601 -- problem with _mpoly_dict_recursive: had to understand some crazy code for multivariate polynomials, then fix it; a pretty serious bug...

• #3544 -- PermutationGroup is_transitive broken: changed wrapping of a Gap function and documented better

• #4274 -- assertion failure in rank for elliptic curves

Graphics

• #2858 -- parametric_plot3d throws an error when the sum of the components cancels a variable: fixed by rewriting to check if is a CallableSymbolicExpression.

• #4818 -- bug in list_plot3d -- invalid index: easy

System and Build

• #773 -- SAGE drops . from path: fixed by patching around a nasty bug in pexpect
• #2129 -- implement "sage -t" for .spyx files; also fixed testing of .py, .sage, .pyx when out of tree to import file, build file, etc.
• #2861 -- scripts do not exit with correct exit code when sys.exit() is used
• #4029 -- sage-env kills the shell when called from "wrong" directory: break sage-env into two files

• #4936 -- massive bloat: make something delete everything in ~/.sage/gap > 1 week old and untouched: fixed by modifying gap.py to do that.

• #5041/4955 -- make it so the magma .sig files in extcode don't get written there by magma: fixed by copying files to a temp dir then loading
• #5044 -- on some systems mwrank dumps core and crashes on exit when run under pexpect: fixed with kill -9
• #5045 -- sage's "make check" should check that the sage build flags (in sage-flags.txt) are right; done, and involved fixing also a bunch of stupid broken return codes

Doctesting

• #3871 -- do not save pngs in SAGE_ROOT; extending #3759 -- pretty easy; just clean up using grep
• #4588 -- doctest -- get rid of the "feature" where docstrings with require, optional, and package all in them are automatically marked optional: deleted that "feature", then spent "hours" putting #optionals in.
• #4665 -- sage/misc/cython.py creates file sage/misc/hello.spyx in tree while doctesting: just fix that doctest (easy)
• #5068 -- change_ring fails for polynomials over finite fields in many cases: subtle caching issues with finite fields, etc.