diff options
Diffstat (limited to 'pkgs/applications/science')
27 files changed, 205 insertions, 135 deletions
diff --git a/pkgs/applications/science/astronomy/gravit/default.nix b/pkgs/applications/science/astronomy/gravit/default.nix index baf9ed7fc184d..d557f32bb6da1 100644 --- a/pkgs/applications/science/astronomy/gravit/default.nix +++ b/pkgs/applications/science/astronomy/gravit/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, SDL, SDL_ttf, SDL_image, libSM, libICE, libGLU, libGL, libpng, lua5, autoconf, automake }: stdenv.mkDerivation rec { - name = "gravit-0.5.1"; + pname = "gravit"; + version = "0.5.1"; src = fetchurl { - url = "https://gravit.slowchop.com/media/downloads/${name}.tgz"; + url = "https://gravit.slowchop.com/media/downloads/gravit-${version}.tgz"; sha256 = "14vf7zj2bgrl96wsl3f1knsggc8h9624354ajzd72l46y09x5ky7"; }; diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index f147c0422e454..b6286d11c8cbd 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -1,11 +1,12 @@ -{lib, stdenv, fetchurl, cmake}: +{ lib, stdenv, fetchurl, cmake }: -stdenv.mkDerivation { - name = "cmtk-3.3.1"; +stdenv.mkDerivation rec { + pname = "cmtk"; + version = "3.3.1"; src = fetchurl { name = "cmtk-source.tar.gz"; - url = "https://www.nitrc.org/frs/download.php/8198/CMTK-3.3.1-Source.tar.gz//?i_agree=1&download_now=1"; + url = "https://www.nitrc.org/frs/download.php/8198/CMTK-${version}-Source.tar.gz//?i_agree=1&download_now=1"; sha256 = "1nmsga9m7vcc4y4a6zl53ra3mwlgjwdgsq1j291awkn7zr1az6qs"; }; @@ -14,13 +15,13 @@ stdenv.mkDerivation { NIX_CFLAGS_COMPILE = lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing"; meta = with lib; { - description = "Computational Morphometry Toolkit "; + description = "Computational Morphometry Toolkit "; longDescription = ''A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O''; maintainers = with maintainers; [ tbenst ]; platforms = platforms.all; - license = licenses.gpl3; - homepage = "https://www.nitrc.org/projects/cmtk/"; + license = licenses.gpl3; + homepage = "https://www.nitrc.org/projects/cmtk/"; }; } diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index 2e11c1d8c58cb..4f23f3f9a82c1 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, cmake, zlib }: -stdenv.mkDerivation { - name = "diamond-0.8.36"; +stdenv.mkDerivation rec { + pname = "diamond"; + version = "0.8.36"; src = fetchurl { - url = "https://github.com/bbuchfink/diamond/archive/v0.8.36.tar.gz"; + url = "https://github.com/bbuchfink/diamond/archive/v${version}.tar.gz"; sha256 = "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh"; }; @@ -30,7 +31,7 @@ stdenv.mkDerivation { B. Buchfink, Xie C., D. Huson, "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12, 59-60 (2015). - ''; + ''; homepage = "https://github.com/bbuchfink/diamond"; license = { fullName = "University of Tuebingen, Benjamin Buchfink"; diff --git a/pkgs/applications/science/biology/ecopcr/default.nix b/pkgs/applications/science/biology/ecopcr/default.nix index 019370378605b..4ed11857a30e5 100644 --- a/pkgs/applications/science/biology/ecopcr/default.nix +++ b/pkgs/applications/science/biology/ecopcr/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, gcc, zlib, python27 }: stdenv.mkDerivation rec { - name = "ecopcr-0.8.0"; + pname = "ecopcr"; + version = "0.8.0"; src = fetchurl { - url = "https://git.metabarcoding.org/obitools/ecopcr/uploads/6f37991b325c8c171df7e79e6ae8d080/${name}.tar.gz"; + url = "https://git.metabarcoding.org/obitools/ecopcr/uploads/6f37991b325c8c171df7e79e6ae8d080/ecopcr-${version}.tar.gz"; sha256 = "10c58hj25z78jh0g3zcbx4890yd2qrvaaanyx8mn9p49mmyf5pk6"; }; diff --git a/pkgs/applications/science/biology/emboss/default.nix b/pkgs/applications/science/biology/emboss/default.nix index 5cbcd46ee07cf..29669d027303a 100644 --- a/pkgs/applications/science/biology/emboss/default.nix +++ b/pkgs/applications/science/biology/emboss/default.nix @@ -1,9 +1,11 @@ -{lib, stdenv, fetchurl, readline, perl, libharu, libX11, libpng, libXt, zlib}: +{ lib, stdenv, fetchurl, readline, perl, libharu, libX11, libpng, libXt, zlib }: + +stdenv.mkDerivation rec { + pname = "emboss"; + version = "6.6.0"; -stdenv.mkDerivation { - name = "emboss-6.6.0"; src = fetchurl { - url = "ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz"; + url = "ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${version}.tar.gz"; sha256 = "7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e"; }; @@ -16,13 +18,13 @@ stdenv.mkDerivation { ''; meta = { - description = "The European Molecular Biology Open Software Suite"; + description = "The European Molecular Biology Open Software Suite"; longDescription = ''EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community, including libraries. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web.''; - license = lib.licenses.gpl2; - homepage = "http://emboss.sourceforge.net/"; + license = lib.licenses.gpl2; + homepage = "http://emboss.sourceforge.net/"; }; } diff --git a/pkgs/applications/science/biology/iv/default.nix b/pkgs/applications/science/biology/iv/default.nix index 72cf9c86e65b3..ba1b91298bb32 100644 --- a/pkgs/applications/science/biology/iv/default.nix +++ b/pkgs/applications/science/biology/iv/default.nix @@ -1,32 +1,43 @@ -{ lib, stdenv, fetchurl, neuron-version -, libX11, libXext, patchelf +{ lib +, stdenv +, fetchurl +, neuron-version +, libX11 +, libXext +, patchelf }: -stdenv.mkDerivation rec - { name = "iv-19"; - src = fetchurl - { url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${neuron-version}/${name}.tar.gz"; - sha256 = "07a3g8zzay4h0bls7fh89dd0phn7s34c2g15pij6dsnwpmjg06yx"; - }; - nativeBuildInputs = [ patchelf ]; - buildInputs = [ libXext ]; - propagatedBuildInputs = [ libX11 ]; - hardeningDisable = [ "format" ]; - postInstall = '' - for dir in $out/*; do # */ - if [ -d $dir/lib ]; then - mv $dir/* $out # */ - rmdir $dir - break - fi - done - '' + lib.optionalString stdenv.isLinux '' - patchelf --add-needed ${libX11}/lib/libX11.so $out/lib/libIVhines.so - ''; - meta = with lib; - { description = "InterViews graphical library for Neuron"; - license = licenses.bsd3; - homepage = "http://www.neuron.yale.edu/neuron"; - platforms = platforms.all; - }; - } +stdenv.mkDerivation rec { + pname = "iv"; + version = "19"; + + src = fetchurl { + url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${neuron-version}/iv-${version}.tar.gz"; + sha256 = "07a3g8zzay4h0bls7fh89dd0phn7s34c2g15pij6dsnwpmjg06yx"; + }; + + nativeBuildInputs = [ patchelf ]; + buildInputs = [ libXext ]; + propagatedBuildInputs = [ libX11 ]; + + hardeningDisable = [ "format" ]; + + postInstall = '' + for dir in $out/*; do # */ + if [ -d $dir/lib ]; then + mv $dir/* $out # */ + rmdir $dir + break + fi + done + '' + lib.optionalString stdenv.isLinux '' + patchelf --add-needed ${libX11}/lib/libX11.so $out/lib/libIVhines.so + ''; + + meta = with lib; { + description = "InterViews graphical library for Neuron"; + license = licenses.bsd3; + homepage = "http://www.neuron.yale.edu/neuron"; + platforms = platforms.all; + }; +} diff --git a/pkgs/applications/science/chemistry/avogadro/default.nix b/pkgs/applications/science/chemistry/avogadro/default.nix index f5c6d79e28aa5..c6339bab1228e 100644 --- a/pkgs/applications/science/chemistry/avogadro/default.nix +++ b/pkgs/applications/science/chemistry/avogadro/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, cmake, qt4, zlib, eigen, openbabel, pkg-config, libGLU, libGL, libX11, doxygen }: stdenv.mkDerivation rec { - name = "avogadro-1.1.1"; + pname = "avogadro"; + version = "1.1.1"; src = fetchurl { - url = "mirror://sourceforge/avogadro/${name}.tar.bz2"; + url = "mirror://sourceforge/avogadro/avogadro-${version}.tar.bz2"; sha256 = "050ag9p4vg7jg8hj1wqfv7lsm6ar2isxjw2vw85s49vsl7g7nvzy"; }; diff --git a/pkgs/applications/science/electronics/archimedes/default.nix b/pkgs/applications/science/electronics/archimedes/default.nix index 731f2db56af53..8bceed08e1db6 100644 --- a/pkgs/applications/science/electronics/archimedes/default.nix +++ b/pkgs/applications/science/electronics/archimedes/default.nix @@ -1,10 +1,11 @@ -{lib, stdenv, fetchurl}: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation rec { - name = "archimedes-2.0.1"; + pname = "archimedes"; + version = "2.0.1"; src = fetchurl { - url = "mirror://gnu/archimedes/${name}.tar.gz"; + url = "mirror://gnu/archimedes/archimedes-${version}.tar.gz"; sha256 = "0jfpnd3pns5wxcxbiw49v5sgpmm5b4v8s4q1a5292hxxk2hzmb3z"; }; diff --git a/pkgs/applications/science/electronics/qfsm/default.nix b/pkgs/applications/science/electronics/qfsm/default.nix index de79abc3e511c..b2e3704cba70f 100644 --- a/pkgs/applications/science/electronics/qfsm/default.nix +++ b/pkgs/applications/science/electronics/qfsm/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, qt4, cmake, graphviz, pkg-config }: stdenv.mkDerivation rec { - name = "qfsm-0.54.0"; + pname = "qfsm"; + version = "0.54.0"; src = fetchurl { - url = "mirror://sourceforge/qfsm/${name}-Source.tar.bz2"; + url = "mirror://sourceforge/qfsm/qfsm-${version}-Source.tar.bz2"; sha256 = "0rl7bc5cr29ng67yij4akciyid9z7npal812ys4c3m229vjvflrb"; }; diff --git a/pkgs/applications/science/electronics/tkgate/1.x.nix b/pkgs/applications/science/electronics/tkgate/1.x.nix index 6a39995855344..f8741cd8d1804 100644 --- a/pkgs/applications/science/electronics/tkgate/1.x.nix +++ b/pkgs/applications/science/electronics/tkgate/1.x.nix @@ -5,10 +5,11 @@ let libiconvLib = lib.optionalString stdenv.isLinux "${glibc.out}/lib"; in stdenv.mkDerivation rec { - name = "tkgate-1.8.7"; + pname = "tkgate"; + version = "1.8.7"; src = fetchurl { - url = "http://www.tkgate.org/downloads/${name}.tgz"; + url = "http://www.tkgate.org/downloads/tkgate-${version}.tgz"; sha256 = "1pqywkidfpdbj18i03h97f4cimld4fb3mqfy8jjsxs12kihm18fs"; }; diff --git a/pkgs/applications/science/geometry/tetgen/1.4.nix b/pkgs/applications/science/geometry/tetgen/1.4.nix index 245d4c12bfe07..684f5913f79fe 100644 --- a/pkgs/applications/science/geometry/tetgen/1.4.nix +++ b/pkgs/applications/science/geometry/tetgen/1.4.nix @@ -1,10 +1,11 @@ -{lib, stdenv, fetchurl}: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation rec { - name = "tetgen-1.4.3"; + pname = "tetgen"; + version = "1.4.3"; src = fetchurl { - url = "${meta.homepage}/files/tetgen1.4.3.tar.gz"; + url = "${meta.homepage}/files/tetgen${version}.tar.gz"; sha256 = "0d70vjqdapmy1ghlsxjlvl5z9yp310zw697bapc4zxmp0sxi29wm"; }; diff --git a/pkgs/applications/science/logic/aspino/default.nix b/pkgs/applications/science/logic/aspino/default.nix index f9cc97893da8f..fc16423b671ef 100644 --- a/pkgs/applications/science/logic/aspino/default.nix +++ b/pkgs/applications/science/logic/aspino/default.nix @@ -8,7 +8,8 @@ let in stdenv.mkDerivation { - name = "aspino-unstable-2017-03-09"; + pname = "aspino"; + version = "unstable-2017-03-09"; src = fetchFromGitHub { owner = "alviano"; diff --git a/pkgs/applications/science/logic/gappa/default.nix b/pkgs/applications/science/logic/gappa/default.nix index be1d6f253bc59..af6673caa54f3 100644 --- a/pkgs/applications/science/logic/gappa/default.nix +++ b/pkgs/applications/science/logic/gappa/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, gmp, mpfr, boost }: -stdenv.mkDerivation { - name = "gappa-1.4.0"; +stdenv.mkDerivation rec { + pname = "gappa"; + version = "1.4.0"; src = fetchurl { - url = "https://gforge.inria.fr/frs/download.php/file/38436/gappa-1.4.0.tar.gz"; + url = "https://gforge.inria.fr/frs/download.php/file/38436/gappa-${version}.tar.gz"; sha256 = "12x42z901pr05ldmparqdi8sq9s7fxbavhzk2dbq3l6hy247dwbb"; }; diff --git a/pkgs/applications/science/logic/hol_light/default.nix b/pkgs/applications/science/logic/hol_light/default.nix index 24faa98f777ba..e66fe992e189a 100644 --- a/pkgs/applications/science/logic/hol_light/default.nix +++ b/pkgs/applications/science/logic/hol_light/default.nix @@ -3,11 +3,11 @@ let load_num = if num == null then "" else - '' - -I ${num}/lib/ocaml/${ocaml.version}/site-lib/num \ - -I ${num}/lib/ocaml/${ocaml.version}/site-lib/top-num \ - -I ${num}/lib/ocaml/${ocaml.version}/site-lib/stublibs \ - ''; + '' + -I ${num}/lib/ocaml/${ocaml.version}/site-lib/num \ + -I ${num}/lib/ocaml/${ocaml.version}/site-lib/top-num \ + -I ${num}/lib/ocaml/${ocaml.version}/site-lib/stublibs \ + ''; start_script = '' @@ -21,19 +21,22 @@ let in stdenv.mkDerivation { - name = "hol_light-2019-10-06"; + pname = "hol_light"; + version = "unstable-2019-10-06"; src = fetchFromGitHub { - owner = "jrh13"; - repo = "hol-light"; - rev = "5c91b2ded8a66db571824ecfc18b4536c103b23e"; + owner = "jrh13"; + repo = "hol-light"; + rev = "5c91b2ded8a66db571824ecfc18b4536c103b23e"; sha256 = "0sxsk8z08ba0q5aixdyczcx5l29lb51ba4ip3d2fry7y604kjsx6"; }; - patches = [(fetchpatch { - url = "https://salsa.debian.org/ocaml-team/hol-light/-/raw/master/debian/patches/0004-Fix-compilation-with-camlp5-7.11.patch"; - sha256 = "180qmxbrk3vb1ix7j77hcs8vsar91rs11s5mm8ir5352rz7ylicr"; - })]; + patches = [ + (fetchpatch { + url = "https://salsa.debian.org/ocaml-team/hol-light/-/raw/master/debian/patches/0004-Fix-compilation-with-camlp5-7.11.patch"; + sha256 = "180qmxbrk3vb1ix7j77hcs8vsar91rs11s5mm8ir5352rz7ylicr"; + }) + ]; buildInputs = [ ocaml camlp5 ]; propagatedBuildInputs = [ num ]; @@ -47,9 +50,9 @@ stdenv.mkDerivation { meta = with lib; { description = "Interactive theorem prover based on Higher-Order Logic"; - homepage = "http://www.cl.cam.ac.uk/~jrh13/hol-light/"; - license = licenses.bsd2; - platforms = platforms.unix; + homepage = "http://www.cl.cam.ac.uk/~jrh13/hol-light/"; + license = licenses.bsd2; + platforms = platforms.unix; maintainers = with maintainers; [ thoughtpolice maggesi vbgl ]; }; } diff --git a/pkgs/applications/science/logic/open-wbo/default.nix b/pkgs/applications/science/logic/open-wbo/default.nix index 77db8ae3384da..193f603656dca 100644 --- a/pkgs/applications/science/logic/open-wbo/default.nix +++ b/pkgs/applications/science/logic/open-wbo/default.nix @@ -1,7 +1,8 @@ { lib, stdenv, fetchFromGitHub, zlib, gmp }: stdenv.mkDerivation { - name = "open-wbo-2.0"; + pname = "open-wbo"; + version = "2.0"; src = fetchFromGitHub { owner = "sat-group"; diff --git a/pkgs/applications/science/logic/prover9/default.nix b/pkgs/applications/science/logic/prover9/default.nix index 7fedca72b6980..2f57fca972974 100644 --- a/pkgs/applications/science/logic/prover9/default.nix +++ b/pkgs/applications/science/logic/prover9/default.nix @@ -1,7 +1,8 @@ -{lib, stdenv, fetchurl}: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation { - name = "prover9-2009-11a"; + pname = "prover9"; + version = "2009-11a"; src = fetchurl { url = "https://www.cs.unm.edu/~mccune/mace4/download/LADR-2009-11A.tar.gz"; @@ -40,6 +41,6 @@ stdenv.mkDerivation { the Otter Prover. This is the LADR command-line version. ''; platforms = lib.platforms.linux; - maintainers = []; + maintainers = [ ]; }; } diff --git a/pkgs/applications/science/logic/redprl/default.nix b/pkgs/applications/science/logic/redprl/default.nix index 43a2ec7e97e23..05a7b63f55681 100644 --- a/pkgs/applications/science/logic/redprl/default.nix +++ b/pkgs/applications/science/logic/redprl/default.nix @@ -1,6 +1,8 @@ { lib, stdenv, fetchgit, mlton }: stdenv.mkDerivation { - name = "redprl-2017-03-28"; + pname = "redprl"; + version = "unstable-2017-03-28"; + src = fetchgit { url = "https://github.com/RedPRL/sml-redprl.git"; rev = "bdf027de732e4a8d10f9f954389dfff0c822f18b"; @@ -18,11 +20,11 @@ stdenv.mkDerivation { mkdir -p $out/bin mv ./bin/redprl $out/bin ''; - meta = { + meta = with lib; { description = "A proof assistant for Nominal Computational Type Theory"; homepage = "http://www.redprl.org/"; - license = lib.licenses.mit; - maintainers = [ lib.maintainers.acowley ]; - platforms = lib.platforms.unix; + license = licenses.mit; + maintainers = with maintainers; [ acowley ]; + platforms = platforms.unix; }; } diff --git a/pkgs/applications/science/logic/sad/default.nix b/pkgs/applications/science/logic/sad/default.nix index fe0ca1b3017ba..a509d70ed4624 100644 --- a/pkgs/applications/science/logic/sad/default.nix +++ b/pkgs/applications/science/logic/sad/default.nix @@ -1,9 +1,10 @@ { lib, stdenv, fetchurl, haskell, spass }: -stdenv.mkDerivation { - name = "system-for-automated-deduction-2.3.25"; +stdenv.mkDerivation rec { + pname = "system-for-automated-deduction"; + version = "2.3.25"; src = fetchurl { - url = "http://nevidal.org/download/sad-2.3-25.tar.gz"; + url = "http://nevidal.org/download/sad-${version}.tar.gz"; sha256 = "10jd93xgarik7xwys5lq7fx4vqp7c0yg1gfin9cqfch1k1v8ap4b"; }; buildInputs = [ haskell.compiler.ghc844 spass ]; @@ -15,7 +16,7 @@ stdenv.mkDerivation { ]; postPatch = '' substituteInPlace Alice/Main.hs --replace init.opt $out/init.opt - ''; + ''; installPhase = '' mkdir -p $out/{bin,provers} install alice $out/bin @@ -23,18 +24,18 @@ stdenv.mkDerivation { substituteAll provers/provers.dat $out/provers/provers.dat substituteAll init.opt $out/init.opt cp -r examples $out - ''; + ''; inherit spass; meta = { description = "A program for automated proving of mathematical texts"; longDescription = '' The system for automated deduction is intended for automated processing of formal mathematical texts written in a special language called ForTheL (FORmal THEory Language) or in a traditional first-order language - ''; + ''; license = lib.licenses.gpl3Plus; maintainers = [ lib.maintainers.schmitthenner ]; homepage = "http://nevidal.org/sad.en.html"; platforms = lib.platforms.linux; - broken = true; # ghc-8.4.4 is gone from Nixpkgs + broken = true; # ghc-8.4.4 is gone from Nixpkgs }; } diff --git a/pkgs/applications/science/math/csdp/default.nix b/pkgs/applications/science/math/csdp/default.nix index 02c4c134f92e9..6ce03008d3a98 100644 --- a/pkgs/applications/science/math/csdp/default.nix +++ b/pkgs/applications/science/math/csdp/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchurl, blas, gfortran, lapack }: -stdenv.mkDerivation { - name = "csdp-6.1.1"; +stdenv.mkDerivation rec { + pname = "csdp"; + version = "6.1.1"; src = fetchurl { - url = "https://www.coin-or.org/download/source/Csdp/Csdp-6.1.1.tgz"; + url = "https://www.coin-or.org/download/source/Csdp/Csdp-${version}.tgz"; sha256 = "1f9ql6cjy2gwiyc51ylfan24v1ca9sjajxkbhszlds1lqmma8n05"; }; diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index 58b2a617bd63f..808d89ef96361 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -1,5 +1,13 @@ -{ lib, stdenv, fetchurl, ocamlPackages, makeWrapper -, libGLU, libGL, freeglut, mpfr, gmp +{ lib +, stdenv +, fetchurl +, ocamlPackages +, makeWrapper +, libGLU +, libGL +, freeglut +, mpfr +, gmp , pkgsHostTarget }: @@ -7,24 +15,32 @@ let inherit (pkgsHostTarget.targetPackages.stdenv) cc; in -stdenv.mkDerivation { - name = "glsurf-3.3.1"; +stdenv.mkDerivation rec { + pname = "glsurf"; + version = "3.3.1"; src = fetchurl { - url = "https://raffalli.eu/~christophe/glsurf/glsurf-3.3.1.tar.gz"; + url = "https://raffalli.eu/~christophe/glsurf/glsurf-${version}.tar.gz"; sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7"; }; nativeBuildInputs = [ makeWrapper ] ++ (with ocamlPackages; [ - ocaml findlib + ocaml + findlib ]); buildInputs = [ - freeglut libGL libGLU mpfr gmp + freeglut + libGL + libGLU + mpfr + gmp ] ++ (with ocamlPackages; [ - camlp4 lablgl camlimages_4_2_4 + camlp4 + lablgl + camlimages_4_2_4 ]); postPatch = '' diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix index 5c0de33a71ae1..3ddcd6206d688 100644 --- a/pkgs/applications/science/math/jags/default.nix +++ b/pkgs/applications/science/math/jags/default.nix @@ -1,9 +1,11 @@ -{lib, stdenv, fetchurl, gfortran, blas, lapack}: +{ lib, stdenv, fetchurl, gfortran, blas, lapack }: stdenv.mkDerivation rec { - name = "JAGS-4.3.0"; + pname = "JAGS"; + version = "4.3.0"; + src = fetchurl { - url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz"; + url = "mirror://sourceforge/mcmc-jags/JAGS-${version}.tar.gz"; sha256 = "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"; }; @@ -15,8 +17,8 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Just Another Gibbs Sampler"; - license = licenses.gpl2; - homepage = "http://mcmc-jags.sourceforge.net"; + license = licenses.gpl2; + homepage = "http://mcmc-jags.sourceforge.net"; maintainers = [ maintainers.andres ]; platforms = platforms.unix; }; diff --git a/pkgs/applications/science/math/mathematica/9.nix b/pkgs/applications/science/math/mathematica/9.nix index 88db3c4b2e92c..90a7ada99504b 100644 --- a/pkgs/applications/science/math/mathematica/9.nix +++ b/pkgs/applications/science/math/mathematica/9.nix @@ -1,4 +1,5 @@ -{ lib, stdenv +{ lib +, stdenv , coreutils , patchelf , requireFile @@ -22,11 +23,11 @@ let throw "Mathematica requires i686-linux or x86_64 linux"; in stdenv.mkDerivation rec { - - name = "mathematica-9.0.0"; + pname = "mathematica"; + version = "9.0.0"; src = requireFile { - name = "Mathematica_9.0.0_LINUX.sh"; + name = "Mathematica_${version}_LINUX.sh"; message = '' This nix expression requires that Mathematica_9.0.0_LINUX.sh is already part of the store. Find the file on your Mathematica CD @@ -61,7 +62,7 @@ stdenv.mkDerivation rec { ldpath = lib.makeLibraryPath buildInputs + lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") - (":" + lib.makeSearchPathOutput "lib" "lib64" buildInputs); + (":" + lib.makeSearchPathOutput "lib" "lib64" buildInputs); phases = "unpackPhase installPhase fixupPhase"; diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix index 588df51554ab9..6456608e7dbc1 100644 --- a/pkgs/applications/science/math/msieve/default.nix +++ b/pkgs/applications/science/math/msieve/default.nix @@ -1,10 +1,11 @@ -{lib, stdenv, fetchurl, zlib, gmp, ecm }: +{ lib, stdenv, fetchurl, zlib, gmp, ecm }: -stdenv.mkDerivation { - name = "msieve-1.53"; +stdenv.mkDerivation rec { + pname = "msieve"; + version = "1.53"; src = fetchurl { - url = "mirror://sourceforge/msieve/msieve/Msieve%20v1.53/msieve153_src.tar.gz"; + url = "mirror://sourceforge/msieve/msieve/Msieve%20v${version}/msieve${lib.replaceStrings ["."] [""] version}_src.tar.gz"; sha256 = "1d1vv7j4rh3nnxsmvafi73qy7lw7n3akjlm5pjl3m936yapvmz65"; }; diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index d53236d8070cc..4545203dacca0 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -1,7 +1,7 @@ { lib, stdenv, fetchurl, unzip }: stdenv.mkDerivation { - name = "perseus-4-beta"; + pname = "perseus"; version = "4-beta"; nativeBuildInputs = [ unzip ]; @@ -34,7 +34,7 @@ stdenv.mkDerivation { ''; homepage = "http://www.sas.upenn.edu/~vnanda/perseus/index.html"; license = lib.licenses.gpl3; - maintainers = with lib.maintainers; [erikryb]; + maintainers = with lib.maintainers; [ erikryb ]; platforms = lib.platforms.linux; }; } diff --git a/pkgs/applications/science/math/ries/default.nix b/pkgs/applications/science/math/ries/default.nix index e46553d7b09ed..eb759723256db 100644 --- a/pkgs/applications/science/math/ries/default.nix +++ b/pkgs/applications/science/math/ries/default.nix @@ -1,10 +1,11 @@ { lib, stdenv, fetchzip }: -stdenv.mkDerivation { - name = "ries-2018-04-11"; +stdenv.mkDerivation rec { + pname = "ries"; + version = "2018.04.11-1"; # upstream does not provide a stable link src = fetchzip { - url = "https://salsa.debian.org/debian/ries/-/archive/debian/2018.04.11-1/ries-debian-2018.04.11-1.zip"; + url = "https://salsa.debian.org/debian/ries/-/archive/debian/${version}/ries-debian-${version}.zip"; sha256 = "1h2wvd4k7f0l0i1vm9niz453xdbcs3nxccmri50qyrzzzc1b0842"; }; diff --git a/pkgs/applications/science/misc/openmvs/default.nix b/pkgs/applications/science/misc/openmvs/default.nix index 731230130caf9..a92920c5e7958 100644 --- a/pkgs/applications/science/misc/openmvs/default.nix +++ b/pkgs/applications/science/misc/openmvs/default.nix @@ -1,9 +1,24 @@ -{ lib, stdenv, fetchFromGitHub, pkg-config, cmake -, eigen, opencv, ceres-solver, cgal, boost, vcg -, gmp, mpfr, glog, gflags, libjpeg_turbo }: +{ lib +, stdenv +, fetchFromGitHub +, pkg-config +, cmake +, eigen +, opencv +, ceres-solver +, cgal +, boost +, vcg +, gmp +, mpfr +, glog +, gflags +, libjpeg_turbo +}: stdenv.mkDerivation { - name = "openmvs-unstable-2018-05-26"; + pname = "openmvs"; + version = "unstable-2018-05-26"; src = fetchFromGitHub { owner = "cdcseacave"; diff --git a/pkgs/applications/science/misc/vite/default.nix b/pkgs/applications/science/misc/vite/default.nix index ed9d185287567..7d284d5eebb7e 100644 --- a/pkgs/applications/science/misc/vite/default.nix +++ b/pkgs/applications/science/misc/vite/default.nix @@ -10,7 +10,8 @@ let }; in stdenv.mkDerivation { - name = "vite-1.2pre${rev}"; + pname = "vite"; + version = "1.2pre${rev}"; src = fetchsvn { url = "svn://scm.gforge.inria.fr/svn/vite/trunk"; |