sage dependency updates

pkgs/applications/science/math/giac/default.nix

@@ -2,32 +2,44 @@
 , gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty
 , readline, gettext, libpng, libao, gfortran, perl
 , enableGUI ? false, libGL, libGLU, xorg, fltk
+, enableMicroPy ? false, python3
 }:
 
 assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "giac${lib.optionalString enableGUI "-with-xcas"}";
-  version = "1.5.0-87"; # TODO try to remove preCheck phase on upgrade
+  version = "1.6.0-47"; # TODO try to remove preCheck phase on upgrade
 
   src = fetchurl {
     url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz";
-    sha256 = "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv";
+    sha256 = "sha256-c5A9/I6L/o3Y3dxEPoTKpw/fJqYMr6euLldaQ1HWT5c=";
   };
 
-  patches = lib.optionals (!enableGUI) [
-    # when enableGui is false, giac is compiled without fltk. That means some
-    # outputs differ in the make check. Patch around this:
+  patches = [
     (fetchpatch {
-      url    = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26";
+      name = "pari_2_11.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/pari_2_11.patch?id=21ba7540d385a9864b44850d6987893dfa16bfc0";
+      sha256 = "sha256-vEo/5MNzMdYRPWgLFPsDcMT1W80Qzj4EPBjx/B8j68k=";
+    })
+  ] ++ lib.optionals (!enableGUI) [
+    # when enableGui is false, giac is compiled without fltk. That
+    # means some outputs differ in the make check. Patch around this:
+    (fetchpatch {
+      name = "nofltk-check.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26";
       sha256 = "0xkmfc028vg5w6va04gp2x2iv31n8v4shd6vbyvk4blzgfmpj2cw";
     })
   ];
 
   postPatch = ''
-    for i in doc/*/Makefile*; do
+    for i in doc/*/Makefile* micropython*/xcas/Makefile*; do
       substituteInPlace "$i" --replace "/bin/cp" "cp";
     done;
+  '' +
+  # workaround for 1.6.0-47, should not be necessary in future versions
+  lib.optionalString (!enableMicroPy) ''
+    sed -i -e 's/micropython-[0-9.]* //' Makefile*
   '';
 
   nativeBuildInputs = [
@@ -44,7 +56,7 @@ stdenv.mkDerivation rec {
     lapack blas
   ] ++ lib.optionals enableGUI [
     libGL libGLU fltk xorg.libX11
-  ];
+  ] ++ lib.optional enableMicroPy python3;
 
   /* fixes:
   configure:16211: checking for main in -lntl
@@ -58,13 +70,12 @@ stdenv.mkDerivation rec {
   outputs = [ "out" ] ++ lib.optional (!enableGUI) "doc";
 
   doCheck = true;
-  preCheck = ''
-    # One test in this file fails. That test just tests a part of the pari
-    # interface that isn't actually used in giac. Of course it would be better
-    # to only remove that one test, but that would require a patch.
-    # Removing the whole test set should be good enough for now.
-    # Upstream report: https://xcas.univ-grenoble-alpes.fr/forum/viewtopic.php?f=4&t=2102#p10326
-    echo > check/chk_fhan11
+  preCheck = lib.optionalString (!enableGUI) ''
+    # even with the nofltk patch, some changes in src/misc.cc (grep
+    # for HAVE_LIBFLTK) made it so that giac behaves differently
+    # when fltk is disabled. disable these tests for now.
+    echo > check/chk_fhan2
+    echo > check/chk_fhan9
   '';
 
   enableParallelBuilding = true;
@@ -75,7 +86,7 @@ stdenv.mkDerivation rec {
     "--enable-ao" "--enable-ecm" "--enable-glpk"
   ] ++ lib.optionals enableGUI [
     "--enable-gui" "--with-x"
-  ];
+  ] ++ lib.optional (!enableMicroPy) "--disable-micropy";
 
   postInstall = ''
     # example Makefiles contain the full path to some commands

pkgs/applications/science/math/palp/default.nix

@@ -10,11 +10,11 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "palp";
-  version = "2.11";
+  version = "2.20";
 
   src = fetchurl {
-    url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz";
-    sha256 = "00jpm73fw9jjq58z6rysr1mwv489j6rpfqqlhm9ab0dln4kyhh05";
+    url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/${pname}-${version}.tar.gz";
+    sha256 = "1q1cl3vpdir16szy0jcadysydcrjp48hqxyx42kr8g9digkqjgkj";
   };
 
   hardeningDisable = [

pkgs/applications/science/math/sage/sage-src.nix

@@ -9,6 +9,20 @@
 # This is done because multiple derivations rely on these sources and they should
 # all get the same sources with the same patches applied.
 
+let
+  # Fetch a diff between `base` and `rev` on sage's git server.
+  # Used to fetch trac tickets by setting the `base` to the last release and the
+  # `rev` to the last commit of the ticket.
+  fetchSageDiff = { base, name, rev, sha256, ...}@args: (
+    fetchpatch ({
+      inherit name sha256;
+      url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
+      # We don't care about sage's own build system (which builds all its dependencies).
+      # Exclude build system changes to avoid conflicts.
+      excludes = [ "build/*" ];
+    } // builtins.removeAttrs args [ "rev" "base" "sha256" ])
+  );
+in
 stdenv.mkDerivation rec {
   version = "9.2";
   pname = "sage-src";
@@ -40,17 +54,13 @@ stdenv.mkDerivation rec {
     # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
     ./patches/sphinx-docbuild-subprocesses.patch
 
-    # Sage's workaround to pretty print dicts (in
-    # src/sage/doctest/forker.py:init_sage) runs too late (after
-    # controller.load_environment(), which imports sage.all.*) to to
-    # affect sage.sandpiles.Sandpile{Config,Divisor}'s pretty printer.
-    # Due to the sandpiles module being lazily loaded, this only
-    # affects the first run (subsequent runs read from an import cache
-    # at ~/.sage/cache and are not affected), which is probably why
-    # other distributions don't hit this bug. This breaks two sandpile
-    # tests, so do the workaround a little bit earlier.
-    # https://trac.sagemath.org/ticket/31053
-    ./patches/register-pretty-printer-earlier.patch
+    # Register sorted dict pprinter earlier (https://trac.sagemath.org/ticket/31053)
+    (fetchSageDiff {
+      base = "9.3.beta4";
+      name = "register-pretty-printer-earlier.patch";
+      rev = "d658230ce06ca19f4a3b3a4576297ee82f2d2151";
+      sha256 = "sha256-9mPUV7K5PoLDH2vVaYaOfvDLDpmxU0Aj7m/eaXYotDs=";
+    })
   ];
 
   # Since sage unfortunately does not release bugfix releases, packagers must
@@ -63,17 +73,20 @@ stdenv.mkDerivation rec {
 
     # fix intermittent errors in Sage 9.2's psage.py (this patch is
     # already included in Sage 9.3): https://trac.sagemath.org/ticket/30730
-    (fetchpatch {
+    (fetchSageDiff {
+      base = "9.2.rc2";
       name = "fix-psage-is-locked.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=75df605f216ddc7b6ca719be942d666b241520e9";
+      rev = "75df605f216ddc7b6ca719be942d666b241520e9";
       sha256 = "0g9pl1wbb3sgs26d3bvv70cpa77sfskylv4kd255y1794f1fgk4q";
     })
 
     # fix intermittent errors in sagespawn.pyx: https://trac.sagemath.org/ticket/31052
-    ./patches/sagespawn-implicit-casting.patch
-
-    # disable pexpect interrupt test (see https://trac.sagemath.org/ticket/30945)
-    ./patches/disable-pexpect-intermittent-failure.patch
+    (fetchSageDiff {
+      base = "9.2";
+      name = "sagespawn-implicit-casting.patch";
+      rev = "2959ac792ebd6107fe87c9af1541083de5ba02d6";
+      sha256 = "sha256-bWIpEGir9Kawak5CJegBMNcHm/CqhWmdru+emeSsvO0=";
+    })
   ];
 
   # Patches needed because of package updates. We could just pin the versions of
@@ -82,20 +95,7 @@ stdenv.mkDerivation rec {
   # compatible with never dependency versions when possible. All these changes
   # should come from or be proposed to upstream. This list will probably never
   # be empty since dependencies update all the time.
-  packageUpgradePatches = let
-    # Fetch a diff between `base` and `rev` on sage's git server.
-    # Used to fetch trac tickets by setting the `base` to the last release and the
-    # `rev` to the last commit of the ticket.
-    fetchSageDiff = { base, rev, name ? "sage-diff-${base}-${rev}.patch", ...}@args: (
-      fetchpatch ({
-        inherit name;
-        url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
-        # We don't care about sage's own build system (which builds all its dependencies).
-        # Exclude build system changes to avoid conflicts.
-        excludes = [ "build/*" ];
-      } // builtins.removeAttrs args [ "rev" "base" ])
-    );
-  in [
+  packageUpgradePatches = [
     # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
     # now set the cache dir to be withing the .sage directory. This is not
     # strictly necessary, but keeps us from littering in the user's HOME.
@@ -105,7 +105,20 @@ stdenv.mkDerivation rec {
     ./patches/ignore-cmp-deprecation.patch
 
     # adapt sage's Image class to pillow 8.0.1 (https://trac.sagemath.org/ticket/30971)
-    ./patches/pillow-update.patch
+    (fetchSageDiff {
+      base = "9.3.beta2";
+      name = "pillow-8.0.1-update.patch";
+      rev = "f05f2d0aac9c4b5abe68105cee2cc7f2c8461847";
+      sha256 = "sha256-uY2UlgSd5hhOUUukB4Xc3Gjy0/e7p/qyq9jdvz10IOs=";
+    })
+
+    # don't use deprecated numpy type aliases (https://trac.sagemath.org/ticket/31364)
+    (fetchSageDiff {
+      base = "9.3.beta7";
+      name = "dont-use-deprecated-numpy-type-aliases.patch";
+      rev = "dfdef60515d4a4269e82d91280f76a7fdf10bf97";
+      sha256 = "sha256-77/3LkT5J7DQN8IPlGJKB6ZcJPaF7xwje06JNns+0AE=";
+    })
 
     # fix test output with sympy 1.7 (https://trac.sagemath.org/ticket/30985)
     ./patches/sympy-1.7-update.patch
@@ -115,6 +128,31 @@ stdenv.mkDerivation rec {
 
     # updated eclib output has punctuation changes and tidier whitespace
     ./patches/eclib-20210223-test-formatting.patch
+
+    # upgrade arb to 2.18.1 (https://trac.sagemath.org/ticket/28623)
+    (fetchSageDiff {
+      base = "9.3.beta3";
+      name = "arb-2.18.1-update.patch";
+      rev = "0c9c4ed35c2eaf34ae0d19387c07b7f460e4abce";
+      sha256 = "sha256-CjOJIsyyVCziAfvE6pWSihPO35IZMcY2/taXAsqhPLY=";
+    })
+
+    # giac 1.6.0-47 update (https://trac.sagemath.org/ticket/30537)
+    (fetchSageDiff {
+      base = "9.3.beta7";
+      name = "giac-1.6.0-47-update.patch";
+      rev = "f05720bf63dfaf33a4e3b6d3ed2c2c0ec46b5d31";
+      sha256 = "sha256-gDUq+84eXd5GxLBWUSI61GMJpBF2KX4LBVOt3mS1NF8=";
+    })
+
+    # Make gcd/lcm interact better with pari and gmpy2 (https://trac.sagemath.org/ticket/30849)
+    # needed for pari 2.13.1 update, which we will do in the future
+    (fetchSageDiff {
+      base = "9.3.beta0";
+      name = "make-gcd-lcm-interact-better-with-pari-and-gmpy2.patch";
+      rev = "75c1516f0abb9e6f8c335e38e4031f6ef674ed30";
+      sha256 = "sha256-RukkieIZcXNrju904H2oyGKdtpdE+9vNzvyjN2IBNg0=";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;

pkgs/development/libraries/arb/default.nix

@@ -1,14 +1,21 @@
-{ lib, stdenv, fetchFromGitHub, mpir, gmp, mpfr, flint }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, mpir
+, gmp
+, mpfr
+, flint
+}:
 
 stdenv.mkDerivation rec {
   pname = "arb";
-  version = "2.17.0";
+  version = "2.19.0";
 
   src = fetchFromGitHub {
     owner = "fredrik-johansson";
     repo = pname;
     rev = version;
-    sha256 = "05lpy3hkl5f8ik19aw40cqydrb932xaf2n8hbq9ib5dnk7f010p1";
+    sha256 = "sha256-J/LQVZ8gmssazE7ru89EtvW6cVjaLEHgUHuwjW1nuOE=";
   };
 
   buildInputs = [ mpir gmp mpfr flint ];