diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math')
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="; }) ]; |