Merge commit '87807e64a5ef5206b745a40af118c7be8db73681'

5 files changed, 75 insertions, 39 deletions

diff --git a/nixpkgs/pkgs/applications/science/math/caffe/default.nix b/nixpkgs/pkgs/applications/science/math/caffe/default.nix
index 565c6a17672d..08bf84be7c89 100644
--- a/nixpkgs/pkgs/applications/science/math/caffe/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/caffe/default.nix
@@ -76,7 +76,7 @@ stdenv.mkDerivation rec {
     let pp = python.pkgs; in ([
       pp.numpy pp.scipy pp.scikitimage pp.h5py
       pp.matplotlib pp.ipython pp.networkx pp.nose
-      pp.pandas pp.dateutil pp.protobuf pp.gflags
+      pp.pandas pp.python-dateutil pp.protobuf pp.gflags
       pp.pyyaml pp.pillow pp.six
     ] ++ lib.optional leveldbSupport pp.leveldb)
   );
diff --git a/nixpkgs/pkgs/applications/science/math/glsurf/default.nix b/nixpkgs/pkgs/applications/science/math/glsurf/default.nix
index 208bb95f930e..58b2a617bd63 100644
--- a/nixpkgs/pkgs/applications/science/math/glsurf/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/glsurf/default.nix
@@ -1,7 +1,12 @@
-{ lib, stdenv, fetchurl, ocamlPackages, libGLU, libGL, freeglut, giflib
-, libmysqlclient, mpfr, gmp, libtiff, libjpeg, libpng
+{ lib, stdenv, fetchurl, ocamlPackages, makeWrapper
+, libGLU, libGL, freeglut, mpfr, gmp
+, pkgsHostTarget
 }:
 
+let
+  inherit (pkgsHostTarget.targetPackages.stdenv) cc;
+in
+
 stdenv.mkDerivation {
   name = "glsurf-3.3.1";
 
@@ -10,17 +15,32 @@ stdenv.mkDerivation {
     sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7";
   };
 
-  buildInputs = [ freeglut libGLU libGL libmysqlclient mpfr giflib gmp
-    libtiff libjpeg libpng ]
-  ++ (with ocamlPackages; [
-    ocaml findlib ocaml_mysql lablgl camlimages_4_1_2 mlgmpidl
+  nativeBuildInputs = [
+    makeWrapper
+  ] ++ (with ocamlPackages; [
+    ocaml findlib
+  ]);
+
+  buildInputs = [
+    freeglut libGL libGLU mpfr gmp
+  ] ++ (with ocamlPackages; [
+    camlp4 lablgl camlimages_4_2_4
   ]);
 
+  postPatch = ''
+    for f in callbacks*/Makefile src/Makefile; do
+      substituteInPlace "$f" --replace "+camlp4" \
+        "${ocamlPackages.camlp4}/lib/ocaml/${ocamlPackages.ocaml.version}/site-lib/camlp4"
+    done
+  '';
+
   installPhase = ''
     mkdir -p $out/bin $out/share/doc/glsurf
     cp ./src/glsurf.opt $out/bin/glsurf
     cp ./doc/doc.pdf $out/share/doc/glsurf
     cp -r ./examples $out/share/doc/glsurf
+
+    wrapProgram "$out/bin/glsurf" --set CC "${cc}/bin/${cc.targetPrefix}cc"
   '';
 
   meta = {
diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 56b6df94e8fb..7807ae613e8c 100644
--- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qalculate-gtk";
-  version = "3.18.0";
+  version = "3.19.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "sha256-hE0di7B6dCnMmMBLgFkb6vPS4hS/7zD6BbviIucrn1I=";
+    sha256 = "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch
deleted file mode 100644
index f17897d4c89f..000000000000
--- a/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
-index 6bad826a88..f4d7b8651c 100644
---- a/src/sage/misc/sagedoc.py
-+++ b/src/sage/misc/sagedoc.py
-@@ -24,7 +24,7 @@ see :trac:`12849`::
-     ....:     for line in fobj:
-     ....:         if "#sage.symbolic.expression.Expression.numerical_approx" in line:
-     ....:             print(line)
--    <code class="sig-name descname">numerical_approx</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">prec</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">digits</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">algorithm</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span>...
-+    <code class="sig-name descname"><span class="pre">numerical_approx</span></code><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">prec</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">digits</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span>...
- 
- Check that sphinx is not imported at Sage start-up::
- 
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index 57234c660a5a..218ab920a872 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -16,7 +16,12 @@ let
   fetchSageDiff = { base, name, rev, sha256, ...}@args: (
     fetchpatch ({
       inherit name sha256;
-      url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}";
+
+      # We used to use
+      # "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}"
+      # but the former way does not squash multiple patches together.
+      url = "https://github.com/sagemath/sage/compare/${base}...${rev}.diff";
+
       # We don't care about sage's own build system (which builds all its dependencies).
       # Exclude build system changes to avoid conflicts.
       excludes = [ "build/*" ];
@@ -79,13 +84,6 @@ stdenv.mkDerivation rec {
     # ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests
     ./patches/ignore-cmp-deprecation.patch
 
-    # sphinx 3.5 pretty-prints code slightly differently than sphinx
-    # 3.1--3.3. a similar patch is available at the sphinx 4 ticket
-    # (https://trac.sagemath.org/ticket/31696), but sphinx 3.5 uses
-    # <code> tags while sphinx 4 uses <span> tags so we cannot just
-    # import the patch from trac.
-    ./patches/sphinx-3.5-code-output.patch
-
     # remove use of matplotlib function deprecated in 3.4
     # https://trac.sagemath.org/ticket/31827
     (fetchSageDiff {
@@ -95,16 +93,47 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-SXcUGBMOoE9HpuBzgKC3P6cUmM5MiktXbe/7dVdrfWo=";
     })
 
-    # https://trac.sagemath.org/ticket/30801. this patch has
-    # positive_review but has not been merged upstream yet, so we
-    # don't use fetchSageDiff because it returns a file that contains
-    # each commit as a separate patch instead of a single diff, and
-    # some commits from the pari update branch are already in 9.3.rc5
-    # (auto-resolvable merge conflicts).
-    (fetchpatch {
+    # pari 2.13 update
+    # https://trac.sagemath.org/ticket/30801
+    #
+    # the last commit in that ticket is
+    # c78b1470fccd915e2fa93f95f2fefba6220fb1f7, but commits after
+    # 10a4531721d2700fd717e2b3a1364508ffd971c3 only deal with 32-bit
+    # and post-26635 breakage, none of which is relevant to us. since
+    # there are post-9.4.beta0 rebases after that, we just skip later
+    # commits.
+    (fetchSageDiff {
+      base = "9.3";
       name = "pari-2.13.1.patch";
-      url = "https://github.com/sagemath/sagetrac-mirror/compare/d6c5cd9be78cc448ee4c54bac93385b1244a234c...10a4531721d2700fd717e2b3a1364508ffd971c3.diff";
-      sha256 = "sha256-zMjRMEReoiTvmt+vvV0Ij1jtyLSLwSXBEVXqgvmq1D4=";
+      rev = "10a4531721d2700fd717e2b3a1364508ffd971c3";
+      sha256 = "sha256-gffWKK9CMREaNOb5zb63iZUgON4FvsPrMQNqe+5ZU9E=";
+    })
+
+    # sympy 1.8 update
+    # https://trac.sagemath.org/ticket/31647
+    (fetchSageDiff {
+      base = "9.4.beta0";
+      name = "sympy-1.8.patch";
+      rev = "fa864b36e15696450c36d54215b1e68183b29d25";
+      sha256 = "sha256-fj/9QEZlVF0fw9NpWflkTuBSKpGjCE6b96ECBgdn77o=";
+    })
+
+    # sphinx 4 update
+    # https://trac.sagemath.org/ticket/31696
+    (fetchSageDiff {
+      base = "9.4.beta3";
+      name = "sphinx-4.patch";
+      rev = "bc84af8c795b7da433d2000afc3626ee65ba28b8";
+      sha256 = "sha256-5Kvs9jarC8xRIU1rdmvIWxQLC25ehiTLJpg5skh8WNM=";
+    })
+
+    # eclib 20210625 update
+    # https://trac.sagemath.org/ticket/31443
+    (fetchSageDiff {
+      base = "9.4.beta3";
+      name = "eclib-20210625.patch";
+      rev = "789550ca04c94acfb1e803251538996a34962038";
+      sha256 = "sha256-VlyEn5hg3joG8t/GwiRfq9TzJ54AoHxLolsNQ3shc2c=";
     })
   ];