diff options
Diffstat (limited to 'pkgs/applications/science')
30 files changed, 369 insertions, 73 deletions
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index eca25774c59..3cb34576c46 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -6,13 +6,13 @@ mkDerivation rec { pname = "stellarium"; - version = "0.19.3"; + version = "0.20.0"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${version}"; - sha256 = "175aj4bgi9b6bif6fvjdlpd68brcwij4x3ml0lxk6i51binv233y"; + sha256 = "1732dxkgyqd4xf0ry7v930vcbv60l8iry596869z1d47j2piibs4"; }; nativeBuildInputs = [ cmake perl wrapQtAppsHook ]; diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix index 78a6f483337..8787c96e5b0 100644 --- a/pkgs/applications/science/biology/deeptools/default.nix +++ b/pkgs/applications/science/biology/deeptools/default.nix @@ -4,11 +4,11 @@ with python.pkgs; buildPythonApplication rec { pname = "deepTools"; - version = "3.3.1"; + version = "3.4.1"; src = fetchPypi { inherit pname version; - sha256 = "08p36p9ncj5s8qf1r7h83x4rnmi63l3yk6mnr3wgpg2qgvwl0hji"; + sha256 = "05zw9gk17hz08hns5lnhn7l13idg9jdz4gdba6m6gbr84yz149gs"; }; propagatedBuildInputs = [ diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index b47ce6ac3a9..1a3762f4326 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1047"; + version = "1060"; src = fetchurl { url = "http://last.cbrc.jp/last-${version}.zip"; - sha256 = "06fj4qfw3dd35y3pky3dnr40v1alf43wjx373rbx1vr3hbgzvgf8"; + sha256 = "0h0604rxg0z0h21dykrnxsb4679zfhibg79gss1v2ik5xpdxl8kk"; }; nativeBuildInputs = [ unzip ]; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 93f66810549..246c9876810 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 = "2.22.0"; + version = "2.22.2"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "1qgg8r81xn2z965v78kfj05vycrd2cz48gxk5csr6kvwk3ba286c"; + sha256 = "11mzz483f89pb2s8jmwhl12d0m6k41kmi4xh0i6hq69rxrqi8l4s"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/seaview/default.nix b/pkgs/applications/science/biology/seaview/default.nix index fea8da41d70..4192de714d0 100644 --- a/pkgs/applications/science/biology/seaview/default.nix +++ b/pkgs/applications/science/biology/seaview/default.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, coreutils, fltk, libjpeg }: stdenv.mkDerivation rec { - version = "5.0"; + version = "5.0.2"; pname = "seaview"; src = fetchurl { url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz"; - sha256 = "0gzjqf5mm91pa1drwxvz229bv6l995npdggngszh6z6j4pfh8j7c"; + sha256 = "0bad0nd18a36g6ysx28j68rbnwqn33ra8inx2lv2igqqcs6i5kif"; }; buildInputs = [ fltk libjpeg ]; @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224. ''; - homepage = http://doua.prabi.fr/software/seaview; + homepage = "http://doua.prabi.fr/software/seaview"; license = licenses.gpl3; maintainers = [ maintainers.iimog ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/stacks/default.nix b/pkgs/applications/science/biology/stacks/default.nix index e778c3bd52c..93a02a46bd8 100644 --- a/pkgs/applications/science/biology/stacks/default.nix +++ b/pkgs/applications/science/biology/stacks/default.nix @@ -2,17 +2,17 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.41"; + version = "2.52"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "0q420rzjb05jfchcls3pysm4hxfgs6xj2jw246isx0il10g93gkq"; + sha256 = "0gq3kbj910jsq591wylzjmd23srjlsssmrckmf46m4ysjqdqd8vm"; }; buildInputs = [ zlib ]; meta = { description = "Software pipeline for building loci from short-read sequences"; - homepage = http://catchenlab.life.illinois.edu/stacks/; + homepage = "http://catchenlab.life.illinois.edu/stacks/"; maintainers = [ stdenv.lib.maintainers.bzizou ]; license = stdenv.lib.licenses.gpl3; }; diff --git a/pkgs/applications/science/chemistry/gwyddion/codegen.patch b/pkgs/applications/science/chemistry/gwyddion/codegen.patch new file mode 100644 index 00000000000..eb306d99f8a --- /dev/null +++ b/pkgs/applications/science/chemistry/gwyddion/codegen.patch @@ -0,0 +1,22 @@ +--- gwyddion-2.55.orig/configure 2019-11-04 01:25:31.000000000 -0800 ++++ gwyddion-2.55/configure 2020-03-20 18:49:43.860452655 -0700 +@@ -18560,7 +18560,7 @@ + fi + if test "x$embed_pygtk" = xno; then + if test "x$PYGTK_CODEGENDIR" = 'x'; then +- PYGTK_CODEGENDIR=`$PKG_CONFIG --variable=codegendir pygtk-2.0` ++ PYGTK_CODEGENDIR=`$PKG_CONFIG --variable=codegendir pygobject-2.0` + fi + else + # Some silly OSes want to remove pygtk2. We can build pygwy without +--- gwyddion-2.55.orig/configure.ac 2019-11-04 01:25:16.000000000 -0800 ++++ gwyddion-2.55/configure.ac 2020-03-20 18:52:55.042724547 -0700 +@@ -270,7 +270,7 @@ + [embed_pygtk=yes; pygwy_warn=" (embedded pygtk2)"]) + if test "x$embed_pygtk" = xno; then + if test "x$PYGTK_CODEGENDIR" = 'x'; then +- PYGTK_CODEGENDIR=`$PKG_CONFIG --variable=codegendir pygtk-2.0` ++ PYGTK_CODEGENDIR=`$PKG_CONFIG --variable=codegendir pygobject-2.0` + fi + else + # Some silly OSes want to remove pygtk2. We can build pygwy without diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix index 12007c940b3..644f609ed0a 100644 --- a/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -1,17 +1,69 @@ -{ stdenv, fetchurl, gtk2, pkgconfig }: +{ stdenv, fetchurl, gtk2, pkg-config, fftw, file, + pythonSupport ? false, pythonPackages ? null, + gnome2 ? null, + openexrSupport ? true, openexr ? null, + libzipSupport ? true, libzip ? null, + libxml2Support ? true, libxml2 ? null, + libwebpSupport ? true, libwebp ? null, + # libXmu is not used if libunique is. + libXmuSupport ? false, xorg ? null, + libxsltSupport ? true, libxslt ? null, + fitsSupport ? true, cfitsio ? null, + zlibSupport ? true, zlib ? null, + libuniqueSupport ? true, libunique ? null, + libpngSupport ? true, libpng ? null, + openglSupport ? !stdenv.isDarwin +}: -with stdenv.lib; +assert openexrSupport -> openexr != null; +assert libzipSupport -> libzip != null; +assert libxml2Support -> libxml2 != null; +assert libwebpSupport -> libwebp != null; +assert libXmuSupport -> xorg != null; +assert libxsltSupport -> libxslt != null; +assert fitsSupport -> cfitsio != null; +assert zlibSupport -> zlib != null; +assert libuniqueSupport -> libunique != null; +assert libpngSupport -> libpng != null; +assert openglSupport -> gnome2 != null; +assert pythonSupport -> (pythonPackages != null && gnome2 != null); -let version = "2.48"; in -stdenv.mkDerivation { +let + inherit (pythonPackages) pygtk pygobject2 python; + +in + +stdenv.mkDerivation rec { pname = "gwyddion"; - inherit version; + version = "2.55"; src = fetchurl { - url = "mirror://sourceforge/gwyddion/files/gwyddion/${version}/gwyddion-${version}.tar.xz"; - sha256 = "119iw58ac2wn4cas6js8m7r1n4gmmkga6b1y711xzcyjp9hshgwx"; + url = "mirror://sourceforge/gwyddion/gwyddion-${version}.tar.xz"; + sha256 = "0l00zszvginpriv12idc0y1x28qmicdmrwkqa007srkxvrdgxwdi"; }; - nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ gtk2 ]; + + nativeBuildInputs = [ pkg-config file ]; + + buildInputs = with stdenv.lib; + [ gtk2 fftw ] ++ + optional openglSupport gnome2.gtkglext ++ + optional openexrSupport openexr ++ + optional libXmuSupport xorg.libXmu ++ + optional fitsSupport cfitsio ++ + optional libpngSupport libpng ++ + optional libxsltSupport libxslt ++ + optional libxml2Support libxml2 ++ + optional libwebpSupport libwebp ++ + optional zlibSupport zlib ++ + optional libuniqueSupport libunique ++ + optional libzipSupport libzip; + + propagatedBuildInputs = with stdenv.lib; + optionals pythonSupport [ pygtk pygobject2 python gnome2.gtksourceview ]; + + # This patch corrects problems with python support, but should apply cleanly + # regardless of whether python support is enabled, and have no effects if + # it is disabled. + patches = [ ./codegen.patch ]; meta = { homepage = http://gwyddion.net/; @@ -28,6 +80,7 @@ stdenv.mkDerivation { spectrophotometry. ''; license = stdenv.lib.licenses.gpl2; - platforms = stdenv.lib.platforms.linux; + platforms = with stdenv.lib.platforms; linux ++ darwin; + maintainers = [ stdenv.lib.maintainers.cge ]; }; } diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 2c155e4e848..c54fb3444bb 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.6.0"; + version = "20.9.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "1vd1hsj36wzghpn6xnppjmva35kdcin7h0xdj3xmi4w5l3qw7fl6"; + sha256 = "1c6q1vb96jsb37g5qbhzcnasd5pdqjyc190yg3caw3gwrd97889q"; }; nativeBuildInputs = [ dpkg makeWrapper ]; @@ -40,7 +40,7 @@ stdenv.mkDerivation rec { meta = { description = "A chemical modelling, analysis and structure drawing program"; - homepage = https://chemaxon.com/products/marvin; + homepage = "https://chemaxon.com/products/marvin"; maintainers = with maintainers; [ fusion809 ]; license = licenses.unfree; platforms = platforms.linux; diff --git a/pkgs/applications/science/electronics/dsview/default.nix b/pkgs/applications/science/electronics/dsview/default.nix index d188365db1d..1e125964d50 100644 --- a/pkgs/applications/science/electronics/dsview/default.nix +++ b/pkgs/applications/science/electronics/dsview/default.nix @@ -1,6 +1,6 @@ { stdenv, fetchFromGitHub, pkgconfig, cmake, libzip, boost, fftw, qtbase, -libusb, wrapQtAppsHook, libsigrok4dsl, libsigrokdecode4dsl +libusb1, wrapQtAppsHook, libsigrok4dsl, libsigrokdecode4dsl }: stdenv.mkDerivation rec { @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake pkgconfig wrapQtAppsHook ]; buildInputs = [ - boost fftw qtbase libusb libzip libsigrokdecode4dsl libsigrok4dsl + boost fftw qtbase libusb1 libzip libsigrokdecode4dsl libsigrok4dsl ]; enableParallelBuilding = true; diff --git a/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix b/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix index c2cfc69c50c..f5f3ce7435a 100644 --- a/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix +++ b/pkgs/applications/science/electronics/dsview/libsigrok4dsl.nix @@ -1,5 +1,5 @@ { stdenv, pkgconfig, autoreconfHook, -glib, libzip, libserialport, check, libusb, libftdi, +glib, libzip, libserialport, check, libusb1, libftdi, systemd, alsaLib, dsview }: @@ -15,7 +15,7 @@ stdenv.mkDerivation { nativeBuildInputs = [ pkgconfig autoreconfHook ]; buildInputs = [ - glib libzip libserialport libusb libftdi systemd check alsaLib + glib libzip libserialport libusb1 libftdi systemd check alsaLib ]; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/electronics/fparser/default.nix b/pkgs/applications/science/electronics/fparser/default.nix new file mode 100644 index 00000000000..55e40ca2b00 --- /dev/null +++ b/pkgs/applications/science/electronics/fparser/default.nix @@ -0,0 +1,26 @@ +{ stdenv +, fetchFromGitHub +, cmake +}: + +stdenv.mkDerivation rec { + pname = "fparser"; + version = "unstable-2015-09-25"; + + src = fetchFromGitHub { + owner = "thliebig"; + repo = "fparser"; + rev = "a59e1f51e32096bfe2a0a2640d5dffc7ae6ba37b"; + sha256 = "0wayml1mlyi922gp6am3fsidhzsilziksdn5kbnpcln01h8555ad"; + }; + + nativeBuildInputs = [ cmake ]; + + meta = with stdenv.lib; { + description = "C++ Library for Evaluating Mathematical Functions"; + homepage = "https://github.com/thliebig/fparser"; + license = licenses.lgpl3; + maintainers = with maintainers; [ matthuszagh ]; + platforms = platforms.linux; + }; +} diff --git a/pkgs/applications/science/electronics/xcircuit/default.nix b/pkgs/applications/science/electronics/xcircuit/default.nix index 418144e6af7..d10b486492e 100644 --- a/pkgs/applications/science/electronics/xcircuit/default.nix +++ b/pkgs/applications/science/electronics/xcircuit/default.nix @@ -2,7 +2,7 @@ , cairo, ghostscript, ngspice, tcl, tk, xorg, zlib }: let - version = "3.9.73"; + version = "3.10.12"; name = "xcircuit-${version}"; inherit (stdenv.lib) getBin; @@ -11,7 +11,7 @@ in stdenv.mkDerivation { src = fetchurl { url = "http://opencircuitdesign.com/xcircuit/archive/${name}.tgz"; - sha256 = "1kj9hayipplzm4960kx48vxddqj154qnxkccaqj9cnkp62b7q3jg"; + sha256 = "1h1ywc3mr7plvwnhdii2zgnnv5ih2nhyl4qbdjpi83dq0aq1s2mn"; }; nativeBuildInputs = [ autoreconfHook automake pkgconfig ]; @@ -30,6 +30,6 @@ in stdenv.mkDerivation { homepage = http://opencircuitdesign.com/xcircuit; license = licenses.gpl2; platforms = platforms.linux; - maintainers = [ maintainers.spacefrogg ]; + maintainers = with maintainers; [ spacefrogg thoughtpolice ]; }; } diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix index f83480cfbaf..e396f1c4a91 100644 --- a/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/pkgs/applications/science/logic/alt-ergo/default.nix @@ -1,26 +1,47 @@ -{ fetchurl, stdenv, which, dune, ocamlPackages }: +{ fetchurl, lib, which, ocamlPackages }: -stdenv.mkDerivation rec { +let pname = "alt-ergo"; - version = "2.3.0"; + version = "2.3.2"; src = fetchurl { - url = "https://alt-ergo.ocamlpro.com/download_manager.php?target=${pname}-${version}.tar.gz"; - name = "${pname}-${version}.tar.gz"; - sha256 = "1ycr3ff0gacq1aqzs16n6swgfniwpim0m7rvhcam64kj0a80c6bz"; + url = "https://alt-ergo.ocamlpro.com/http/alt-ergo-${version}/alt-ergo-${version}.tar.gz"; + sha256 = "130hisjzkaslygipdaaqib92spzx9rapsd45dbh5ssczjn5qnhb9"; }; - buildInputs = [ dune which ] ++ (with ocamlPackages; [ - ocaml findlib camlzip lablgtk menhir num ocplib-simplex psmt2-frontend seq zarith - ]); - preConfigure = "patchShebangs ./configure"; + nativeBuildInputs = [ which ]; + +in + +let alt-ergo-lib = ocamlPackages.buildDunePackage rec { + pname = "alt-ergo-lib"; + inherit version src preConfigure nativeBuildInputs; + configureFlags = pname; + propagatedBuildInputs = with ocamlPackages; [ num ocplib-simplex stdlib-shims zarith ]; +}; in + +let alt-ergo-parsers = ocamlPackages.buildDunePackage rec { + pname = "alt-ergo-parsers"; + inherit version src preConfigure nativeBuildInputs; + configureFlags = pname; + buildInputs = with ocamlPackages; [ menhir ]; + propagatedBuildInputs = [ alt-ergo-lib ] ++ (with ocamlPackages; [ camlzip psmt2-frontend ]); +}; in + +ocamlPackages.buildDunePackage { + + inherit pname version src preConfigure nativeBuildInputs; + + configureFlags = pname; + + buildInputs = [ alt-ergo-parsers ocamlPackages.menhir ]; + meta = { description = "High-performance theorem prover and SMT solver"; homepage = "https://alt-ergo.ocamlpro.com/"; - license = stdenv.lib.licenses.ocamlpro_nc; - platforms = stdenv.lib.platforms.linux ++ stdenv.lib.platforms.darwin; - maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; + license = lib.licenses.ocamlpro_nc; + maintainers = [ lib.maintainers.thoughtpolice ]; }; } diff --git a/pkgs/applications/science/logic/cadical/default.nix b/pkgs/applications/science/logic/cadical/default.nix new file mode 100644 index 00000000000..5e6c0d55b7d --- /dev/null +++ b/pkgs/applications/science/logic/cadical/default.nix @@ -0,0 +1,29 @@ +{ stdenv, fetchFromGitHub }: + +stdenv.mkDerivation rec { + pname = "cadical"; + version = "1.2.1"; + + src = fetchFromGitHub { + owner = "arminbiere"; + repo = "cadical"; + rev = "rel-${version}"; + hash = "sha256:1a66xkw42ad330fvw8i0sawrmg913m8wrq5c85lw5qandkwvxdi6"; + }; + + dontAddPrefix = true; + installPhase = '' + install -Dm0755 build/cadical "$out/bin/cadical" + install -Dm0755 build/mobical "$out/bin/mobical" + mkdir -p "$out/share/doc/${pname}-${version}/" + install -Dm0755 {LICEN?E,README*,VERSION} "$out/share/doc/${pname}-${version}/" + ''; + + meta = with stdenv.lib; { + description = "Simplified Satisfiability Solver"; + maintainers = with maintainers; [ shnarazk ]; + platforms = platforms.unix; + license = licenses.mit; + homepage = "http://fmv.jku.at/cadical"; + }; +} diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 85c5d23ffca..52a587ccb48 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -33,6 +33,7 @@ let "8.10.1" = "072v2zkjzf7gj48137wpr3c9j0hg9pdhlr5l8jrgrwynld8fp7i4"; "8.10.2" = "0znxmpy71bfw0p6x47i82jf5k7v41zbz9bdpn901ysn3ir8l3wrz"; "8.11.0" = "1rfdic6mp7acx2zfwz7ziqk12g95bl9nyj68z4n20a5bcjv2pxpn"; + "8.11.1" = "0qriy9dy36dajsv5qmli8gd6v55mah02ya334nw49ky19v7518m0"; }.${version}; coq-version = stdenv.lib.versions.majorMinor version; versionAtLeast = stdenv.lib.versionAtLeast coq-version; diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index cfd645a3c73..594f596b5ef 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.7.2"; + version = "3.8.0"; src = fetchFromGitHub { owner = "leanprover-community"; repo = "lean"; rev = "v${version}"; - sha256 = "0d9lz0mbxyaaykkvk2p8w2hcif9cx0ksihgh7qhxf417bz6msgc1"; + sha256 = "0frs2vhxlzdliyydb462c1886dn585zd7yp7hdxzsri2v6gdh89g"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/logic/mcy/default.nix b/pkgs/applications/science/logic/mcy/default.nix index ec9af192631..a9366d56058 100644 --- a/pkgs/applications/science/logic/mcy/default.nix +++ b/pkgs/applications/science/logic/mcy/default.nix @@ -7,13 +7,13 @@ let in stdenv.mkDerivation { pname = "mcy"; - version = "2020.03.16"; + version = "2020.03.21"; src = fetchFromGitHub { owner = "YosysHQ"; repo = "mcy"; - rev = "562c02375067428bb657f57faa5131ee1ab44051"; - sha256 = "0q77v2hxnmv61zx5bl4lrqiavgvsiyb5qxdp9hnihimj1m30bc5h"; + rev = "bac92b8aad9bf24714fda70d3750bb50d6d96177"; + sha256 = "0mmg6zd5cbn8g0am9c3naamg0lq67yyy117fzn2ydigcyia7vmnp"; }; buildInputs = [ python ]; diff --git a/pkgs/applications/science/logic/poly/default.nix b/pkgs/applications/science/logic/poly/default.nix index c833b22e49b..ee50a2d8504 100644 --- a/pkgs/applications/science/logic/poly/default.nix +++ b/pkgs/applications/science/logic/poly/default.nix @@ -2,13 +2,14 @@ stdenv.mkDerivation rec { pname = "libpoly"; - version = "0.1.7"; + version = "0.1.8"; src = fetchFromGitHub { owner = "SRI-CSL"; repo = "libpoly"; - rev = "v${version}"; - sha256 = "0i5ar4lhs88glk0rvkmag656ii434i6i1q5dspx6d0kyg78fii64"; + # they've pushed to the release branch, use explicit tag + rev = "refs/tags/v${version}"; + sha256 = "1n3gijksnl2ybznq4lkwm2428f82423sxq18gnb2g1kiwqlzdaa3"; }; nativeBuildInputs = [ cmake ]; @@ -16,7 +17,7 @@ stdenv.mkDerivation rec { buildInputs = [ gmp python ]; meta = with stdenv.lib; { - homepage = https://github.com/SRI-CSL/libpoly; + homepage = "https://github.com/SRI-CSL/libpoly"; description = "C library for manipulating polynomials"; license = licenses.lgpl3; platforms = platforms.all; diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix index 48c48836b06..b180cf307f0 100644 --- a/pkgs/applications/science/logic/symbiyosys/default.nix +++ b/pkgs/applications/science/logic/symbiyosys/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation { pname = "symbiyosys"; - version = "2020.02.11"; + version = "2020.03.24"; src = fetchFromGitHub { owner = "YosysHQ"; repo = "SymbiYosys"; - rev = "0a7013017f9d583ef6cc8d10712f4bf11cf6e024"; - sha256 = "08xz8sgvs1qy7jxp8ma5yl49i6nl7k6bkhry4afdvwg3fvwis39c"; + rev = "8a62780b9df4d2584e41cdd42cab92fddcd75b31"; + sha256 = "0ss5mrzwff2dny8kfciqbrz67m6k52yvc1shd7gk3qb99x7g7fp8"; }; buildInputs = [ python3 ]; diff --git a/pkgs/applications/science/math/cemu/default.nix b/pkgs/applications/science/math/cemu/default.nix new file mode 100644 index 00000000000..f91e5be5170 --- /dev/null +++ b/pkgs/applications/science/math/cemu/default.nix @@ -0,0 +1,53 @@ +{ fetchFromGitHub +, stdenv +, mkDerivation +, SDL2 +, libGL +, libarchive +, libusb +, qtbase +, qmake +, git +, libpng_apng +, pkgconfig +}: + +mkDerivation rec { + pname = "CEmu"; + version = "1.3"; + src = fetchFromGitHub { + owner = "CE-Programming"; + repo = "CEmu"; + rev = "v${version}"; + sha256 = "1wcdnzcqscawj6jfdj5wwmw9g9vsd6a1rx0rrramakxzf8b7g47r"; + fetchSubmodules = true; + }; + + nativeBuildInputs = [ + qmake + git + pkgconfig + ]; + + buildInputs = [ + SDL2 + libGL + libarchive + libusb + qtbase + libpng_apng + ]; + + qmakeFlags = [ + "gui/qt" + ]; + + meta = with stdenv.lib; { + changelog = "https://github.com/CE-Programming/CEmu/releases/tag/v${version}"; + description = "Third-party TI-84 Plus CE / TI-83 Premium CE emulator, focused on developer features"; + homepage = "https://ce-programming.github.io/CEmu"; + license = licenses.gpl3; + maintainers = with maintainers; [ luc65r ]; + platforms = [ "x86_64-linux" "x86_64-darwin" ]; + }; +} diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index e65cf52d581..2c4d5f254da 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { pname = "gmsh"; - version = "4.5.4"; + version = "4.5.6"; src = fetchurl { url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "1k9f7qxlwja9i40qy55070sjnr21bl165677mdqw7qyb8d7wgy6c"; + sha256 = "0gs65bgr1ph5lz7r6manqj8cra30s7c94pxilkd2z0p5vq6fpsj6"; }; buildInputs = [ openblasCompat gmm fltk libjpeg zlib libGLU libGL diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix index 7cd1b2eb99f..5553bb0505f 100644 --- a/pkgs/applications/science/math/mathematica/default.nix +++ b/pkgs/applications/science/math/mathematica/default.nix @@ -9,6 +9,7 @@ , freetype , gcc , glib +, libssh2 , ncurses , opencv , openssl @@ -44,9 +45,11 @@ stdenv.mkDerivation rec { gcc.cc gcc.libc glib + libssh2 ncurses opencv openssl + stdenv.cc.cc.lib unixODBC xkeyboard_config libxml2 @@ -93,7 +96,7 @@ stdenv.mkDerivation rec { # Fix library paths cd $out/libexec/Mathematica/Executables for path in mathematica MathKernel Mathematica WolframKernel wolfram math; do - sed -i -e "2iexport LD_LIBRARY_PATH=${zlib}/lib:\''${LD_LIBRARY_PATH}\n" $path + sed -i -e "2iexport LD_LIBRARY_PATH=${zlib}/lib:${stdenv.cc.cc.lib}/lib:${libssh2}/lib:\''${LD_LIBRARY_PATH}\n" $path done # Fix xkeyboard config path for Qt @@ -102,7 +105,7 @@ stdenv.mkDerivation rec { done # Remove some broken libraries - rm $out/libexec/Mathematica/SystemFiles/Libraries/Linux-x86-64/libz.so* + rm -f $out/libexec/Mathematica/SystemFiles/Libraries/Linux-x86-64/libz.so* ''; preFixup = '' diff --git a/pkgs/applications/science/math/mathematica/l10ns.nix b/pkgs/applications/science/math/mathematica/l10ns.nix index 51fb489be7e..c75c91be059 100644 --- a/pkgs/applications/science/math/mathematica/l10ns.nix +++ b/pkgs/applications/science/math/mathematica/l10ns.nix @@ -8,6 +8,12 @@ let allVersions = with lib; flip map # N.B. Versions in this list should be ordered from newest to oldest. [ { + version = "12.1.0"; + lang = "en"; + language = "English"; + sha256 = "15m9l20jvkxh5w6mbp81ys7mx2lx5j8acw5gz0il89lklclgb8z7"; + } + { version = "12.0.0"; lang = "en"; language = "English"; diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix index e9fd21b46d8..4912b82d158 100644 --- a/pkgs/applications/science/math/palp/default.nix +++ b/pkgs/applications/science/math/palp/default.nix @@ -4,10 +4,12 @@ , doSymlink ? true # symlink the executables to the default location (without dimension postfix) }: +let + dim = toString dimensions; +in stdenv.mkDerivation rec { + pname = "palp"; version = "2.1"; - dim = toString dimensions; - name = "palp-${dim}d-${version}"; src = fetchurl { url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz"; @@ -75,7 +77,7 @@ stdenv.mkDerivation rec { algorithms work in any dimension and our key routine for vertex and facet enumeration compares well with existing packages. ''; - homepage = http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html; + homepage = "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/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index c23debdd7a4..e393111590a 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 = "3.8.0"; + version = "3.8.0a"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "0nsg6dzg5r7rzqr671nvrf1c50rjwpz7bxv5f20i4s7agizgv840"; + sha256 = "0bjd61bbc5b2i09kz3ss01c0xmxrhmiv5wpbhhplkp3yhw2qrf3m"; }; patchPhase = '' diff --git a/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch b/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch new file mode 100644 index 00000000000..197d1347d53 --- /dev/null +++ b/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch @@ -0,0 +1,25 @@ +From 0eaef67b683683fb423fcb2d5096b3cdf9a4a9cd Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Maciej=20Kr=C3=BCger?= <mkg20001@gmail.com> +Date: Sun, 22 Mar 2020 12:26:10 +0100 +Subject: [PATCH] Patch plugindir to output + +--- + configure.ac | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index 50edb74..639ee86 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -50,7 +50,7 @@ PKG_CHECK_MODULES([glib], [glib-2.0 >= 2.40 gio-unix-2.0 gmodule-2.0 ]) + PKG_CHECK_MODULES([cairo], [cairo]) + PKG_CHECK_MODULES([rofi], [rofi >= 1.5.4]) + +-[rofi_PLUGIN_INSTALL_DIR]="`$PKG_CONFIG --variable=pluginsdir rofi`" ++[rofi_PLUGIN_INSTALL_DIR]="`echo $out/lib/rofi`" + AC_SUBST([rofi_PLUGIN_INSTALL_DIR]) + + LT_INIT([disable-static]) +-- +2.25.1 + diff --git a/pkgs/applications/science/math/rofi-calc/default.nix b/pkgs/applications/science/math/rofi-calc/default.nix new file mode 100644 index 00000000000..842265cf3d5 --- /dev/null +++ b/pkgs/applications/science/math/rofi-calc/default.nix @@ -0,0 +1,54 @@ +{ stdenv +, fetchFromGitHub +, autoreconfHook +, pkgconfig +, rofi-unwrapped +, libqalculate +, glib +, cairo +, gobject-introspection +, wrapGAppsHook +}: + +stdenv.mkDerivation rec { + pname = "rofi-calc"; + version = "1.6"; + + src = fetchFromGitHub { + owner = "svenstaro"; + repo = pname; + rev = "v${version}"; + sha256 = "00pz0s99pihjdjy8pl4ckg2qciyp32k439lmjb5iazwck512ar92"; + }; + + nativeBuildInputs = [ + autoreconfHook + pkgconfig + gobject-introspection + wrapGAppsHook + ]; + + buildInputs = [ + rofi-unwrapped + libqalculate + glib + cairo + ]; + + patches = [ + ./0001-Patch-plugindir-to-output.patch + ]; + + postPatch = '' + sed "s|qalc_binary = \"qalc\"|qalc_binary = \"${libqalculate}/bin/qalc\"|" -i src/calc.c + ''; + + meta = with stdenv.lib; { + description = "Do live calculations in rofi!"; + homepage = "https://github.com/svenstaro/rofi-calc"; + license = licenses.mit; + maintainers = with maintainers; [ luc65r albakham ]; + platforms = [ "x86_64-linux" "x86_64-darwin" ]; + }; +} + diff --git a/pkgs/applications/science/misc/rink/default.nix b/pkgs/applications/science/misc/rink/default.nix index 1bb74ec17a3..839fc8f9546 100644 --- a/pkgs/applications/science/misc/rink/default.nix +++ b/pkgs/applications/science/misc/rink/default.nix @@ -16,8 +16,8 @@ rustPlatform.buildRustPackage rec { cargoSha256 = "0shlh0m9k0iqxpv9zmiw7a6v197swrvpz9x6qzhximzkdwni9gz9"; - buildInputs = [ pkgconfig ]; - propagatedBuildInputs = [ openssl gmp ncurses ]; + nativeBuildInputs = [ pkgconfig ]; + buildInputs = [ openssl gmp ncurses ]; # Some tests fail and/or attempt to use internet servers. doCheck = false; diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 27bf47e890a..34bdaf6bacf 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -2,7 +2,7 @@ python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "5.10.0"; + version = "5.13.0"; propagatedBuildInputs = with python3Packages; [ appdirs @@ -22,13 +22,13 @@ python3Packages.buildPythonApplication rec { src = python3Packages.fetchPypi { inherit pname version; - sha256 = "0n8d5c8sc90kfdw740ad9ffbkg1ic3k1pmlnk68qr4w4vc98pym3"; + sha256 = "11snr7sgv70d3y63s5svijfx8f4xpggh96g8chr6lccl4mi1s9x9"; }; doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json meta = with stdenv.lib; { - homepage = http://snakemake.bitbucket.io; + homepage = "http://snakemake.bitbucket.io"; license = licenses.mit; description = "Python-based execution environment for make-like workflows"; longDescription = '' |