diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math')
103 files changed, 5866 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/math/LiE/default.nix b/nixpkgs/pkgs/applications/science/math/LiE/default.nix new file mode 100644 index 000000000000..f5f3bb0a42b1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/LiE/default.nix @@ -0,0 +1,47 @@ +{ stdenv, fetchurl +, bison, readline }: + +stdenv.mkDerivation { + version = "2.2.2"; + # The current version of LiE is 2.2.2, which is more or less unchanged + # since about the year 2000. Minor bugfixes do get applied now and then. + pname = "lie"; + + meta = { + description = "A Computer algebra package for Lie group computations"; + homepage = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/"; + license = stdenv.lib.licenses.lgpl3; # see the website + + longDescription = '' + LiE is a computer algebra system that is specialised in computations + involving (reductive) Lie groups and their representations. It is + publically available for free in source code. For a description of its + characteristics, we refer to the following sources of information. + ''; # take from the website + + platforms = stdenv.lib.platforms.linux; + maintainers = [ ]; # this package is probably not going to change anyway + }; + + src = fetchurl { + url = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/conLiE.tar.gz"; + sha256 = "07lbj75qqr4pq1j1qz8fyfnmrz1gnk92lnsshxycfavxl5zzdmn4"; + }; + + buildInputs = [ bison readline ]; + + patchPhase = '' + substituteInPlace make_lie \ + --replace \`/bin/pwd\` $out + ''; + + installPhase = '' + mkdir -vp $out/bin + + cp -v Lie.exe $out + cp -v lie $out/bin + + cp -v LEARN* $out + cp -v INFO* $out + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix new file mode 100644 index 000000000000..52da3b4a1ac9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/R/default.nix @@ -0,0 +1,118 @@ +{ stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng +, libtiff, ncurses, pango, pcre2, perl, readline, tcl, texLive, tk, xz, zlib +, less, texinfo, graphviz, icu, pkgconfig, bison, imake, which, jdk, blas, lapack +, curl, Cocoa, Foundation, libobjc, libcxx, tzdata, fetchpatch +, withRecommendedPackages ? true +, enableStrictBarrier ? false +# R as of writing does not support outputting both .so and .a files; it outputs: +# --enable-R-static-lib conflicts with --enable-R-shlib and will be ignored +, static ? false +}: + +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + name = "R-4.0.0"; + + src = fetchurl { + url = "https://cran.r-project.org/src/base/R-4/${name}.tar.gz"; + sha256 = "0h1995smlyiyhx7gpg9paxsfqrcn6g9bbp5h9r47i6an3clv1gh6"; + }; + + dontUseImakeConfigure = true; + + buildInputs = [ + bzip2 gfortran libX11 libXmu libXt libXt libjpeg libpng libtiff ncurses + pango pcre2 perl readline texLive xz zlib less texinfo graphviz icu + pkgconfig bison imake which blas lapack curl tcl tk jdk + ] ++ stdenv.lib.optionals stdenv.isDarwin [ Cocoa Foundation libobjc libcxx ]; + + patches = [ + ./no-usr-local-search-paths.patch + ./fix-failing-test.patch + ]; + + prePatch = stdenv.lib.optionalString stdenv.isDarwin '' + substituteInPlace configure --replace "-install_name libR.dylib" "-install_name $out/lib/R/lib/libR.dylib" + ''; + + dontDisableStatic = static; + + preConfigure = '' + configureFlagsArray=( + --disable-lto + --with${stdenv.lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages + --with-blas="-L${blas}/lib -lblas" + --with-lapack="-L${lapack}/lib -llapack" + --with-readline + --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh" + --with-cairo + --with-libpng + --with-jpeglib + --with-libtiff + --with-ICU + ${stdenv.lib.optionalString enableStrictBarrier "--enable-strict-barrier"} + ${if static then "--enable-R-static-lib" else "--enable-R-shlib"} + AR=$(type -p ar) + AWK=$(type -p gawk) + CC=$(type -p cc) + CXX=$(type -p c++) + FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran" + JAVA_HOME="${jdk}" + RANLIB=$(type -p ranlib) + R_SHELL="${stdenv.shell}" + '' + stdenv.lib.optionalString stdenv.isDarwin '' + --disable-R-framework + OBJC="clang" + CPPFLAGS="-isystem ${libcxx}/include/c++/v1" + LDFLAGS="-L${libcxx}/lib" + '' + '' + ) + echo >>etc/Renviron.in "TCLLIBPATH=${tk}/lib" + echo >>etc/Renviron.in "TZDIR=${tzdata}/share/zoneinfo" + ''; + + installTargets = [ "install" "install-info" "install-pdf" ]; + + # The store path to "which" is baked into src/library/base/R/unix/system.unix.R, + # but Nix cannot detect it as a run-time dependency because the installed file + # is compiled and compressed, which hides the store path. + postFixup = "echo ${which} > $out/nix-support/undetected-runtime-dependencies"; + + doCheck = true; + preCheck = "export TZ=CET; bin/Rscript -e 'sessionInfo()'"; + + enableParallelBuilding = true; + + setupHook = ./setup-hook.sh; + + meta = with stdenv.lib; { + homepage = "http://www.r-project.org/"; + description = "Free software environment for statistical computing and graphics"; + license = licenses.gpl2Plus; + + longDescription = '' + GNU R is a language and environment for statistical computing and + graphics that provides a wide variety of statistical (linear and + nonlinear modelling, classical statistical tests, time-series + analysis, classification, clustering, ...) and graphical + techniques, and is highly extensible. One of R's strengths is the + ease with which well-designed publication-quality plots can be + produced, including mathematical symbols and formulae where + needed. R is an integrated suite of software facilities for data + manipulation, calculation and graphical display. It includes an + effective data handling and storage facility, a suite of operators + for calculations on arrays, in particular matrices, a large, + coherent, integrated collection of intermediate tools for data + analysis, graphical facilities for data analysis and display + either on-screen or on hardcopy, and a well-developed, simple and + effective programming language which includes conditionals, loops, + user-defined recursive functions and input and output facilities. + ''; + + platforms = platforms.all; + hydraPlatforms = platforms.linux; + + maintainers = with maintainers; [ peti timokau ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch new file mode 100644 index 000000000000..5fb3b3b9c317 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/R/fix-failing-test.patch @@ -0,0 +1,25 @@ +From e8f54bc562eb301d204b5f880614be58a2b39a2b Mon Sep 17 00:00:00 2001 +From: maechler <maechler@00db46b3-68df-0310-9c12-caf00c1e9a41> +Date: Mon, 30 Mar 2020 19:15:59 +0000 +Subject: [PATCH] no longer fail in norm() check for broken OpenBLAS Lapack + 3.9.0 + +git-svn-id: https://svn.r-project.org/R/trunk@78112 00db46b3-68df-0310-9c12-caf00c1e9a41 +--- + tests/reg-tests-1d.R | 3 ++- + 1 file changed, 2 insertions(+), 1 deletion(-) + +diff --git a/tests/reg-tests-1d.R b/tests/reg-tests-1d.R +index 6b7de765a95..fafd6911e7a 100644 +--- a/tests/reg-tests-1d.R ++++ b/tests/reg-tests-1d.R +@@ -3836,7 +3836,8 @@ stopifnot(is.na( norm(diag(c(1, NA)), "2") )) + ## norm(<matrix-w-NA>, "F") + (m <- cbind(0, c(NA, 0), 0:-1)) + nTypes <- eval(formals(base::norm)$type) # "O" "I" "F" "M" "2" +-stopifnot(is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN ++print( # stopifnot( -- for now, as Lapack is still broken in some OpenBLAS -- FIXME ++ is.na( print(vapply(nTypes, norm, 0., x = m)) )) # print(): show NA *or* NaN + ## "F" gave non-NA with LAPACK 3.9.0, before our patch in R-devel and R-patched + + diff --git a/nixpkgs/pkgs/applications/science/math/R/no-usr-local-search-paths.patch b/nixpkgs/pkgs/applications/science/math/R/no-usr-local-search-paths.patch new file mode 100644 index 000000000000..6c7f6d4ee02a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/R/no-usr-local-search-paths.patch @@ -0,0 +1,24 @@ +diff -ubr R-3.0.1-orig/configure R-3.0.1/configure +--- R-3.0.1-orig/configure 2013-07-04 10:46:42.336133947 +0200 ++++ R-3.0.1/configure 2013-07-04 10:46:17.181919960 +0200 +@@ -3800,13 +3800,13 @@ + : ${LIBnn=$libnn} + ## We provide these defaults so that headers and libraries in + ## '/usr/local' are found (by the native tools, mostly). +-if test -f "/sw/etc/fink.conf"; then +- : ${CPPFLAGS="-I/sw/include -I/usr/local/include"} +- : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"} +-else +- : ${CPPFLAGS="-I/usr/local/include"} +- : ${LDFLAGS="-L/usr/local/${LIBnn}"} +-fi ++# if test -f "/sw/etc/fink.conf"; then ++# : ${CPPFLAGS="-I/sw/include -I/usr/local/include"} ++# : ${LDFLAGS="-L/sw/lib -L/usr/local/lib"} ++# else ++# : ${CPPFLAGS="-I/usr/local/include"} ++# : ${LDFLAGS="-L/usr/local/${LIBnn}"} ++# fi + + ## take care not to override the command-line setting + if test "${libdir}" = '${exec_prefix}/lib'; then diff --git a/nixpkgs/pkgs/applications/science/math/R/setup-hook.sh b/nixpkgs/pkgs/applications/science/math/R/setup-hook.sh new file mode 100644 index 000000000000..6951e2a4b61b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/R/setup-hook.sh @@ -0,0 +1,7 @@ +addRLibPath () { + if [[ -d "$1/library" ]]; then + addToSearchPath R_LIBS_SITE "$1/library" + fi +} + +addEnvHooks "$targetOffset" addRLibPath diff --git a/nixpkgs/pkgs/applications/science/math/almonds/default.nix b/nixpkgs/pkgs/applications/science/math/almonds/default.nix new file mode 100644 index 000000000000..9edb0747b31e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/almonds/default.nix @@ -0,0 +1,26 @@ +{ stdenv, python3, fetchFromGitHub, ncurses }: + +with python3.pkgs; buildPythonApplication rec { + pname = "almonds"; + version = "1.25b"; + + src = fetchFromGitHub { + owner = "Tenchi2xh"; + repo = "Almonds"; + rev = version; + sha256 = "0j8d8jizivnfx8lpc4w6sbqj5hq35nfz0vdg7ld80sc5cs7jr3ws"; + }; + + nativeBuildInputs = [ pytest ]; + buildInputs = [ ncurses ]; + propagatedBuildInputs = [ pillow ]; + + checkPhase = "py.test"; + + meta = with stdenv.lib; { + description = "Terminal Mandelbrot fractal viewer"; + homepage = "https://github.com/Tenchi2xh/Almonds"; + license = licenses.mit; + maintainers = with maintainers; [ infinisil ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/bcal/default.nix b/nixpkgs/pkgs/applications/science/math/bcal/default.nix new file mode 100644 index 000000000000..18b6e051b3f2 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/bcal/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, python3Packages, readline }: + +with stdenv.lib; + +stdenv.mkDerivation rec { + pname = "bcal"; + version = "1.9"; + + src = fetchFromGitHub { + owner = "jarun"; + repo = "bcal"; + rev = "v${version}"; + sha256 = "0h6qi5rvzl6c6fsfdpdb3l4jcgip03l18i0b1x08z1y89i56y8mm"; + }; + + nativeBuildInputs = [ python3Packages.pytest ]; + + buildInputs = [ readline ]; + + doCheck = true; + checkPhase = '' + python3 -m pytest test.py + ''; + + installFlags = [ "DESTDIR=$(out)" "PREFIX=" ]; + + meta = { + description = "Storage conversion and expression calculator"; + homepage = "https://github.com/jarun/bcal"; + license = licenses.gpl3; + platforms = [ "aarch64-linux" "x86_64-darwin" "x86_64-linux" ]; + maintainers = with maintainers; [ jfrankenau ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/bliss/default.nix b/nixpkgs/pkgs/applications/science/math/bliss/default.nix new file mode 100644 index 000000000000..361b08846626 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/bliss/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchurl, unzip, doxygen }: + +stdenv.mkDerivation rec { + pname = "bliss"; + version = "0.73"; + + src = fetchurl { + url = "http://www.tcs.hut.fi/Software/bliss/${pname}-${version}.zip"; + sha256 = "f57bf32804140cad58b1240b804e0dbd68f7e6bf67eba8e0c0fa3a62fd7f0f84"; + }; + + patches = fetchurl { + url = "http://scip.zib.de/download/bugfixes/scip-5.0.1/bliss-0.73.patch"; + sha256 = "815868d6586bcd49ff3c28e14ccb536d38b2661151088fe08187c13909c5dab0"; + }; + + nativeBuildInputs = [ unzip doxygen ]; + + preBuild = '' + doxygen Doxyfile + ''; + + installPhase = '' + mkdir -p $out/bin $out/share/doc/bliss $out/lib $out/include/bliss + mv bliss $out/bin + mv html/* COPYING* $out/share/doc/bliss + mv *.a $out/lib + mv *.h *.hh $out/include/bliss + ''; + + 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."; + homepage = "http://www.tcs.hut.fi/Software/bliss/"; + license = licenses.lgpl3; + platforms = [ "i686-linux" "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/caffe/darwin.patch b/nixpkgs/pkgs/applications/science/math/caffe/darwin.patch new file mode 100644 index 000000000000..e8fa6a683f73 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/caffe/darwin.patch @@ -0,0 +1,47 @@ +diff --git a/Makefile b/Makefile +index c823f66e..65b90c5e 100644 +--- a/Makefile ++++ b/Makefile +@@ -32,9 +32,9 @@ SRC_DIRS := $(shell find * -type d -exec bash -c "find {} -maxdepth 1 \ + LIBRARY_NAME := $(PROJECT) + LIB_BUILD_DIR := $(BUILD_DIR)/lib + STATIC_NAME := $(LIB_BUILD_DIR)/lib$(LIBRARY_NAME).a +-DYNAMIC_VERSION_MAJOR := 1 +-DYNAMIC_VERSION_MINOR := 0 +-DYNAMIC_VERSION_REVISION := 0 ++DYNAMIC_VERSION_MAJOR := 1 ++DYNAMIC_VERSION_MINOR := 0 ++DYNAMIC_VERSION_REVISION := 0 + DYNAMIC_NAME_SHORT := lib$(LIBRARY_NAME).so + #DYNAMIC_SONAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR) + DYNAMIC_VERSIONED_NAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR).$(DYNAMIC_VERSION_MINOR).$(DYNAMIC_VERSION_REVISION) +diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake +index c48255c8..cf4c580e 100644 +--- a/cmake/Dependencies.cmake ++++ b/cmake/Dependencies.cmake +@@ -105,7 +105,6 @@ if(USE_OPENCV) + endif() + + # ---[ BLAS +-if(NOT APPLE) + set(BLAS "Atlas" CACHE STRING "Selected BLAS library") + set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL") + +@@ -123,17 +122,6 @@ if(NOT APPLE) + list(APPEND Caffe_LINKER_LIBS PUBLIC ${MKL_LIBRARIES}) + list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_MKL) + endif() +-elseif(APPLE) +- find_package(vecLib REQUIRED) +- list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${vecLib_INCLUDE_DIR}) +- list(APPEND Caffe_LINKER_LIBS PUBLIC ${vecLib_LINKER_LIBS}) +- +- if(VECLIB_FOUND) +- if(NOT vecLib_INCLUDE_DIR MATCHES "^/System/Library/Frameworks/vecLib.framework.*") +- list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_ACCELERATE) +- endif() +- endif() +-endif() + + # ---[ Python + if(BUILD_python) diff --git a/nixpkgs/pkgs/applications/science/math/caffe/default.nix b/nixpkgs/pkgs/applications/science/math/caffe/default.nix new file mode 100644 index 000000000000..4a6a2dc6c7e0 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/caffe/default.nix @@ -0,0 +1,142 @@ +{ config, stdenv, lib +, fetchFromGitHub +, fetchurl +, cmake +, boost +, gflags +, glog +, hdf5-cpp +, opencv3 +, protobuf +, doxygen +, blas +, Accelerate, CoreGraphics, CoreVideo +, lmdbSupport ? true, lmdb +, leveldbSupport ? true, leveldb, snappy +, cudaSupport ? config.cudaSupport or false, cudatoolkit +, cudnnSupport ? cudaSupport, cudnn ? null +, ncclSupport ? false, nccl ? null +, pythonSupport ? false, python ? null, numpy ? null +, substituteAll +}: + +assert leveldbSupport -> (leveldb != null && snappy != null); +assert cudnnSupport -> cudaSupport; +assert ncclSupport -> cudaSupport; +assert pythonSupport -> (python != null && numpy != null); + +let + toggle = bool: if bool then "ON" else "OFF"; + + test_model_weights = fetchurl { + url = "http://dl.caffe.berkeleyvision.org/bvlc_reference_caffenet.caffemodel"; + sha256 = "472d4a06035497b180636d8a82667129960371375bd10fcb6df5c6c7631f25e0"; + }; + +in + +stdenv.mkDerivation rec { + pname = "caffe"; + version = "1.0"; + + src = fetchFromGitHub { + owner = "BVLC"; + repo = "caffe"; + rev = version; + sha256 = "104jp3cm823i3cdph7hgsnj6l77ygbwsy35mdmzhmsi4jxprd9j3"; + }; + + enableParallelBuilding = true; + + nativeBuildInputs = [ cmake doxygen ]; + + cmakeFlags = + # It's important that caffe is passed the major and minor version only because that's what + # boost_python expects + [ (if pythonSupport then "-Dpython_version=${python.pythonVersion}" else "-DBUILD_python=OFF") + "-DBLAS=open" + ] ++ (if cudaSupport then [ + "-DCUDA_ARCH_NAME=All" + "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc" + ] else [ "-DCPU_ONLY=ON" ]) + ++ ["-DUSE_NCCL=${toggle ncclSupport}"] + ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"] + ++ ["-DUSE_LMDB=${toggle lmdbSupport}"]; + + buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv3 blas ] + ++ lib.optional cudaSupport cudatoolkit + ++ lib.optional cudnnSupport cudnn + ++ lib.optional lmdbSupport lmdb + ++ lib.optional ncclSupport nccl + ++ lib.optionals leveldbSupport [ leveldb snappy ] + ++ lib.optionals pythonSupport [ python numpy ] + ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ] + ; + + propagatedBuildInputs = lib.optionals pythonSupport ( + # requirements.txt + let pp = python.pkgs; in ([ + pp.numpy pp.scipy pp.scikitimage pp.h5py + pp.matplotlib pp.ipython pp.networkx pp.nose + pp.pandas pp.dateutil pp.protobuf pp.gflags + pp.pyyaml pp.pillow pp.six + ] ++ lib.optional leveldbSupport pp.leveldb) + ); + + outputs = [ "bin" "out" ]; + propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle + + patches = [ + ./darwin.patch + ] ++ lib.optional pythonSupport (substituteAll { + src = ./python.patch; + inherit (python.sourceVersion) major minor; # Should be changed in case of PyPy + }); + + postPatch = lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") '' + # CUDA 9.0 doesn't support sm_20 + sed -i 's,20 21(20) ,,' cmake/Cuda.cmake + ''; + + preConfigure = lib.optionalString pythonSupport '' + # We need this when building with Python bindings + export BOOST_LIBRARYDIR="${boost.out}/lib"; + ''; + + postInstall = '' + # Internal static library. + rm $out/lib/libproto.a + + # Install models + cp -a ../models $out/share/Caffe/models + + moveToOutput "bin" "$bin" + '' + lib.optionalString pythonSupport '' + mkdir -p $out/${python.sitePackages} + mv $out/python/caffe $out/${python.sitePackages} + rm -rf $out/python + ''; + + doInstallCheck = false; # build takes more than 30 min otherwise + installCheckPhase = '' + model=bvlc_reference_caffenet + m_path="$out/share/Caffe/models/$model" + $bin/bin/caffe test \ + -model "$m_path/deploy.prototxt" \ + -solver "$m_path/solver.prototxt" \ + -weights "${test_model_weights}" + ''; + + meta = with stdenv.lib; { + description = "Deep learning framework"; + longDescription = '' + Caffe is a deep learning framework made with expression, speed, and + modularity in mind. It is developed by the Berkeley Vision and Learning + Center (BVLC) and by community contributors. + ''; + homepage = "http://caffe.berkeleyvision.org/"; + maintainers = with maintainers; [ jb55 ]; + license = licenses.bsd2; + platforms = platforms.linux ++ platforms.darwin; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/caffe/python.patch b/nixpkgs/pkgs/applications/science/math/caffe/python.patch new file mode 100644 index 000000000000..dac5071aa08c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/caffe/python.patch @@ -0,0 +1,70 @@ +commit b14ca23651d390fcae4a929dedc7c33a83453a66 +Author: Frederik Rietdijk <fridh@fridh.nl> +Date: Sun Feb 17 08:41:27 2019 +0100 + + Find boost_pythonXX + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 08f56a33..0a04592a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -99,10 +99,10 @@ add_subdirectory(docs) + add_custom_target(lint COMMAND ${CMAKE_COMMAND} -P ${PROJECT_SOURCE_DIR}/cmake/lint.cmake) + + # ---[ pytest target +-if(BUILD_python) +- add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python ) +- add_dependencies(pytest pycaffe) +-endif() ++# if(BUILD_python) ++# add_custom_target(pytest COMMAND python${python_version} -m unittest discover -s caffe/test WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/python ) ++# add_dependencies(pytest pycaffe) ++# endif() + + # ---[ uninstall target + configure_file( +diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake +index 4a5bac47..be026d43 100644 +--- a/cmake/Dependencies.cmake ++++ b/cmake/Dependencies.cmake +@@ -141,37 +141,14 @@ if(BUILD_python) + # use python3 + find_package(PythonInterp 3.0) + find_package(PythonLibs 3.0) +- find_package(NumPy 1.7.1) +- # Find the matching boost python implementation +- set(version ${PYTHONLIBS_VERSION_STRING}) +- +- STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} ) +- find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}") +- set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND}) +- +- while(NOT "${version}" STREQUAL "" AND NOT Boost_PYTHON_FOUND) +- STRING( REGEX REPLACE "([0-9.]+).[0-9]+" "\\1" version ${version} ) +- +- STRING( REGEX REPLACE "[^0-9]" "" boost_py_version ${version} ) +- find_package(Boost 1.46 COMPONENTS "python-py${boost_py_version}") +- set(Boost_PYTHON_FOUND ${Boost_PYTHON-PY${boost_py_version}_FOUND}) +- +- STRING( REGEX MATCHALL "([0-9.]+).[0-9]+" has_more_version ${version} ) +- if("${has_more_version}" STREQUAL "") +- break() +- endif() +- endwhile() +- if(NOT Boost_PYTHON_FOUND) +- find_package(Boost 1.46 COMPONENTS python) +- endif() + else() + # disable Python 3 search + find_package(PythonInterp 2.7) + find_package(PythonLibs 2.7) +- find_package(NumPy 1.7.1) +- find_package(Boost 1.46 COMPONENTS python) + endif() +- if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON_FOUND) ++ find_package(NumPy 1.7.1) ++ find_package(Boost 1.46 REQUIRED COMPONENTS python@major@@minor@) ++ if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON@major@@minor@_FOUND) + set(HAVE_PYTHON TRUE) + if(BUILD_python_layer) + list(APPEND Caffe_DEFINITIONS PRIVATE -DWITH_PYTHON_LAYER) diff --git a/nixpkgs/pkgs/applications/science/math/calc/default.nix b/nixpkgs/pkgs/applications/science/math/calc/default.nix new file mode 100644 index 000000000000..8e50f48b286b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/calc/default.nix @@ -0,0 +1,48 @@ +{ stdenv, lib, fetchurl, utillinux, makeWrapper +, enableReadline ? true, readline, ncurses }: + +stdenv.mkDerivation rec { + pname = "calc"; + version = "2.12.7.2"; + + src = fetchurl { + urls = [ + "https://github.com/lcn2/calc/releases/download/${version}/${pname}-${version}.tar.bz2" + "http://www.isthe.com/chongo/src/calc/${pname}-${version}.tar.bz2" + ]; + sha256 = "147wmbajcxv6wp92j6pizq4plrr1sb7jirifr1477bx33hc49bsp"; + }; + + patchPhase = '' + substituteInPlace Makefile \ + --replace '-install_name ''${LIBDIR}/libcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcalc''${LIB_EXT_VERSION}' \ + --replace '-install_name ''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}' '-install_name ''${T}''${LIBDIR}/libcustcalc''${LIB_EXT_VERSION}' + ''; + + buildInputs = [ utillinux makeWrapper ] + ++ lib.optionals enableReadline [ readline ncurses ]; + + makeFlags = [ + "T=$(out)" + "INCDIR=" + "BINDIR=/bin" + "LIBDIR=/lib" + "CALC_SHAREDIR=/share/calc" + "CALC_INCDIR=/include" + "MANDIR=/share/man/man1" + + # Handle LDFLAGS defaults in calc + "DEFAULT_LIB_INSTALL_PATH=$(out)/lib" + ] ++ lib.optionals enableReadline [ + "READLINE_LIB=-lreadline" + "USE_READLINE=-DUSE_READLINE" + ]; + + meta = with lib; { + description = "C-style arbitrary precision calculator"; + homepage = "http://www.isthe.com/chongo/tech/comp/calc/"; + license = licenses.lgpl21; + maintainers = with maintainers; [ matthewbauer ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch b/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch new file mode 100644 index 000000000000..5b8f492a8e7c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/calculix/calculix.patch @@ -0,0 +1,31 @@ +diff --git a/ccx_2.15/src/Makefile b/ccx_2.15/src/Makefile +index 9cab2fc..6e977b8 100755 +--- a/ccx_2.15/src/Makefile ++++ b/ccx_2.15/src/Makefile +@@ -1,6 +1,6 @@ + + CFLAGS = -Wall -O3 -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE -DNETWORKOUT +-FFLAGS = -Wall -O3 ++FFLAGS = -Wall -O3 + + CC=cc + FC=gfortran +@@ -18,15 +18,10 @@ OCCXF = $(SCCXF:.f=.o) + OCCXC = $(SCCXC:.c=.o) + OCCXMAIN = $(SCCXMAIN:.c=.o) + +-DIR=../../../SPOOLES.2.2 ++LIBS = -lpthread -lm -lc -lspooles -larpack -lblas -llapack + +-LIBS = \ +- $(DIR)/spooles.a \ +- ../../../ARPACK/libarpack_INTEL.a \ +- -lpthread -lm -lc +- +-ccx_2.15: $(OCCXMAIN) ccx_2.15.a $(LIBS) +- ./date.pl; $(CC) $(CFLAGS) -c ccx_2.15.c; $(FC) -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.15.a $(LIBS) ++ccx_2.15: $(OCCXMAIN) ccx_2.15.a ++ $(CC) $(CFLAGS) -c ccx_2.15.c; $(FC) -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.15.a $(LIBS) + + ccx_2.15.a: $(OCCXF) $(OCCXC) + ar vr $@ $? diff --git a/nixpkgs/pkgs/applications/science/math/calculix/default.nix b/nixpkgs/pkgs/applications/science/math/calculix/default.nix new file mode 100644 index 000000000000..44882594550b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/calculix/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchurl, gfortran, arpack, spooles, blas, lapack }: + +stdenv.mkDerivation rec { + pname = "calculix"; + version = "2.15"; + + src = fetchurl { + url = "http://www.dhondt.de/ccx_${version}.src.tar.bz2"; + sha256 = "0d4axfxgm3ag4p2vx9rjcky7c122k99a2nhv1jv53brm35rblzdw"; + }; + + nativeBuildInputs = [ gfortran ]; + + buildInputs = [ arpack spooles blas lapack ]; + + NIX_CFLAGS_COMPILE = "-I${spooles}/include/spooles"; + + patches = [ + ./calculix.patch + ]; + + postPatch = '' + cd ccx*/src + ''; + + installPhase = '' + install -Dm0755 ccx_${version} $out/bin/ccx + ''; + + meta = with stdenv.lib; { + homepage = "http://www.calculix.de/"; + description = "Three-dimensional structural finite element program"; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ gebner ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/cbc/default.nix b/nixpkgs/pkgs/applications/science/math/cbc/default.nix new file mode 100644 index 000000000000..b75f3d3f7868 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/cbc/default.nix @@ -0,0 +1,30 @@ +{ lib, stdenv, fetchurl, zlib, bzip2 }: + +stdenv.mkDerivation rec { + pname = "cbc"; + version = "2.10.3"; + + src = fetchurl { + url = "https://www.coin-or.org/download/source/Cbc/Cbc-${version}.tgz"; + sha256 = "1zzcg40ky5v96s7br2hqlkqdspwrn43kf3757g6c35wl29bq6f5d"; + }; + + configureFlags = [ "-C" ]; + + enableParallelBuilding = true; + + hardeningDisable = [ "format" ]; + + buildInputs = [ zlib bzip2 ]; + + # FIXME: move share/coin/Data to a separate output? + + meta = { + homepage = "https://projects.coin-or.org/Cbc"; + license = lib.licenses.epl10; + maintainers = [ lib.maintainers.eelco ]; + platforms = lib.platforms.linux ++ lib.platforms.darwin; + broken = stdenv.isAarch64; # Missing <immintrin.h> after 2.10.0 + description = "A mixed integer programming solver"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/cemu/default.nix b/nixpkgs/pkgs/applications/science/math/cemu/default.nix new file mode 100644 index 000000000000..b41135229dd7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/cemu/default.nix @@ -0,0 +1,53 @@ +{ fetchFromGitHub +, stdenv +, mkDerivation +, SDL2 +, libGL +, libarchive +, libusb-compat-0_1 +, qtbase +, qmake +, git +, libpng_apng +, pkgconfig +}: + +mkDerivation rec { + pname = "CEmu"; + version = "1.3"; + src = fetchFromGitHub { + owner = "CE-Programming"; + repo = "CEmu"; + rev = "v${version}"; + sha256 = "1wcdnzcqscawj6jfdj5wwmw9g9vsd6a1rx0rrramakxzf8b7g47r"; + fetchSubmodules = true; + }; + + nativeBuildInputs = [ + qmake + git + pkgconfig + ]; + + buildInputs = [ + SDL2 + libGL + libarchive + libusb-compat-0_1 + qtbase + libpng_apng + ]; + + qmakeFlags = [ + "gui/qt" + ]; + + meta = with stdenv.lib; { + changelog = "https://github.com/CE-Programming/CEmu/releases/tag/v${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/nixpkgs/pkgs/applications/science/math/clp/default.nix b/nixpkgs/pkgs/applications/science/math/clp/default.nix new file mode 100644 index 000000000000..5e770cec13b3 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/clp/default.nix @@ -0,0 +1,22 @@ +{ stdenv, fetchurl, zlib }: + +stdenv.mkDerivation rec { + version = "1.17.5"; + pname = "clp"; + src = fetchurl { + url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz"; + sha256 = "0y5wg4lfffy5vh8gc20v68pmmv241ndi2jgm9pgvk39b00bzkaa9"; + }; + + propagatedBuildInputs = [ zlib ]; + + doCheck = true; + + meta = with stdenv.lib; { + license = licenses.epl10; + homepage = "https://github.com/coin-or/Clp"; + description = "An open-source linear programming solver written in C++"; + platforms = platforms.darwin ++ [ "x86_64-linux" ]; + maintainers = [ maintainers.vbgl ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/cntk/default.nix b/nixpkgs/pkgs/applications/science/math/cntk/default.nix new file mode 100644 index 000000000000..401454a6b69b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/cntk/default.nix @@ -0,0 +1,105 @@ +{ lib, stdenv, fetchgit, fetchFromGitHub, cmake +, openblas, blas, lapack, opencv3, libzip, boost, protobuf, openmpi +, onebitSGDSupport ? false +, cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11 +, cudnnSupport ? cudaSupport, cudnn +}: + +assert cudnnSupport -> cudaSupport; +assert blas.implementation == "openblas" && lapack.implementation == "openblas"; + +let + # Old specific version required for CNTK. + cub = fetchFromGitHub { + owner = "NVlabs"; + repo = "cub"; + rev = "1.7.4"; + sha256 = "0ksd5n1lxqhm5l5cd2lps4cszhjkf6gmzahaycs7nxb06qci8c66"; + }; + +in stdenv.mkDerivation rec { + pname = "CNTK"; + version = "2.7"; + + # Submodules + src = fetchgit { + url = "https://github.com/Microsoft/CNTK"; + rev = "v${version}"; + sha256 = "18l9k7s966a26ywcf7flqyhm61788pcb9fj3wk61jrmgkhy2pcns"; + }; + + nativeBuildInputs = [ cmake ] ++ lib.optional cudaSupport addOpenGLRunpath; + + # Force OpenMPI to use g++ in PATH. + OMPI_CXX = "g++"; + + buildInputs = [ openblas opencv3 libzip boost protobuf openmpi ] + ++ lib.optional cudaSupport cudatoolkit + ++ lib.optional cudnnSupport cudnn; + + configureFlags = [ + "--with-opencv=${opencv3}" + "--with-libzip=${libzip.dev}" + "--with-openblas=${openblas}" + "--with-boost=${boost.dev}" + "--with-protobuf=${protobuf}" + "--with-mpi=${openmpi}" + "--cuda=${if cudaSupport then "yes" else "no"}" + # FIXME + "--asgd=no" + ] ++ lib.optionals cudaSupport [ + "--with-cuda=${cudatoolkit}" + "--with-gdk-include=${cudatoolkit}/include" + "--with-gdk-nvml-lib=${nvidia_x11}/lib" + "--with-cub=${cub}" + ] ++ lib.optional onebitSGDSupport "--1bitsgd=yes"; + + configurePhase = '' + sed -i \ + -e 's,^GIT_STATUS=.*,GIT_STATUS=,' \ + -e 's,^GIT_COMMIT=.*,GIT_COMMIT=v${version},' \ + -e 's,^GIT_BRANCH=.*,GIT_BRANCH=v${version},' \ + -e 's,^BUILDER=.*,BUILDER=nixbld,' \ + -e 's,^BUILDMACHINE=.*,BUILDMACHINE=machine,' \ + -e 's,^BUILDPATH=.*,BUILDPATH=/homeless-shelter,' \ + -e '/git does not exist/d' \ + Tools/generate_build_info + + patchShebangs . + mkdir build + cd build + ${lib.optionalString cudnnSupport '' + mkdir cuda + ln -s ${cudnn}/include cuda + export configureFlags="$configureFlags --with-cudnn=$PWD" + ''} + + ../configure $configureFlags + ''; + + installPhase = '' + mkdir -p $out/bin + # Moving to make patchelf remove references later. + mv lib $out + cp bin/cntk $out/bin + ''; + + postFixup = lib.optionalString cudaSupport '' + for lib in $out/lib/*; do + addOpenGLRunpath "$lib" + done + ''; + + enableParallelBuilding = true; + + meta = with lib; { + # Newer cub is included with cudatoolkit now and it breaks the build. + # https://github.com/Microsoft/CNTK/issues/3191 + broken = cudaSupport; + homepage = "https://github.com/Microsoft/CNTK"; + description = "An open source deep-learning toolkit"; + license = if onebitSGDSupport then licenses.unfreeRedistributable else licenses.mit; + platforms = [ "x86_64-linux" ]; + maintainers = with maintainers; [ abbradar ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/colpack/default.nix b/nixpkgs/pkgs/applications/science/math/colpack/default.nix new file mode 100644 index 000000000000..13a75ce4db2d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/colpack/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchFromGitHub, autoconf, automake, libtool, gettext }: + +stdenv.mkDerivation rec { + + pname = "ColPack"; + version = "1.0.10"; + + src = fetchFromGitHub { + owner = "CSCsw"; + repo = pname; + rev = "v" + version; + sha256 = "1p05vry940mrjp6236c0z83yizmw9pk6ly2lb7d8rpb7j9h03glr"; + }; + + buildInputs = [ autoconf automake gettext libtool ]; + + configurePhase = '' + autoreconf -vif + ./configure --prefix=$out --enable-openmp + ''; + + meta = with stdenv.lib; { + description = "A package comprising of implementations of algorithms for + vertex coloring and derivative computation"; + homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities"; + license = licenses.lgpl3; + platforms = platforms.linux; + maintainers = with maintainers; [ edwtjo ]; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/math/cplex/default.nix b/nixpkgs/pkgs/applications/science/math/cplex/default.nix new file mode 100644 index 000000000000..ec13f5252f13 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/cplex/default.nix @@ -0,0 +1,87 @@ +{ stdenv, makeWrapper, openjdk, gtk2, xorg, glibcLocales, releasePath ? null }: + +# To use this package, you need to download your own cplex installer from IBM +# and override the releasePath attribute to point to the location of the file. +# +# Note: cplex creates an individual build for each license which screws +# somewhat with the use of functions like requireFile as the hash will be +# different for every user. + +stdenv.mkDerivation rec { + pname = "cplex"; + version = "128"; + + src = + if releasePath == null then + throw '' + This nix expression requires that the cplex installer is already + downloaded to your machine. Get it from IBM: + https://developer.ibm.com/docloud/blog/2017/12/20/cplex-optimization-studio-12-8-now-available/ + + Set `cplex.releasePath = /path/to/download;` in your + ~/.config/nixpkgs/config.nix for `nix-*` commands, or + `config.cplex.releasePath = /path/to/download;` in your + `configuration.nix` for NixOS. + '' + else + releasePath; + + nativeBuildInputs = [ makeWrapper ]; + buildInputs = [ openjdk gtk2 xorg.libXtst glibcLocales ]; + + unpackPhase = "cp $src $name"; + + patchPhase = '' + sed -i -e 's|/usr/bin/tr"|tr" |' $name + ''; + + buildPhase = '' + sh $name -i silent -DLICENSE_ACCEPTED=TRUE -DUSER_INSTALL_DIR=$out + ''; + + installPhase = '' + mkdir -p $out/bin + ln -s $out/opl/bin/x86-64_linux/oplrun\ + $out/opl/bin/x86-64_linux/oplrunjava\ + $out/opl/oplide/oplide\ + $out/cplex/bin/x86-64_linux/cplex\ + $out/cpoptimizer/bin/x86-64_linux/cpoptimizer\ + $out/bin + ''; + + fixupPhase = + let + libraryPath = stdenv.lib.makeLibraryPath [ stdenv.cc.cc gtk2 xorg.libXtst ]; + in '' + interpreter=${stdenv.glibc}/lib/ld-linux-x86-64.so.2 + + for pgm in $out/opl/bin/x86-64_linux/oplrun $out/opl/bin/x86-64_linux/oplrunjava $out/opl/oplide/oplide; + do + patchelf --set-interpreter "$interpreter" $pgm; + wrapProgram $pgm \ + --prefix LD_LIBRARY_PATH : $out/opl/bin/x86-64_linux:${libraryPath} \ + --set LOCALE_ARCHIVE ${glibcLocales}/lib/locale/locale-archive; + done + + for pgm in $out/cplex/bin/x86-64_linux/cplex $out/cpoptimizer/bin/x86-64_linux/cpoptimizer $out/opl/oplide/jre/bin/*; + do + if grep ELF $pgm > /dev/null; + then + patchelf --set-interpreter "$interpreter" $pgm; + fi + done + ''; + + passthru = { + libArch = "x86-64_linux"; + libSuffix = "${version}0"; + }; + + meta = with stdenv.lib; { + description = "Optimization solver for mathematical programming"; + homepage = "https://www.ibm.com/be-en/marketplace/ibm-ilog-cplex"; + license = licenses.unfree; + platforms = [ "x86_64-linux" ]; + maintainers = with maintainers; [ bfortz ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/csdp/default.nix b/nixpkgs/pkgs/applications/science/math/csdp/default.nix new file mode 100644 index 000000000000..ef9d5e733ca7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/csdp/default.nix @@ -0,0 +1,29 @@ +{ lib, stdenv, fetchurl, blas, gfortran, lapack }: + +stdenv.mkDerivation { + name = "csdp-6.1.1"; + + src = fetchurl { + url = "https://www.coin-or.org/download/source/Csdp/Csdp-6.1.1.tgz"; + sha256 = "1f9ql6cjy2gwiyc51ylfan24v1ca9sjajxkbhszlds1lqmma8n05"; + }; + + buildInputs = [ blas gfortran.cc.lib lapack ]; + + postPatch = '' + substituteInPlace Makefile --replace /usr/local/bin $out/bin + ''; + + preInstall = '' + rm -f INSTALL + mkdir -p $out/bin + ''; + + meta = { + homepage = "https://projects.coin-or.org/Csdp"; + license = lib.licenses.cpl10; + maintainers = [ lib.maintainers.roconnor ]; + description = "A C Library for Semidefinite Programming"; + platforms = stdenv.lib.platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/ecm/default.nix b/nixpkgs/pkgs/applications/science/math/ecm/default.nix new file mode 100644 index 000000000000..3e8e5879950b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/ecm/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchurl, gmp, m4 }: + +let + pname = "ecm"; + version = "7.0.4"; + name = "${pname}-${version}"; +in + +stdenv.mkDerivation { + inherit name; + + src = fetchurl { + url = "http://gforge.inria.fr/frs/download.php/file/36224/ecm-${version}.tar.gz"; + sha256 = "0hxs24c2m3mh0nq1zz63z3sb7dhy1rilg2s1igwwcb26x3pb7xqc"; + }; + + # See https://trac.sagemath.org/ticket/19233 + configureFlags = stdenv.lib.optional stdenv.isDarwin "--disable-asm-redc"; + + buildInputs = [ m4 gmp ]; + + doCheck = true; + + meta = { + description = "Elliptic Curve Method for Integer Factorization"; + license = stdenv.lib.licenses.gpl2Plus; + homepage = "http://ecm.gforge.inria.fr/"; + maintainers = [ stdenv.lib.maintainers.roconnor ]; + platforms = with stdenv.lib.platforms; linux ++ darwin; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/eukleides/default.nix b/nixpkgs/pkgs/applications/science/math/eukleides/default.nix new file mode 100644 index 000000000000..879ad96a9367 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/eukleides/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchurl, bison, flex, texinfo, readline, texLive }: + +let + name = "eukleides"; + version = "1.5.4"; +in +stdenv.mkDerivation { + name = "${name}-${version}"; + + src = fetchurl { + url = "http://www.eukleides.org/files/${name}-${version}.tar.bz2"; + sha256 = "0s8cyh75hdj89v6kpm3z24i48yzpkr8qf0cwxbs9ijxj1i38ki0q"; + }; + + buildInputs = [bison flex texinfo readline texLive]; + + preConfigure = "sed -i 's/ginstall-info/install-info/g' doc/Makefile"; + installPhase = "mkdir -p $out/bin ; make PREFIX=$out install"; + + meta = { + description = "Geometry Drawing Language"; + homepage = "http://www.eukleides.org/"; + license = stdenv.lib.licenses.gpl2; + + longDescription = '' + Eukleides is a computer language devoted to elementary plane + geometry. It aims to be a fairly comprehensive system to create + geometric figures, either static or dynamic. Eukleides allows to + handle basic types of data: numbers and strings, as well as + geometric types of data: points, vectors, sets (of points), lines, + circles and conics. + ''; + + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.peti ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/form/default.nix b/nixpkgs/pkgs/applications/science/math/form/default.nix new file mode 100644 index 000000000000..091372792901 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/form/default.nix @@ -0,0 +1,22 @@ +{ stdenv, fetchurl, gmp, zlib }: + +stdenv.mkDerivation { + version = "4.2.1"; + pname = "form"; + + # This tarball is released by author, it is not downloaded from tag, so can't use fetchFromGitHub + src = fetchurl { + url = "https://github.com/vermaseren/form/releases/download/v4.2.1/form-4.2.1.tar.gz"; + sha256 = "0a0smc10gm85vxd85942n5azy88w5qs5avbqrw0lw0yb9injswpj"; + }; + + buildInputs = [ gmp zlib ]; + + meta = with stdenv.lib; { + description = "The FORM project for symbolic manipulation of very big expressions"; + homepage = "https://www.nikhef.nl/~form/"; + license = licenses.gpl3; + maintainers = [ maintainers.veprbl ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/fricas/default.nix b/nixpkgs/pkgs/applications/science/math/fricas/default.nix new file mode 100644 index 000000000000..39ca53c47e6e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/fricas/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }: + +let + version = "1.3.4"; + name = "fricas-" + version; +in +stdenv.mkDerivation { + inherit name; + + src = fetchurl { + url = "mirror://sourceforge/fricas/files/fricas/${version}/${name}-full.tar.bz2"; + sha256 = "156k9az1623y5808j845c56z2nvvdrm48dzg1v0ivpplyl7vp57x"; + }; + + buildInputs = [ sbcl libX11 libXpm libICE libSM libXt libXau libXdmcp ]; + + dontStrip = true; + + meta = { + homepage = "http://fricas.sourceforge.net/"; + description = "An advanced computer algebra system"; + license = stdenv.lib.licenses.bsd3; + + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.sprock ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/gap/default.nix b/nixpkgs/pkgs/applications/science/math/gap/default.nix new file mode 100644 index 000000000000..87f4fa120387 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/gap/default.nix @@ -0,0 +1,180 @@ +{ stdenv +, lib +, fetchurl +, fetchpatch +, makeWrapper +, m4 +, gmp +# one of +# - "minimal" (~400M): +# Install the bare minimum of packages required by gap to start. +# This is likely to break a lot of stuff. Do not expect upstream support with +# this configuration. +# - "standard" (~700M): +# Install the "standard packages" which gap autoloads by default. These +# packages are effectively considered a part of gap. +# - "full" (~1.7G): +# Install all available packages. This takes a lot of space. +, packageSet ? "standard" +# Kept for backwards compatibility. Overrides packageSet to "full". +, keepAllPackages ? false +}: +let + # packages absolutely required for gap to start + # `*` represents the version where applicable + requiredPackages = [ + "GAPDoc-*" + "primgrp-*" + "SmallGrp-*" + "transgrp" + ]; + # packages autoloaded by default if available + autoloadedPackages = [ + "atlasrep" + "autpgrp-*" + "alnuth-*" + "crisp-*" + "ctbllib" + "FactInt-*" + "fga" + "irredsol-*" + "laguna-*" + "polenta-*" + "polycyclic-*" + "resclasses-*" + "sophus-*" + "tomlib-*" + ]; + keepAll = keepAllPackages || (packageSet == "full"); + packagesToKeep = requiredPackages ++ lib.optionals (packageSet == "standard") autoloadedPackages; + + # Generate bash script that removes all packages from the `pkg` subdirectory + # that are not on the whitelist. The whitelist consists of strings expected by + # `find`'s `-name`. + removeNonWhitelistedPkgs = whitelist: '' + find pkg -type d -maxdepth 1 -mindepth 1 \ + '' + (lib.concatStringsSep "\n" (map (str: "-not -name '${str}' \\") whitelist)) + '' + -exec echo "Removing package {}" \; \ + -exec rm -r '{}' \; + ''; +in +stdenv.mkDerivation rec { + pname = "gap"; + # https://www.gap-system.org/Releases/ + version = "4.10.2"; + + src = fetchurl { + url = "https://www.gap-system.org/pub/gap/gap-${lib.versions.major version}.${lib.versions.minor version}/tar.bz2/gap-${version}.tar.bz2"; + sha256 = "0cp6ddk0469zzv1m1vair6gm27ic6c5m77ri8rn0znq3gaps6x94"; + }; + + # remove all non-essential packages (which take up a lot of space) + preConfigure = lib.optionalString (!keepAll) (removeNonWhitelistedPkgs packagesToKeep) + '' + patchShebangs . + ''; + + configureFlags = [ "--with-gmp=system" ]; + + buildInputs = [ + m4 + gmp + ]; + + nativeBuildInputs = [ + makeWrapper + ]; + + patches = [ + # https://github.com/gap-system/gap/pull/3294 + (fetchpatch { + name = "add-make-install-targets.patch"; + url = "https://github.com/gap-system/gap/commit/3361c172e6c5ff3bb3f01ba9d6f1dd4ad42cea80.patch"; + sha256 = "1kwp9qnfvmlbpf1c3rs6j5m2jz22rj7a4hb5x1gj9vkpiyn5pdyj"; + }) + ]; + + # "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"; + + preInstallCheck = '' + # gap tests check that the home directory exists + export HOME="$TMP/gap-home" + mkdir -p "$HOME" + + # make sure gap is in PATH + export PATH="$out/bin:$PATH" + + # make sure we don't accidentally use the wrong gap binary + rm -r bin + + # like the defaults the Makefile, but use gap from PATH instead of the + # one from builddir + installCheckFlagsArray+=( + "TESTGAP=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r -A" + "TESTGAPauto=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r" + ) + ''; + + 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 + popd + ''; + + installTargets = [ + "install-libgap" + "install-headers" + ]; + + # full `make install` is not yet implemented, just for libgap and headers + postInstall = '' + # Install config.h, which is not currently handled by `make install-headers` + cp gen/config.h "$out/include/gap" + + mkdir -p "$out/bin" "$out/share/gap/" + + mkdir -p "$out/share/gap" + echo "Copying files to target directory" + cp -ar . "$out/share/gap/build-dir" + + makeWrapper "$out/share/gap/build-dir/bin/gap.sh" "$out/bin/gap" \ + --set GAP_DIR $out/share/gap/build-dir + ''; + + preFixup = '' + # patchelf won't strip references to the build dir if it still exists + rm -rf pkg + ''; + + meta = with lib; { + description = "Computational discrete algebra system"; + maintainers = with maintainers; + [ + raskin + chrisjefferson + timokau + ]; + platforms = platforms.all; + broken = stdenv.isDarwin; + # keeping all packages increases the package size considerably, wchich + # is why a local build is preferable in that situation. The timeframe + # is reasonable and that way the binary cache doesn't get overloaded. + hydraPlatforms = lib.optionals (!keepAllPackages) meta.platforms; + license = licenses.gpl2; + homepage = "http://gap-system.org/"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/geogebra/default.nix b/nixpkgs/pkgs/applications/science/math/geogebra/default.nix new file mode 100644 index 000000000000..1dd92267a837 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/geogebra/default.nix @@ -0,0 +1,63 @@ +{ stdenv, fetchurl, jre, makeDesktopItem, makeWrapper, language ? "en_US" }: + +stdenv.mkDerivation rec { + pname = "geogebra"; + version = "5-0-574-0"; + + preferLocalBuild = true; + + src = fetchurl { + urls = [ + "https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2" + "http://web.archive.org/https://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2" + ]; + sha256 = "0jbci4spqkf33yb079lsnsc684y4mdf1p8lm9r0037av8jlsrgrc"; + }; + + srcIcon = fetchurl { + url = "http://static.geogebra.org/images/geogebra-logo.svg"; + sha256 = "01sy7ggfvck350hwv0cla9ynrvghvssqm3c59x4q5lwsxjsxdpjm"; + }; + + desktopItem = makeDesktopItem { + name = "geogebra"; + exec = "geogebra"; + icon = "geogebra"; + desktopName = "Geogebra"; + genericName = "Geogebra"; + comment = meta.description; + categories = "Education;Science;Math;"; + mimeType = "application/vnd.geogebra.file;application/vnd.geogebra.tool;"; + }; + + buildInputs = [ makeWrapper ]; + + installPhase = '' + install -D geogebra/* -t "$out/libexec/geogebra/" + + makeWrapper "$out/libexec/geogebra/geogebra" "$out/bin/geogebra" \ + --set JAVACMD "${jre}/bin/java" \ + --set GG_PATH "$out/libexec/geogebra" \ + --add-flags "--language=${language}" + + install -Dm644 "${desktopItem}/share/applications/"* \ + -t $out/share/applications/ + + install -Dm644 "${srcIcon}" \ + "$out/share/icons/hicolor/scalable/apps/geogebra.svg" + ''; + + meta = with stdenv.lib; { + description = "Dynamic mathematics software with graphics, algebra and spreadsheets"; + longDescription = '' + Dynamic mathematics software for all levels of education that brings + together geometry, algebra, spreadsheets, graphing, statistics and + calculus in one easy-to-use package. + ''; + homepage = "https://www.geogebra.org/"; + maintainers = with maintainers; [ ma27 ]; + license = with licenses; [ gpl3 cc-by-nc-sa-30 geogebra ]; + platforms = platforms.all; + hydraPlatforms = []; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/getdp/default.nix b/nixpkgs/pkgs/applications/science/math/getdp/default.nix new file mode 100644 index 000000000000..ae93e89f1416 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/getdp/default.nix @@ -0,0 +1,28 @@ +{ stdenv, fetchurl, cmake, gfortran, blas, lapack, openmpi, petsc, python3 }: + +stdenv.mkDerivation rec { + name = "getdp-${version}"; + version = "3.3.0"; + src = fetchurl { + url = "http://getdp.info/src/getdp-${version}-source.tgz"; + sha256 = "1pfviy2bw8z5y6c15czvlvyjjg9pvpgrj9fr54xfi2gmvs7zkgpf"; + }; + + nativeBuildInputs = [ cmake gfortran ]; + buildInputs = [ blas lapack openmpi petsc python3 ]; + + meta = with stdenv.lib; { + description = "A General Environment for the Treatment of Discrete Problems"; + longDescription = '' + GetDP is a free finite element solver using mixed elements to discretize + de Rham-type complexes in one, two and three dimensions. The main + feature of GetDP is the closeness between the input data defining + discrete problems (written by the user in ASCII data files) and the + symbolic mathematical expressions of these problems. + ''; + homepage = "http://getdp.info/"; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ wucke13 ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/gfan/default.nix b/nixpkgs/pkgs/applications/science/math/gfan/default.nix new file mode 100644 index 000000000000..72d1a548c530 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/gfan/default.nix @@ -0,0 +1,27 @@ +{stdenv, fetchurl, gmp, mpir, cddlib}: +stdenv.mkDerivation rec { + pname = "gfan"; + version = "0.6.2"; + + src = fetchurl { + url = "http://home.math.au.dk/jensen/software/gfan/gfan${version}.tar.gz"; + sha256 = "02pihqb1lb76a0xbfwjzs1cd6ay3ldfxsm8dvsbl6qs3vkjxax56"; + }; + + patchPhase = stdenv.lib.optionalString stdenv.isDarwin '' + substituteInPlace Makefile --replace "-fno-guess-branch-probability" "" + ''; + + buildFlags = [ "CC=cc" "CXX=c++" "cddnoprefix=1" ]; + installFlags = [ ''PREFIX=$(out)'' ]; + buildInputs = [ gmp mpir cddlib ]; + + meta = { + inherit version; + description = ''A software package for computing Gröbner fans and tropical varieties''; + license = stdenv.lib.licenses.gpl2 ; + maintainers = [stdenv.lib.maintainers.raskin]; + platforms = stdenv.lib.platforms.unix; + homepage = "http://home.math.au.dk/jensen/software/gfan/gfan.html"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/giac/default.nix b/nixpkgs/pkgs/applications/science/math/giac/default.nix new file mode 100644 index 000000000000..ea9c921f19e1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/giac/default.nix @@ -0,0 +1,110 @@ +{ stdenv, lib, fetchurl, fetchpatch, texlive, bison, flex, lapack, blas +, gmp, mpfr, pari, ntl, gsl, mpfi, ecm, glpk, nauty +, readline, gettext, libpng, libao, gfortran, perl +, enableGUI ? false, libGL ? null, libGLU ? null, xorg ? null, fltk ? null +}: + +assert enableGUI -> libGLU != null && libGL != null && xorg != null && fltk != null; +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + pname = "giac${lib.optionalString enableGUI "-with-xcas"}"; + version = "1.5.0-21"; # TODO try to remove preCheck phase on upgrade + + src = fetchurl { + url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz"; + sha256 = "1b9khiv0mk2xzw1rblm2jy6qsf8y6f9k7qy15sxpb21d72hzzbl2"; + }; + + patches = stdenv.lib.optionals (!enableGUI) [ + # when enableGui is false, giac is compiled without fltk. That means some + # outputs differ in the make check. Patch around this: + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/giac/patches/nofltk-check.patch?id=7553a3c8dfa7bcec07241a07e6a4e7dcf5bb4f26"; + sha256 = "0xkmfc028vg5w6va04gp2x2iv31n8v4shd6vbyvk4blzgfmpj2cw"; + }) + ]; + + postPatch = '' + for i in doc/*/Makefile*; do + substituteInPlace "$i" --replace "/bin/cp" "cp"; + done; + ''; + + nativeBuildInputs = [ + texlive.combined.scheme-small bison flex + ]; + + # perl is only needed for patchShebangs fixup. + buildInputs = [ + gmp mpfr pari ntl gsl blas mpfi glpk nauty + readline gettext libpng libao perl ecm + # gfortran.cc default output contains static libraries compiled without -fPIC + # we want libgfortran.so.3 instead + (stdenv.lib.getLib gfortran.cc) + lapack blas + ] ++ stdenv.lib.optionals enableGUI [ + libGL libGLU fltk xorg.libX11 + ]; + + /* fixes: + configure:16211: checking for main in -lntl + configure:16230: g++ -o conftest -g -O2 conftest.cpp -lntl -llapack -lblas -lgfortran -ldl -lpng16 -lm -lmpfi -lmpfr -lgmp >&5 + /nix/store/y9c1v4x7y39j2rfbg17agjwqdzxpsn18-ntl-11.3.2/lib/libntl.so: undefined reference to `pthread_key_create' + */ + NIX_CFLAGS_LINK="-lpthread"; + + # xcas Phys and Turtle menus are broken with split outputs + # and interactive use is likely to need docs + outputs = [ "out" ] ++ stdenv.lib.optional (!enableGUI) "doc"; + + doCheck = true; + preCheck = '' + # One test in this file fails. That test just tests a part of the pari + # interface that isn't actually used in giac. Of course it would be better + # to only remove that one test, but that would require a patch. + # Removing the whole test set should be good enough for now. + # Upstream report: https://xcas.univ-grenoble-alpes.fr/forum/viewtopic.php?f=4&t=2102#p10326 + echo > check/chk_fhan11 + ''; + + enableParallelBuilding = true; + + configureFlags = [ + "--enable-gc" "--enable-png" "--enable-gsl" "--enable-lapack" + "--enable-pari" "--enable-ntl" "--enable-gmpxx" # "--enable-cocoa" + "--enable-ao" "--enable-ecm" "--enable-glpk" + ] ++ stdenv.lib.optionals enableGUI [ + "--enable-gui" "--with-x" + ]; + + postInstall = '' + # example Makefiles contain the full path to some commands + # notably texlive, and we don't want texlive to become a runtime + # dependency + for file in $(find $out -name Makefile) ; do + sed -i "s@/nix/store/[^/]*/bin/@@" "$file" ; + done; + + # reference cycle + rm "$out/share/giac/doc/el/"{casinter,tutoriel}/Makefile + + if [ -n "$doc" ]; then + mkdir -p "$doc/share/giac" + mv "$out/share/giac/doc" "$doc/share/giac" + mv "$out/share/giac/examples" "$doc/share/giac" + fi + '' + stdenv.lib.optionalString (!enableGUI) '' + for i in pixmaps application-registry applications icons; do + rm -r "$out/share/$i"; + done; + ''; + + meta = with stdenv.lib; { + description = "A free computer algebra system (CAS)"; + homepage = "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html"; + license = licenses.gpl3Plus; + platforms = platforms.linux ++ (optionals (!enableGUI) platforms.darwin); + maintainers = [ maintainers.symphorien ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/ginac/default.nix b/nixpkgs/pkgs/applications/science/math/ginac/default.nix new file mode 100644 index 000000000000..701445f90100 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/ginac/default.nix @@ -0,0 +1,28 @@ +{ stdenv, fetchurl, cln, pkgconfig, readline, gmp, python }: + +stdenv.mkDerivation rec { + name = "ginac-1.7.9"; + + src = fetchurl { + url = "${meta.homepage}/${name}.tar.bz2"; + sha256 = "08cqc87qq4w6z3l053x5gfqsa4zkgkicq8skxsbsj39nli1zzkb7"; + }; + + propagatedBuildInputs = [ cln ]; + + buildInputs = [ readline ] ++ stdenv.lib.optional stdenv.isDarwin gmp; + + nativeBuildInputs = [ pkgconfig python ]; + + preConfigure = "patchShebangs ginsh"; + + configureFlags = [ "--disable-rpath" ]; + + meta = with stdenv.lib; { + description = "GiNaC is Not a CAS"; + homepage = "http://www.ginac.de/"; + maintainers = with maintainers; [ lovek323 ]; + license = licenses.gpl2; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/glsurf/default.nix b/nixpkgs/pkgs/applications/science/math/glsurf/default.nix new file mode 100644 index 000000000000..09d0d5241687 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/glsurf/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchurl, ocamlPackages, libGLU, libGL, freeglut +, libmysqlclient, mpfr, gmp, libtiff, libjpeg, libpng, giflib +}: + +stdenv.mkDerivation { + name = "glsurf-3.3.1"; + + src = fetchurl { + url = "https://raffalli.eu/~christophe/glsurf/glsurf-3.3.1.tar.gz"; + sha256 = "0w8xxfnw2snflz8wdr2ca9f5g91w5vbyp1hwlx1v7vg83d4bwqs7"; + }; + + buildInputs = [ freeglut libGLU libGL libmysqlclient mpfr gmp + libtiff libjpeg libpng giflib ] + ++ (with ocamlPackages; [ + ocaml findlib ocaml_mysql lablgl camlimages_4_0 mlgmpidl + ]); + + installPhase = '' + mkdir -p $out/bin $out/share/doc/glsurf + cp ./src/glsurf.opt $out/bin/glsurf + cp ./doc/doc.pdf $out/share/doc/glsurf + cp -r ./examples $out/share/doc/glsurf + ''; + + meta = { + homepage = "https://raffalli.eu/~christophe/glsurf/"; + description = "A program to draw implicit surfaces and curves"; + license = stdenv.lib.licenses.lgpl21; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix new file mode 100644 index 000000000000..946beff8003f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix @@ -0,0 +1,29 @@ +{ stdenv, fetchurl, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg +, zlib, libGL, libGLU, xorg, opencascade-occt }: + +assert (!blas.isILP64) && (!lapack.isILP64); + +stdenv.mkDerivation rec { + pname = "gmsh"; + version = "4.5.6"; + + src = fetchurl { + url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; + sha256 = "0gs65bgr1ph5lz7r6manqj8cra30s7c94pxilkd2z0p5vq6fpsj6"; + }; + + buildInputs = [ blas lapack gmm fltk libjpeg zlib libGLU libGL + libGLU xorg.libXrender xorg.libXcursor xorg.libXfixes xorg.libXext + xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM xorg.libICE + opencascade-occt + ]; + + nativeBuildInputs = [ cmake gfortran ]; + + meta = { + description = "A three-dimensional finite element mesh generator"; + homepage = "http://gmsh.info/"; + platforms = [ "x86_64-linux" ]; + license = stdenv.lib.licenses.gpl2Plus; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix new file mode 100644 index 000000000000..1aa7bce07c5d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix @@ -0,0 +1,58 @@ +{ stdenv, lib, fetchurl, autoPatchelfHook, python }: + +let + majorVersion = "8.1"; +in stdenv.mkDerivation rec { + pname = "gurobi"; + version = "${majorVersion}.0"; + + src = with stdenv.lib; fetchurl { + url = "http://packages.gurobi.com/${versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; + sha256 = "1yjqbzqnq4jjkjm616d36bgd3rmqr0a1ii17n0prpdjzmdlq63dz"; + }; + + sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; + + nativeBuildInputs = [ autoPatchelfHook ]; + buildInputs = [ (python.withPackages (ps: [ ps.gurobipy ])) ]; + + buildPhase = '' + cd src/build + make + cd ../.. + ''; + + installPhase = '' + mkdir -p $out/bin + cp bin/* $out/bin/ + rm $out/bin/gurobi.env + rm $out/bin/gurobi.sh + rm $out/bin/python2.7 + + cp lib/gurobi.py $out/bin/gurobi.sh + + mkdir -p $out/include + cp include/gurobi*.h $out/include/ + + mkdir -p $out/lib + cp lib/*.jar $out/lib/ + cp lib/libGurobiJni*.so $out/lib/ + cp lib/libgurobi*.so* $out/lib/ + cp lib/libgurobi*.a $out/lib/ + cp src/build/*.a $out/lib/ + + mkdir -p $out/share/java + ln -s $out/lib/gurobi.jar $out/share/java/ + ln -s $out/lib/gurobi-javadoc.jar $out/share/java/ + ''; + + passthru.libSuffix = lib.replaceStrings ["."] [""] majorVersion; + + meta = with stdenv.lib; { + description = "Optimization solver for mathematical programming"; + homepage = "https://www.gurobi.com"; + license = licenses.unfree; + platforms = [ "x86_64-linux" ]; + maintainers = with maintainers; [ jfrankenau ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/hmetis/default.nix b/nixpkgs/pkgs/applications/science/math/hmetis/default.nix new file mode 100644 index 000000000000..b5e99a8dd75b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/hmetis/default.nix @@ -0,0 +1,42 @@ +{ stdenv, fetchurl, ghostscript }: + +stdenv.mkDerivation rec { + pname = "hmetis"; + version = "1.5"; + + src = fetchurl { + url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/hmetis/hmetis-${version}-linux.tar.gz"; + sha256 = "e835a098c046e9c26cecb8addfea4d18ff25214e49585ffd87038e72819be7e1"; + }; + + nativeBuildInputs = [ ghostscript ]; + + binaryFiles = "hmetis khmetis shmetis"; + + patchPhase = '' + for binaryfile in $binaryFiles; do + patchelf \ + --set-interpreter ${stdenv.glibc}/lib/ld-linux.so.2 \ + --set-rpath ${stdenv.glibc}/lib \ + $binaryfile + done + ''; + + buildPhase = '' + gs -sOutputFile=manual.pdf -sDEVICE=pdfwrite -SNOPAUSE -dBATCH manual.ps + ''; + + installPhase = '' + mkdir -p $out/bin $out/share/doc/hmetis $out/lib + mv $binaryFiles $out/bin + mv manual.pdf $out/share/doc/hmetis + mv libhmetis.a $out/lib + ''; + + meta = with stdenv.lib; { + description = "hMETIS is a set of programs for partitioning hypergraphs"; + homepage = "http://glaros.dtc.umn.edu/gkhome/metis/hmetis/overview"; + license = licenses.unfree; + platforms = [ "i686-linux" "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/jags/default.nix b/nixpkgs/pkgs/applications/science/math/jags/default.nix new file mode 100644 index 000000000000..122c62888476 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/jags/default.nix @@ -0,0 +1,19 @@ +{stdenv, fetchurl, gfortran, blas, lapack}: + +stdenv.mkDerivation rec { + name = "JAGS-4.3.0"; + src = fetchurl { + url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz"; + sha256 = "1z3icccg2ic56vmhyrpinlsvpq7kcaflk1731rgpvz9bk1bxvica"; + }; + buildInputs = [gfortran blas lapack]; + configureFlags = [ "--with-blas=-lblas" "--with-lapack=-llapack" ]; + + meta = with stdenv.lib; { + description = "Just Another Gibbs Sampler"; + license = licenses.gpl2; + homepage = "http://mcmc-jags.sourceforge.net"; + maintainers = [ maintainers.andres ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix b/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix new file mode 100644 index 000000000000..f39c6a04d190 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/lp_solve/default.nix @@ -0,0 +1,49 @@ +{ stdenv, fetchurl }: + +stdenv.mkDerivation rec { + + pname = "lp_solve"; + version = "5.5.2.5"; + + src = fetchurl { + url = "mirror://sourceforge/project/lpsolve/lpsolve/${version}/lp_solve_${version}_source.tar.gz"; + sha256 = "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0"; + }; + + patches = [ ./isnan.patch ]; + + buildCommand = '' + . $stdenv/setup + tar xvfz $src + ( + cd lp_solve* + eval patchPhase + ) + ( + cd lp_solve*/lpsolve55 + bash ccc + mkdir -pv $out/lib + cp -v bin/*/* $out/lib + ) + ( + cd lp_solve*/lp_solve + bash ccc + mkdir -pv $out/bin + cp -v bin/*/* $out/bin + ) + ( + mkdir -pv $out/include + cp -v lp_solve*/*.h $out/include + ) + ''; + + meta = with stdenv.lib; { + description = "A Mixed Integer Linear Programming (MILP) solver"; + homepage = "http://lpsolve.sourceforge.net"; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ smironov ]; + platforms = platforms.unix; + }; + +} + diff --git a/nixpkgs/pkgs/applications/science/math/lp_solve/isnan.patch b/nixpkgs/pkgs/applications/science/math/lp_solve/isnan.patch new file mode 100644 index 000000000000..bc1983d4423d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/lp_solve/isnan.patch @@ -0,0 +1,13 @@ +diff -u a/lp_lib.h b/lp_lib.h +--- a/lp_lib.h 2016-05-04 19:45:15.753143720 +0900 ++++ b/lp_lib.h 2016-05-04 19:53:59.536920722 +0900 +@@ -59,9 +59,6 @@ + # if defined _WIN32 && !defined __GNUC__ + # define isnan _isnan + # endif +-#if defined NOISNAN +-# define isnan(x) FALSE +-#endif + + #define SETMASK(variable, mask) variable |= mask + #define CLEARMASK(variable, mask) variable &= ~(mask) diff --git a/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix b/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix new file mode 100644 index 000000000000..438a84c0e0be --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix @@ -0,0 +1,40 @@ +{ stdenv +, fetchFromBitbucket +, fetchpatch +, autoreconfHook +}: + +stdenv.mkDerivation rec { + version = "1.2"; + pname = "lrcalc"; + + src = fetchFromBitbucket { + owner = "asbuch"; + repo = "lrcalc"; + rev = "lrcalc-${version}"; + sha256 = "1c12d04jdyxkkav4ak8d1aqrv594gzihwhpxvc6p9js0ry1fahss"; + }; + + doCheck = true; + + nativeBuildInputs = [ + autoreconfHook + ]; + + patches = [ + # Fix include syntax: + # For private includes, use `#include "..."` instead of `#include <...>` + (fetchpatch { + url = "https://bitbucket.org/asbuch/lrcalc/commits/226981a0/raw/"; + sha256 = "02kaqx5s3l642rhh28kn2wg9wr098vzpknxyl4pv627lqa3lv9vm"; + }) + ]; + + meta = with stdenv.lib; { + description = "Littlewood-Richardson calculator"; + homepage = "http://math.rutgers.edu/~asbuch/lrcalc/"; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ timokau ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/10.nix b/nixpkgs/pkgs/applications/science/math/mathematica/10.nix new file mode 100644 index 000000000000..277fb1984c44 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/mathematica/10.nix @@ -0,0 +1,136 @@ +{ stdenv +, coreutils +, patchelf +, requireFile +, alsaLib +, fontconfig +, freetype +, gcc +, glib +, ncurses +, opencv2 +, openssl +, unixODBC +, xorg +, libxml2 +, libuuid +}: + +let + platform = + if stdenv.hostPlatform.system == "i686-linux" || stdenv.hostPlatform.system == "x86_64-linux" then + "Linux" + else + throw "Mathematica requires i686-linux or x86_64 linux"; +in +stdenv.mkDerivation rec { + version = "10.0.2"; + + pname = "mathematica"; + + src = requireFile rec { + name = "Mathematica_${version}_LINUX.sh"; + message = '' + This nix expression requires that ${name} is + already part of the store. Find the file on your Mathematica CD + and add it to the nix store with nix-store --add-fixed sha256 <FILE>. + ''; + sha256 = "1d2yaiaikzcacjamlw64g3xkk81m3pb4vz4an12cv8nb7kb20x9l"; + }; + + buildInputs = [ + coreutils + patchelf + alsaLib + coreutils + fontconfig + freetype + gcc.cc + gcc.libc + glib + ncurses + opencv2 + openssl + unixODBC + libxml2 + libuuid + ] ++ (with xorg; [ + libX11 + libXext + libXtst + libXi + libXmu + libXrender + libxcb + libXcursor + libXfixes + libXrandr + libICE + libSM + ]); + + ldpath = stdenv.lib.makeLibraryPath buildInputs + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") + (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); + + phases = "unpackPhase installPhase fixupPhase"; + + unpackPhase = '' + echo "=== Extracting makeself archive ===" + # find offset from file + offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src) + dd if="$src" ibs=$offset skip=1 | tar -xf - + cd Unix + ''; + + installPhase = '' + cd Installer + # don't restrict PATH, that has already been done + sed -i -e 's/^PATH=/# PATH=/' MathInstaller + + echo "=== Running MathInstaller ===" + ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -platforms=${platform} -silent + ''; + + preFixup = '' + echo "=== PatchElfing away ===" + # This code should be a bit forgiving of errors, unfortunately + set +e + find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do + type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/') + if [ -z "$type" ]; then + : + elif [ "$type" == "EXEC" ]; then + echo "patching $f executable <<" + patchelf --shrink-rpath "$f" + patchelf \ + --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + elif [ "$type" == "DYN" ]; then + echo "patching $f library <<" + patchelf \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + else + echo "not patching $f <<: unknown elf type" + fi + done + ''; + + # all binaries are already stripped + dontStrip = true; + + # we did this in prefixup already + dontPatchELF = true; + + meta = { + description = "Wolfram Mathematica computational software system"; + homepage = "http://www.wolfram.com/mathematica/"; + license = stdenv.lib.licenses.unfree; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/11.nix b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix new file mode 100644 index 000000000000..1c698a5e5428 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix @@ -0,0 +1,150 @@ +{ stdenv +, coreutils +, patchelf +, requireFile +, callPackage +, alsaLib +, dbus +, fontconfig +, freetype +, gcc +, glib +, ncurses +, opencv2 +, openssl +, unixODBC +, xkeyboard_config +, xorg +, zlib +, libxml2 +, libuuid +, lang ? "en" +, libGL +, libGLU +}: + +let + l10n = + import ./l10ns.nix { + lib = stdenv.lib; + inherit requireFile lang; + majorVersion = "11"; + }; +in +stdenv.mkDerivation rec { + inherit (l10n) version name src; + + buildInputs = [ + coreutils + patchelf + alsaLib + coreutils + dbus + fontconfig + freetype + gcc.cc + gcc.libc + glib + ncurses + opencv2 + openssl + unixODBC + xkeyboard_config + libxml2 + libuuid + zlib + libGL + libGLU + ] ++ (with xorg; [ + libX11 + libXext + libXtst + libXi + libXmu + libXrender + libxcb + libXcursor + libXfixes + libXrandr + libICE + libSM + ]); + + ldpath = stdenv.lib.makeLibraryPath buildInputs + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") + (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); + + phases = "unpackPhase installPhase fixupPhase"; + + unpackPhase = '' + echo "=== Extracting makeself archive ===" + # find offset from file + offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src) + dd if="$src" ibs=$offset skip=1 | tar -xf - + cd Unix + ''; + + installPhase = '' + cd Installer + # don't restrict PATH, that has already been done + sed -i -e 's/^PATH=/# PATH=/' MathInstaller + sed -i -e 's/\/bin\/bash/\/bin\/sh/' MathInstaller + + echo "=== Running MathInstaller ===" + ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -silent + + # Fix library paths + cd $out/libexec/Mathematica/Executables + for path in mathematica MathKernel Mathematica WolframKernel wolfram math; do + sed -i -e 's#export LD_LIBRARY_PATH$#export LD_LIBRARY_PATH=${zlib}/lib:\''${LD_LIBRARY_PATH}#' $path + done + + # Fix xkeyboard config path for Qt + for path in mathematica Mathematica; do + line=$(grep -n QT_PLUGIN_PATH $path | sed 's/:.*//') + sed -i -e "$line iexport QT_XKB_CONFIG_ROOT=\"${xkeyboard_config}/share/X11/xkb\"" $path + done + ''; + + preFixup = '' + echo "=== PatchElfing away ===" + # This code should be a bit forgiving of errors, unfortunately + set +e + find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do + type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/') + if [ -z "$type" ]; then + : + elif [ "$type" == "EXEC" ]; then + echo "patching $f executable <<" + patchelf --shrink-rpath "$f" + patchelf \ + --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + elif [ "$type" == "DYN" ]; then + echo "patching $f library <<" + patchelf \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + else + echo "not patching $f <<: unknown elf type" + fi + done + ''; + + # all binaries are already stripped + dontStrip = true; + + # we did this in prefixup already + dontPatchELF = true; + + meta = { + description = "Wolfram Mathematica computational software system"; + homepage = "http://www.wolfram.com/mathematica/"; + license = stdenv.lib.licenses.unfree; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/9.nix b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix new file mode 100644 index 000000000000..d0967485c01f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/mathematica/9.nix @@ -0,0 +1,122 @@ +{ stdenv +, coreutils +, patchelf +, requireFile +, alsaLib +, fontconfig +, freetype +, gcc +, glib +, ncurses +, opencv2 +, openssl +, unixODBC +, xorg +}: + +let + platform = + if stdenv.hostPlatform.system == "i686-linux" || stdenv.hostPlatform.system == "x86_64-linux" then + "Linux" + else + throw "Mathematica requires i686-linux or x86_64 linux"; +in +stdenv.mkDerivation rec { + + name = "mathematica-9.0.0"; + + src = requireFile { + name = "Mathematica_9.0.0_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 + and add it to the nix store with nix-store --add-fixed sha256 <FILE>. + ''; + sha256 = "106zfaplhwcfdl9rdgs25x83xra9zcny94gb22wncbfxvrsk3a4q"; + }; + + buildInputs = [ + coreutils + patchelf + alsaLib + coreutils + fontconfig + freetype + gcc.cc + gcc.libc + glib + ncurses + opencv2 + openssl + unixODBC + ] ++ (with xorg; [ + libX11 + libXext + libXtst + libXi + libXmu + libXrender + libxcb + ]); + + ldpath = stdenv.lib.makeLibraryPath buildInputs + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") + (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); + + phases = "unpackPhase installPhase fixupPhase"; + + unpackPhase = '' + echo "=== Extracting makeself archive ===" + # find offset from file + offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src) + dd if="$src" ibs=$offset skip=1 | tar -xf - + cd Unix + ''; + + installPhase = '' + cd Installer + # don't restrict PATH, that has already been done + sed -i -e 's/^PATH=/# PATH=/' MathInstaller + + echo "=== Running MathInstaller ===" + ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -platforms=${platform} -silent + ''; + + preFixup = '' + echo "=== PatchElfing away ===" + find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do + type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/') + if [ -z "$type" ]; then + : + elif [ "$type" == "EXEC" ]; then + echo "patching $f executable <<" + patchelf \ + --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + --set-rpath "${ldpath}" \ + "$f" + patchelf --shrink-rpath "$f" + elif [ "$type" == "DYN" ]; then + echo "patching $f library <<" + patchelf \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + else + echo "not patching $f <<: unknown elf type" + fi + done + ''; + + # all binaries are already stripped + dontStrip = true; + + # we did this in prefixup already + dontPatchELF = true; + + meta = { + description = "Wolfram Mathematica computational software system"; + homepage = "http://www.wolfram.com/mathematica/"; + license = stdenv.lib.licenses.unfree; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix new file mode 100644 index 000000000000..94d72eec6ae4 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix @@ -0,0 +1,156 @@ +{ stdenv +, coreutils +, patchelf +, requireFile +, callPackage +, alsaLib +, dbus +, fontconfig +, freetype +, gcc +, glib +, libssh2 +, ncurses +, opencv2 +, openssl +, unixODBC +, xkeyboard_config +, xorg +, zlib +, libxml2 +, libuuid +, lang ? "en" +, libGL +, libGLU +}: + +let + l10n = + import ./l10ns.nix { + lib = stdenv.lib; + inherit requireFile lang; + }; +in +stdenv.mkDerivation rec { + inherit (l10n) version name src; + + buildInputs = [ + coreutils + patchelf + alsaLib + coreutils + dbus + fontconfig + freetype + gcc.cc + gcc.libc + glib + libssh2 + ncurses + opencv2 + openssl + stdenv.cc.cc.lib + unixODBC + xkeyboard_config + libxml2 + libuuid + zlib + libGL + libGLU + ] ++ (with xorg; [ + libX11 + libXext + libXtst + libXi + libXmu + libXrender + libxcb + libXcursor + libXfixes + libXrandr + libICE + libSM + ]); + + ldpath = stdenv.lib.makeLibraryPath buildInputs + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") + (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); + + unpackPhase = '' + echo "=== Extracting makeself archive ===" + # find offset from file + offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src) + dd if="$src" ibs=$offset skip=1 | tar -xf - + cd Unix + ''; + + installPhase = '' + cd Installer + # don't restrict PATH, that has already been done + sed -i -e 's/^PATH=/# PATH=/' MathInstaller + sed -i -e 's/\/bin\/bash/\/bin\/sh/' MathInstaller + + echo "=== Running MathInstaller ===" + ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -silent + + # 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:${stdenv.cc.cc.lib}/lib:${libssh2}/lib:\''${LD_LIBRARY_PATH}\n" $path + done + + # Fix xkeyboard config path for Qt + for path in mathematica Mathematica; do + sed -i -e "2iexport QT_XKB_CONFIG_ROOT=\"${xkeyboard_config}/share/X11/xkb\"\n" $path + done + + # Remove some broken libraries + rm -f $out/libexec/Mathematica/SystemFiles/Libraries/Linux-x86-64/libz.so* + ''; + + preFixup = '' + echo "=== PatchElfing away ===" + # This code should be a bit forgiving of errors, unfortunately + set +e + find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do + type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/') + if [ -z "$type" ]; then + : + elif [ "$type" == "EXEC" ]; then + echo "patching $f executable <<" + patchelf --shrink-rpath "$f" + patchelf \ + --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + elif [ "$type" == "DYN" ]; then + echo "patching $f library <<" + patchelf \ + --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \ + "$f" \ + && patchelf --shrink-rpath "$f" \ + || echo unable to patch ... ignoring 1>&2 + else + echo "not patching $f <<: unknown elf type" + fi + done + ''; + + dontBuild = true; + + # all binaries are already stripped + dontStrip = true; + + # we did this in prefixup already + dontPatchELF = true; + + meta = with stdenv.lib; { + description = "Wolfram Mathematica computational software system"; + homepage = "http://www.wolfram.com/mathematica/"; + license = licenses.unfree; + maintainers = with maintainers; [ herberteuler ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix b/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix new file mode 100644 index 000000000000..c75c91be059c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix @@ -0,0 +1,60 @@ +{ lib +, requireFile +, lang +, majorVersion ? null +}: + +let allVersions = with lib; flip map + # N.B. Versions in this list should be ordered from newest to oldest. + [ + { + version = "12.1.0"; + lang = "en"; + language = "English"; + sha256 = "15m9l20jvkxh5w6mbp81ys7mx2lx5j8acw5gz0il89lklclgb8z7"; + } + { + version = "12.0.0"; + lang = "en"; + language = "English"; + sha256 = "b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7"; + } + { + version = "11.3.0"; + lang = "en"; + language = "English"; + sha256 = "0fcfe208c1eac8448e7be3af0bdb84370b17bd9c5d066c013928c8ee95aed10e"; + } + { + version = "11.2.0"; + lang = "ja"; + language = "Japanese"; + sha256 = "916392edd32bed8622238df435dd8e86426bb043038a3336f30df10d819b49b1"; + } + ] + ({ version, lang, language, sha256 }: { + inherit version lang; + name = "mathematica-${version}" + optionalString (lang != "en") "-${lang}"; + src = requireFile rec { + name = "Mathematica_${version}" + optionalString (lang != "en") "_${language}" + "_LINUX.sh"; + message = '' + This nix expression requires that ${name} is + already part of the store. Find the file on your Mathematica CD + and add it to the nix store with nix-store --add-fixed sha256 <FILE>. + ''; + inherit sha256; + }; + }); +minVersion = + with lib; + if majorVersion == null + then elemAt (builtins.splitVersion (elemAt allVersions 0).version) 0 + else majorVersion; +maxVersion = toString (1 + builtins.fromJSON minVersion); +in +with lib; +findFirst (l: (l.lang == lang + && l.version >= minVersion + && l.version < maxVersion)) + (throw "Version ${minVersion} in language ${lang} not supported") + allVersions diff --git a/nixpkgs/pkgs/applications/science/math/maxima/5.41.nix b/nixpkgs/pkgs/applications/science/math/maxima/5.41.nix new file mode 100644 index 000000000000..829dffc6116e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/maxima/5.41.nix @@ -0,0 +1,102 @@ +{ stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null +, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false +}: + +let + name = "maxima"; + # old version temporarily kept for sage, see discussion at + # https://github.com/NixOS/nixpkgs/commit/82254747af35f3e0e0d6f78023ded3a81e25331b + version = "5.41.0"; + + searchPath = + stdenv.lib.makeBinPath + (stdenv.lib.filter (x: x != null) [ sbcl ecl rlwrap tk gnuplot ]); +in +stdenv.mkDerivation ({ + inherit version; + name = "${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/nixpkgs/pkgs/applications/science/math/maxima/default.nix b/nixpkgs/pkgs/applications/science/math/maxima/default.nix new file mode 100644 index 000000000000..49ff0d5d5a05 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/maxima/default.nix @@ -0,0 +1,104 @@ +{ stdenv, fetchurl, fetchpatch, sbcl, texinfo, perl, python, makeWrapper, rlwrap ? null +, tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false +}: + +let + name = "maxima"; + version = "5.42.2"; + + 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 = "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn"; + }; + + buildInputs = stdenv.lib.filter (x: x != null) [ + sbcl ecl texinfo perl python makeWrapper + gnuplot # required in the test suite + ]; + + 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"; + }) + ]; + + # The test suite is disabled since 5.42.2 because of the following issues: + # + # Errors found in /build/maxima-5.42.2/share/linearalgebra/rtest_matrixexp.mac, problems: + # (20 21 22) + # Error found in rtest_arag, problem: + # (error break) + # 3 tests failed out of 3,881 total tests. + # + # These failures don't look serious. It would be nice to fix them, but I + # don't know how and probably won't have the time to find out. + doCheck = false; # try to re-enable after next version update + + 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/nixpkgs/pkgs/applications/science/math/maxima/known-ecl-failures.patch b/nixpkgs/pkgs/applications/science/math/maxima/known-ecl-failures.patch new file mode 100644 index 000000000000..f1d612d993e6 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/maxima/known-ecl-failures.patch @@ -0,0 +1,21 @@ +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/nixpkgs/pkgs/applications/science/math/msieve/default.nix b/nixpkgs/pkgs/applications/science/math/msieve/default.nix new file mode 100644 index 000000000000..db7a1c149068 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/msieve/default.nix @@ -0,0 +1,30 @@ +{stdenv, fetchurl, zlib, gmp, ecm }: + +stdenv.mkDerivation { + name = "msieve-1.53"; + + src = fetchurl { + url = "mirror://sourceforge/msieve/msieve/Msieve%20v1.53/msieve153_src.tar.gz"; + sha256 = "1d1vv7j4rh3nnxsmvafi73qy7lw7n3akjlm5pjl3m936yapvmz65"; + }; + + buildInputs = [ zlib gmp ecm ]; + + ECM = if ecm == null then "0" else "1"; + + # Doesn't hurt Linux but lets clang-based platforms like Darwin work fine too + makeFlags = [ "CC=cc" "all" ]; + + installPhase = '' + mkdir -p $out/bin/ + cp msieve $out/bin/ + ''; + + meta = { + description = "A C library implementing a suite of algorithms to factor large integers"; + license = stdenv.lib.licenses.publicDomain; + homepage = "http://msieve.sourceforge.net/"; + maintainers = [ stdenv.lib.maintainers.roconnor ]; + platforms = [ "x86_64-linux" ] ++ stdenv.lib.platforms.darwin; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/mxnet/default.nix b/nixpkgs/pkgs/applications/science/math/mxnet/default.nix new file mode 100644 index 000000000000..b006a9dd18d1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/mxnet/default.nix @@ -0,0 +1,55 @@ +{ config, stdenv, lib, fetchurl, bash, cmake +, opencv3, gtest, blas, perl +, cudaSupport ? config.cudaSupport or false, cudatoolkit, nvidia_x11 +, cudnnSupport ? cudaSupport, cudnn +}: + +assert cudnnSupport -> cudaSupport; + +stdenv.mkDerivation rec { + pname = "mxnet"; + version = "1.6.0"; + + src = fetchurl { + url = "https://github.com/apache/incubator-mxnet/releases/download/${version}/apache-mxnet-src-${version}-incubating.tar.gz"; + sha256 = "1vvdb7pfh63kb9fzs6gqp95q550a3ck4cj9mqxlk9wwhkh30dsq1"; + }; + + nativeBuildInputs = [ cmake perl ]; + + buildInputs = [ opencv3 gtest blas ] + ++ lib.optionals cudaSupport [ cudatoolkit nvidia_x11 ] + ++ lib.optional cudnnSupport cudnn; + + cmakeFlags = + [ "-DUSE_MKL_IF_AVAILABLE=OFF" ] + ++ (if cudaSupport then [ + "-DUSE_OLDCMAKECUDA=ON" # see https://github.com/apache/incubator-mxnet/issues/10743 + "-DCUDA_ARCH_NAME=All" + "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc" + ] else [ "-DUSE_CUDA=OFF" ]) + ++ lib.optional (!cudnnSupport) "-DUSE_CUDNN=OFF"; + + postPatch = '' + substituteInPlace 3rdparty/mkldnn/tests/CMakeLists.txt \ + --replace "/bin/bash" "${bash}/bin/bash" + + # Build against the system version of OpenMP. + # https://github.com/apache/incubator-mxnet/pull/12160 + rm -rf 3rdparty/openmp + ''; + + postInstall = '' + rm "$out"/lib/*.a + ''; + + enableParallelBuilding = true; + + meta = with stdenv.lib; { + description = "Lightweight, Portable, Flexible Distributed/Mobile Deep Learning with Dynamic, Mutation-aware Dataflow Dep Scheduler"; + homepage = "https://mxnet.incubator.apache.org/"; + maintainers = with maintainers; [ abbradar ]; + license = licenses.asl20; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/nasc/default.nix b/nixpkgs/pkgs/applications/science/math/nasc/default.nix new file mode 100644 index 000000000000..002acbf3875f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/nasc/default.nix @@ -0,0 +1,70 @@ +{ stdenv +, fetchFromGitHub +, fetchpatch +, pkgconfig +, vala +, gtk3 +, glib +, pantheon +, libsoup +, gtksourceview +, libgee +, cmake +, libqalculate +, cln +, wrapGAppsHook +}: + +stdenv.mkDerivation rec { + pname = "nasc"; + version = "0.5.4"; + + src = fetchFromGitHub { + owner = "parnold-x"; + repo = pname; + rev = version; + sha256 = "036v3dx8yasp19j88lflibqnpfi5d0nk7qkcnr80zn1lvawf4wgn"; + }; + + patches = [ + # fix build with gcc9 + (fetchpatch { + url = "https://github.com/parnold-x/nasc/commit/46b9b80e228b6b86001bded45d85e073a9411549.patch"; + sha256 = "1sm2aw0xhw2chk036r231nmp2f2ypxcmzggwljkn7wfzgg3h1mx3"; + }) + ]; + + nativeBuildInputs = [ + cmake + vala + pkgconfig + wrapGAppsHook + ]; + + buildInputs = [ + cln + libsoup + gtk3 + glib + gtksourceview + libgee + libqalculate + pantheon.elementary-icon-theme + pantheon.granite + ]; + + meta = with stdenv.lib; { + description = "Do maths like a normal person"; + longDescription = '' + It’s an app where you do maths like a normal person. It lets you + type whatever you want and smartly figures out what is math and + spits out an answer on the right pane. Then you can plug those + answers in to future equations and if that answer changes, so does + the equations it’s used in. + ''; + homepage = "https://github.com/parnold-x/nasc"; + maintainers = with maintainers; [ samdroid-apps ]; + platforms = platforms.linux; + license = licenses.gpl3Plus; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/nauty/default.nix b/nixpkgs/pkgs/applications/science/math/nauty/default.nix new file mode 100644 index 000000000000..64cc4a9aa003 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/nauty/default.nix @@ -0,0 +1,42 @@ +{ stdenv +, lib +, fetchurl +}: +stdenv.mkDerivation rec { + pname = "nauty"; + version = "26r12"; + src = fetchurl { + url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz"; + sha256 = "1p4mxf8q5wm47nxyskxbqwa5p1vvkycv1zgswvnk9nsn6vff0al6"; + }; + outputs = [ "out" "dev" ]; + configureFlags = { + # Prevent nauty from sniffing some cpu features. While those are very + # widely available, it can lead to nasty bugs when they are not available: + # https://groups.google.com/forum/#!topic/sage-packaging/Pe4SRDNYlhA + default = [ "--disable-clz" "--disable-popcnt" ]; + westmere = [ "--disable-clz" ]; + sandybridge = [ "--disable-clz" ]; + ivybridge = [ "--disable-clz" ]; + }.${stdenv.hostPlatform.platform.gcc.arch or "default"} or []; + installPhase = '' + mkdir -p "$out"/{bin,share/doc/nauty} "$dev"/{lib,include/nauty} + + find . -type f -perm -111 \! -name '*.*' \! -name configure -exec cp '{}' "$out/bin" \; + cp [Rr][Ee][Aa][Dd]* COPYRIGHT This* [Cc]hange* "$out/share/doc/nauty" + + cp *.h "$dev/include/nauty" + for i in *.a; do + cp "$i" "$dev/lib/lib$i"; + done + ''; + checkTarget = "checks"; + meta = with lib; { + inherit version; + description = ''Programs for computing automorphism groups of graphs and digraphs''; + license = licenses.asl20; + maintainers = with maintainers; [ raskin timokau ]; + platforms = platforms.unix; + homepage = "http://pallini.di.uniroma1.it/"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/nota/default.nix b/nixpkgs/pkgs/applications/science/math/nota/default.nix new file mode 100644 index 000000000000..897785ef6e8b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/nota/default.nix @@ -0,0 +1,40 @@ +{ mkDerivation, haskellPackages, fetchurl, lib }: + +mkDerivation rec { + pname = "nota"; + version = "1.0"; + + # Can't use fetchFromGitLab since codes.kary.us doesn't support https + src = fetchurl { + url = "http://codes.kary.us/nota/nota/-/archive/V${version}/nota-V${version}.tar.bz2"; + sha256 = "0bbs6bm9p852hvqadmqs428ir7m65h2prwyma238iirv42pk04v8"; + }; + + postUnpack = '' + export sourceRoot=$sourceRoot/source + ''; + + isLibrary = false; + isExecutable = true; + + libraryHaskellDepends = with haskellPackages; [ + base + bytestring + array + split + scientific + parsec + ansi-terminal + regex-compat + containers + terminal-size + numbers + text + time + ]; + + description = "The most beautiful command line calculator"; + homepage = "https://kary.us/nota"; + license = lib.licenses.mpl20; + maintainers = with lib.maintainers; [ dtzWill ]; +} diff --git a/nixpkgs/pkgs/applications/science/math/palp/default.nix b/nixpkgs/pkgs/applications/science/math/palp/default.nix new file mode 100644 index 000000000000..4912b82d158f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/palp/default.nix @@ -0,0 +1,88 @@ +{ stdenv +, fetchurl +, dimensions ? 6 # works for <= dimensions dimensions, but is only optimized for that exact value +, doSymlink ? true # symlink the executables to the default location (without dimension postfix) +}: + +let + dim = toString dimensions; +in +stdenv.mkDerivation rec { + pname = "palp"; + version = "2.1"; + + src = fetchurl { + url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/palp-${version}.tar.gz"; + sha256 = "1s7s2lc5f0ig1yy7ygsh3sddm3sbq4mxwybqsj8lp9wjdxs7qfrs"; + }; + + hardeningDisable = [ + "format" + "strictoverflow" # causes runtime failure (tested in checkPhase) + ]; + + patchPhase = stdenv.lib.optionalString stdenv.isDarwin '' + substituteInPlace GNUmakefile --replace gcc cc + ''; + + preBuild = '' + echo Building PALP optimized for ${dim} dimensions + sed -i "s/^#define[^a-zA-Z]*POLY_Dmax.*/#define POLY_Dmax ${dim}/" Global.h + ''; + + # palp has no tests of its own. This test is an adapted sage test that failed + # when #28029 was merged. + doCheck = true; + checkPhase = '' + ./nef.x -f -N << EOF | grep -q 'np=' + 3 6 + 1 0 0 -1 0 0 + 0 1 0 0 -1 0 + 0 0 1 0 0 -1 + EOF + ''; + + installPhase = '' + mkdir -p "$out/bin" + for file in poly class cws nef mori; do + cp -p $file.x "$out/bin/$file-${dim}d.x" + done + '' + stdenv.lib.optionalString doSymlink '' + cd "$out/bin" + for file in poly class cws nef mori; do + ln -sf $file-6d.x $file.x + done + ''; + + meta = with stdenv.lib; { + description = "A Package for Analyzing Lattice Polytopes"; + longDescription = '' + A Package for Analyzing Lattice Polytopes (PALP) is a set of C + programs for calculations with lattice polytopes and applications to + toric geometry. + + It contains routines for vertex and facet enumeration, computation of + incidences and symmetries, as well as completion of the set of lattice + points in the convex hull of a given set of points. In addition, there + are procedures specialised to reflexive polytopes such as the + enumeration of reflexive subpolytopes, and applications to toric + geometry and string theory, like the computation of Hodge data and + fibration structures for toric Calabi-Yau varieties. The package is + well tested and optimised in speed as it was used for time consuming + tasks such as the classification of reflexive polyhedra in 4 + dimensions and the creation and manipulation of very large lists of + 5-dimensional polyhedra. + + While originally intended for low-dimensional applications, the + 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"; + # 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. + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/pari/default.nix b/nixpkgs/pkgs/applications/science/math/pari/default.nix new file mode 100644 index 000000000000..8b5176c94f69 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/pari/default.nix @@ -0,0 +1,91 @@ +{ stdenv +, fetchurl +, fetchpatch +, gmp +, readline +, libX11 +, tex +, perl +, withThread ? true, libpthreadstubs +}: + +assert withThread -> libpthreadstubs != null; + +stdenv.mkDerivation rec { + pname = "pari"; + version = "2.11.3"; + + src = fetchurl { + url = "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz"; + sha256 = "1jd65h2psrmba2dx7rkf5qidf9ka0cwbsg20pd18k45ggr30l467"; + }; + + patches = [ + # https://trac.sagemath.org/ticket/29313#comment:1 + (fetchpatch { + name = "backport-bug-fix.patch"; + url = "https://git.archlinux.org/svntogit/community.git/plain/repos/community-x86_64/c7a1d35f.patch?h=packages/pari&id=27893d227290dc3821d68aa25877d9765c204dad"; + sha256 = "0vm0fwyzj66cr32imip6srksd47s2s2sjl1rb26ph8gpfi3nalii"; + }) + ]; + + buildInputs = [ + gmp + readline + libX11 + tex + perl + ] ++ stdenv.lib.optionals withThread [ + libpthreadstubs + ]; + + configureScript = "./Configure"; + configureFlags = [ + "--with-gmp=${gmp.dev}" + "--with-readline=${readline.dev}" + ] ++ stdenv.lib.optional stdenv.isDarwin "--host=x86_64-darwin" + ++ stdenv.lib.optional withThread "--mt=pthread"; + + preConfigure = '' + export LD=$CC + ''; + + postConfigure = stdenv.lib.optionalString stdenv.isDarwin '' + echo 'echo x86_64-darwin' > config/arch-osname + ''; + + makeFlags = [ "all" ]; + + meta = with stdenv.lib; { + description = "Computer algebra system for high-performance number theory computations"; + longDescription = '' + PARI/GP is a widely used computer algebra system designed for fast + computations in number theory (factorizations, algebraic number theory, + elliptic curves...), but also contains a large number of other useful + functions to compute with mathematical entities such as matrices, + polynomials, power series, algebraic numbers etc., and a lot of + transcendental functions. PARI is also available as a C library to allow + for faster computations. + + Originally developed by Henri Cohen and his co-workers (Université + Bordeaux I, France), PARI is now under the GPL and maintained by Karim + Belabas with the help of many volunteer contributors. + + - PARI is a C library, allowing fast computations. + - gp is an easy-to-use interactive shell giving access to the + PARI functions. + - GP is the name of gp's scripting language. + - gp2c, the GP-to-C compiler, combines the best of both worlds + by compiling GP scripts to the C language and transparently loading + the resulting functions into gp. (gp2c-compiled scripts will typically + run 3 or 4 times faster.) gp2c currently only understands a subset + of the GP language. + ''; + homepage = "http://pari.math.u-bordeaux.fr"; + downloadPage = "http://pari.math.u-bordeaux.fr/download.html"; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ ertes raskin AndersonTorres timokau ]; + platforms = platforms.linux ++ platforms.darwin; + updateWalker = true; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix b/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix new file mode 100644 index 000000000000..4fa63e8edabd --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchurl +, pari, perl }: + +stdenv.mkDerivation rec { + + pname = "gp2c"; + version = "0.0.11pl3"; + + src = fetchurl { + url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${pname}-${version}.tar.gz"; + sha256 = "0yymbrgyjw500hqgmkj5m4nmscd7c9rs9w2c96lxgrcyab8krhrm"; + }; + + buildInputs = [ pari perl ]; + + configureFlags = [ + "--with-paricfg=${pari}/lib/pari/pari.cfg" + "--with-perl=${perl}/bin/perl" ]; + + meta = with stdenv.lib; { + description = "A compiler to translate GP scripts to PARI programs"; + homepage = "http://pari.math.u-bordeaux.fr/"; + downloadPage = "http://pari.math.u-bordeaux.fr/download.html"; + license = licenses.gpl2Plus; + maintainers = with maintainers; [ AndersonTorres ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/pcalc/default.nix b/nixpkgs/pkgs/applications/science/math/pcalc/default.nix new file mode 100644 index 000000000000..f372357fe7d8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/pcalc/default.nix @@ -0,0 +1,26 @@ +{ stdenv, fetchgit, bison, flex }: + +with stdenv.lib; + +stdenv.mkDerivation rec { + pname = "pcalc"; + version = "20141224"; + + src = fetchgit { + url = "git://git.code.sf.net/p/pcalc/code"; + rev = "181d60d3c880da4344fef7138065943eb3b9255f"; + sha256 = "1hd5bh20j5xzvv6qa0fmzmv0h8sf38r7zgi7y0b6nk17pjq33v90"; + }; + + makeFlags = [ "DESTDIR= BINDIR=$(out)/bin" ]; + buildInputs = [ bison flex ]; + + meta = { + homepage = "http://pcalc.sourceforge.net/"; + description = "Programmer's calculator"; + license = licenses.gpl2; + maintainers = with stdenv.lib.maintainers; [ ftrvxmtrx ]; + platforms = stdenv.lib.platforms.linux; + inherit version; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/perseus/default.nix b/nixpkgs/pkgs/applications/science/math/perseus/default.nix new file mode 100644 index 000000000000..55293e6c8a79 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/perseus/default.nix @@ -0,0 +1,40 @@ +{ stdenv, fetchurl, unzip }: + +stdenv.mkDerivation { + name = "perseus-4-beta"; + version = "4-beta"; + buildInputs = [ unzip ]; + + hardeningDisable = [ "stackprotector" ]; + + src = fetchurl { + url = "http://www.sas.upenn.edu/~vnanda/source/perseus_4_beta.zip"; + sha256 = "09brijnqabhgfjlj5wny0bqm5dwqcfkp1x5wif6yzdmqh080jybj"; + }; + + sourceRoot = "."; + + buildPhase = '' + g++ Pers.cpp -O3 -fpermissive -o perseus + ''; + + installPhase = '' + mkdir -p $out/bin + cp perseus $out/bin + ''; + + meta = { + description = "The Persistent Homology Software"; + longDescription = '' + Persistent homology - or simply, persistence - is an algebraic + topological invariant of a filtered cell complex. Perseus + computes this invariant for a wide class of filtrations built + around datasets arising from point samples, images, distance + matrices and so forth. + ''; + homepage = "http://www.sas.upenn.edu/~vnanda/perseus/index.html"; + license = stdenv.lib.licenses.gpl3; + maintainers = with stdenv.lib.maintainers; [erikryb]; + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/polymake/default.nix b/nixpkgs/pkgs/applications/science/math/polymake/default.nix new file mode 100644 index 000000000000..d4f13f84f81c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/polymake/default.nix @@ -0,0 +1,47 @@ +{ stdenv, fetchurl +, ninja, libxml2, libxslt, readline, perl, gmp, mpfr, boost +, bliss, ppl, singular, cddlib, lrs, nauty +, ant, openjdk +, perlPackages +, makeWrapper +}: + +stdenv.mkDerivation rec { + pname = "polymake"; + version = "3.2.rc4"; + + src = fetchurl { + url = "https://polymake.org/lib/exe/fetch.php/download/polymake-3.2r4.tar.bz2"; + sha256 = "02jpkvy1cc6kc23vkn7nkndzr40fq1gkb3v257bwyi1h5d37fyqy"; + }; + + buildInputs = [ + libxml2 libxslt readline perl gmp mpfr boost + bliss ppl singular cddlib lrs nauty + openjdk + ] ++ + (with perlPackages; [ + XMLLibXML XMLLibXSLT XMLWriter TermReadLineGnu TermReadKey + ]); + + nativeBuildInputs = [ + makeWrapper ninja ant perl + ]; + + ninjaFlags = [ "-C" "build/Opt" ]; + + postInstall = '' + for i in "$out"/bin/*; do + wrapProgram "$i" --prefix PERL5LIB : "$PERL5LIB" + done + ''; + + meta = { + inherit version; + description = "Software for research in polyhedral geometry"; + license = stdenv.lib.licenses.gpl2 ; + maintainers = [stdenv.lib.maintainers.raskin]; + platforms = stdenv.lib.platforms.linux; + homepage = "https://www.polymake.org/doku.php"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/pspp/default.nix b/nixpkgs/pkgs/applications/science/math/pspp/default.nix new file mode 100644 index 000000000000..95c2c3931b3c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/pspp/default.nix @@ -0,0 +1,53 @@ +{ stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk3, gsl +, pkgconfig, gtksourceview, pango, gettext, dconf +, makeWrapper, gsettings-desktop-schemas, hicolor-icon-theme +, texinfo, ssw +}: + +stdenv.mkDerivation rec { + pname = "pspp"; + version = "1.2.0"; + + src = fetchurl { + url = "mirror://gnu/pspp/${pname}-${version}.tar.gz"; + sha256 = "07pp27zycrb5x927jwaj9r3q7hy915jh51xs85zxby6gfiwl63m5"; + }; + + nativeBuildInputs = [ pkgconfig texinfo ]; + buildInputs = [ libxml2 readline zlib perl cairo gtk3 gsl + gtksourceview pango gettext + makeWrapper gsettings-desktop-schemas hicolor-icon-theme ssw + ]; + + doCheck = false; + + enableParallelBuilding = true; + + preFixup = '' + wrapProgram "$out/bin/psppire" \ + --prefix XDG_DATA_DIRS : "$out/share" \ + --prefix XDG_DATA_DIRS : "$XDG_ICON_DIRS" \ + --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH" \ + --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules" + ''; + + meta = { + homepage = "https://www.gnu.org/software/pspp/"; + description = "A free replacement for SPSS, a program for statistical analysis of sampled data"; + license = stdenv.lib.licenses.gpl3Plus; + + longDescription = '' + PSPP is a program for statistical analysis of sampled data. It is + a Free replacement for the proprietary program SPSS. + + PSPP can perform descriptive statistics, T-tests, anova, linear + and logistic regression, cluster analysis, factor analysis, + non-parametric tests and more. Its backend is designed to perform + its analyses as fast as possible, regardless of the size of the + input data. You can use PSPP with its graphical interface or the + more traditional syntax commands. + ''; + + platforms = stdenv.lib.platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/pynac/default.nix b/nixpkgs/pkgs/applications/science/math/pynac/default.nix new file mode 100644 index 000000000000..82e331216712 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/pynac/default.nix @@ -0,0 +1,48 @@ +{ stdenv +, fetchFromGitHub +, autoreconfHook +, pkgconfig +, flint +, gmp +, python2 +, singular +}: + +stdenv.mkDerivation rec { + version = "0.7.26"; + pname = "pynac"; + + src = fetchFromGitHub { + owner = "pynac"; + repo = "pynac"; + rev = "pynac-${version}"; + sha256 = "09d2p74x1arkydlxy6pw4p4byi7r8q7f29w373h4d8a215kadc6d"; + }; + + buildInputs = [ + flint + gmp + singular + singular + python2 + ]; + + nativeBuildInputs = [ + autoreconfHook + pkgconfig + ]; + + meta = with stdenv.lib; { + description = "Python is Not a CAS -- modified version of Ginac"; + longDescription = '' + Pynac -- "Python is Not a CAS" is a modified version of Ginac that + replaces the depency of GiNaC on CLN by a dependency instead of Python. + It is a lite version of GiNaC as well, not implementing all the features + of the full GiNaC, and it is *only* meant to be used as a Python library. + ''; + homepage = "http://pynac.org"; + license = licenses.gpl3; + maintainers = with maintainers; [ timokau ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix new file mode 100644 index 000000000000..e393111590a8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -0,0 +1,30 @@ +{ stdenv, fetchFromGitHub, intltool, autoreconfHook, pkgconfig, libqalculate, gtk3, wrapGAppsHook }: + +stdenv.mkDerivation rec { + pname = "qalculate-gtk"; + version = "3.8.0a"; + + src = fetchFromGitHub { + owner = "qalculate"; + repo = "qalculate-gtk"; + rev = "v${version}"; + sha256 = "0bjd61bbc5b2i09kz3ss01c0xmxrhmiv5wpbhhplkp3yhw2qrf3m"; + }; + + patchPhase = '' + substituteInPlace src/main.cc --replace 'getPackageDataDir().c_str()' \"$out/share\" + ''; + + hardeningDisable = [ "format" ]; + + nativeBuildInputs = [ intltool pkgconfig autoreconfHook wrapGAppsHook ]; + buildInputs = [ libqalculate gtk3 ]; + enableParallelBuilding = true; + + meta = with stdenv.lib; { + description = "The ultimate desktop calculator"; + homepage = "http://qalculate.github.io"; + maintainers = with maintainers; [ gebner ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/ratpoints/default.nix b/nixpkgs/pkgs/applications/science/math/ratpoints/default.nix new file mode 100644 index 000000000000..fb205a69f038 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/ratpoints/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchurl, fetchpatch, gmp }: +stdenv.mkDerivation rec { + pname = "ratpoints"; + version = "2.1.3.p4"; + + src = fetchurl { + url = "http://www.mathe2.uni-bayreuth.de/stoll/programs/ratpoints-${version}.tar.gz"; + sha256 = "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4"; + }; + + enableParallelBuilding = true; + + patches = [ + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/sturm_and_rp_private.patch?id=1615f58890e8f9881c4228c78a6b39b9aab1303a"; + sha256 = "0q3wajncyfr3gahd8gwk9x7g56zw54lpywrl63lqk7drkf60mrcl"; + }) + ]; + + buildInputs = [ gmp ]; + + makeFlags = [ "CC=cc" ]; + buildFlags = stdenv.lib.optional stdenv.isDarwin ["CCFLAGS2=-lgmp -lc -lm" "CCFLAGS=-UUSE_SSE"]; + installFlags = [ "INSTALL_DIR=$(out)" ]; + + preInstall = ''mkdir -p "$out"/{bin,share,lib,include}''; + + meta = { + inherit version; + description = ''A program to find rational points on hyperelliptic curves''; + license = stdenv.lib.licenses.gpl2Plus; + maintainers = [stdenv.lib.maintainers.raskin]; + platforms = stdenv.lib.platforms.unix; + homepage = "http://www.mathe2.uni-bayreuth.de/stoll/programs/"; + updateWalker = true; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/ries/default.nix b/nixpkgs/pkgs/applications/science/math/ries/default.nix new file mode 100644 index 000000000000..4adf3ef2096e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/ries/default.nix @@ -0,0 +1,21 @@ +{ stdenv, fetchzip }: +stdenv.mkDerivation { + name = "ries-2018-04-11"; + + # upstream does not provide a stable link + src = fetchzip { + url = "https://salsa.debian.org/debian/ries/-/archive/debian/2018.04.11-1/ries-debian-2018.04.11-1.zip"; + sha256 = "1h2wvd4k7f0l0i1vm9niz453xdbcs3nxccmri50qyrzzzc1b0842"; + }; + + makeFlags = [ "PREFIX=$(out)" ]; + + meta = with stdenv.lib; { + homepage = "https://mrob.com/pub/ries/"; + description = "Tool to produce a list of equations that approximately solve to a given number"; + platforms = platforms.all; + maintainers = with maintainers; [ symphorien ]; + license = licenses.gpl3Plus; + }; +} + diff --git a/nixpkgs/pkgs/applications/science/math/ripser/default.nix b/nixpkgs/pkgs/applications/science/math/ripser/default.nix new file mode 100644 index 000000000000..1c8ced5ed222 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/ripser/default.nix @@ -0,0 +1,67 @@ +{ stdenv, fetchurl, fetchFromGitHub +, assembleReductionMatrix ? false +, useCoefficients ? false +, indicateProgress ? false +, useGoogleHashmap ? false, sparsehash ? null +, fileFormat ? "lowerTriangularCsv" +}: + +with stdenv.lib; + +assert assertOneOf "fileFormat" fileFormat + ["lowerTriangularCsv" "upperTriangularCsv" "dipha"]; +assert useGoogleHashmap -> sparsehash != null; + +let + inherit (stdenv.lib) optional; + version = "1.0"; +in +stdenv.mkDerivation { + pname = "ripser"; + inherit version; + + src = fetchFromGitHub { + owner = "Ripser"; + repo = "ripser"; + rev = "f69c6af6ca6883dd518c48faf41cf8901c379598"; + sha256 = "1mw2898s7l29hgajsaf75bs9bjn2sn4g2mvmh41a602jpwp9r0rz"; + }; + + #Patch from dev branch to make compilation work. + #Will be removed when it gets merged into master. + patches = [(fetchurl { + url = "https://github.com/Ripser/ripser/commit/dc78d8ce73ee35f3828f0aad67a4e53620277ebf.patch"; + sha256 = "1y93aqpqz8fm1cxxrf90dhh67im3ndkr8dnxgbw5y96296n4r924"; + })]; + + buildInputs = optional useGoogleHashmap sparsehash; + + buildFlags = [ + "-std=c++11" + "-Ofast" + "-D NDEBUG" + ] + ++ optional assembleReductionMatrix "-D ASSEMBLE_REDUCTION_MATRIX" + ++ optional useCoefficients "-D USE_COEFFICIENTS" + ++ optional indicateProgress "-D INDICATE_PROGRESS" + ++ optional useGoogleHashmap "-D USE_GOOGLE_HASHMAP" + ++ optional (fileFormat == "lowerTriangularCsv") "-D FILE_FORMAT_LOWER_TRIANGULAR_CSV" + ++ optional (fileFormat == "upperTriangularCsv") "-D FILE_FORMAT_UPPER_TRIANGULAR_CSV" + ++ optional (fileFormat == "dipha") "-D FILE_FORMAT_DIPHA" + ; + + buildPhase = "c++ ripser.cpp -o ripser $buildFlags"; + + installPhase = '' + mkdir -p $out/bin + cp ripser $out/bin + ''; + + meta = { + description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes"; + homepage = "https://github.com/Ripser/ripser"; + license = stdenv.lib.licenses.lgpl3; + maintainers = with stdenv.lib.maintainers; [erikryb]; + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch b/nixpkgs/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch new file mode 100644 index 000000000000..197d1347d535 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/rofi-calc/0001-Patch-plugindir-to-output.patch @@ -0,0 +1,25 @@ +From 0eaef67b683683fb423fcb2d5096b3cdf9a4a9cd Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Maciej=20Kr=C3=BCger?= <mkg20001@gmail.com> +Date: Sun, 22 Mar 2020 12:26:10 +0100 +Subject: [PATCH] Patch plugindir to output + +--- + configure.ac | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/configure.ac b/configure.ac +index 50edb74..639ee86 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -50,7 +50,7 @@ PKG_CHECK_MODULES([glib], [glib-2.0 >= 2.40 gio-unix-2.0 gmodule-2.0 ]) + PKG_CHECK_MODULES([cairo], [cairo]) + PKG_CHECK_MODULES([rofi], [rofi >= 1.5.4]) + +-[rofi_PLUGIN_INSTALL_DIR]="`$PKG_CONFIG --variable=pluginsdir rofi`" ++[rofi_PLUGIN_INSTALL_DIR]="`echo $out/lib/rofi`" + AC_SUBST([rofi_PLUGIN_INSTALL_DIR]) + + LT_INIT([disable-static]) +-- +2.25.1 + diff --git a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix new file mode 100644 index 000000000000..84adb2358d24 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix @@ -0,0 +1,54 @@ +{ stdenv +, fetchFromGitHub +, autoreconfHook +, pkgconfig +, rofi-unwrapped +, libqalculate +, glib +, cairo +, gobject-introspection +, wrapGAppsHook +}: + +stdenv.mkDerivation rec { + pname = "rofi-calc"; + version = "1.7"; + + src = fetchFromGitHub { + owner = "svenstaro"; + repo = pname; + rev = "v${version}"; + sha256 = "046x2zpvza7n0m81s75qkvmnpkvsvvyqqqjxcqzj7by0llpqs7wa"; + }; + + 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/nixpkgs/pkgs/applications/science/math/sage/README.md b/nixpkgs/pkgs/applications/science/math/sage/README.md new file mode 100644 index 000000000000..26e91fc63133 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/README.md @@ -0,0 +1,78 @@ +# Sage on nixos + +Sage is a pretty complex package that depends on many other complex packages and patches some of those. As a result, the sage nix package is also quite complex. + +Don't feel discouraged to fix, simplify or improve things though. The individual files have comments explaining their purpose. The most importent ones are `default.nix` linking everything together, `sage-src.nix` adding patches and `sagelib.nix` building the actual sage package. + +## The sage build is broken + +First you should find out which change to nixpkgs is at fault (if you don't already know). You can use `git-bisect` for that (see the manpage). + +If the build broke as a result of a package update, try those solutions in order: + +- search the [sage trac](https://trac.sagemath.org/) for keywords like "Upgrade <package>". Maybe somebody has already proposed a patch that fixes the issue. You can then add a `fetchpatch` to `sage-src.nix`. + +- check if [gentoo](https://github.com/cschwan/sage-on-gentoo/tree/master/sci-mathematics/sage), [debian](https://salsa.debian.org/science-team/sagemath/tree/master/debian) or [arch linux](https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath) already solved the problem. You can then again add a `fetchpatch` to `sage-src.nix`. If applicable you should also [propose the patch upstream](#proposing-a-sage-patch). + +- fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch: + +``` +[user@localhost ~]$ git clone git://github.com/sagemath/sage.git +[user@localhost ~]$ cd sage +[user@localhost sage]$ git checkout 8.2 # substitute the relevant version here +``` + +Then make the needed changes and generate a patch with `git diff`: + +``` +[user@localhost ~]$ <make changes> +[user@localhost ~]$ git diff -u > /path/to/nixpkgs/pkgs/applications/science/math/sage/patches/name-of-patch.patch +``` + +Now just add the patch to `sage-src.nix` and test your changes. If they fix the problem, [propose them upstream](#proposing-a-sage-patch) and add a link to the trac ticket. + +- pin the package version in `default.nix` and add a note that explains why that is necessary. + + +## Proposing a sage patch + +You can [login the sage trac using GitHub](https://trac.sagemath.org/login). Your username will then be `gh-<your-github-name>`. The only other way is to request a trac account via email. After that refer to [git the hard way](http://doc.sagemath.org/html/en/developer/manual_git.html#chapter-manual-git) in the sage documentation. The "easy way" requires a non-GitHub account (requested via email) and a special tool. The "hard way" is really not all that hard if you're a bit familiar with git. + +Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then: + +``` +[user@localhost ~]$ git clone git://github.com/sagemath/sage.git +[user@localhost ~]$ cd sage +[user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master +[user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop +[user@localhost sage]$ <make changes> +[user@localhost sage]$ git add . +[user@localhost sage]$ git commit +[user@localhost sage]$ git show # review your changes +[user@localhost sage]$ git push --set-upstream trac u/gh-<your-github-username>/<your-branch-name> +``` + +You now created a branch on the trac server (you *must* follow the naming scheme as you only have push access to branches with the `u/gh-<your-github-username>/` prefix). +Now you can [create a new trac ticket](https://trac.sagemath.org/newticket). +- Write a description of the change +- set the type and component as appropriate +- write your real name in the "Authors" field +- write `u/gh-<your-github-username>/<your-branch-name>` in the "Branch" field +- click "Create ticket" +- click "Modify" on the top right of your ticket (for some reason you can only change the ticket status after you have created it) +- set the ticket status from `new` to `needs_review` +- click "Save changes" + +Refer to sages [Developer's Guide](http://doc.sagemath.org/html/en/developer/index.html) for further details. + +## I want to update sage + +You'll need to change the `version` field in `sage-src.nix`. Afterwards just try to build and let nix tell you which patches no longer apply (hopefully because they were adopted upstream). Remove those. + +Hopefully the build will succeed now. If it doesn't and the problem is obvious, fix it as described in [The sage build is broken](#the-sage-build-is-broken). +If the problem is not obvious, you can try to first update sage to an intermediate version (remember that you can also set the `version` field to any git revision of sage) and locate the sage commit that introduced the issue. You can even use `git-bisect` for that (it will only be a bit tricky to keep track of which patches to apply). Hopefully after that the issue will be obvious. + +## Well, that didn't help! + +If you couldn't fix the problem, create a GitHub issue on the nixpkgs repo and ping @timokau (or whoever is listed in the `maintainers` list of the sage package). +Describe what you did and why it didn't work. Afterwards it would be great if you help the next guy out and improve this documentation! diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix new file mode 100644 index 000000000000..caf51c3da251 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/default.nix @@ -0,0 +1,172 @@ +{ pkgs +, withDoc ? false +}: + +# Here sage and its dependencies are put together. Some dependencies may be pinned +# as a last resort. Patching sage for compatibility with newer dependency versions +# is always preferred, see `sage-src.nix` for that. + +let + inherit (pkgs) symlinkJoin callPackage nodePackages; + + # https://trac.sagemath.org/ticket/15980 for tracking of python3 support + python = pkgs.python2.override { + packageOverrides = self: super: { + # python packages that appear unmaintained and were not accepted into the nixpkgs + # tree because of that. These packages are only dependencies of the more-or-less + # deprecated sagenb. However sagenb is still a default dependency and the doctests + # depend on it. + # See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion. + # The dependency on the sage notebook (and therefore these packages) will be + # removed in the future: + # https://trac.sagemath.org/ticket/25837 + flask-oldsessions = self.callPackage ./flask-oldsessions.nix {}; + flask-openid = self.callPackage ./flask-openid.nix {}; + python-openid = self.callPackage ./python-openid.nix {}; + sagenb = self.callPackage ./sagenb.nix { + mathjax = nodePackages.mathjax; + }; + + # Package with a cyclic dependency with sage + pybrial = self.callPackage ./pybrial.nix {}; + + # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies + sagelib = self.callPackage ./sagelib.nix { + inherit flint ecl arb; + inherit sage-src env-locations pynac singular; + linbox = pkgs.linbox.override { withSage = true; }; + pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + }; + }; + }; + + jupyter-kernel-definition = { + displayName = "SageMath ${sage-src.version}"; + argv = [ + "${sage-with-env}/bin/sage" # FIXME which sage + "--python" + "-m" + "sage.repl.ipython_kernel" + "-f" + "{connection_file}" + ]; + language = "sagemath"; + # just one 16x16 logo is available + logo32 = "${sage-src}/doc/common/themes/sage/static/sageicon.png"; + logo64 = "${sage-src}/doc/common/themes/sage/static/sageicon.png"; + }; + + # A bash script setting various environment variables to tell sage where + # the files its looking fore are located. Also see `sage-env`. + env-locations = callPackage ./env-locations.nix { + inherit pari_data ecl; + inherit singular maxima-ecl; + cysignals = python.pkgs.cysignals; + three = nodePackages.three; + mathjax = nodePackages.mathjax; + }; + + # The shell file that gets sourced on every sage start. Will also source + # the env-locations file. + sage-env = callPackage ./sage-env.nix { + sagelib = python.pkgs.sagelib; + inherit env-locations; + inherit python ecl singular palp flint pynac pythonEnv maxima-ecl; + pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + }; + + # The documentation for sage, building it takes a lot of ram. + sagedoc = callPackage ./sagedoc.nix { + inherit sage-with-env; + inherit python maxima-ecl; + }; + + # sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run. + sage-with-env = callPackage ./sage-with-env.nix { + inherit pythonEnv; + inherit sage-env; + inherit pynac singular maxima-ecl; + pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + three = nodePackages.three; + }; + + # Doesn't actually build anything, just runs sages testsuite. This is a + # separate derivation to make it possible to re-run the tests without + # rebuilding sagelib (which takes ~30 minutes). + # Running the tests should take something in the order of 1h. + sage-tests = callPackage ./sage-tests.nix { + inherit sage-with-env; + }; + + sage-src = callPackage ./sage-src.nix {}; + + pythonRuntimeDeps = with python.pkgs; [ + sagelib + pybrial + sagenb + cvxopt + networkx + service-identity + psutil + sympy + fpylll + matplotlib + tkinter # optional, as a matplotlib backend (use with `%matplotlib tk`) + scipy + ipywidgets + rpy2 + sphinx + typing + pillow + ]; + + pythonEnv = python.buildEnv.override { + extraLibs = pythonRuntimeDeps; + ignoreCollisions = true; + } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible + + arb = pkgs.arb.override { inherit flint; }; + + singular = pkgs.singular.override { inherit flint; }; + + # https://trac.sagemath.org/ticket/26625 + maxima-ecl = pkgs.maxima-ecl; + + # *not* to confuse with the python package "pynac" + pynac = pkgs.pynac.override { inherit singular flint; }; + + # With openblas (64 bit), the tests fail the same way as when sage is build with + # openblas instead of openblasCompat. Apparently other packages somehow use flints + # blas when it is available. Alternative would be to override flint to use + # openblasCompat. + flint = pkgs.flint.override { withBlas = false; }; + + # Multiple palp dimensions need to be available and sage expects them all to be + # in the same folder. + palp = symlinkJoin { + name = "palp-${pkgs.palp.version}"; + paths = [ + (pkgs.palp.override { dimensions = 4; doSymlink = false; }) + (pkgs.palp.override { dimensions = 5; doSymlink = false; }) + (pkgs.palp.override { dimensions = 6; doSymlink = true; }) + (pkgs.palp.override { dimensions = 11; doSymlink = false; }) + ]; + }; + + # Sage expects those in the same directory. + pari_data = symlinkJoin { + name = "pari_data"; + paths = with pkgs; [ + pari-galdata + pari-seadata-small + ]; + }; + + # https://trac.sagemath.org/ticket/22191 + ecl = pkgs.ecl_16_1_2; +in +# A wrapper around sage that makes sure sage finds its docs (if they were build). +callPackage ./sage.nix { + inherit sage-tests sage-with-env sagedoc jupyter-kernel-definition; + inherit withDoc; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/dist-tests.nix b/nixpkgs/pkgs/applications/science/math/sage/dist-tests.nix new file mode 100644 index 000000000000..24a86a8f37a4 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/dist-tests.nix @@ -0,0 +1,17 @@ +# Lists past failures and files associated with it. The intention is to build +# up a subset of a testsuite that catches 95% of failures that are relevant for +# distributions while only taking ~5m to run. This in turn makes it more +# reasonable to re-test sage on dependency changes and makes it easier for +# users to override the sage derivation. +# This is an experiment for now. If it turns out that there really is a small +# subset of files responsible for the vast majority of packaging tests, we can +# think about moving this upstream. +[ + "src/sage/env.py" # [1] + "src/sage/misc/persist.pyx" # [1] + "src/sage/misc/inline_fortran.py" # [1] + "src/sage/repl/ipython_extension.py" # [1] +] + +# Numbered list of past failures to annotate files with +# [1] PYTHONPATH related issue https://github.com/NixOS/nixpkgs/commit/ec7f569211091282410050e89e68832d4fe60528 diff --git a/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix b/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix new file mode 100644 index 000000000000..bda2d23b9e52 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix @@ -0,0 +1,49 @@ +{ writeTextFile +, pari_data +, pari +, singular +, maxima-ecl +, conway_polynomials +, graphs +, elliptic_curves +, polytopes_db +, gap +, ecl +, combinatorial_designs +, jmol +, mathjax +, three +, cysignals +}: + +# A bash script setting various environment variables to tell sage where +# the files its looking fore are located. Also see `sage-env`. +writeTextFile rec { + name = "sage-env-locations"; + destination = "/${name}"; + text = '' + export GP_DATA_DIR="${pari_data}/share/pari" + export PARI_DATA_DIR="${pari_data}" + export GPHELP="${pari}/bin/gphelp" + export GPDOCDIR="${pari}/share/pari/doc" + export SINGULARPATH='${singular}/share/singular' + export SINGULAR_SO='${singular}/lib/libSingular.so' + export GAP_SO='${gap}/lib/libgap.so' + export SINGULAR_EXECUTABLE='${singular}/bin/Singular' + export MAXIMA_FAS='${maxima-ecl}/lib/maxima/${maxima-ecl.version}/binary-ecl/maxima.fas' + export MAXIMA_PREFIX="${maxima-ecl}" + export CONWAY_POLYNOMIALS_DATA_DIR='${conway_polynomials}/share/conway_polynomials' + export GRAPHS_DATA_DIR='${graphs}/share/graphs' + export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves' + export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes' + export GAP_ROOT_DIR='${gap}/share/gap/build-dir' + export ECLDIR='${ecl}/lib/ecl-${ecl.version}/' + export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs" + export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona" + export JMOL_DIR="${jmol}/share/jmol" # point to the directory that contains JmolData.jar + export JSMOL_DIR="${jmol}/share/jsmol" + export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax" + export THREEJS_DIR="${three}/lib/node_modules/three" + export SAGE_INCLUDE_DIRECTORIES="${cysignals}/lib/python2.7/site-packages" + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix b/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix new file mode 100644 index 000000000000..403dc8708fab --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/flask-oldsessions.nix @@ -0,0 +1,36 @@ +{ stdenv +, buildPythonPackage +, fetchFromGitHub +, python +, flask +}: + +buildPythonPackage rec { + pname = "Flask-OldSessions"; + version = "0.10"; + + # no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1 + src = fetchFromGitHub { + owner = "mitsuhiko"; + repo = "flask-oldsessions"; + rev = version; + sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn"; + }; + + propagatedBuildInputs = [ + flask + ]; + + # missing module flask.testsuite, probably assumes an old version of flask + doCheck = false; + checkPhase = '' + ${python.interpreter} run-tests.py + ''; + + meta = with stdenv.lib; { + description = "Provides a session class that works like the one in Flask before 0.10."; + license = licenses.bsd2; + maintainers = with maintainers; [ timokau ]; + homepage = "https://github.com/mitsuhiko/flask-oldsessions"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix b/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix new file mode 100644 index 000000000000..527173dec80a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/flask-openid.nix @@ -0,0 +1,28 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, flask +, python-openid +}: + +buildPythonPackage rec { + pname = "Flask-OpenID"; + version = "1.2.5"; + + src = fetchPypi { + inherit pname version; + sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss"; + }; + + propagatedBuildInputs = [ + flask + python-openid + ]; + + meta = with stdenv.lib; { + description = "Adds openid support to flask applications"; + license = licenses.bsd2; + maintainers = with maintainers; [ timokau ]; + homepage = "https://pythonhosted.org/Flask-OpenID/"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch new file mode 100644 index 000000000000..8cd80281d0e4 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch @@ -0,0 +1,35 @@ +From 8218bd4fdeb4c92de8af0d3aabec55980fc4fb3d Mon Sep 17 00:00:00 2001 +From: Timo Kaufmann <timokau@zoho.com> +Date: Sun, 21 Oct 2018 17:52:40 +0200 +Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested + +--- + src/sage/doctest/control.py | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py +index bf18df8b2b..935c67abf7 100644 +--- a/src/sage/doctest/control.py ++++ b/src/sage/doctest/control.py +@@ -362,7 +362,8 @@ class DocTestController(SageObject): + if not optionaltag_regex.search(o): + raise ValueError('invalid optional tag {!r}'.format(o)) + +- options.optional |= auto_optional_tags ++ if "sage" in options.optional: ++ options.optional |= auto_optional_tags + + self.options = options + +@@ -765,7 +766,7 @@ class DocTestController(SageObject): + sage: DC = DocTestController(DD, [dirname]) + sage: DC.expand_files_into_sources() + sage: sorted(DC.sources[0].options.optional) # abs tol 1 +- ['guava', 'magma', 'py2'] ++ ['guava', 'magma'] + + We check that files are skipped appropriately:: + +-- +2.18.1 + diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch new file mode 100644 index 000000000000..e687281ad1a7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch @@ -0,0 +1,19 @@ +diff --git a/src/sage/repl/configuration.py b/src/sage/repl/configuration.py +index 67d7d2accf..18279581e2 100644 +--- a/src/sage/repl/configuration.py ++++ b/src/sage/repl/configuration.py +@@ -9,10 +9,11 @@ the IPython simple prompt is being used:: + sage: cmd = 'print([sys.stdin.isatty(), sys.stdout.isatty()])' + sage: import pexpect + sage: output = pexpect.run( +- ....: 'bash -c \'echo "{0}" | sage\''.format(cmd), ++ ....: 'bash -c \'export SAGE_BANNER=no; echo "{0}" | sage\''.format(cmd), + ....: ).decode('utf-8', 'surrogateescape') +- sage: 'sage: [False, True]' in output +- True ++ sage: print(output) ++ sage...[False, True] ++ sage...Exiting Sage ... + """ + + #***************************************************************************** diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch new file mode 100644 index 000000000000..3f844e1b1ef5 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch @@ -0,0 +1,95 @@ +diff --git a/src/sage/env.py b/src/sage/env.py +index 061b94f3f1..67cd091540 100644 +--- a/src/sage/env.py ++++ b/src/sage/env.py +@@ -189,88 +189,13 @@ var('MAXIMA_FAS') + var('SAGE_BANNER', '') + var('SAGE_IMPORTALL', 'yes') + +- +-def _get_shared_lib_filename(libname, *additional_libnames): +- """ +- Return the full path to a shared library file installed in the standard +- location for the system within the ``LIBDIR`` prefix (or +- ``$SAGE_LOCAL/lib`` in the case of manual build of Sage). +- +- This can also be passed more than one library name (e.g. for cases where +- some library may have multiple names depending on the platform) in which +- case the first one found is returned. +- +- This supports most *NIX variants (in which ``lib<libname>.so`` is found +- under ``$SAGE_LOCAL/lib``), macOS (same, but with the ``.dylib`` +- extension), and Cygwin (under ``$SAGE_LOCAL/bin/cyg<libname>.dll``, +- or ``$SAGE_LOCAL/bin/cyg<libname>-*.dll`` for versioned DLLs). +- +- For distributions like Debian that use a multiarch layout, we also try the +- multiarch lib paths (i.e. ``/usr/lib/<arch>/``). +- +- Returns ``None`` if the file does not exist. +- +- EXAMPLES:: +- +- sage: import sys +- sage: from fnmatch import fnmatch +- sage: from sage.env import _get_shared_lib_filename +- sage: lib_filename = _get_shared_lib_filename("Singular", +- ....: "singular-Singular") +- sage: if sys.platform == 'cygwin': +- ....: pattern = "*/cygSingular-*.dll" +- ....: elif sys.platform == 'darwin': +- ....: pattern = "*/libSingular.dylib" +- ....: else: +- ....: pattern = "*/lib*Singular.so" +- sage: fnmatch(lib_filename, pattern) +- True +- sage: _get_shared_lib_filename("an_absurd_lib") is None +- True +- """ +- +- for libname in (libname,) + additional_libnames: +- if sys.platform == 'cygwin': +- bindir = sysconfig.get_config_var('BINDIR') +- pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)] +- filenames = [] +- for pat in pats: +- filenames += glob.glob(os.path.join(bindir, pat)) +- +- # Note: This is not very robust, since if there are multi DLL +- # versions for the same library this just selects one more or less +- # at arbitrary. However, practically speaking, on Cygwin, there +- # will only ever be one version +- if filenames: +- return filenames[-1] +- else: +- if sys.platform == 'darwin': +- ext = 'dylib' +- else: +- ext = 'so' +- +- libdirs = [sysconfig.get_config_var('LIBDIR')] +- multilib = sysconfig.get_config_var('MULTILIB') +- if multilib: +- libdirs.insert(0, os.path.join(libdirs[0], multilib)) +- +- for libdir in libdirs: +- basename = 'lib{}.{}'.format(libname, ext) +- filename = os.path.join(libdir, basename) +- if os.path.exists(filename): +- return filename +- +- # Just return None if no files were found +- return None +- +- + # locate singular shared object + # On Debian it's libsingular-Singular so try that as well +-SINGULAR_SO = _get_shared_lib_filename('Singular', 'singular-Singular') ++SINGULAR_SO = '/default' + var('SINGULAR_SO', SINGULAR_SO) + + # locate libgap shared object +-GAP_SO= _get_shared_lib_filename('gap','') ++GAP_SO= '/default' + var('GAP_SO', GAP_SO) + + # post process diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/docutils-0.15.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/docutils-0.15.patch new file mode 100644 index 000000000000..63f5d2e146dd --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/docutils-0.15.patch @@ -0,0 +1,24 @@ +diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py +index 4849c2bffa..76b7bc8602 100644 +--- a/src/sage/misc/sphinxify.py ++++ b/src/sage/misc/sphinxify.py +@@ -25,6 +25,7 @@ from __future__ import absolute_import, print_function + import os + import re + import shutil ++import warnings + from tempfile import mkdtemp + from sphinx.application import Sphinx + +@@ -120,7 +121,10 @@ smart_quotes = no""") + # buildername, confoverrides, status, warning, freshenv). + sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format, + confoverrides, None, None, True) +- sphinx_app.build(None, [rst_name]) ++ with warnings.catch_warnings(): ++ # Quick and dirty workaround for https://trac.sagemath.org/ticket/28856#comment:19 ++ warnings.simplefilter("ignore") ++ sphinx_app.build(None, [rst_name]) + sys.path = old_sys_path + + # We need to remove "_" from __builtin__ that the gettext module installs diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/fix-ecl-race.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/fix-ecl-race.patch new file mode 100644 index 000000000000..6056416c3a28 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/fix-ecl-race.patch @@ -0,0 +1,19 @@ +diff --git a/src/sage/doctest/forker.py b/src/sage/doctest/forker.py +index 02e18e67e7..2ebf6eb35f 100644 +--- a/src/sage/doctest/forker.py ++++ b/src/sage/doctest/forker.py +@@ -1075,6 +1075,14 @@ class SageDocTestRunner(doctest.DocTestRunner, object): + sage: set(ex2.predecessors) == set([ex0,ex1]) + True + """ ++ ++ # Fix ECL dir race conditions by using a separate dir for each process ++ # (https://trac.sagemath.org/ticket/26968) ++ os.environ['MAXIMA_USERDIR'] = "{}/sage-maxima-{}".format( ++ tempfile.gettempdir(), ++ os.getpid() ++ ) ++ + if isinstance(globs, RecordingDict): + globs.start() + example.sequence_number = len(self.history) diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch new file mode 100644 index 000000000000..11ca74819615 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch @@ -0,0 +1,24 @@ +diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py +index bd6b76ab82..ccf1203dec 100644 +--- a/src/sage/tests/cmdline.py ++++ b/src/sage/tests/cmdline.py +@@ -837,8 +837,6 @@ def test_executable(args, input="", timeout=100.0, **kwds): + /// + 4 + }}} +- sage: err # py2 +- '' + sage: ret + 0 + +@@ -871,8 +869,8 @@ def test_executable(args, input="", timeout=100.0, **kwds): + sage: output = tmp_filename(ext='.sws') + sage: with open(input, 'w') as F: + ....: _ = F.write(s) +- sage: test_executable(["sage", "--rst2sws", input, output]) # py2 +- ('', '', 0) ++ sage: test_executable(["sage", "--rst2sws", input, output])[2] # py2 ++ 0 + sage: import tarfile # py2 + sage: f = tarfile.open(output, 'r') # py2 + sage: print(f.extractfile('sage_worksheet/worksheet.html').read()) # py2 diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch new file mode 100644 index 000000000000..c5f95b498d53 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch @@ -0,0 +1,12 @@ +diff --git a/src/sage/all.py b/src/sage/all.py +index c87c9372e9..862fca4fcc 100644 +--- a/src/sage/all.py ++++ b/src/sage/all.py +@@ -306,6 +306,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0)) + # Ignore all deprecations from IPython etc. + warnings.filterwarnings('ignore', category=DeprecationWarning, + module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)') ++warnings.filterwarnings('ignore', category=DeprecationWarning, message=r".*The import 'werkzeug.ImmutableDict' is deprecated") + # Ignore collections.abc warnings, there are a lot of them but they are + # harmless. + warnings.filterwarnings('ignore', category=DeprecationWarning, diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch new file mode 100644 index 000000000000..49cdfd189b92 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch @@ -0,0 +1,20 @@ +diff --git a/src/sage/doctest/parsing.py b/src/sage/doctest/parsing.py +index 6bdc9a0..31fc780 100644 +--- a/src/sage/doctest/parsing.py ++++ b/src/sage/doctest/parsing.py +@@ -40,6 +40,7 @@ from .external import available_software + + float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)') + optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))') ++pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.') + find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M) + find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M) + random_marker = re.compile('.*random', re.I) +@@ -935,6 +936,7 @@ class SageOutputChecker(doctest.OutputChecker): + <type 'float'> + """ + got = self.human_readable_escape_sequences(got) ++ got = pari_stack_warning_regex.sub('', got) + if isinstance(want, MarkedOutput): + if want.random: + return True diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch new file mode 100644 index 000000000000..1b64f39fe60f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch @@ -0,0 +1,28 @@ +diff --git a/src/sage/all.py b/src/sage/all.py +index ca309ef..be3186b 100644 +--- a/src/sage/all.py ++++ b/src/sage/all.py +@@ -298,6 +298,23 @@ warnings.filterwarnings('ignore', module='matplotlib[.]font_manager') + warnings.filterwarnings('default', + '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.') + ++# Hotpatch around https://bugs.python.org/issue5755 which won't be fixed for ++# python 2.7. Idea by https://stackoverflow.com/a/36293331. ++from distutils.command.build_ext import build_ext ++from distutils.sysconfig import customize_compiler ++ ++_build_extensions = build_ext.build_extensions ++ ++def build_extensions_patched(self): ++ customize_compiler(self.compiler) ++ try: ++ self.compiler.compiler_so.remove("-Wstrict-prototypes") ++ except (AttributeError, ValueError): ++ pass ++ _build_extensions(self) ++ ++build_ext.build_extensions = build_extensions_patched ++ + + # Set a new random number seed as the very last thing + # (so that printing initial_seed() and using that seed diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/sagenb-cmp-deprecation.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sagenb-cmp-deprecation.patch new file mode 100644 index 000000000000..9f502a669517 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/sagenb-cmp-deprecation.patch @@ -0,0 +1,13 @@ +diff --git a/sagenb/__init__.py b/sagenb/__init__.py +index 4db0d2cb..2fc5f01e 100644 +--- a/sagenb/__init__.py ++++ b/sagenb/__init__.py +@@ -1,3 +1,8 @@ + # -*- coding: utf-8 -* + # init ++import warnings + from . import storage ++ ++# deprecation in attrs, needs to be fixed in twisted ++warnings.filterwarnings('ignore', category=DeprecationWarning, ++ message=r'The usage of `cmp` is deprecated and will be removed.*') diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch new file mode 100644 index 000000000000..56f092796229 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch @@ -0,0 +1,58 @@ +diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py +index 73a078e619..059125c59f 100644 +--- a/src/sage_setup/docbuild/__init__.py ++++ b/src/sage_setup/docbuild/__init__.py +@@ -86,27 +86,6 @@ def builder_helper(type): + """ + Returns a function which builds the documentation for + output type ``type``. +- +- TESTS: +- +- Check that :trac:`25161` has been resolved:: +- +- sage: from sage_setup.docbuild import DocBuilder, setup_parser +- sage: DocBuilder._options = setup_parser().parse_args([])[0] # builder_helper needs _options to be set +- +- sage: import sage_setup.docbuild.sphinxbuild +- sage: def raiseBaseException(): +- ....: raise BaseException("abort pool operation") +- sage: original_runsphinx, sage_setup.docbuild.sphinxbuild.runsphinx = sage_setup.docbuild.sphinxbuild.runsphinx, raiseBaseException +- +- sage: from sage_setup.docbuild import builder_helper, build_ref_doc +- sage: from sage_setup.docbuild import _build_many as build_many +- sage: helper = builder_helper("html") +- sage: try: +- ....: build_many(build_ref_doc, [("docname", "en", "html", {})]) +- ....: except Exception as E: +- ....: "Non-exception during docbuild: abort pool operation" in str(E) +- True + """ + def f(self, *args, **kwds): + output_dir = self._output_dir(type) +@@ -128,10 +107,9 @@ def builder_helper(type): + logger.debug(build_command) + + # Run Sphinx with Sage's special logger +- sys.argv = ["sphinx-build"] + build_command.split() +- from .sphinxbuild import runsphinx ++ args = "python -um sage_setup.docbuild.sphinxbuild -N".split() + build_command.split() + try: +- runsphinx() ++ subprocess.check_call(args) + except Exception: + if ABORT_ON_ERROR: + raise +diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py +index fe7eba43b2..463790965c 100644 +--- a/src/sage_setup/docbuild/sphinxbuild.py ++++ b/src/sage_setup/docbuild/sphinxbuild.py +@@ -321,3 +321,8 @@ def runsphinx(): + sys.stderr = saved_stderr + sys.stdout.flush() + sys.stderr.flush() ++ ++if __name__ == '__main__': ++ import sys ++ sys.argv[0] = "sphinx-build" ++ runsphinx() diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/sympow-cache.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sympow-cache.patch new file mode 100644 index 000000000000..20020d610f80 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/patches/sympow-cache.patch @@ -0,0 +1,21 @@ +diff --git a/src/sage/lfunctions/sympow.py b/src/sage/lfunctions/sympow.py +index 1640ac4f6a..03578be7b8 100644 +--- a/src/sage/lfunctions/sympow.py ++++ b/src/sage/lfunctions/sympow.py +@@ -50,6 +50,7 @@ from __future__ import print_function, absolute_import + + import os + ++from sage.env import DOT_SAGE + from sage.structure.sage_object import SageObject + from sage.misc.all import pager, verbose + import sage.rings.all +@@ -76,7 +77,7 @@ class Sympow(SageObject): + """ + Used to call sympow with given args + """ +- cmd = 'sympow %s'%args ++ cmd = 'env SYMPOW_CACHEDIR="%s/sympow///" sympow %s' % (DOT_SAGE, args) + v = os.popen(cmd).read().strip() + verbose(v, level=2) + return v diff --git a/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix b/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix new file mode 100644 index 000000000000..718414126ae8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/pybrial.nix @@ -0,0 +1,25 @@ +{ stdenv +, fetchFromGitHub +, buildPythonPackage +, brial +}: +# This has a cyclic dependency with sage. I don't include sage in the +# buildInputs and let python figure it out at runtime. Because of this, +# I don't include the package in the main nipxkgs tree. It wouldn't be useful +# outside of sage anyways (as you could just directly depend on sage and use +# it). +buildPythonPackage rec { + pname = "pyBRiAl"; + version = brial.version; + + # included with BRiAl source + src = brial.src; + + sourceRoot = "source/sage-brial"; + + meta = with stdenv.lib; { + description = "python implementation of BRiAl"; + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix b/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix new file mode 100644 index 000000000000..4c7fdadadaf0 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix @@ -0,0 +1,40 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, isPy3k +, django +, nose +, twill +, pycrypto +}: + +buildPythonPackage rec { + pname = "python-openid"; + version = "2.2.5"; + + disabled = isPy3k; + + src = fetchPypi { + inherit pname version; + sha256 = "1vvhxlghjan01snfdc4k7ykd80vkyjgizwgg9bncnin8rqz1ricj"; + }; + + propagatedBuildInputs = [ + pycrypto + ]; + + # Cannot access the djopenid example module. + # I don't know how to fix that (adding the examples dir to PYTHONPATH doesn't work) + doCheck = false; + checkInputs = [ nose django twill ]; + checkPhase = '' + nosetests + ''; + + meta = with stdenv.lib; { + description = "OpenID library for Python"; + license = licenses.asl20; + maintainers = with maintainers; [ timokau ]; + homepage = "https://github.com/openid/python-openid/"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix new file mode 100644 index 000000000000..626e1bf1ea92 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix @@ -0,0 +1,187 @@ +{ stdenv +, lib +, writeTextFile +, python +, sagelib +, env-locations +, gfortran +, bash +, coreutils +, gnused +, gnugrep +, binutils +, pythonEnv +, python3 +, pkg-config +, pari +, gap +, ecl +, maxima-ecl +, singular +, fflas-ffpack +, givaro +, gd +, libpng +, linbox +, m4ri +, giac +, palp +, rWrapper +, gfan +, cddlib +, jmol +, tachyon +, glpk +, eclib +, sympow +, nauty +, sqlite +, ppl +, ecm +, lcalc +, rubiks +, flintqs +, blas +, lapack +, flint +, gmp +, mpfr +, pynac +, zlib +, gsl +, ntl +, jdk +, less +}: + +assert (!blas.isILP64) && (!lapack.isILP64); + +# This generates a `sage-env` shell file that will be sourced by sage on startup. +# It sets up various environment variables, telling sage where to find its +# dependencies. + +let + runtimepath = (lib.makeBinPath ([ + "@sage-local@" + "@sage-local@/build" + pythonEnv + # empty python env to add python wrapper that clears PYTHONHOME (see + # wrapper.nix). This is necessary because sage will call the python3 binary + # (from python2 code). The python2 PYTHONHOME (again set in wrapper.nix) + # will then confuse python3, if it is not overwritten. + python3.buildEnv + gfortran # for inline fortran + stdenv.cc # for cython + bash + coreutils + gnused + gnugrep + binutils.bintools + pkg-config + pari + gap + ecl + maxima-ecl + singular + giac + palp + # needs to be rWrapper since the default `R` doesn't include R's default libraries + rWrapper + gfan + cddlib + jmol + tachyon + glpk + eclib + sympow + nauty + sqlite + ppl + ecm + lcalc + rubiks + flintqs + jdk # only needed for `jmol` which may be replaced in the future + less # needed to prevent transient test errors until https://github.com/ipython/ipython/pull/11864 is resolved + ] + )); +in +writeTextFile rec { + name = "sage-env"; + destination = "/${name}"; + text = '' + export PKG_CONFIG_PATH='${lib.makeSearchPathOutput "dev" "lib/pkgconfig" [ + # This should only be needed during build. However, since the doctests + # also test the cython build (for example in src/sage/misc/cython.py), + # it is also needed for the testsuite to pass. We could fix the + # testsuite instead, but since all the packages are also runtime + # dependencies it doesn't really hurt to include them here. + singular + blas lapack + fflas-ffpack givaro + gd + libpng zlib + gsl + linbox + m4ri + ] + }' + export SAGE_ROOT='${sagelib.src}' + export SAGE_LOCAL='@sage-local@' + export SAGE_SHARE='${sagelib}/share' + orig_path="$PATH" + export PATH='${runtimepath}' + + # set dependent vars, like JUPYTER_CONFIG_DIR + source "${sagelib.src}/src/bin/sage-env" + export PATH="$RUNTIMEPATH_PREFIX:${runtimepath}:$orig_path" # sage-env messes with PATH + + export SAGE_LOGS="$TMPDIR/sage-logs" + export SAGE_DOC="''${SAGE_DOC_OVERRIDE:-doc-placeholder}" + export SAGE_DOC_SRC="''${SAGE_DOC_SRC_OVERRIDE:-${sagelib.src}/src/doc}" + + # set locations of dependencies + . ${env-locations}/sage-env-locations + + # needed for cython + export CC='${stdenv.cc}/bin/${stdenv.cc.targetPrefix}cc' + # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar + export LDFLAGS='${ + lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [ + flint + gap + glpk + gmp + mpfr + pari + pynac + zlib + eclib + gsl + ntl + jmol + sympow + ]) + }' + export CFLAGS='${ + lib.concatStringsSep " " (map (pkg: "-isystem ${pkg}/include") [ + singular + gmp.dev + glpk + flint + gap + pynac + mpfr.dev + ]) + }' + + export SAGE_LIB='${sagelib}/${python.sitePackages}' + + export SAGE_EXTCODE='${sagelib.src}/src/ext' + + # for find_library + export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH" + ''; +} // { + lib = sagelib; # equivalent of `passthru`, which `writeTextFile` doesn't support +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix new file mode 100644 index 000000000000..4791d12450a9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -0,0 +1,179 @@ +{ stdenv +, fetchFromGitHub +, fetchpatch +, runtimeShell +}: + +# This file is responsible for fetching the sage source and adding necessary patches. +# It does not actually build anything, it just copies the patched sources to $out. +# This is done because multiple derivations rely on these sources and they should +# all get the same sources with the same patches applied. + +stdenv.mkDerivation rec { + version = "8.9"; + pname = "sage-src"; + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sage"; + rev = version; + sha256 = "1bwga58x3s8z42w5h51c232f91ndsc1861dlb1glhax3pn0rhn3a"; + }; + + # Patches needed because of particularities of nix or the way this is packaged. + # The goal is to upstream all of them and get rid of this list. + nixPatches = [ + # https://trac.sagemath.org/ticket/25358 + (fetchpatch { + name = "safe-directory-test-without-patch.patch"; + url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=dc673c17555efca611f68398d5013b66e9825463"; + sha256 = "1hhannz7xzprijakn2w2d0rhd5zv2zikik9p51i87bas3nc658f7"; + }) + + # `is_unitary` test in `matrix_double_dense.pyx` fails with some BLAS implementations + # https://trac.sagemath.org/ticket/29297 should be included in 9.1 + (fetchpatch { + name = "is_unitary-special-case.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=cc3eb9ffa991e328b09028d32aab7e7cc2ddbb6a"; + sha256 = "0jq4w8hnp5c9q99011ldr4n3knvm1rx2g85z0hidv3i9x868p0ay"; + }) + + # Unfortunately inclusion in upstream sage was rejected. Instead the bug was + # fixed in python, but of course not backported to 2.7. So we'll probably + # have to keep this around until 2.7 is deprecated. + # https://trac.sagemath.org/ticket/25316 + # https://github.com/python/cpython/pull/7476 + ./patches/python-5755-hotpatch.patch + + # Make sure py2/py3 tests are only run when their expected context (all "sage" + # tests) are also run. That is necessary to test dochtml individually. See + # https://trac.sagemath.org/ticket/26110 for an upstream discussion. + ./patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch + + # Fixes a potential race condition which can lead to transient doctest failures. + ./patches/fix-ecl-race.patch + + # Not necessary since library location is set explicitly + # https://trac.sagemath.org/ticket/27660#ticket + ./patches/do-not-test-find-library.patch + + # Parallelize docubuild using subprocesses, fixing an isolation issue. See + # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE + ./patches/sphinx-docbuild-subprocesses.patch + + # Fix doctest failures with docutils 0.15: + # https://nix-cache.s3.amazonaws.com/log/dzmzrb2zvardsmpy7idg7djkizmkzdhs-sage-tests-8.9.drv + # https://trac.sagemath.org/ticket/28856#comment:19 + ./patches/docutils-0.15.patch + ]; + + # Since sage unfortunately does not release bugfix releases, packagers must + # fix those bugs themselves. This is for critical bugfixes, where "critical" + # == "causes (transient) doctest failures / somebody complained". + bugfixPatches = [ + # To help debug the transient error in + # https://trac.sagemath.org/ticket/23087 when it next occurs. + ./patches/configurationpy-error-verbose.patch + ]; + + # Patches needed because of package updates. We could just pin the versions of + # dependencies, but that would lead to rebuilds, confusion and the burdons of + # maintaining multiple versions of dependencies. Instead we try to make sage + # compatible with never dependency versions when possible. All these changes + # should come from or be proposed to upstream. This list will probably never + # be empty since dependencies update all the time. + packageUpgradePatches = let + # Fetch a diff between `base` and `rev` on sage's git server. + # Used to fetch trac tickets by setting the `base` to the last release and the + # `rev` to the last commit of the ticket. + fetchSageDiff = { base, rev, name ? "sage-diff-${base}-${rev}.patch", ...}@args: ( + fetchpatch ({ + inherit name; + url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}"; + # We don't care about sage's own build system (which builds all its dependencies). + # Exclude build system changes to avoid conflicts. + excludes = [ "build/*" ]; + } // builtins.removeAttrs args [ "rev" "base" ]) + ); + in [ + # New glpk version has new warnings, filter those out until upstream sage has found a solution + # Should be fixed with glpk > 4.65. + # https://trac.sagemath.org/ticket/24824 + ./patches/pari-stackwarn.patch # not actually necessary since the pari upgrade, but necessary for the glpk patch to apply + (fetchpatch { + url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/dt-version-glpk-4.65-ignore-warnings.patch"; + sha256 = "0b9293v73wb4x13wv5zwyjgclc01zn16msccfzzi6znswklgvddp"; + stripLen = 1; + }) + + # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can + # now set the cache dir to be withing the .sage directory. This is not + # strictly necessary, but keeps us from littering in the user's HOME. + ./patches/sympow-cache.patch + + # https://trac.sagemath.org/ticket/28472 + (fetchpatch { + name = "eclib-20190909.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=d27dc479a5772d59e4bc85d805b6ffd595284f1d"; + sha256 = "1nf1s9y7n30lhlbdnam7sghgaq9nasmv96415gl5jlcf7a3hlxk3"; + }) + + # ignore a deprecation warning for usage of `cmp` in the attrs library in the doctests + ./patches/ignore-cmp-deprecation.patch + + # Werkzeug has deprecated ImmutableDict, but it is still used in legacy + # sagenb. That's no big issue since sagenb will be removed soon anyways. + ./patches/ignore-werkzeug-immutable-dict-deprecation.patch + + # threejs r109 (#28560) + (fetchpatch { + name = "threejs-r109.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=fcc11d6effa39f375bc5f4ea5831fb7a2f2767da"; + sha256 = "0hnmc8ld3bblks0hcjvjjaydkgwdr1cs3dbl2ys4gfq964pjgqwc"; + }) + + # https://trac.sagemath.org/ticket/28911 + (fetchpatch { + name = "sympy-1.5.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=c6d0308db15efd611211d26cfcbefbd180fc0831"; + sha256 = "0nwai2jr22h49km4hx3kwafs3mzsc5kwsv7mqwjf6ibwfx2bbgyq"; + }) + + # https://trac.sagemath.org/ticket/29313 (patch from ArchLinux) + (fetchpatch { + name = "pari-2.11.3.patch"; + url = "https://aur.archlinux.org/cgit/aur.git/plain/sagemath-pari-2.11.3.patch?h=sagemath-git&id=02e1d58bd1cd70935d69a4990469d18be6bd2c43"; + sha256 = "0z07444zvijyw96d11q7j81pvg7ysd6ycf1bbbjr6za9y74hv7d2"; + }) + ]; + + patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches; + + postPatch = '' + # make sure shebangs etc are fixed, but sage-python23 still works + find . -type f -exec sed \ + -e 's/sage-python23/python/g' \ + -i {} \; + + echo '#!${runtimeShell} + python "$@"' > build/bin/sage-python23 + + # Make sure sage can at least be imported without setting any environment + # variables. It won't be close to feature complete though. + sed -i \ + "s|var('SAGE_LOCAL',.*|var('SAGE_LOCAL', '$out/src')|" \ + src/sage/env.py + + # Do not use sage-env-config (generated by ./configure). + # Instead variables are set manually. + echo '# do nothing' > src/bin/sage-env-config + ''; + + configurePhase = "# do nothing"; + + buildPhase = "# do nothing"; + + installPhase = '' + cp -r . "$out" + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix new file mode 100644 index 000000000000..451edb8f085e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix @@ -0,0 +1,61 @@ +{ stdenv +, lib +, sage-with-env +, makeWrapper +, files ? null # "null" means run all tests +, longTests ? true # run tests marked as "long time" (roughly doubles runtime) +# Run as many tests as possible in approximately n seconds. This will give each +# file to test a "time budget" and stop tests if it is exceeded. 300 is the +# upstream default value. +# https://trac.sagemath.org/ticket/25270 for details. +, timeLimit ? null +}: + +# for a quick test of some source files: +# nix-build -E 'with (import ./. {}); sage.tests.override { files = [ "src/sage/misc/cython.py" ];}' + +let + src = sage-with-env.env.lib.src; + runAllTests = files == null; + testArgs = if runAllTests then "--all" else testFileList; + patienceSpecifier = if longTests then "--long" else ""; + timeSpecifier = if timeLimit == null then "" else "--short ${toString timeLimit}"; + relpathToArg = relpath: lib.escapeShellArg "${src}/${relpath}"; # paths need to be absolute + testFileList = lib.concatStringsSep " " (map relpathToArg files); +in +stdenv.mkDerivation { + version = src.version; + pname = "sage-tests"; + inherit src; + + buildInputs = [ + makeWrapper + sage-with-env + ]; + + dontUnpack = true; + configurePhase = "#do nothing"; + buildPhase = "#do nothing"; + + installPhase = '' + # This output is not actually needed for anything, the package just + # exists to decouple the sage build from its t ests. + + mkdir -p "$out/bin" + # Like a symlink, but make sure that $0 points to the original. + makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage" + ''; + + doInstallCheck = true; + installCheckPhase = '' + export HOME="$TMPDIR/sage-home" + mkdir -p "$HOME" + + # avoid running out of memory with many threads in subprocesses, see + # https://github.com/NixOS/nixpkgs/pull/65802 + export GLIBC_TUNABLES=glibc.malloc.arena_max=4 + + echo "Running sage tests with arguments ${timeSpecifier} ${patienceSpecifier} ${testArgs}" + "sage" -t --timeout=0 --nthreads "$NIX_BUILD_CORES" --optional=sage ${timeSpecifier} ${patienceSpecifier} ${testArgs} + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix new file mode 100644 index 000000000000..87c1e07f5307 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix @@ -0,0 +1,137 @@ +{ stdenv +, lib +, makeWrapper +, sage-env +, blas +, lapack +, pkg-config +, three +, singular +, gap +, giac +, maxima-ecl +, pari +, gmp +, gfan +, python2 +, flintqs +, eclib +, ntl +, ecm +, pynac +, pythonEnv +}: + +# lots of segfaults with (64 bit) blas +assert (!blas.isILP64) && (!lapack.isILP64); + +# Wrapper that combined `sagelib` with `sage-env` to produce an actually +# executable sage. No tests are run yet and no documentation is built. + +let + buildInputs = [ + pythonEnv # for patchShebangs + makeWrapper + pkg-config + blas lapack + singular + three + pynac + giac + gap + pari + gmp + gfan + maxima-ecl + eclib + flintqs + ntl + ecm + ]; + + # remove python prefix, replace "-" in the name by "_", apply patch_names + # python2.7-some-pkg-1.0 -> some_pkg-1.0 + pkg_to_spkg_name = pkg: patch_names: let + parts = lib.splitString "-" pkg.name; + # remove python2.7- + stripped_parts = if (builtins.head parts) == python2.libPrefix then builtins.tail parts else parts; + version = lib.last stripped_parts; + orig_pkgname = lib.init stripped_parts; + pkgname = patch_names (lib.concatStringsSep "_" orig_pkgname); + in pkgname + "-" + version; + + + # return the names of all dependencies in the transitive closure + transitiveClosure = dep: + if dep == null then + # propagatedBuildInputs might contain null + # (although that might be considered a programming error in the derivation) + [] + else + [ dep ] ++ ( + if builtins.hasAttr "propagatedBuildInputs" dep then + lib.unique (builtins.concatLists (map transitiveClosure dep.propagatedBuildInputs)) + else + [] + ); + + allInputs = lib.remove null (buildInputs ++ pythonEnv.extraLibs); + transitiveDeps = lib.unique (builtins.concatLists (map transitiveClosure allInputs )); + # fix differences between spkg and sage names + # (could patch sage instead, but this is more lightweight and also works for packages depending on sage) + patch_names = builtins.replaceStrings [ + "zope.interface" + "node_three" + ] [ + "zope_interface" + "threejs" + ]; + # spkg names (this_is_a_package-version) of all transitive deps + input_names = map (dep: pkg_to_spkg_name dep patch_names) transitiveDeps; +in +stdenv.mkDerivation rec { + version = src.version; + pname = "sage-with-env"; + src = sage-env.lib.src; + + inherit buildInputs; + + configurePhase = "#do nothing"; + + buildPhase = '' + mkdir installed + for pkg in ${lib.concatStringsSep " " input_names}; do + touch "installed/$pkg" + done + + # threejs version is in format 0.<version>.minor, but sage currently still + # relies on installed_packages for the online version of threejs to work + # and expects the format r<version>. This is a hotfix for now. + # upstream: https://trac.sagemath.org/ticket/26434 + rm "installed/threejs"* + touch "installed/threejs-r${lib.versions.minor three.version}" + ''; + + installPhase = '' + mkdir -p "$out/var/lib/sage" + cp -r installed "$out/var/lib/sage" + + mkdir -p "$out/etc" + # sage tests will try to create this file if it doesn't exist + touch "$out/etc/sage-started.txt" + + mkdir -p "$out/build" + + # the scripts in src/bin will find the actual sage source files using environment variables set in `sage-env` + cp -r src/bin "$out/bin" + cp -r build/bin "$out/build/bin" + + cp -f '${sage-env}/sage-env' "$out/bin/sage-env" + substituteInPlace "$out/bin/sage-env" \ + --subst-var-by sage-local "$out" + ''; + + passthru = { + env = sage-env; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage.nix b/nixpkgs/pkgs/applications/science/math/sage/sage.nix new file mode 100644 index 000000000000..4fa8ae6270ba --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sage.nix @@ -0,0 +1,68 @@ +{ stdenv +, makeWrapper +, sage-tests +, sage-with-env +, jupyter-kernel-definition +, jupyter-kernel +, sagedoc +, withDoc +}: + +# A wrapper that makes sure sage finds its docs (if they were build) and the +# jupyter kernel spec. + +let + # generate kernel spec + default kernels + kernel-specs = jupyter-kernel.create { + definitions = jupyter-kernel.default // { + sagemath = jupyter-kernel-definition; + }; + }; +in +stdenv.mkDerivation rec { + version = src.version; + pname = "sage"; + src = sage-with-env.env.lib.src; + + buildInputs = [ + makeWrapper + + # This is a hack to make sure sage-tests is evaluated. It doesn't acutally + # produce anything of value, it just decouples the tests from the build. + sage-tests + ]; + + dontUnpack = true; + configurePhase = "#do nothing"; + buildPhase = "#do nothing"; + + installPhase = '' + mkdir -p "$out/bin" + makeWrapper "${sage-with-env}/bin/sage" "$out/bin/sage" \ + --set SAGE_DOC_SRC_OVERRIDE "${src}/src/doc" ${ + stdenv.lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage" + } \ + --prefix JUPYTER_PATH : "${kernel-specs}" + ''; + + doInstallCheck = withDoc; + installCheckPhase = '' + export HOME="$TMPDIR/sage-home" + mkdir -p "$HOME" + "$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)' + ''; + + passthru = { + tests = sage-tests; + quicktest = sage-tests.override { longTests = false; timeLimit = 600; }; # as many tests as possible in ~10m + doc = sagedoc; + lib = sage-with-env.env.lib; + kernelspec = jupyter-kernel-definition; + }; + + meta = with stdenv.lib; { + description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"; + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagedoc.nix b/nixpkgs/pkgs/applications/science/math/sage/sagedoc.nix new file mode 100644 index 000000000000..bf618fe64f45 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sagedoc.nix @@ -0,0 +1,84 @@ +{ stdenv +, sage-with-env +, python +, maxima-ecl +, tachyon +, jmol +, cddlib +}: + +stdenv.mkDerivation rec { + version = src.version; + pname = "sagedoc"; + src = sage-with-env.env.lib.src; + + + # Building the documentation has many dependencies, because all documented + # modules are imported and because matplotlib is used to produce plots. + buildInputs = [ + sage-with-env.env.lib + python + maxima-ecl + tachyon + jmol + cddlib + ] ++ (with python.pkgs; [ + psutil + future + sphinx + sagenb + scipy + sympy + matplotlib + pillow + networkx + ipykernel + ipywidgets + jupyter_client + typing + pybrial + ]); + + unpackPhase = '' + export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage" + export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc" + + cp -r "${src}/src/doc" "$SAGE_DOC_SRC_OVERRIDE" + chmod -R 755 "$SAGE_DOC_SRC_OVERRIDE" + ''; + + buildPhase = '' + export SAGE_NUM_THREADS="$NIX_BUILD_CORES" + export HOME="$TMPDIR/sage_home" + mkdir -p "$HOME" + + # needed to link them in the sage docs using intersphinx + export PPLPY_DOCS=${python.pkgs.pplpy.doc}/share/doc/pplpy + + ${sage-with-env}/bin/sage -python -m sage_setup.docbuild \ + --mathjax \ + --no-pdf-links \ + all html + ''; + + installPhase = '' + cd "$SAGE_DOC_OVERRIDE" + + mkdir -p "$out/share/doc/sage" + cp -r html "$out"/share/doc/sage + + # Replace duplicated files by symlinks (Gentoo) + cd "$out"/share/doc/sage + mv html/en/_static{,.tmp} + for _dir in `find -name _static` ; do + rm -r $_dir + ln -s /share/doc/sage/html/en/_static $_dir + done + mv html/en/_static{.tmp,} + ''; + + doCheck = true; + checkPhase = '' + ${sage-with-env}/bin/sage -t --optional=dochtml --all + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix new file mode 100644 index 000000000000..830d806a8bcd --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix @@ -0,0 +1,156 @@ +{ sage-src +, env-locations +, perl +, buildPythonPackage +, arb +, blas +, lapack +, brial +, cliquer +, cypari2 +, cysignals +, cython +, ecl +, eclib +, ecm +, flint +, gd +, givaro +, glpk +, gsl +, iml +, jinja2 +, lcalc +, lrcalc +, gap +, linbox +, m4ri +, m4rie +, libmpc +, mpfi +, ntl +, numpy +, pari +, pkgconfig +, pkg-config +, planarity +, ppl +, pynac +, python +, ratpoints +, readline +, rankwidth +, symmetrica +, zn_poly +, fflas-ffpack +, boost +, singular +, pip +, jupyter_core +, libhomfly +, libbraiding +, gmpy2 +, pplpy +}: + +assert (!blas.isILP64) && (!lapack.isILP64); + +# This is the core sage python package. Everything else is just wrappers gluing +# stuff together. It is not very useful on its own though, since it will not +# find many of its dependencies without `sage-env`, will not be tested without +# `sage-tests` and will not have html docs without `sagedoc`. + +buildPythonPackage rec { + format = "other"; + version = src.version; + pname = "sagelib"; + src = sage-src; + + nativeBuildInputs = [ + iml + perl + jupyter_core + pkg-config + pip # needed to query installed packages + ]; + + buildInputs = [ + gd + readline + iml + ]; + + propagatedBuildInputs = [ + cypari2 + jinja2 + numpy + pkgconfig + boost + arb + brial + cliquer + ecl + eclib + ecm + fflas-ffpack + flint + givaro + glpk + gsl + lcalc + gap + libmpc + linbox + lrcalc + m4ri + m4rie + mpfi + ntl + blas + lapack + pari + planarity + ppl + pynac + rankwidth + ratpoints + singular + symmetrica + zn_poly + pip + cython + cysignals + libhomfly + libbraiding + gmpy2 + pplpy + ]; + + buildPhase = '' + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="$SAGE_ROOT" + export SAGE_SHARE="$SAGE_LOCAL/share" + + # set locations of dependencies (needed for nbextensions like threejs) + . ${env-locations}/sage-env-locations + + export JUPYTER_PATH="$SAGE_LOCAL/jupyter" + export PATH="$SAGE_ROOT/build/bin:$SAGE_ROOT/src/bin:$PATH" + + export SAGE_NUM_THREADS="$NIX_BUILD_CORES" + + mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython" + mkdir -p "var/lib/sage/installed" + + source build/bin/sage-dist-helpers + cd src + + ${python.interpreter} -u setup.py --no-user-cfg build + ''; + + installPhase = '' + ${python.interpreter} -u setup.py --no-user-cfg install --prefix=$out + + rm -r "$out/${python.sitePackages}/sage/cython_debug" + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix b/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix new file mode 100644 index 000000000000..77b2168ad974 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/sage/sagenb.nix @@ -0,0 +1,57 @@ +{ stdenv +, python +, buildPythonPackage +, fetchFromGitHub +, mathjax +, twisted +, flask +, flask-oldsessions +, flask-openid +, flask-autoindex +, flask-babel +}: + +# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage. +# Deprecated, hopefully soon to be removed. See +# https://trac.sagemath.org/ticket/25837 + +buildPythonPackage rec { + pname = "sagenb"; + version = "1.1.2"; + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sagenb"; + rev = version; + sha256 = "0bxvhr03qh2nsjdfc4pyfiqrn9jhp3vf7irsc9gqx0185jlblbxs"; + }; + + patches = [ + # cmp deprecation in attrs needs to be handled in twisted + ./patches/sagenb-cmp-deprecation.patch + ]; + + propagatedBuildInputs = [ + twisted + flask + flask-oldsessions + flask-openid + flask-autoindex + flask-babel + ]; + + # tests depend on sage + doCheck = false; + + meta = with stdenv.lib; { + description = "Sage Notebook"; + license = licenses.gpl3Plus; + maintainers = with maintainers; [ timokau ]; + }; + + # let sagenb use mathjax + postInstall = '' + mkdir -p "$out/${python.sitePackages}/sagenb/data" + ln -s ${mathjax}/lib/node_modules/mathjax "$out/${python.sitePackages}/sagenb/data/mathjax" + ''; +} diff --git a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix new file mode 100644 index 000000000000..f9abdee2d148 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix @@ -0,0 +1,104 @@ +{ stdenv, fetchurl, lib, xorg }: + +let + name = "scilab-bin-${ver}"; + + ver = "6.0.2"; + + badArch = throw "${name} requires i686-linux or x86_64-linux"; + + architecture = + if stdenv.hostPlatform.system == "i686-linux" then + "i686" + else if stdenv.hostPlatform.system == "x86_64-linux" then + "x86_64" + else + badArch; +in +stdenv.mkDerivation { + inherit name; + + src = fetchurl { + url = "https://www.scilab.org/download/${ver}/scilab-${ver}.bin.linux-${architecture}.tar.gz"; + sha256 = + if stdenv.hostPlatform.system == "i686-linux" then + "0fgjc2ak3b2qi6yin3fy50qwk2bcj0zbz1h4lyyic9n1n1qcliib" + else if stdenv.hostPlatform.system == "x86_64-linux" then + "05clcdgry90drirl3swbxn5q36fmgknnhs6h5pr7mmrzfr6r818w" + else + badArch; + }; + + libPath = lib.makeLibraryPath [ + stdenv.cc.cc + xorg.libX11 + xorg.libXext + xorg.libXi + xorg.libXrender + xorg.libXtst + xorg.libXxf86vm + ]; + + phases = [ "unpackPhase" "fixupPhase" "installPhase" ]; + + fixupPhase = '' + sed -i 's|\$(/bin/|$(|g' bin/scilab + sed -i 's|/usr/bin/||g' bin/scilab + + sci="$out/opt/scilab-${ver}" + fullLibPath="$sci/lib/scilab:$sci/lib/thirdparty:$libPath" + fullLibPath="$fullLibPath:$sci/lib/thirdparty/redist" + + patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \ + --set-rpath "$fullLibPath" bin/scilab-bin + find . -name '*.so' -type f | while read file; do + patchelf --set-rpath "$fullLibPath" "$file" 2>/dev/null + done + ''; + + installPhase = '' + mkdir -p "$out/opt/scilab-${ver}" + cp -r . "$out/opt/scilab-${ver}/" + + # Create bin/ dir + mkdir "$out/bin" + + # Creating executable symlinks + ln -s "$out/opt/scilab-${ver}/bin/scilab" "$out/bin/scilab" + ln -s "$out/opt/scilab-${ver}/bin/scilab-cli" "$out/bin/scilab-cli" + ln -s "$out/opt/scilab-${ver}/bin/scilab-adv-cli" "$out/bin/scilab-adv-cli" + + # Creating desktop config dir + mkdir -p "$out/share/applications" + + # Moving desktop config files + mv $out/opt/scilab-${ver}/share/applications/*.desktop $out/share/applications + + # Fixing Exec paths and launching each app with a terminal + sed -i -e "s|Exec=|Exec=$out/opt/scilab-${ver}/bin/|g" \ + -e "s|Terminal=.*$|Terminal=true|g" $out/share/applications/*.desktop + + # Moving icons to the appropriate locations + for path in $out/opt/scilab-${ver}/share/icons/hicolor/*/*/* + do + newpath=$(echo $path | sed 's|/opt/scilab-${ver}||g') + filename=$(echo $path | sed 's|.*/||g') + dir=$(echo $newpath | sed "s|$filename||g") + mkdir -p $dir + mv $path $newpath + done + + # Removing emptied folders + rm -rf $out/opt/scilab-${ver}/share/{applications,icons} + + # Moving other share/ folders + mv $out/opt/scilab-${ver}/share/{appdata,locale,mime} $out/share + ''; + + meta = { + homepage = "http://www.scilab.org/"; + description = "Scientific software package for numerical computations (Matlab lookalike)"; + # see http://www.scilab.org/legal_notice + license = "Scilab"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/scilab/default.nix b/nixpkgs/pkgs/applications/science/math/scilab/default.nix new file mode 100644 index 000000000000..24b3feef51e1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/scilab/default.nix @@ -0,0 +1,66 @@ +{stdenv, fetchurl, lib, gfortran +, ncurses +, withXaw3d ? false +#, withPVMlib ? false +, tcl, tk, withTk ? true +, gtk2, withGtk ? false # working ? +#, withF2c ? false +, ocaml, withOCaml ? true +#, withJava ? false +#, atlasMath, withAtlas ? false +, xlibsWrapper, withX ? true +}: + +stdenv.mkDerivation rec { + version = "4.1.2"; + pname = "scilab"; + src = fetchurl { + url = "https://www.scilab.org/download/${version}/${pname}-${version}-src.tar.gz"; + sha256 = "1adk6jqlj7i3gjklvlf1j3il1nb22axnp4rvwl314an62siih0sc"; + }; + + buildInputs = [gfortran ncurses] + ++ lib.optionals withGtk [gtk2] + ++ lib.optionals withOCaml [ocaml] + ++ lib.optional withX xlibsWrapper + ; + + +/* + --with-atlas-library=DIR Atlas library files are in DIR and we use Atlas +*/ + configureFlags = [ + # use gcc C compiler and gnu Fortran compiler (g77 or gfortran) + "--with-gcc" "--with-g77" + # do not compile with PVM library + "--without-pvm" + # compile with GTK + (stdenv.lib.enableFeature withGtk "gtk") + (stdenv.lib.enableFeature withGtk "gtk2") + # compile with ocaml + (stdenv.lib.withFeature withOCaml "ocaml") + # do not compile Java interface + "--without-java" + # use the X Window System + (stdenv.lib.withFeature withX "x") + # compile with TCL/TK + ] ++ lib.optionals withTk [ + "--with-tk" + "--with-tcl-library=${tcl}/lib" + "--with-tcl-include=${tcl}/include" + "--with-tk-library=${tk}/lib" + "--with-tk-include=${tk}/include" + ] # use Xaw3d widgets given with Scilab + ++ lib.optional (!withXaw3d) "--with-local-xaw" + ; + + makeFlags = [ "all" ]; + + meta = { + homepage = "http://www.scilab.org/"; + description = "Scientific software package for numerical computations (Matlab lookalike)"; + # see http://www.scilab.org/legal + license = "SciLab"; + broken = true; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/scotch/default.nix b/nixpkgs/pkgs/applications/science/math/scotch/default.nix new file mode 100644 index 000000000000..75a6b2dba68c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/scotch/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchurl, bison, openmpi, flex, zlib}: + +stdenv.mkDerivation rec { + version = "6.0.4"; + pname = "scotch"; + src_name = "scotch_${version}"; + + buildInputs = [ bison openmpi flex zlib ]; + + src = fetchurl { + url = "https://gforge.inria.fr/frs/download.php/file/34618/${src_name}.tar.gz"; + sha256 = "f53f4d71a8345ba15e2dd4e102a35fd83915abf50ea73e1bf6efe1bc2b4220c7"; + }; + + sourceRoot = "${src_name}/src"; + + preConfigure = '' + ln -s Make.inc/Makefile.inc.x86-64_pc_linux2 Makefile.inc + ''; + + buildFlags = [ "scotch ptscotch" ]; + installFlags = [ "prefix=\${out}" ]; + + meta = { + description = "Graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering"; + longDescription = '' + Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, + and sparse matrix ordering. + ''; + homepage = "http://www.labri.fr/perso/pelegrin/scotch"; + license = stdenv.lib.licenses.cecill-c; + maintainers = [ stdenv.lib.maintainers.bzizou ]; + platforms = stdenv.lib.platforms.linux; + }; +} + diff --git a/nixpkgs/pkgs/applications/science/math/singular/default.nix b/nixpkgs/pkgs/applications/science/math/singular/default.nix new file mode 100644 index 000000000000..a8c4f6bb9a09 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/singular/default.nix @@ -0,0 +1,118 @@ +{ stdenv, fetchurl, gmp, bison, perl, ncurses, readline, coreutils, pkgconfig +, lib +, fetchpatch +, autoreconfHook +, file +, flint +, ntl +, cddlib +, enableFactory ? true +, enableGfanlib ? true +}: + +stdenv.mkDerivation rec { + pname = "singular"; + version = "4.1.1p2"; + + src = let + # singular sorts its tarballs in directories by base release (without patch version) + # for example 4.1.1p1 will be in the directory 4-1-1 + baseVersion = builtins.head (lib.splitString "p" version); + urlVersion = builtins.replaceStrings [ "." ] [ "-" ] baseVersion; + in + fetchurl { + url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/${urlVersion}/singular-${version}.tar.gz"; + sha256 = "07x9kri8vl4galik7lr6pscq3c51n8570pyw64i7gbj0m706f7wf"; + }; + + configureFlags = [ + "--with-ntl=${ntl}" + ] ++ lib.optionals enableFactory [ + "--enable-factory" + ] ++ lib.optionals enableGfanlib [ + "--enable-gfanlib" + ]; + + postUnpack = '' + patchShebangs . + ''; + + patches = [ + # NTL error handler was introduced in the library part, preventing users of + # the library from implementing their own error handling + # https://www.singular.uni-kl.de/forum/viewtopic.php?t=2769 + (fetchpatch { + name = "move_error_handler_out_of_libsingular.patch"; + # rebased version of https://github.com/Singular/Sources/commit/502cf86d0bb2a96715be6764774b64a69c1ca34c.patch + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/singular/patches/singular-ntl-error-handler.patch?h=50b9ae2fd233c30860e1cbb3e63a26f2cc10560a"; + sha256 = "0vgh4m9zn1kjl0br68n04j4nmn5i1igfn28cph0chnwf7dvr9194"; + }) + ]; + + # For reference (last checked on commit 75f460d): + # https://github.com/Singular/Sources/blob/spielwiese/doc/Building-Singular-from-source.md + # https://github.com/Singular/Sources/blob/spielwiese/doc/external-packages-dynamic-modules.md + buildInputs = [ + # necessary + gmp + # by upstream recommended but optional + ncurses + readline + ntl + flint + ] ++ lib.optionals enableGfanlib [ + cddlib + ]; + nativeBuildInputs = [ + bison + perl + pkgconfig + autoreconfHook + ]; + + preAutoreconf = '' + find . -type f -readable -writable -exec sed \ + -e 's@/bin/rm@${coreutils}&@g' \ + -e 's@/bin/uname@${coreutils}&@g' \ + -e 's@/usr/bin/file@${file}/bin/file@g' \ + -i '{}' ';' + ''; + + hardeningDisable = lib.optional stdenv.isi686 "stackprotector"; + + # The Makefile actually defaults to `make install` anyway + buildPhase = '' + # do nothing + ''; + + installPhase = '' + mkdir -p "$out" + cp -r Singular/LIB "$out/lib" + make install + + # Make sure patchelf picks up the right libraries + rm -rf libpolys factory resources omalloc Singular + ''; + + # simple test to make sure singular starts and finds its libraries + doInstallCheck = true; + installCheckPhase = '' + "$out/bin/Singular" -c 'LIB "freegb.lib"; exit;' + if [ $? -ne 0 ]; then + echo >&2 "Error loading the freegb library in Singular." + exit 1 + fi + ''; + + enableParallelBuilding = true; + + meta = with lib; { + description = "A CAS for polynomial computations"; + maintainers = with maintainers; [ raskin timokau ]; + # 32 bit x86 fails with some link error: `undefined reference to `__divmoddi4@GCC_7.0.0'` + platforms = subtractLists platforms.i686 platforms.unix; + license = licenses.gpl3; # Or GPLv2 at your option - but not GPLv4 + homepage = "http://www.singular.uni-kl.de"; + downloadPage = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/speedcrunch/default.nix b/nixpkgs/pkgs/applications/science/math/speedcrunch/default.nix new file mode 100644 index 000000000000..4bb39ab73f5f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/speedcrunch/default.nix @@ -0,0 +1,37 @@ +{ mkDerivation, lib, fetchgit, cmake, qtbase, qttools }: + +mkDerivation rec { + pname = "speedcrunch"; + version = "0.12.0"; + + src = fetchgit { + # the tagging is not standard, so you probably need to check this when updating + rev = "refs/tags/release-${version}"; + url = "https://bitbucket.org/heldercorreia/speedcrunch"; + sha256 = "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"; + }; + + buildInputs = [ qtbase qttools ]; + + nativeBuildInputs = [ cmake ]; + + preConfigure = '' + cd src + ''; + + meta = with lib; { + homepage = "http://speedcrunch.org"; + license = licenses.gpl2Plus; + description = "A fast power user calculator"; + longDescription = '' + SpeedCrunch is a fast, high precision and powerful desktop calculator. + Among its distinctive features are a scrollable display, up to 50 decimal + precisions, unlimited variable storage, intelligent automatic completion + full keyboard-friendly and more than 15 built-in math function. + ''; + maintainers = with maintainers; [ gebner ]; + inherit (qtbase.meta) platforms; + # works with qt 5.6 and qt 5.8 + broken = builtins.compareVersions qtbase.version "5.7.0" == 0; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix b/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix new file mode 100644 index 000000000000..b363137fb99c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/symmetrica/default.nix @@ -0,0 +1,36 @@ +{ stdenv +, lib +, fetchFromGitLab +, fetchpatch +, autoreconfHook +}: +stdenv.mkDerivation rec { + pname = "symmetrica"; + version = "3.0.1"; + + # Fork of the original symmetrica, which can be found here + # http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/index.html + # "This fork was created to modernize the codebase, and to resume making + # releases with the fixes that have accrued over the years." + # Also see https://trac.sagemath.org/ticket/29061#comment:3. + src = fetchFromGitLab { + owner = "sagemath"; + repo = "symmetrica"; + rev = version; + sha256 = "0wfmrzw82f5i91d7rf24mcdqcj2fmgrgy02pw4pliz7ncwaq14w3"; + }; + + nativeBuildInputs = [ + autoreconfHook + ]; + + enableParallelBuilding = true; + + meta = with lib; { + description = ''A collection of routines for representation theory and combinatorics''; + license = licenses.isc; + maintainers = with maintainers; [raskin timokau]; + platforms = platforms.unix; + homepage = "https://gitlab.com/sagemath/symmetrica"; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/weka/default.nix b/nixpkgs/pkgs/applications/science/math/weka/default.nix new file mode 100644 index 000000000000..c4fc19d6c6b7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/weka/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchurl, jre, unzip, makeWrapper }: + +stdenv.mkDerivation rec { + pname = "weka"; + version = "3.9.2"; + + src = fetchurl { + url = "mirror://sourceforge/weka/${stdenv.lib.replaceChars ["."]["-"] "${pname}-${version}"}.zip"; + sha256 = "0zwmhspmqb0a7cm6k6i0s6q3w19ws1g9dx3cp2v3g3vsif6cdh31"; + }; + + buildInputs = [ unzip makeWrapper ]; + + # The -Xmx1000M comes suggested from their download page: + # http://www.cs.waikato.ac.nz/ml/weka/downloading.html + installPhase = '' + mkdir -pv $out/share/weka + cp -Rv * $out/share/weka + + makeWrapper ${jre}/bin/java $out/bin/weka \ + --add-flags "-Xmx1000M -jar $out/share/weka/weka.jar" + ''; + + meta = { + homepage = "http://www.cs.waikato.ac.nz/ml/weka/"; + description = "Collection of machine learning algorithms for data mining tasks"; + license = stdenv.lib.licenses.gpl2Plus; + maintainers = [ stdenv.lib.maintainers.mimame ]; + platforms = stdenv.lib.platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix new file mode 100644 index 000000000000..4d6e4bea34e6 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchFromGitHub +, wrapGAppsHook, cmake, gettext +, maxima, wxGTK, gnome3 }: + +stdenv.mkDerivation rec { + pname = "wxmaxima"; + version = "20.02.4"; + + src = fetchFromGitHub { + owner = "wxMaxima-developers"; + repo = "wxmaxima"; + rev = "Version-${version}"; + sha256 = "106a7jrjwfmymzj70nsv44fm3jbxngr8pmkaghhpwy0ln38lhf54"; + }; + + buildInputs = [ wxGTK maxima gnome3.adwaita-icon-theme ]; + + nativeBuildInputs = [ wrapGAppsHook cmake gettext ]; + + preConfigure = '' + gappsWrapperArgs+=(--prefix PATH ":" ${maxima}/bin) + ''; + + meta = with stdenv.lib; { + description = "Cross platform GUI for the computer algebra system Maxima"; + license = licenses.gpl2; + homepage = "https://wxmaxima-developers.github.io/wxmaxima/"; + platforms = platforms.linux; + maintainers = [ maintainers.peti ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/yacas/default.nix b/nixpkgs/pkgs/applications/science/math/yacas/default.nix new file mode 100644 index 000000000000..c19d8f0fbc17 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/yacas/default.nix @@ -0,0 +1,39 @@ +{ stdenv, fetchFromGitHub, cmake, perl +, enableGui ? false, qt5 +, enableJupyter ? false, boost, jsoncpp, openssl, zmqpp +}: + +stdenv.mkDerivation rec { + pname = "yacas"; + version = "1.8.0"; + + src = fetchFromGitHub { + owner = "grzegorzmazur"; + repo = "yacas"; + rev = "v${version}"; + sha256 = "0fwd98dwq6g0md3yhgyl30i377593b8rw6gsvffzvs11g3aqf1ga"; + }; + + hardeningDisable = [ "format" ]; + + cmakeFlags = [ + "-DENABLE_CYACAS_GUI=${if enableGui then "ON" else "OFF"}" + "-DENABLE_CYACAS_KERNEL=${if enableJupyter then "ON" else "OFF"}" + ]; + + # Perl is only for the documentation + nativeBuildInputs = [ cmake perl ]; + buildInputs = [ + ] ++ stdenv.lib.optionals enableGui (with qt5; [ qtbase qtwebkit ]) + ++ stdenv.lib.optionals enableJupyter [ boost jsoncpp openssl zmqpp ] + ; + + meta = { + description = "Easy to use, general purpose Computer Algebra System"; + homepage = "http://www.yacas.org/"; + license = stdenv.lib.licenses.gpl2Plus; + maintainers = with stdenv.lib.maintainers; [viric]; + platforms = with stdenv.lib.platforms; linux; + broken = enableGui || enableJupyter; + }; +} |