Upgrade to 8.1

[saraedum]

🤔: These packages are probably not the right version in conda-forge but they should not matter for the conda release.

Base SPKGs that have changed between 7.6 and 8.1 (from git diff 7.6..8.1 build/.)

• [x] 🤔 upgrade configure (~212~ → 247)

Standard SPKGs that have changed.

• [x] upgrade arb (~2.8.1.p1~ → 2.11.1.p0) and drop patches/flint_includes.patch
• [x] upgrade BRiAl (~0.8.5~ → 1.0.1.p1) and patch with patches/BooleConstant_not_const.patch, and some changes in spkg-install
• [x] upgrade conway_polynomials (~0.4.p0~ → 0.5) and changes to spkg-install
• [x] 🤔 add curl (7.56.1)
• [x] add cypari2 (1.1.3)
• [x] upgrade cysignals (~1.3.2~ → 1.6.5)
• [x] upgrade cython (~0.25.2~ → 0.27.2), drop patches/pxi_sys_path.patch,
• [x] upgrade docutils (~0.12.p0~ → 0.13.1)
• [x] upgrade ecl (~16.1.2.p2~ → 16.1.2.p4), add patches/flisten-bug.patch, patches/format-directive-limit.patch
• [x] upgrade eclib (~20170104~ → 20171002)
• [x] upgrade ecm (~6.4.4.p0~ → 7.0.4.p0), drop patches/asm-align.patch, patches/cygwin.patch.
• [x] upgrade ~libfplll~ *fplll (~5.0.3rc0~ → 5.2.0)
• [x] upgrade fpylll (~0.2.3dev → 0.3.0dev.p0), add patches/ticket-24191.patch (patched in upstream, but only relevant on Cygwin.)
• [x] ~upgrade~ GAP (~jm5-2015-02-01~ → 04jul17), ~drop patches/gap3_init.patch, patches/gap3_startup.patch and patches/gap3_makefile.patch, and a few changes in spkg-install~ (I got that one wrong. They did not upgrade gap-4 but gap-3.)
• [x] 🤔 upgrade GAP3(~jm5-2015-02-01~ → 04jul17), drop patches/gap3_init.patch, patches/gap3_startup.patch and patches/gap3_makefile.patch, and a few changes in spkg-install; we got away without it so far, so GAP-3 does not seem to be necessary.
• [x] upgrade gc (~7.2f.p0~ → 7.2f.p1)
• [x] 🤔 upgrade gcc (~5.4.0~ → 7.2.0)
• [x] upgrade gf2x (~1.1.p1~ → 1.2), add patches/0001-generic_really_is_generic.patch, and drop lots of other patches, disable tuning for SAGE_FAT_BINARY.
• [x] upgrade gfan (~0.5.p1~ → 0.5.p2), modifies patch to Makefile
• [x] upgrade Giac (~1.2.3.25~ → 1.2.4.47.p0) which now requires libpng, drop patches/configdotguess.patch, add patches/libpng16.patch, and drop patches/ticket-22315.patch
• [x] upgrade glpk (~4.60.p0~ → 4.63.p1), add patches/glp_exact_verbosity.patch
• [x] upgrade GSL (~2.1.p1~ → 2.3)
• [x] upgrade ipython-genutils (~0.1.0.p0~ → 0.2.0)
• [x] upgrade jupyter-client (~4.4.0~ → 5.1.0)
• [x] upgrade lcalc (~1.23.p14~ → 1.23.p15), changes patched Makefile
• [x] upgrade libpng (~1.2.51.p0~ → 1.6.29), drop patches/pngconf.h.patch, and drop Darwin patches in spkg-install
• [x] upgrade LinBox (~1.4,2~ → 1.4.2.p1), add patches/linbox-PR50.patch and patches/ticket-23029.patch
• [x] upgrade MPFR (~3.1.5~ → 3.1.5.p0), add patches/clang_workaround.patch
• [x] upgrade nbformat (~4.2.0~ → 4.4.0)
• [x] upgrade NTL (~10.1.0~ → 10.3.0)
• [x] upgrade NumPy (~1.11.1.p0~ → 1.13.3.p0), add patches/PEP_3141.patch, drop patches/numpy-1.10.1-asarray_conversion.patch, drop patches/numpy-1.11.1-newlib-xlocale.patch.
• [x] upgrade OpenBLAS (~0.2.19.p0~ → 0.2.20.p1), add patches/88a35ff457f55e527e0e8a503a0dc61976c1846d.patch, modify some build related patches
• [x] upgrade PARI/GP (~2.9.1.p2~ → 2.10-1280-g88fb5b3.p0), modifies lots of patches; it seems that we can get away with 2.9.4 if we patch away the ellratpoints call (see the recent discussion with the ArchLinux maintainer.)
• [x] add pcre (8.40.p0) [the exact versioin should not matter, and the patches are about Cygwin.]
• [x] upgrade pip (~8.1.2.p1~ → 9.0.1)
• [x] upgrade planarity (~2.2.0~ → 3.0.0.5), drop patches/malloc.patch, patches/without_nauty.patch
• [x] upgrade polytopes_db (~20120220~ → 20170220)
• [x] upgrade prompt_toolkit (~1.0.3.p0~ → 1.0.9)
• [x] upgrade psutil (~4.3.1.p0~ → 5.2.0.p0)
• [x] upgrade pygments (~2.1.3.p1~ → 2.2.0.p0)
• [x] upgrade Pynac (~0.7.5~ → 0.7.12), drop patches/funcmap-fix.patch
• [x] upgrade Python3 (~3.5.1~ → 3.6.1.p1)
• [x] 🤔 upgrade R (~3.2.4-revised.p0~ → 3.4.2.p0), with quite a few patch changes; let's try to get away with an older R. The major version is correct so it might just work™.
• [x] add Requests (2.13.0)
• [x] 🤔 upgrade sagenb_export (~2.0.p0~ → 3.2); I think we can get away without this. I am not sure but I had the feeling that sagenb (the Sage Notebook?) is going away anyway.
• [x] upgrade SciPy (~0.17.1.p0~ → 0.19.1)
• [x] upgrade Singular (~4.1.0p1~ → 4.1.0p3.p0) which drops lots of patches
• [x] upgrade six (~1.10.0.p0~ → 1.11.0)
• [x] upgrade sphinx (~1.4.4.p0~ → 1.6.3.p1) with changed patches (not sure what's going on here but I don't want to patch sphinx in conda for Sage)
• [x] upgrade SQLite (~autoconf-3130000~ → autoconf-3170000)
• [x] upgrade sympow (~1.018.1.p11~ → 1.018.1.p12), adds patches/initialize-tacks.patch
• [x] upgrade sympy (~1.0.p1~ → 1.1.1), replaces undeffun patch.
• [x] upgrade tachyon (~0.98.9.p5~ → 0.98.9.p6)
• [x] add typing (3.6.1)
• [x] add Yasm (1.3.0)
• [x] upgrade zeromq (~4.0.5~ → 4.0.5.p1) with build changes only
• [x] upgrade zlib (~1.2.8.p0~ → 1.2.11)

Optional SPKGs that have changed. 😞: Proper support for optional packages won't come before Sage 8.3 with the inclusion of https://trac.sagemath.org/ticket/20382. These packages are probably not present in conda-forge but it does not matter at the moment as they would not be detected by Sage anyway.

• [x] 🤔 upgrade autotools (~20141105~ → 20141105.p0)
• [x] upgrade cmake (~3.2.3~ → 3.8.1) with patches/osx10.10.patch for OS X and some minor changes in spkg-install.
• [x] 😞 upgrade Coxeter (~3.0_beta2~ → 3.1.sage) ?
• [x] 😞 upgrade CryptoMiniSat (~2.9.6~ → 5.0.1) and apply patches/osx_install_nameQA.patch, and changes in spkg-install (https://github.com/conda-forge/staged-recipes/pull/5185, https://github.com/msoos/cryptominisat/issues/459)
• [x] 😞 add Deformation (d05941b)
• [x] 😞 upgrade dot2tex (~2.9.0.p1~ → 2.9.0.p2), and add graphviz as a requirement in spkg-install
• [x] 😞 upgrade FriCAS (~1.2.7~ → 1.3.2), drop patches/uffi.patch,
• [x] 😞 upgrade gambit (~14.1.0~ → 15.1.1), add patches/b91115633dbf6f64745fda2db7fbb83f918dd500.patch
• [x] 😞 add Jupyter kernel for GAP (0.9)
• [x] 😞 upgrade giacpy (~0.6~ → 0.6.6)
• [x] upgrade GMP (~5.1.3~ → 6.1.2)
• [x] 😞 upgrade gmpy2 (~2.0.8~ → 2.0.8.p0), add patches/no_set_memory_functions.patch
• [x] 😞 upgrade libhomfly (~1.0~ → 1.0r2)
• [x] 😞 upgrade Meataxe (~2.4.24.p1~ → 2.4.24.p3), add patches/TrueRowSize.patch, patches/mtxdirs.patch
• [x] 😞 add Mpfrcx (0.4.2)
• [x] 😞 upgrade MPIR (~2.7.2.p0~ → 3.0.0-644faf502c56f97d9accd301965fc57d6ec70868), drop patches/PR185.patch, and some changes to spkg-install
• [x] 😞 upgrade normaliz (~3.1.4~ → 3.2.1), and add /patches/22684_cone_reduce_memory_usage.patch
• [x] 😞 upgrade OpenSSL (~1.0.2j~ → 1.0.2m)
• [x] 😞 upgrade Ore_algebra (~0.2.p0~ → 0.3)
• [x] 😞 upgrade pynormaliz (~1.0~ → 1.5)
• [x] 😞 upgrade pysingular (~0.9.1~ → 0.9.5)
• [x] 😞 upgrade Python (~2.7.13.p0~ → 2.7.14.p2), add patches/linux_linking_issue_25229.patch
• [x] 😞 upgrade rst2ipynb (~0.2.1~ → 0.2.2.p0), adds patches/check-pandoc.patch
• [x] 😞 upgrade sagenb (~0.13~ → 1.0.1)
• [x] 😞 add SIP (4.18)
• [x] 😞 add SIROCCO (2.0)

Experimental SPKGs that have changed.

• [x] 😞 upgrade polymake (~3.0r2~ → 3.1), add patches/fix-compilation-with-gcc7.patch
• [x] 😞 upgrade scipoptsuite (~3.2.1~ → 4.0.0), with many changed patches

New runtime dependencies:

• [x] cypari is now a standard SPKG
• [x] fplll is now a standard SPKG
• [x] pcre is now a standard SPKG
• [x] Requests is now a standard SPKG

New build-time dependencies:

• [x] sympy (doc build dependency)
• [x] typing (doc build dependency)

[isuruf]

You can cc me to any of the PRs. Also it would be good to have separate lists for standard, optional packages

[saraedum]

@isuruf I think that I am done with the dependencies except for the two open PRs. I guess it's time to try to upgrade the sagemath recipe itself.

[saraedum]

Closed with #11.