Merge pull request #39981 from timokau/sage-on-nixos

Sage on nixos

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

@@ -2,9 +2,11 @@
 , fetchPypi
 , buildPythonPackage
 , cython
-, sphinx
+, pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
 }:
 
+assert pariSupport -> pari != null;
+
 buildPythonPackage rec {
   pname = "cysignals";
   version = "1.7.1";
@@ -14,6 +16,8 @@ buildPythonPackage rec {
     sha256 = "15nky8siwlc7s8v23vv4m0mnxa1z6jcs2qfr26m2mkw9j9g2na2j";
   };
 
+  # explicit check:
+  # build/src/cysignals/implementation.c:27:2: error: #error "cysignals must be compiled without _FORTIFY_SOURCE"
   hardeningDisable = [
     "fortify"
   ];
@@ -26,6 +30,10 @@ buildPythonPackage rec {
     export PATH="$out/bin:$PATH"
   '';
 
+  buildInputs = lib.optionals pariSupport [
+    pari
+  ];
+
   propagatedBuildInputs = [
     cython
   ];

pkgs/development/python-modules/flask-autoindex/default.nix

@@ -1,7 +1,6 @@
 { stdenv
 , buildPythonPackage
-, fetchpatch
-, fetchPypi
+, fetchFromGitHub
 , flask
 , flask-silk
 , future
@@ -9,11 +8,16 @@
 
 buildPythonPackage rec {
   pname = "Flask-AutoIndex";
-  version = "0.6";
+  version = "2018-06-28";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "19b10mb1nrqfjyafki6wnrbn8mqi30bbyyiyvp5xssc74pciyfqs";
+  # master fixes various issues (binary generation, flask syntax) and has no
+  # major changes
+  # new release requested: https://github.com/sublee/flask-autoindex/issues/38
+  src = fetchFromGitHub {
+    owner = "sublee";
+    repo = "flask-autoindex";
+    rev = "e3d449a89d56bf4c171c7c8d90af028e579782cf";
+    sha256 = "0bwq2nid4h8vrxspggk064vra4wd804cl2ryyx4j2d1dyywmgjgy";
   };
 
   propagatedBuildInputs = [
@@ -22,15 +26,6 @@ buildPythonPackage rec {
     future
   ];
 
-  patches = [
-    # fix generated binary, see https://github.com/sublee/flask-autoindex/pull/32
-    (fetchpatch {
-      name = "fix_binary.patch";
-      url = "https://github.com/sublee/flask-autoindex/pull/32.patch";
-      sha256 = "1v2r0wvi7prhipjq89774svv6aqj0a13mdfj07pdlkpzfbf029dn";
-    })
-  ];
-
   meta = with stdenv.lib; {
     description = "The mod_autoindex for Flask";
     longDescription = ''

pkgs/development/python-modules/flask-silk/default.nix

@@ -1,16 +1,20 @@
 { stdenv
 , buildPythonPackage
-, fetchPypi
+, fetchFromGitHub
 , flask
 }:
 
 buildPythonPackage rec {
   pname = "Flask-Silk";
-  version = "0.2";
+  version = "2018-06-28";
 
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1gjzighx4f0w39sq9xvzr1kwb4y7yv9qrgzvli1p89gy16piz8l0";
+  # master fixes flask import syntax and has no major changes
+  # new release requested: https://github.com/sublee/flask-silk/pull/6
+  src = fetchFromGitHub {
+    owner = "sublee";
+    repo = "flask-silk";
+    rev = "3a8166550f9a0ec52edae7bf31d9818c4c15c531";
+    sha256 = "0mplziqw52jfspas6vsm210lmxqqzgj0dxm8y0i3gpbyyykwcmh0";
   };
 
   propagatedBuildInputs = [

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

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, fetchpatch
 , glibcLocales
 , mpmath
 }:
@@ -25,10 +26,26 @@ buildPythonPackage rec {
     export LANG="en_US.UTF-8"
   '';
 
+  patches = [
+    # see https://trac.sagemath.org/ticket/20204 and https://github.com/sympy/sympy/issues/12825
+    # There is also an upstream patch for this, included in the next release (PR #128826).
+    # However that doesn't quite fix the issue yet. Apparently some changes by sage are required.
+    # TODO re-evaluate the change once a new sympy version is released (open a sage trac ticket about
+    # it).
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympy/patches/03_undeffun_sage.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "1mh2va1rlgizgvx8yzqwgvbf5wvswarn511002b361mc8yy0bnhr";
+    })
+    (fetchpatch {
+      url = "https://github.com/sympy/sympy/pull/13276.patch";
+      sha256 = "1rz74b5c74vwh3pj9axxgh610i02l3555vvsvr4a15ya7siw7zxh";
+    })
+  ];
+
   meta = {
     description = "A Python library for symbolic mathematics";
     homepage    = http://www.sympy.org/;
     license     = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ lovek323 ];
   };
-}
+}