diff options
Diffstat (limited to 'pkgs/applications/science')
13 files changed, 16 insertions, 139 deletions
diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index 59b173ac98c..cfd1206f231 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { buildInputs = [ libyamlcpp ]; meta = with stdenv.lib; { - description = "dcm2niix DICOM to NIfTI converter"; + description = "DICOM to NIfTI converter"; longDescription = '' dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 5a1bb187886..014ae14cc79 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = false; meta = with stdenv.lib; { - description = "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data"; + description = "Program for quantifying abundances of transcripts from RNA-Seq data"; homepage = "https://pachterlab.github.io/kallisto"; license = licenses.bsd2; platforms = platforms.linux; diff --git a/pkgs/applications/science/electronics/openhantek6022/default.nix b/pkgs/applications/science/electronics/openhantek6022/default.nix index ad8fa3c7a7a..acdac346fd3 100644 --- a/pkgs/applications/science/electronics/openhantek6022/default.nix +++ b/pkgs/applications/science/electronics/openhantek6022/default.nix @@ -2,13 +2,13 @@ mkDerivation rec { pname = "openhantek6022"; - version = "3.1.2"; + version = "3.1.3"; src = fetchFromGitHub { owner = "OpenHantek"; repo = "OpenHantek6022"; rev = version; - sha256 = "104j7d3i5y6jd20c2z3l10sr6sgdy8iki3g9mlwhddnr8x6nzc03"; + sha256 = "1n4l8ks5808d99zj1vj0ck0v1lb9s7iv3ahww7ximbf9iha39pbm"; }; nativeBuildInputs = [ cmake makeWrapper ]; diff --git a/pkgs/applications/science/logic/coq2html/default.nix b/pkgs/applications/science/logic/coq2html/default.nix index 2e56eda893e..e53e8e7392c 100644 --- a/pkgs/applications/science/logic/coq2html/default.nix +++ b/pkgs/applications/science/logic/coq2html/default.nix @@ -1,6 +1,6 @@ { stdenv, fetchgit, ocaml }: -let +let version = "20170720"; in @@ -22,7 +22,7 @@ stdenv.mkDerivation { ''; meta = with stdenv.lib; { - description = "coq2html is an HTML documentation generator for Coq source files"; + description = "HTML documentation generator for Coq source files"; longDescription = '' coq2html is an HTML documentation generator for Coq source files. It is an alternative to the standard coqdoc documentation generator diff --git a/pkgs/applications/science/logic/ott/default.nix b/pkgs/applications/science/logic/ott/default.nix index ecc253a64d9..48ad63eaa99 100644 --- a/pkgs/applications/science/logic/ott/default.nix +++ b/pkgs/applications/science/logic/ott/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { postInstall = "opaline -prefix $out"; meta = { - description = "Ott: tool for the working semanticist"; + description = "A tool for the working semanticist"; longDescription = '' Ott is a tool for writing definitions of programming languages and calculi. It takes as input a definition of a language syntax and diff --git a/pkgs/applications/science/machine-learning/labelimg/default.nix b/pkgs/applications/science/machine-learning/labelimg/default.nix index 05c56b0b095..18c304e8316 100644 --- a/pkgs/applications/science/machine-learning/labelimg/default.nix +++ b/pkgs/applications/science/machine-learning/labelimg/default.nix @@ -28,7 +28,7 @@ makeWrapperArgs+=("''${qtWrapperArgs[@]}") ''; meta = with stdenv.lib; { - description = "LabelImg is a graphical image annotation tool and label object bounding boxes in images"; + description = "A graphical image annotation tool and label object bounding boxes in images"; homepage = "https://github.com/tzutalin/labelImg"; license = licenses.mit; platforms = platforms.linux; diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 717b240c1cc..25ee66e8f75 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -12,11 +12,11 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { - name = "R-4.0.2"; + name = "R-4.0.3"; src = fetchurl { url = "https://cran.r-project.org/src/base/R-4/${name}.tar.gz"; - sha256 = "0xdy3dy2bzdiba8z94hjykyra8si8a5q15s0bri7c26scjrymg6k"; + sha256 = "03cypg2qf7v9mq9mr9alz9w5y9m5kdgwbc97bp26pyymg253m609"; }; dontUseImakeConfigure = true; diff --git a/pkgs/applications/science/math/bliss/default.nix b/pkgs/applications/science/math/bliss/default.nix index 52b05646a70..9ab90134aad 100644 --- a/pkgs/applications/science/math/bliss/default.nix +++ b/pkgs/applications/science/math/bliss/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - description = "bliss is an open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs"; + description = "An open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs"; homepage = "http://www.tcs.hut.fi/Software/bliss/"; license = licenses.lgpl3; platforms = [ "i686-linux" "x86_64-linux" ]; diff --git a/pkgs/applications/science/math/maxima/5.41.nix b/pkgs/applications/science/math/maxima/5.41.nix deleted file mode 100644 index 829dffc6116..00000000000 --- a/pkgs/applications/science/math/maxima/5.41.nix +++ /dev/null @@ -1,102 +0,0 @@ -{ stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null -, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false -}: - -let - name = "maxima"; - # old version temporarily kept for sage, see discussion at - # https://github.com/NixOS/nixpkgs/commit/82254747af35f3e0e0d6f78023ded3a81e25331b - version = "5.41.0"; - - searchPath = - stdenv.lib.makeBinPath - (stdenv.lib.filter (x: x != null) [ sbcl ecl rlwrap tk gnuplot ]); -in -stdenv.mkDerivation ({ - inherit version; - name = "${name}-${version}"; - - src = fetchurl { - url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz"; - sha256 = "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"; - }; - - buildInputs = stdenv.lib.filter (x: x != null) [ - sbcl ecl texinfo perl python makeWrapper - ]; - - postInstall = '' - # Make sure that maxima can find its runtime dependencies. - for prog in "$out/bin/"*; do - wrapProgram "$prog" --prefix PATH ":" "$out/bin:${searchPath}" - done - # Move emacs modules and documentation into the right place. - mkdir -p $out/share/emacs $out/share/doc - ln -s ../maxima/${version}/emacs $out/share/emacs/site-lisp - ln -s ../maxima/${version}/doc $out/share/doc/maxima - '' - + (stdenv.lib.optionalString ecl-fasl '' - cp src/binary-ecl/maxima.fas* "$out/lib/maxima/${version}/binary-ecl/" - '') - ; - - patches = [ - # fix path to info dir (see https://trac.sagemath.org/ticket/11348) - (fetchpatch { - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/infodir.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; - sha256 = "09v64n60f7i6frzryrj0zd056lvdpms3ajky4f9p6kankhbiv21x"; - }) - - # fix https://sourceforge.net/p/maxima/bugs/2596/ - (fetchpatch { - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/matrixexp.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; - sha256 = "06961hn66rhjijfvyym21h39wk98sfxhp051da6gz0n9byhwc6zg"; - }) - - # undo https://sourceforge.net/p/maxima/code/ci/f5e9b0f7eb122c4e48ea9df144dd57221e5ea0ca, see see https://trac.sagemath.org/ticket/13364#comment:93 - (fetchpatch { - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/undoing_true_false_printing_patch.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; - sha256 = "0fvi3rcjv6743sqsbgdzazy9jb6r1p1yq63zyj9fx42wd1hgf7yx"; - }) - - # upstream bug https://sourceforge.net/p/maxima/bugs/2520/ (not fixed) - # introduced in https://trac.sagemath.org/ticket/13364 - (fetchpatch { - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/0001-taylor2-Avoid-blowing-the-stack-when-diff-expand-isn.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; - sha256 = "0xa0b6cr458zp7lc7qi0flv5ar0r3ivsqhjl0c3clv86di2y522d"; - }) - ] ++ stdenv.lib.optionals ecl-fasl [ - # build fasl, needed for ECL support - (fetchpatch { - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/maxima/patches/maxima.system.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; - sha256 = "18zafig8vflhkr80jq2ivk46k92dkszqlyq8cfmj0b2vcfjwwbar"; - }) - # There are some transient test failures. I hope this disables all those tests. - # If those test failures ever happen in the non-ecl version, that should be - # reportetd upstream. - ./known-ecl-failures.patch - ]; - - # Failures in the regression test suite won't abort the build process. We run - # the suite only so that potential errors show up in the build log. See also: - # https://sourceforge.net/tracker/?func=detail&aid=3365831&group_id=4933&atid=104933. - doCheck = true; - - enableParallelBuilding = true; - - meta = { - description = "Computer algebra system"; - homepage = "http://maxima.sourceforge.net"; - license = stdenv.lib.licenses.gpl2; - - longDescription = '' - Maxima is a fairly complete computer algebra system written in - lisp with an emphasis on symbolic computation. It is based on - DOE-MACSYMA and licensed under the GPL. Its abilities include - symbolic integration, 3D plotting, and an ODE solver. - ''; - - platforms = stdenv.lib.platforms.unix; - maintainers = [ stdenv.lib.maintainers.peti ]; - }; -}) diff --git a/pkgs/applications/science/math/maxima/known-ecl-failures.patch b/pkgs/applications/science/math/maxima/known-ecl-failures.patch deleted file mode 100644 index f1d612d993e..00000000000 --- a/pkgs/applications/science/math/maxima/known-ecl-failures.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff --git a/tests/testsuite.lisp b/tests/testsuite.lisp -index 45a81f4..36c35b8 100644 ---- a/tests/testsuite.lisp -+++ b/tests/testsuite.lisp -@@ -25,13 +25,14 @@ - ((mlist simp) "rtest10" 24 25) - ((mlist) "rtest11" #+(or gcl cmucl ccl64) 158 #+(or gcl cmucl ccl64) 174 #+gcl 175) - "rtest13" "rtest13s" -- "rtest14" -+ ;; "rtest14" ;; some tests sometimes fail with ecl, hard to reproduce. Observed failing: 250, 267, 297, 307, 310, 312, 315, 319 - "rtest15" - ;; ccl versions 1.11 and earlier fail test 50. Mark it as a - ;; known failure. Presumably 1.12 will have this fixed. - ((mlist simp) "rtest16" #+ccl 50) - "rtestode" "rtestode_zp" -- "rtest3" "rtest8" -+ "rtest3" -+ ((mlist simp) "rtest8" 104) ;; fails with ecl - ((mlist simp) "rtest12" 76 78) - "rexamples" - ((mlist simp) "rtesthyp" 105 112 113 123 124 128) diff --git a/pkgs/applications/science/math/rofi-calc/default.nix b/pkgs/applications/science/math/rofi-calc/default.nix index 40b2711ff65..ebf2d2f0475 100644 --- a/pkgs/applications/science/math/rofi-calc/default.nix +++ b/pkgs/applications/science/math/rofi-calc/default.nix @@ -12,13 +12,13 @@ stdenv.mkDerivation rec { pname = "rofi-calc"; - version = "1.8"; + version = "1.9"; src = fetchFromGitHub { owner = "svenstaro"; repo = pname; rev = "v${version}"; - sha256 = "0vwb9c3xvd2cms6cw8j8parg7w4bsxvvrd1wgggr8sz2p8rrvy5p"; + sha256 = "ZGY4ZtAG/ZnEnC80modZBV4RdRQElbkjeoKCEFVrncE="; }; nativeBuildInputs = [ @@ -48,7 +48,7 @@ stdenv.mkDerivation rec { homepage = "https://github.com/svenstaro/rofi-calc"; license = licenses.mit; maintainers = with maintainers; [ luc65r albakham ]; - platforms = [ "x86_64-linux" "x86_64-darwin" ]; + platforms = with platforms; linux; }; } diff --git a/pkgs/applications/science/misc/openmodelica/default.nix b/pkgs/applications/science/misc/openmodelica/default.nix index 50d4dcc1a9f..268ae53401f 100644 --- a/pkgs/applications/science/misc/openmodelica/default.nix +++ b/pkgs/applications/science/misc/openmodelica/default.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation { ''; meta = with stdenv.lib; { - description = "OpenModelica is an open-source Modelica-based modeling and simulation environment"; + description = "An open-source Modelica-based modeling and simulation environment"; homepage = "https://openmodelica.org"; license = licenses.gpl3; maintainers = with maintainers; [ smironov ]; diff --git a/pkgs/applications/science/programming/scyther/default.nix b/pkgs/applications/science/programming/scyther/default.nix index d1e948fe187..ca6b57de611 100644 --- a/pkgs/applications/science/programming/scyther/default.nix +++ b/pkgs/applications/science/programming/scyther/default.nix @@ -13,7 +13,7 @@ let }; meta = with lib; { - description = "Scyther is a tool for the automatic verification of security protocols"; + description = "A tool for the automatic verification of security protocols"; homepage = "https://www.cs.ox.ac.uk/people/cas.cremers/scyther/"; license = licenses.gpl2; maintainers = with maintainers; [ infinisil ]; |