diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
27 files changed, 168 insertions, 86 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/nixpkgs/pkgs/applications/science/biology/ants/default.nix index 20eedfaaa16..cb88e92fe1c 100644 --- a/nixpkgs/pkgs/applications/science/biology/ants/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/ants/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk }: +{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7 }: stdenv.mkDerivation rec { pname = "ANTs"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { ]; nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ itk4 vtk ]; + buildInputs = [ itk4 vtk_7 ]; cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/bppsuite/default.nix b/nixpkgs/pkgs/applications/science/biology/bppsuite/default.nix new file mode 100644 index 00000000000..564a38708bc --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bppsuite/default.nix @@ -0,0 +1,21 @@ +{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq, bpp-phyl, bpp-popgen }: + +stdenv.mkDerivation rec { + pname = "bppsuite"; + + inherit (bpp-core) version; + + src = fetchFromGitHub { + owner = "BioPP"; + repo = pname; + rev = "v${version}"; + sha256 = "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ bpp-core bpp-seq bpp-phyl bpp-popgen ]; + + meta = bpp-core.meta // { + changelog = "https://github.com/BioPP/bppsuite/blob/master/ChangeLog"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index 1a3762f4326..fc302522215 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1060"; + version = "1061"; src = fetchurl { url = "http://last.cbrc.jp/last-${version}.zip"; - sha256 = "0h0604rxg0z0h21dykrnxsb4679zfhibg79gss1v2ik5xpdxl8kk"; + sha256 = "1jbvcxfy5xrf90qbhif0bd6aywm9rjqrm0sx24yr312f7r7c1dnx"; }; nativeBuildInputs = [ unzip ]; diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index 5073d0f0f32..4b455eaca6f 100644 --- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.22.4"; + version = "2.22.8"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0gzna5df8nk42l7mc0qbp9h73gwr1030jnw10fawjp6ql6213kdd"; + sha256 = "0g387jlf7r1p2kx8gya3vxksbjy3y2ywxa7yjqmxg3y8725fyixl"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix index 9512a288d80..1a22544c270 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.10.0"; + version = "20.12.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "042ndlns48pa6mn6wyrp4q9c1v0a2vzcnhw5l766zdnxdjyv0acx"; + sha256 = "1imfr56nbq2mbcyapwa8xmcmj5rjhbjz9r438387s73kd1avd6yl"; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix index 9fc1111c7b9..b7ab5fa70d9 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix @@ -8,7 +8,7 @@ , oceSupport ? false, opencascade , withOCCT ? true, opencascade-occt , ngspiceSupport ? true, libngspice -, scriptingSupport ? true, swig, python, pythonPackages, wxPython +, scriptingSupport ? true, swig, python, wxPython , debug ? false, valgrind , withI18n ? true }: diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix index 2aa2686a29a..a99f1b2d8d7 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix @@ -8,7 +8,7 @@ , oceSupport ? false, opencascade , withOCCT ? true, opencascade-occt , ngspiceSupport ? true, libngspice -, scriptingSupport ? true, swig, python3, python3Packages +, scriptingSupport ? true, swig, python3 , debug ? false, valgrind , with3d ? true , withI18n ? true @@ -31,9 +31,9 @@ let # but brings high DPI support? else wxGTK31.override { withGtk2 = false; }; - pythonPackages = python3Packages; + pythonPackages = python.pkgs; python = python3; - wxPython = python3Packages.wxPython_4_0; + wxPython = pythonPackages.wxPython_4_0; in stdenv.mkDerivation rec { diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix index 2b7c91751e5..4a9ed0cb86d 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,49 +3,49 @@ { "kicad" = { kicadVersion = { - version = "5.1.5"; + version = "5.1.6"; src = { - rev = "52549c5d09cbfb0e807fcbcb07819bc9f7861544"; - sha256 = "15h3rwisjss3fdc9bam9n2wq94slhacc3fbg14bnzf4n5agsnv5b"; + rev = "c6e7f7de7df655fd59b57823499efc443009de6b"; + sha256 = "1pa3z0h0679jmgxlzc833h6q85b5paxdp69kf2h93vkaryj58622"; }; }; libVersion = { - version = "5.1.5"; + version = "5.1.6"; libSources = { - i18n.rev = "5122cbec6563fb7c8d6f960a639ac470353af91b"; - i18n.sha256 = "1rfpifl8vky1gba2angizlb2n7mwmsiai3r6ip6qma60wdj8sbd3"; - symbols.rev = "dd122ec170b49e032179511c9d263126f52f4020"; - symbols.sha256 = "048b07ffsaav1ssrchw2p870lvb4rsyb5vnniy670k7q9p16qq6h"; - templates.rev = "94761f10d06582b33cd55ea2149d72f269f65580"; - templates.sha256 = "0cs3bm3zb5ngw5ldn0lzw5bvqm4kvcidyrn76438alffwiz2b15g"; - footprints.rev = "e076f8f271f8db96d5fec45616b7554caebb7ef7"; - footprints.sha256 = "1c4whgn14qhz4yqkl46w13p6rpv1k0hsc9s9h9368fxfcz9knb2j"; - packages3d.rev = "8d233cdcb109aa1c3b8ba4c934ee31f6a3b6e1f4"; - packages3d.sha256 = "0cff2ms1bsw530kqb1fr1m2pjixyxzwa81mxgac3qpbcf8fnpvaz"; + i18n.rev = "5ad171ce5c8d90f4740517c2adecb310d8be51bd"; + i18n.sha256 = "0qryi8xjm23ka363zfl7bbga0v5c31fr3d4nyxp3m168vkv9zhha"; + symbols.rev = "5150eaa2a7d15cfc6bb1459c527c4ebaa66d7708"; + symbols.sha256 = "12w3rdy085drlikkpb27n9ni7cyg9l0pqy7hnr86cxjcw3l5wcx6"; + templates.rev = "9213d439f757e6049b7e54f3ea08272a0d0f44a9"; + templates.sha256 = "1hppcsrkn4dk6ggby6ckh0q65qxkywrbyxa4lwpaf7pxjyv498xg"; + footprints.rev = "a61b4e49762fb355f654e65a1c7db1aaf7bb2332"; + footprints.sha256 = "1kmf91a5mmvj9izrv40mkaw1w36yjgn8daczd9rq2wlmd0rdp1zx"; + packages3d.rev = "150ff1caf0b01dc04c84f4f966f4f88fedfa8f8c"; + packages3d.sha256 = "0b9jglf77fy0n0r8xs4yqkv6zvipyfvp0z5dnqlzp32csy5aqpi1"; }; }; }; "kicad-unstable" = { kicadVersion = { - version = "2020-05-06"; + version = "2020-05-14"; src = { - rev = "c92181621e2e51dc8aae1bd9f4483bb3301ffaa5"; - sha256 = "0s50xn5gbjy7yxnp9yiynxvxi2mkcrp6yghgdzclpm40rnfyi0v5"; + rev = "3b8465359135e9f6dea4b0a5fcb62377753fe890"; + sha256 = "18xsg2s0pxx176rnblygq1f8xpmryw59lcjzm897gifz0sj0nhvx"; }; }; libVersion = { - version = "2020-05-06"; + version = "2020-05-14"; libSources = { - i18n.rev = "f29cab831eb823165fa2c5efab5d9c9b443e62e2"; - i18n.sha256 = "0cc0zvpml75yxphay3281f762ls08fzvv538cd5hmkr8xqlj3vbi"; - symbols.rev = "d4245ae8cf633095a0994ab01492bd56cd124112"; - symbols.sha256 = "11pynjgji3skw42q5mryz98f8z418k43jy6s2k90w6jv638z3cb0"; + i18n.rev = "c4460d0d8e1075691d43dc928ffc332fa1282592"; + i18n.sha256 = "1gkrbfyfzsr5q7sahhlyhgfpfwm6b83lzf0q1v854gwxdfabvi0y"; + symbols.rev = "614b5f6256fbae82c2bba399086506bbe435bd94"; + symbols.sha256 = "10ix3wdcl832r4ha5q8phpx8j97gzngb41nczdli1qkhjmiw9y8r"; templates.rev = "7db8d4d0ea0711f1961d117853547fb3edbc3857"; templates.sha256 = "1hppcsrkn4dk6ggby6ckh0q65qxkywrbyxa4lwpaf7pxjyv498xg"; - footprints.rev = "3bff23ee339bc48490bb39deba5d8b2f1f42733e"; - footprints.sha256 = "0430r8k49ib6w1sjr8fx42szbz960yhlzg4w80jl5bwasq67nqwd"; - packages3d.rev = "889a3dd550233ec51baed4a04a01d4cc64a8d747"; - packages3d.sha256 = "152zv4j51v8skqlvrabblpcqpbn5yf3grisjj8vnwf7kdd41chb2"; + footprints.rev = "240804c6c89b66af808379e1fc94ea6011433cbe"; + footprints.sha256 = "1jh71004lrn7bl384zfmbqqdbs28gjb6diwn6hyb587jpivdnl3g"; + packages3d.rev = "9b560cf94a35b692ca516d37bdaf392ce10e549d"; + packages3d.sha256 = "0b9jglf77fy0n0r8xs4yqkv6zvipyfvp0z5dnqlzp32csy5aqpi1"; }; }; }; diff --git a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix index 5e6c0d55b7d..6a90f50b5aa 100644 --- a/nixpkgs/pkgs/applications/science/logic/cadical/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cadical/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation rec { owner = "arminbiere"; repo = "cadical"; rev = "rel-${version}"; - hash = "sha256:1a66xkw42ad330fvw8i0sawrmg913m8wrq5c85lw5qandkwvxdi6"; + sha256 = "1a66xkw42ad330fvw8i0sawrmg913m8wrq5c85lw5qandkwvxdi6"; }; dontAddPrefix = true; diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix index 315900d42b9..39e7cbe7f3c 100644 --- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix @@ -34,6 +34,7 @@ let "8.10.2" = "0znxmpy71bfw0p6x47i82jf5k7v41zbz9bdpn901ysn3ir8l3wrz"; "8.11.0" = "1rfdic6mp7acx2zfwz7ziqk12g95bl9nyj68z4n20a5bcjv2pxpn"; "8.11.1" = "0qriy9dy36dajsv5qmli8gd6v55mah02ya334nw49ky19v7518m0"; + "8.11.2" = "0f77ccyxdgbf1nrj5fa8qvrk1cyfy06fv8gj9kzfvlcgn0cf48sa"; }.${version}; coq-version = stdenv.lib.versions.majorMinor version; versionAtLeast = stdenv.lib.versionAtLeast coq-version; diff --git a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix index 8c1b3bd0369..591b04ab062 100644 --- a/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/cryptominisat/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "cryptominisat"; - version = "5.7.0"; + version = "5.7.1"; src = fetchFromGitHub { owner = "msoos"; repo = "cryptominisat"; rev = version; - sha256 = "0ny5ln8fc0irprs04qw01c9mppps8q27lkx01a549zazwhj4b5rm"; + sha256 = "16lydnbd4rxfyabvvw7l4hbbby3yprcqqzrydd3n8rjbxibi4xyf"; }; buildInputs = [ python3 boost ]; diff --git a/nixpkgs/pkgs/applications/science/logic/elan/default.nix b/nixpkgs/pkgs/applications/science/logic/elan/default.nix index 743bbf163c2..7a7da2c5f5d 100644 --- a/nixpkgs/pkgs/applications/science/logic/elan/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/elan/default.nix @@ -2,16 +2,16 @@ rustPlatform.buildRustPackage rec { pname = "elan"; - version = "0.10.0"; + version = "0.10.2"; src = fetchFromGitHub { owner = "kha"; repo = "elan"; rev = "v${version}"; - sha256 = "0aw538shvpfbk481y0gw3z97nsazdnk8qh8fwsb6ji62p2r51v6f"; + sha256 = "0ycw1r364g5gwh8796dpv1israpg7zqwx8mcvnacv2lqj5iijmby"; }; - cargoSha256 = "0zg3q31z516049v9fhli4yxldx9fg31k2qfx4ag8rmyvpgy9xh6c"; + cargoSha256 = "0hcaiy046d2gnkp6sfpnkkprb3nd94i9q8dgqxxpwrc1j157x6z9"; nativeBuildInputs = [ pkgconfig ]; diff --git a/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/nixpkgs/pkgs/applications/science/logic/lean/default.nix index ed077b03908..2f5943dfa9b 100644 --- a/nixpkgs/pkgs/applications/science/logic/lean/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/lean/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.13.1"; + version = "3.14.0"; src = fetchFromGitHub { owner = "leanprover-community"; repo = "lean"; rev = "v${version}"; - sha256 = "1ak5l40h5yjlbzz92l724l6bm5q341cg6k1yk13sbwn42l8szsar"; + sha256 = "1dlzap3j26rh93ick1lqb7g3jkqjpd33gl4gqfcbx22v62258y5b"; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/logic/proverif/default.nix b/nixpkgs/pkgs/applications/science/logic/proverif/default.nix index 931ad2fc4f3..6a9367b30aa 100644 --- a/nixpkgs/pkgs/applications/science/logic/proverif/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/proverif/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "proverif"; - version = "2.00"; + version = "2.01"; src = fetchurl { url = "http://prosecco.gforge.inria.fr/personal/bblanche/proverif/proverif${version}.tar.gz"; - sha256 = "0vjphj85ch9q39vc7sd6n4vxy5bplp017vlshk989yhfwb00r37y"; + sha256 = "01wp5431c77z0aaa99h8bnm5yhr6jslpqc8iyg0a7gxfqnb19gxi"; }; buildInputs = with ocamlPackages; [ ocaml findlib lablgtk ]; diff --git a/nixpkgs/pkgs/applications/science/logic/sad/default.nix b/nixpkgs/pkgs/applications/science/logic/sad/default.nix index f9b82b5d733..f1066abf693 100644 --- a/nixpkgs/pkgs/applications/science/logic/sad/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/sad/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation { }; buildInputs = [ haskell.compiler.ghc844 spass ]; patches = [ - ./patch + ./patch.patch # Since the LTS 12.0 update, <> is an operator in Prelude, colliding with # the <> operator with a different meaning defined by this package ./monoid.patch diff --git a/nixpkgs/pkgs/applications/science/logic/sad/patch b/nixpkgs/pkgs/applications/science/logic/sad/patch.patch index a5b1d617708..a5b1d617708 100644 --- a/nixpkgs/pkgs/applications/science/logic/sad/patch +++ b/nixpkgs/pkgs/applications/science/logic/sad/patch.patch diff --git a/nixpkgs/pkgs/applications/science/math/clp/default.nix b/nixpkgs/pkgs/applications/science/math/clp/default.nix index 5e770cec13b..97ef3dd7543 100644 --- a/nixpkgs/pkgs/applications/science/math/clp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/clp/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, zlib }: stdenv.mkDerivation rec { - version = "1.17.5"; + version = "1.17.6"; pname = "clp"; src = fetchurl { url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz"; - sha256 = "0y5wg4lfffy5vh8gc20v68pmmv241ndi2jgm9pgvk39b00bzkaa9"; + sha256 = "0ap1f0lxppa6pnbc4bg7ih7a96avwaki482nig8w5fr3vg9wvkzr"; }; propagatedBuildInputs = [ zlib ]; diff --git a/nixpkgs/pkgs/applications/science/math/gap/default.nix b/nixpkgs/pkgs/applications/science/math/gap/default.nix index 87f4fa12038..04a49becc97 100644 --- a/nixpkgs/pkgs/applications/science/math/gap/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gap/default.nix @@ -3,7 +3,7 @@ , fetchurl , fetchpatch , makeWrapper -, m4 +, readline , gmp # one of # - "minimal" (~400M): @@ -64,7 +64,7 @@ stdenv.mkDerivation rec { version = "4.10.2"; src = fetchurl { - url = "https://www.gap-system.org/pub/gap/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2"; + url = "https://files.gap-system.org/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2"; sha256 = "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"; }; @@ -73,10 +73,8 @@ stdenv.mkDerivation rec { patchShebangs . ''; - configureFlags = [ "--with-gmp=system" ]; - buildInputs = [ - m4 + readline gmp ]; @@ -91,14 +89,31 @@ stdenv.mkDerivation rec { url = "https://github.com/gap-system/gap/commit/3361c172e6c5ff3bb3f01ba9d6f1dd4ad42cea80.patch"; sha256 = "1kwp9qnfvmlbpf1c3rs6j5m2jz22rj7a4hb5x1gj9vkpiyn5pdyj"; }) + + # Fix for locale specific tests causing issues. Already upstream. + # Backport of https://github.com/gap-system/gap/pull/4022 + # WHEN REMOVING: also remove the`rm tst/testinstall/strings.tst` line in + # `postPatch` below. That line is necessary since the patch is not intended + # for gap 4.10. + (fetchpatch { + name = "remove-locale-specific-tests.patch"; + url = "https://github.com/gap-system/gap/commit/c18b0c4215b5212a2cc4f305e2d5b94ba716bee8.patch"; + excludes = ["tst/testinstall/stringobj.tst"]; + sha256 = "1mz5b4mbw2jdd1ypp5s0dy6pp0jsvwsxr2dm4kbkls20r1r192sc"; + }) ]; + postPatch = '' + # File not covered by the remove-locale-specific-tests.patch patch above. + rm tst/testinstall/strings.tst + ''; + # "teststandard" is a superset of testinstall. It takes ~1h instead of ~1min. # tests are run twice, once with all packages loaded and once without # checkTarget = "teststandard"; doInstallCheck = true; - installCheckTarget = "testinstall"; + installCheckTarget = "check"; preInstallCheck = '' # gap tests check that the home directory exists @@ -119,16 +134,6 @@ stdenv.mkDerivation rec { ) ''; - postCheck = '' - # The testsuite doesn't exit with a non-zero exit code on failure. - # It leaves its logs in dev/log however. - - # grep for error messages - if grep ^##### dev/log/*; then - exit 1 - fi - ''; - postBuild = '' pushd pkg bash ../bin/BuildPackages.sh @@ -170,11 +175,11 @@ stdenv.mkDerivation rec { ]; platforms = platforms.all; broken = stdenv.isDarwin; - # keeping all packages increases the package size considerably, wchich - # is why a local build is preferable in that situation. The timeframe - # is reasonable and that way the binary cache doesn't get overloaded. + # keeping all packages increases the package size considerably, which is + # why a local build is preferable in that situation. The timeframe is + # reasonable and that way the binary cache doesn't get overloaded. hydraPlatforms = lib.optionals (!keepAllPackages) meta.platforms; license = licenses.gpl2; - homepage = "http://gap-system.org/"; + homepage = "https://www.gap-system.org"; }; } diff --git a/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/nixpkgs/pkgs/applications/science/math/nauty/default.nix index 64cc4a9aa00..c1d408213b9 100644 --- a/nixpkgs/pkgs/applications/science/math/nauty/default.nix +++ b/nixpkgs/pkgs/applications/science/math/nauty/default.nix @@ -4,10 +4,10 @@ }: stdenv.mkDerivation rec { pname = "nauty"; - version = "26r12"; + version = "27r1"; src = fetchurl { url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz"; - sha256 = "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"; + sha256 = "1nym0p2djws8ylkpr0kgpxfa6fxdlh46cmvz0gn5vd02jzgs0aww"; }; outputs = [ "out" "dev" ]; configureFlags = { @@ -37,6 +37,10 @@ stdenv.mkDerivation rec { license = licenses.asl20; maintainers = with maintainers; [ raskin timokau ]; platforms = platforms.unix; + # I'm not sure if the filename will remain the same for future changelog or + # if it will track changes to minor releases. Lets see. Better than nothing + # in any case. + changelog = "http://pallini.di.uniroma1.it/changes24-27.txt"; homepage = "http://pallini.di.uniroma1.it/"; }; } diff --git a/nixpkgs/pkgs/applications/science/math/palp/default.nix b/nixpkgs/pkgs/applications/science/math/palp/default.nix index 42259a2c689..c383438002f 100644 --- a/nixpkgs/pkgs/applications/science/math/palp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/palp/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz"; - sha256 = "09l4ysrdkqs91igg1faah75ay6ii684634ggvcxbkjsck65378l4"; + sha256 = "00jpm73fw9jjq58z6rysr1mwv489j6rpfqqlhm9ab0dln4kyhh05"; }; hardeningDisable = [ diff --git a/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix b/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix index b4e4adbfa6f..0db007f543f 100644 --- a/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix @@ -1,14 +1,23 @@ -{ stdenv, fetchurl, jre, makeWrapper }: +{ stdenv, fetchurl, jre, makeWrapper, substituteAll, coreutils }: stdenv.mkDerivation rec { pname = "cytoscape"; - version = "3.7.2"; + version = "3.8.0"; src = fetchurl { - url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-${version}.tar.gz"; - sha256 = "125vgr8vqbmy2nsm1yl0h0q8p49lxxqfw5cmxzbx1caklcn4rryc"; + url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz"; + sha256 = "0kksx12m83cjprdygmcc286990byf25yqfx5s7c07cizc21aavyg"; }; + patches = [ + # By default, gen_vmoptions.sh tries to store custom options in $out/share + # at run time. This patch makes sure $HOME is used instead. + (substituteAll { + src = ./gen_vmoptions_to_homedir.patch; + inherit coreutils; + }) + ]; + buildInputs = [jre makeWrapper]; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch b/nixpkgs/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch new file mode 100644 index 00000000000..e31681e8541 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch @@ -0,0 +1,19 @@ +diff -Nur a/gen_vmoptions.sh b/gen_vmoptions.sh +--- a/gen_vmoptions.sh 2020-03-30 21:57:47.000000000 +0100 ++++ b/gen_vmoptions.sh 2020-05-05 09:49:57.974989824 +0100 +@@ -1,13 +1,10 @@ + #!/bin/sh + # Generates the Cytoscape.vmoptions file + +-script_path="$(dirname -- $0)" +- +-#vm_options_path="$HOME/.cytoscape" +-vm_options_path=$script_path ++vm_options_path="$HOME/.cytoscape" + + if [ ! -e $vm_options_path ]; then +- /bin/mkdir $vm_options_path ++ @coreutils@/bin/mkdir $vm_options_path + fi + + # Determine amount of physical memory present: diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix index 72217689ff1..91c3b8c779c 100644 --- a/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix +++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/control.nix @@ -8,7 +8,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.9"; + version = "7.6.13"; python = python2.withPackages ( @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb"; - sha256 = "1fh7ybbp3qlqzh18c4gva3aaymv7d31mqchrv235a1axldha1s9s"; + sha256 = "0qfvhwc29cgqkwf2bkhq4gr2d1c4jgccfs58916ss03n4rwz9gng"; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix b/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix index a35df650300..cdeed6536ef 100644 --- a/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/nixpkgs/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -11,7 +11,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.9"; + version = "7.6.13"; in stdenv.mkDerivation rec { inherit version; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb"; - sha256 = "04wr86g11wpmsczzwzak4gvalcihb47rn3zp6qriawhxyac9nf93"; + sha256 = "09yfvk16j1iwx8h1xg678ks3bc8760gfdn7n32j8r893kd32cwyk"; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix index 741330e4ad2..63a727f9c88 100644 --- a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix @@ -2,7 +2,7 @@ python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "5.16.0"; + version = "5.17.0"; propagatedBuildInputs = with python3Packages; [ appdirs @@ -22,7 +22,7 @@ python3Packages.buildPythonApplication rec { src = python3Packages.fetchPypi { inherit pname version; - sha256 = "0jlf3y8b1gdv5xz37yk9b5g2b65zkk45p15x0ypvd2blpzy80537"; + sha256 = "0y652i3saqq2z61yvk0i6q3lnq2xfrygcxms5gygspj71q2n4f7k"; }; doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json diff --git a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix index 314fc522500..a672272e9e6 100644 --- a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "sherpa"; - version = "2.2.9"; + version = "2.2.10"; src = fetchurl { url = "https://www.hepforge.org/archive/sherpa/SHERPA-MC-${version}.tar.gz"; - sha256 = "1z7vws97k6zfzyqx0dkv2kq8d83dibi73i5jiqk5a22yplp6bnjh"; + sha256 = "1iwa17s8ipj6a2b8zss5csb1k5y9s5js38syvq932rxcinbyjsl4"; }; buildInputs = [ gfortran sqlite lhapdf rivet ]; diff --git a/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix new file mode 100644 index 00000000000..85838b04cbf --- /dev/null +++ b/nixpkgs/pkgs/applications/science/physics/xflr5/default.nix @@ -0,0 +1,23 @@ +{ stdenv, lib, fetchurl, wrapQtAppsHook, qmake }: + +stdenv.mkDerivation rec { + pname = "xflr5"; + version = "6.47"; + + src = fetchurl { + url = "mirror://sourceforge/xflr5/${pname}_v${version}_src.tar.gz"; + sha256 = "02x3r9iv3ndwxa65mxn9m5dlhcrnjiq7cffi6rmb456gs3v3dnav"; + }; + + enableParallelBuilding = true; + + nativeBuildInputs = [ qmake wrapQtAppsHook ]; + + meta = with stdenv.lib; { + description = "An analysis tool for airfoils, wings and planes"; + homepage = https://sourceforge.net/projects/xflr5/; + license = licenses.gpl3; + maintainers = [ maintainers.esclear ]; + platforms = platforms.linux; + }; +}
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