eclib: 20171219 -> 20180710

Also includes the necessary sage compatibility patch, borrowed from
ArchLinux.

pkgs/applications/science/math/sage/patches/eclib-20180710.patch

@@ -0,0 +1,40 @@
+diff --git a/src/sage/interfaces/mwrank.py b/src/sage/interfaces/mwrank.py
+index 4417b59276..ae57ca2991 100644
+--- a/src/sage/interfaces/mwrank.py
++++ b/src/sage/interfaces/mwrank.py
+@@ -54,8 +54,9 @@ def Mwrank(options="", server=None, server_tmpdir=None):
+         sage: M = Mwrank('-v 0 -l')
+         sage: print(M('0 0 1 -1 0'))
+         Curve [0,0,1,-1,0] :    Rank = 1
+-        Generator 1 is [0:-1:1]; height 0.0511114082399688
+-        Regulator = 0.0511114082399688
++        Generator 1 is [0:-1:1]; height 0.051111408239969
++        Regulator = 0.051111408239969
++
+     """
+     global instances
+     try:
+diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp
+index 5fd5693b53..d12468faa8 100644
+--- a/src/sage/libs/eclib/wrap.cpp
++++ b/src/sage/libs/eclib/wrap.cpp
+@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose)
+ 
+ 
+ int mw_process(struct Curvedata* curve, struct mw* m,
+-                      const struct bigint* x, const struct bigint* y,
+-                      const struct bigint* z, int sat)
++                      const bigint* x, const bigint* y,
++                      const bigint* z, int sat)
+ {
+   Point P(*curve, *x, *y, *z);
+   if (!P.isvalid())
+@@ -188,7 +188,7 @@ int mw_rank(struct mw* m)
+ }
+ 
+ /* Returns index and unsat long array, which user must deallocate */
+-int mw_saturate(struct mw* m, struct bigint* index, char** unsat,
++int mw_saturate(struct mw* m, bigint* index, char** unsat,
+                        long sat_bd, int odd_primes_only)
+ {
+   vector<long> v;

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

@@ -176,6 +176,9 @@ stdenv.mkDerivation rec {
 
     # https://trac.sagemath.org/ticket/24838 rebased
     ./patches/pynac-0.7.22.patch
+
+    # https://trac.sagemath.org/ticket/25862
+    ./patches/eclib-20180710.patch
   ];
 
   patches = nixPatches ++ packageUpgradePatches;

pkgs/development/libraries/eclib/default.nix

@@ -1,5 +1,6 @@
 { stdenv
 , fetchFromGitHub
+, fetchpatch
 , autoreconfHook
 , libtool
 , gettext
@@ -17,13 +18,25 @@ assert withFlint -> flint != null;
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "eclib";
-  version = "20171219";
+  version = "20180710"; # upgrade might break the sage interface
+  # sage tests to run:
+  # src/sage/interfaces/mwrank.py
+  # src/sage/libs/eclib
+  # ping @timokau for more info
   src = fetchFromGitHub {
     owner = "JohnCremona";
     repo = "${pname}";
     rev = "v${version}";
-    sha256 = "1yw488ng0labpxqqpxq0710qnndxl8plvcaqklpbwwd62a47knlr";
+    sha256 = "1kmwpw971sipb4499c9b35q5pz6sms5qndqrvq7396d8hhwjg1i2";
   };
+  patches = [
+    # One of the headers doesn't get installed.
+    # See https://github.com/NixOS/nixpkgs/pull/43476.
+    (fetchpatch {
+      url = "https://github.com/JohnCremona/eclib/pull/42/commits/c9b96429815e31a6e3372c106e31eef2a96431f9.patch";
+      sha256 = "0cw26h94m66rbh8jjsfnb1bvc6z7ybh8zcp8xl5nhxjxiawhcl73";
+    })
+  ];
   buildInputs = [
     pari
     ntl
@@ -35,12 +48,12 @@ stdenv.mkDerivation rec {
     autoreconfHook
   ];
   doCheck = true;
-  meta = {
+  meta = with stdenv.lib; {
     inherit version;
     description = ''Elliptic curve tools'';
     homepage = https://github.com/JohnCremona/eclib;
-    license = stdenv.lib.licenses.gpl2Plus;
-    maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ raskin timokau ];
+    platforms = platforms.all;
   };
 }

pkgs/development/python-modules/cvxopt/default.nix

@@ -46,6 +46,11 @@ buildPythonPackage rec {
     export CVXOPT_FFTW_INC_DIR=${fftw.dev}/include
   '';
 
+  # https://github.com/cvxopt/cvxopt/issues/122
+  # This is fixed on staging (by #43234, status 2018-07-15), but until that
+  # lands we should disable the tests. Otherwise the 99% of use cases that
+  # should be unaffected by that failure are affected.
+  doCheck = false;
   checkPhase = ''
     ${python.interpreter} -m unittest discover -s tests
   '';