diff options
Diffstat (limited to 'pkgs/applications/science')
10 files changed, 79 insertions, 44 deletions
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 5073d0f0f324..1e678d4b6ed3 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.22.4"; + version = "2.22.7"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0gzna5df8nk42l7mc0qbp9h73gwr1030jnw10fawjp6ql6213kdd"; + sha256 = "09q66lhjnprkw8azavwzwv9dlhr9b4x0dbz6fym0i2wbhylqp4w6"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index 2b7c91751e54..4a9ed0cb86dc 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/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/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 315900d42b9b..39e7cbe7f3cc 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/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/pkgs/applications/science/logic/elan/default.nix b/pkgs/applications/science/logic/elan/default.nix index 743bbf163c2f..7a7da2c5f5d2 100644 --- a/pkgs/applications/science/logic/elan/default.nix +++ b/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${version}"; - sha256 = "0aw538shvpfbk481y0gw3z97nsazdnk8qh8fwsb6ji62p2r51v6f"; + sha256 = "0ycw1r364g5gwh8796dpv1israpg7zqwx8mcvnacv2lqj5iijmby"; }; - cargoSha256 = "0zg3q31z516049v9fhli4yxldx9fg31k2qfx4ag8rmyvpgy9xh6c"; + cargoSha256 = "0hcaiy046d2gnkp6sfpnkkprb3nd94i9q8dgqxxpwrc1j157x6z9"; nativeBuildInputs = [ pkgconfig ]; diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index 64cc4a9aa003..c1d408213b98 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -4,10 +4,10 @@ }: stdenv.mkDerivation rec { pname = "nauty"; - version = "26r12"; + version = "27r1"; src = fetchurl { url = "http://pallini.di.uniroma1.it/nauty${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/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix index 4912b82d158f..c0100422c64a 100644 --- a/pkgs/applications/science/math/palp/default.nix +++ b/pkgs/applications/science/math/palp/default.nix @@ -9,16 +9,15 @@ let in stdenv.mkDerivation rec { pname = "palp"; - version = "2.1"; + version = "2.11"; src = fetchurl { url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz"; - sha256 = "1s7s2lc5f0ig1yy7ygsh3sddm3sbq4mxwybqsj8lp9wjdxs7qfrs"; + sha256 = "0pv3rmgk8xc8z98w173f1jxc1cd67cdl8mjjgmgp3mcvifcfsrjl"; }; hardeningDisable = [ "format" - "strictoverflow" # causes runtime failure (tested in checkPhase) ]; patchPhase = stdenv.lib.optionalString stdenv.isDarwin '' @@ -78,6 +77,9 @@ stdenv.mkDerivation rec { facet enumeration compares well with existing packages. ''; homepage = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html"; + # Not really a changelog, but a one-line summary of each update that should + # be reviewed on update. + changelog = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html"; # Just a link on the website pointing to gpl -- now gplv3. When the last # version was released that pointed to gplv2 however, so thats probably # the right license. diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index b4e4adbfa6f2..0db007f543f3 100644 --- a/pkgs/applications/science/misc/cytoscape/default.nix +++ b/pkgs/applications/science/misc/cytoscape/default.nix @@ -1,14 +1,23 @@ -{ stdenv, fetchurl, jre, makeWrapper }: +{ stdenv, fetchurl, jre, makeWrapper, substituteAll, coreutils }: stdenv.mkDerivation rec { pname = "cytoscape"; - version = "3.7.2"; + version = "3.8.0"; src = fetchurl { - url = "https://github.com/cytoscape/cytoscape/releases/download/${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 $HOME is used instead. + (substituteAll { + src = ./gen_vmoptions_to_homedir.patch; + inherit coreutils; + }) + ]; + buildInputs = [jre makeWrapper]; installPhase = '' diff --git a/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch new file mode 100644 index 000000000000..e31681e8541f --- /dev/null +++ b/pkgs/applications/science/misc/cytoscape/gen_vmoptions_to_homedir.patch @@ -0,0 +1,19 @@ +diff -Nur a/gen_vmoptions.sh b/gen_vmoptions.sh +--- a/gen_vmoptions.sh 2020-03-30 21:57:47.000000000 +0100 ++++ b/gen_vmoptions.sh 2020-05-05 09:49:57.974989824 +0100 +@@ -1,13 +1,10 @@ + #!/bin/sh + # Generates the Cytoscape.vmoptions file + +-script_path="$(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 $vm_options_path + fi + + # Determine amount of physical memory present: diff --git a/pkgs/applications/science/misc/foldingathome/control.nix b/pkgs/applications/science/misc/foldingathome/control.nix index 72217689ff18..91c3b8c779cd 100644 --- a/pkgs/applications/science/misc/foldingathome/control.nix +++ b/pkgs/applications/science/misc/foldingathome/control.nix @@ -8,7 +8,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.9"; + version = "7.6.13"; python = python2.withPackages ( @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb"; - sha256 = "1fh7ybbp3qlqzh18c4gva3aaymv7d31mqchrv235a1axldha1s9s"; + sha256 = "0qfvhwc29cgqkwf2bkhq4gr2d1c4jgccfs58916ss03n4rwz9gng"; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/misc/foldingathome/viewer.nix b/pkgs/applications/science/misc/foldingathome/viewer.nix index a35df650300b..cdeed6536efa 100644 --- a/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -11,7 +11,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.9"; + version = "7.6.13"; in stdenv.mkDerivation rec { inherit version; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb"; - sha256 = "04wr86g11wpmsczzwzak4gvalcihb47rn3zp6qriawhxyac9nf93"; + sha256 = "09yfvk16j1iwx8h1xg678ks3bc8760gfdn7n32j8r893kd32cwyk"; }; nativeBuildInputs = [ |