diff options
Diffstat (limited to 'pkgs/applications/science')
10 files changed, 62 insertions, 47 deletions
diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index ca80262eb76..43007cb1f0f 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -35,10 +35,10 @@ in stdenv.mkDerivation rec { pname = "gwyddion"; - version = "2.58"; + version = "2.59"; src = fetchurl { url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; - sha256 = "sha256-0xNnzYkuW3nEsO2o+0WEA+Z71XWoq6FYXm342OWO9Sw="; + sha256 = "sha256-APMOJeZt/zp8JvXghKZ5lQFRKWO/4TVDORok8qAgEBk="; }; nativeBuildInputs = [ pkg-config file ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index c645693e19a..92606f3f909 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -17,14 +17,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.31.41"; + version = "14.31.42"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - sha256 = "sha256-dI1WkQgFikxaIjjqVKZcsGvc3QIu/NMIcRW3N8PGbkY="; + sha256 = "sha256-q81dUSxrKT3nzX0bFclolsyguQxXKlsiX9GCwEvOpAw="; }; patchPhase = '' diff --git a/pkgs/applications/science/logic/elan/default.nix b/pkgs/applications/science/logic/elan/default.nix index d20be86daf0..a49262e7cb6 100644 --- a/pkgs/applications/science/logic/elan/default.nix +++ b/pkgs/applications/science/logic/elan/default.nix @@ -7,16 +7,16 @@ in rustPlatform.buildRustPackage rec { pname = "elan"; - version = "1.0.2"; + version = "1.0.6"; src = fetchFromGitHub { owner = "leanprover"; repo = "elan"; rev = "v${version}"; - sha256 = "sha256-nK4wvxK5Ne1+4kaMts6pIr5FvXBgXJsGdn68gGEZUdk="; + sha256 = "sha256-Ns8vSS/PDlfopigW4Nz3fdR9PCMG8gDoL36+/s0Qkeo="; }; - cargoSha256 = "sha256-ptSbpq1ePNWmdBGfKtqFGfkdimDjU0YEo4F8VPtQMt4="; + cargoSha256 = "sha256-NDtldiVo4SyE88f6ntKn1WJDFdvwN5Ps4DxQH15iNZE="; nativeBuildInputs = [ pkg-config makeWrapper ]; diff --git a/pkgs/applications/science/logic/hol/default.nix b/pkgs/applications/science/logic/hol/default.nix index 569c455e653..8427249c4ce 100644 --- a/pkgs/applications/science/logic/hol/default.nix +++ b/pkgs/applications/science/logic/hol/default.nix @@ -81,7 +81,7 @@ stdenv.mkDerivation { ''; homepage = "http://hol.sourceforge.net/"; license = licenses.bsd3; - platforms = [ "x86_64-linux" ]; + platforms = platforms.unix; maintainers = with maintainers; [ mudri ]; }; } diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index 214f4e218fd..ea2cd356e31 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.30.0"; + version = "3.31.0"; src = fetchFromGitHub { owner = "leanprover-community"; @@ -11,8 +11,8 @@ stdenv.mkDerivation rec { # from. this is then used to check whether an olean file should be # rebuilt. don't use a tag as rev because this will get replaced into # src/githash.h.in in preConfigure. - rev = "a5822ea47ebc52eec6323d8f1b60f6ec025daf99"; - sha256 = "sha256-gJhbkl19iilNyfCt2TfPmghYA3yCjg6kS+yk/x/k14Y="; + rev = "333783350cd3fe38f25fed1da7d6a433d8f85b77"; + sha256 = "sha256-N8Ju7pSGssvt84/0e1o6G/p7fWM1c0Mzw+ftL1/++J4="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix index defe218b119..ef2d97ef6bf 100644 --- a/pkgs/applications/science/logic/tlaplus/toolbox.nix +++ b/pkgs/applications/science/logic/tlaplus/toolbox.nix @@ -1,5 +1,5 @@ { lib, fetchzip, makeWrapper, makeDesktopItem, stdenv -, gtk3, libXtst, glib, zlib +, gtk3, libXtst, glib, zlib, wrapGAppsHook }: let @@ -25,7 +25,11 @@ in stdenv.mkDerivation rec { sha256 = "02a2y2mkfab5cczw8g604m61h4xr0apir49zbd1aq6mmgcgngw80"; }; - nativeBuildInputs = [ makeWrapper ]; + buildInputs = [ gtk3 ]; + + nativeBuildInputs = [ makeWrapper wrapGAppsHook ]; + + dontWrapGApps = true; phases = [ "installPhase" ]; @@ -36,6 +40,9 @@ in stdenv.mkDerivation rec { cp -r "$src" "$out/toolbox" chmod -R +w "$out/toolbox" + fixupPhase + gappsWrapperArgsHook + patchelf \ --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \ "$out/toolbox/toolbox" @@ -52,7 +59,8 @@ in stdenv.mkDerivation rec { makeWrapper $out/toolbox/toolbox $out/bin/tla-toolbox \ --run "set -x; cd $out/toolbox" \ --add-flags "-data ~/.tla-toolbox" \ - --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ gtk3 libXtst glib zlib ]}" + --prefix LD_LIBRARY_PATH : "${lib.makeLibraryPath [ gtk3 libXtst glib zlib ]}" \ + "''${gappsWrapperArgs[@]}" echo -e "\nCreating TLA Toolbox icons..." pushd "$src" diff --git a/pkgs/applications/science/math/caffe/default.nix b/pkgs/applications/science/math/caffe/default.nix index 565c6a17672..08bf84be7c8 100644 --- a/pkgs/applications/science/math/caffe/default.nix +++ b/pkgs/applications/science/math/caffe/default.nix @@ -76,7 +76,7 @@ stdenv.mkDerivation rec { let pp = python.pkgs; in ([ pp.numpy pp.scipy pp.scikitimage pp.h5py pp.matplotlib pp.ipython pp.networkx pp.nose - pp.pandas pp.dateutil pp.protobuf pp.gflags + pp.pandas pp.python-dateutil pp.protobuf pp.gflags pp.pyyaml pp.pillow pp.six ] ++ lib.optional leveldbSupport pp.leveldb) ); diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 56b6df94e8f..7807ae613e8 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "qalculate-gtk"; - version = "3.18.0"; + version = "3.19.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "sha256-hE0di7B6dCnMmMBLgFkb6vPS4hS/7zD6BbviIucrn1I="; + sha256 = "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"; }; hardeningDisable = [ "format" ]; diff --git a/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch b/pkgs/applications/science/math/sage/patches/sphinx-3.5-code-output.patch deleted file mode 100644 index f17897d4c89..00000000000 --- a/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/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 57234c660a5..1ed174ebd46 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/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 +93,38 @@ 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="; }) ]; |