Merge pull request #146711 from AndersonTorres/new-misc

pari update

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

@@ -1,10 +1,11 @@
-{ lib, stdenv
+{ lib
+, stdenv
 , fetchurl
 , gmp
-, readline
 , libX11
-, tex
 , perl
+, readline
+, tex
 , withThread ? true, libpthreadstubs
 }:
 
@@ -12,7 +13,7 @@ assert withThread -> libpthreadstubs != null;
 
 stdenv.mkDerivation rec {
   pname = "pari";
-  version = "2.13.1";
+  version = "2.13.3";
 
   src = fetchurl {
     urls = [
@@ -20,30 +21,25 @@ stdenv.mkDerivation rec {
       # old versions are at the url below
       "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${lib.versions.majorMinor version}/${pname}-${version}.tar.gz"
     ];
-    sha256 = "sha256-gez31wzNquIwFlz/Ynyc4uwpe48i+fQHQiedhfht/LE=";
+    hash = "sha256-zLp/FgbGhU8UQ2N7tXrQlY1Bx/R1P4roRZ8dZMJnoco=";
   };
 
-  patches = [
-    # rebased version of 3edb98db78, see
-    # https://pari.math.u-bordeaux.fr/cgi-bin/bugreport.cgi?bug=2284
-    ./rnfdisc.patch
-  ];
-
   buildInputs = [
     gmp
-    readline
     libX11
-    tex
     perl
+    readline
+    tex
   ] ++ lib.optionals withThread [
     libpthreadstubs
   ];
 
   configureScript = "./Configure";
   configureFlags = [
-    "--with-gmp=${gmp.dev}"
-    "--with-readline=${readline.dev}"
-  ] ++ lib.optional stdenv.isDarwin "--host=x86_64-darwin"
+    "--with-gmp=${lib.getDev gmp}"
+    "--with-readline=${lib.getDev readline}"
+  ]
+  ++ lib.optional stdenv.isDarwin "--host=x86_64-darwin"
   ++ lib.optional withThread "--mt=pthread";
 
   preConfigure = ''
@@ -57,6 +53,7 @@ stdenv.mkDerivation rec {
   makeFlags = [ "all" ];
 
   meta = with lib; {
+    homepage = "http://pari.math.u-bordeaux.fr";
     description = "Computer algebra system for high-performance number theory computations";
     longDescription = ''
        PARI/GP is a widely used computer algebra system designed for fast
@@ -81,7 +78,6 @@ stdenv.mkDerivation rec {
          3 or 4 times faster.) gp2c currently only understands a subset of the
          GP language.
     '';
-    homepage = "http://pari.math.u-bordeaux.fr";
     downloadPage = "http://pari.math.u-bordeaux.fr/download.html";
     license = licenses.gpl2Plus;
     maintainers = with maintainers; [ ertes AndersonTorres ] ++ teams.sage.members;

pkgs/applications/science/math/pari/gp2c.nix

@@ -1,7 +1,9 @@
-{ lib, stdenv
-, pari
+{ lib
+, stdenv
 , fetchurl
-, perl }:
+, pari
+, perl
+}:
 
 stdenv.mkDerivation rec {
   pname = "gp2c";
@@ -12,11 +14,15 @@ stdenv.mkDerivation rec {
     sha256 = "039ip7qkwwv46wrcdrz7y12m30kazzkjr44kqbc0h137g4wzd7zf";
   };
 
-  buildInputs = [ pari perl ];
+  buildInputs = [
+    pari
+    perl
+  ];
 
   configureFlags = [
     "--with-paricfg=${pari}/lib/pari/pari.cfg"
-    "--with-perl=${perl}/bin/perl" ];
+    "--with-perl=${perl}/bin/perl"
+  ];
 
   meta = with lib; {
     description =  "A compiler to translate GP scripts to PARI programs";

pkgs/applications/science/math/pari/rnfdisc.patch

@@ -1,51 +0,0 @@
-commit 0d8a3ac970291c62b56104172418b3f2ca30927c
-Author: Bill Allombert <Bill.Allombert@math.u-bordeaux.fr>
-Date:   Sun Mar 28 13:27:24 2021 +0200
-
-    rnfdisc_factored: remove spurious Q_primpart [#2284]
-
-diff --git a/src/basemath/base2.c b/src/basemath/base2.c
-index 7e7d0db9d..c461826f4 100644
---- a/src/basemath/base2.c
-+++ b/src/basemath/base2.c
-@@ -3582,7 +3582,7 @@ rnfdisc_factored(GEN nf, GEN pol, GEN *pd)
- 
-   nf = checknf(nf);
-   pol = rnfdisc_get_T(nf, pol, &lim);
--  disc = nf_to_scalar_or_basis(nf, nfX_disc(nf, Q_primpart(pol)));
-+  disc = nf_to_scalar_or_basis(nf, nfX_disc(nf, pol));
-   pol = nfX_to_monic(nf, pol, NULL);
-   fa = idealfactor_partial(nf, disc, lim);
-   P = gel(fa,1); l = lg(P);
-diff --git a/src/test/32/rnf b/src/test/32/rnf
-index 1e743f415..c016dce00 100644
---- a/src/test/32/rnf
-+++ b/src/test/32/rnf
-@@ -853,9 +853,10 @@ error("inconsistent dimensions in idealtwoelt.")
- 0
- 0
- 1
--[[7361, 3786, 318, 5823; 0, 1, 0, 0; 0, 0, 1, 0; 0, 0, 0, 1], [-3, 6, -2, 0]
--~]
--[2, -1]
-+[[433, 322, 318, 1318/17; 0, 1, 0, 12/17; 0, 0, 1, 5/17; 0, 0, 0, 1/17], [25
-+/17, -12/17, 12/17, 16/17]~]
-+[1, -1]
-+[[12, 0, 0, 0; 0, 12, 4, 0; 0, 0, 4, 0; 0, 0, 0, 4], [6, 5, -1, 2]~]
-   ***   at top-level: rnfdedekind(nf,P,pr2,1)
-   ***                 ^-----------------------
-   *** rnfdedekind: sorry, Dedekind in the difficult case is not yet implemented.
-diff --git a/src/test/in/rnf b/src/test/in/rnf
-index 7851ae291..318d5349e 100644
---- a/src/test/in/rnf
-+++ b/src/test/in/rnf
-@@ -212,6 +212,9 @@ k = nfinit(y^4 + 10*y^2 + 17);
- rnfdisc(k, x^2 - x + 1/Mod(y,k.pol))
- rnfdisc(k, x^2 - x + 1/2)
- 
-+k = nfinit(y^4 - 10*y^2 + 1);
-+rnfdisc(k,x^2-(y^3/2+y^2-5*y/2+1))
-+
- \\ ERRORS, keep at end of file
- rnfdedekind(nf, P, pr2, 1)
- rnfdedekind(nf, P)

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

@@ -23,6 +23,12 @@ let
       # branches (wip patches from tickets), but exports each commit as a separate
       # patch, so merge commits can lead to conflicts. Used if squashed == false.
       #
+      # The above is the preferred option. To use it, find a Trac ticket and pass the
+      # "Commit" field from the ticket as "rev", choosing "base" as an appropriate
+      # release tag, i.e. a tag that doesn't cause the patch to include a lot of
+      # unrelated changes. If there is no such tag (due to nonlinear history, for
+      # example), there are two other options, listed below.
+      #
       # 2) From GitHub's sagemath/sage repo. This lets us use a GH feature that allows
       # us to choose between a .patch file, with one patch per commit, or a .diff file,
       # which squashes all commits into a single diff. This is used if squashed ==
@@ -118,6 +124,14 @@ stdenv.mkDerivation rec {
       rev = "beed4e16aff32e47d0c3b1c58cb1e2f4c38590f8";
       sha256 = "sha256-3eJPfWfCrCAQ5filIn7FbzjRQeO9QyTIVl/HyRuqFtE=";
     })
+
+    # https://trac.sagemath.org/ticket/32797
+    (fetchSageDiff {
+      base = "9.5.beta7";
+      name = "pari-2.13.3-update.patch";
+      rev = "f5f7a86908daf60b25e66e6a189c51ada7e0a732";
+      sha256 = "sha256-H/caGx3q4KcdsyGe+ojV9bUTQ5y0siqM+QHgDbeEnbw=";
+    })
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;