diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/math')
17 files changed, 218 insertions, 1030 deletions
diff --git a/nixpkgs/pkgs/applications/science/math/gap/default.nix b/nixpkgs/pkgs/applications/science/math/gap/default.nix index 2927701dbd71..e12353878149 100644 --- a/nixpkgs/pkgs/applications/science/math/gap/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gap/default.nix @@ -1,62 +1,137 @@ { stdenv +, lib , fetchurl , fetchpatch +, makeWrapper , m4 , gmp -# don't remove any packages -- results in a ~1.3G size increase -# see https://github.com/NixOS/nixpkgs/pull/38754 for a discussion -, keepAllPackages ? true +# 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-*" + ]; + standardPackages = requiredPackages ++ autoloadedPackages; + 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 '${str}' \\") whitelist)) + '' + -exec echo "Removing package {}" \; \ + -exec rm -r '{}' \; + ''; +in stdenv.mkDerivation rec { pname = "gap"; # https://www.gap-system.org/Releases/ - # newer versions (4.9.0) are available, but still considered beta (https://github.com/gap-system/gap/wiki/GAP-4.9-release-notes) - version = "4r8p10"; - pkgVer = "2018_01_15-13_02"; - name = "${pname}-${version}"; - - src = let - # 4r8p10 -> 48 - majorminor = stdenv.lib.replaceStrings ["r"] [""] ( - builtins.head (stdenv.lib.splitString "p" version) # 4r8p10 -> 4r8 - ); - in - fetchurl { - url = "https://www.gap-system.org/pub/gap/gap${majorminor}/tar.bz2/gap${version}_${pkgVer}.tar.bz2"; - sha256 = "0wzfdjnn6sfiaizbk5c7x44rhbfayis4lf57qbqqg84c7dqlwr6f"; + version = "4.10.0"; + + 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 = "1dmb8v4p7j1nnf7sx8sg54b49yln36bi9acwp7w1d3a1nxj17ird"; }; # remove all non-essential packages (which take up a lot of space) - preConfigure = stdenv.lib.optionalString (!keepAllPackages) '' - find pkg -type d -maxdepth 1 -mindepth 1 \ - -not -name 'GAPDoc-*' \ - -not -name 'autpgrp*' \ - -exec echo "Removing package {}" \; \ - -exec rm -r {} \; + preConfigure = lib.optionalString (!keepAll) (removeNonWhitelistedPkgs packagesToKeep) + '' + patchShebangs . ''; configureFlags = [ "--with-gmp=system" ]; - buildInputs = [ m4 gmp ]; + + buildInputs = [ + m4 + gmp + ]; + + nativeBuildInputs = [ + makeWrapper + ]; patches = [ - # fix infinite loop in writeandcheck() when writing an error message fails. + # bugfix: https://github.com/gap-system/gap/pull/3102 + (fetchpatch { + name = "fix-infinite-loop-in-writeandcheck.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/0001-a-version-of-the-writeandcheck.patch-from-Sage-that-.patch?id=5e61d7b6a0da3aa53d8176fa1fb9353cc559b098"; + sha256 = "1zkv8bbiw3jdn54sqqvfkdkfsd7jxzq0bazwsa14g4sh2265d28j"; + }) + + # needed for libgap (sage): https://github.com/gap-system/gap/pull/3043 + (fetchpatch { + name = "add-error-messages-helper.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/0002-kernel-add-helper-function-for-writing-error-message.patch?id=5e61d7b6a0da3aa53d8176fa1fb9353cc559b098"; + sha256 = "0c4ry5znb6hwwp8ld6k62yw8w6cqldflw3x49bbzizbmipfpidh5"; + }) + + # needed for libgap (sage): https://github.com/gap-system/gap/pull/3096 (fetchpatch { - url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/writeandcheck.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; - sha256 = "1r1511x4kc2i2mbdq1b61rb6p3misvkf1v5qy3z6fmn6vqwziaz1"; + name = "gap-enter.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/gap/patches/0003-Prototype-for-GAP_Enter-Leave-macros-to-bracket-use-.patch?id=5e61d7b6a0da3aa53d8176fa1fb9353cc559b098"; + sha256 = "12fg8mb8rm6khsz1r4k3k26jrkx4q1rv13hcrfnlhn0m7iikvc3q"; }) ]; - doCheck = true; - checkTarget = "testinstall"; # "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"; - preCheck = '' + 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:$PATH" + + # make sure we don't accidentally use the wrong gap binary + rm -r bin + + # like the defaults the Makefile, but use gap from PATH instead of the + # one from builddir + installCheckFlagsArray+=( + "TESTGAP=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r -A" + "TESTGAPauto=gap --quitonbreak -b -m 100m -o 1g -q -x 80 -r" + ) ''; postCheck = '' @@ -75,28 +150,44 @@ stdenv.mkDerivation rec { popd ''; - installPhase = '' + installTargets = [ + "install-libgap" + "install-headers" + ]; + + # full `make install` is not yet implemented, just for libgap and headers + postInstall = '' + # Install config.h, which is not currently handled by `make install-headers` + cp gen/config.h "$out/include/gap" + mkdir -p "$out/bin" "$out/share/gap/" - cp -r . "$out/share/gap/build-dir" + mkdir -p "$out/share/gap" + echo "Copying files to target directory" + cp -ar . "$out/share/gap/build-dir" - sed -e "/GAP_DIR=/aGAP_DIR='$out/share/gap/build-dir/'" -i "$out/share/gap/build-dir/bin/gap.sh" + makeWrapper "$out/share/gap/build-dir/bin/gap.sh" "$out/bin/gap" \ + --set GAP_DIR $out/share/gap/build-dir + ''; - ln -s "$out/share/gap/build-dir/bin/gap.sh" "$out/bin/gap" + preFixup = '' + # patchelf won't strip references to the build dir if it still exists + rm -rf pkg ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Computational discrete algebra system"; maintainers = with maintainers; [ raskin chrisjefferson + timokau ]; platforms = platforms.all; # keeping all packages increases the package size considerably, wchich # is why a local build is preferable in that situation. The timeframe # is reasonable and that way the binary cache doesn't get overloaded. - hydraPlatforms = stdenv.lib.optionals (!keepAllPackages) meta.platforms; + hydraPlatforms = lib.optionals (!keepAllPackages) meta.platforms; license = licenses.gpl2; homepage = http://gap-system.org/; }; diff --git a/nixpkgs/pkgs/applications/science/math/getdp/default.nix b/nixpkgs/pkgs/applications/science/math/getdp/default.nix new file mode 100644 index 000000000000..74e4b052fdb5 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/getdp/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchurl, cmake, gfortran, openblas, openmpi, python3 }: + +stdenv.mkDerivation rec { + name = "getdp-${version}"; + version = "3.0.4"; + src = fetchurl { + url = "http://getdp.info/src/getdp-${version}-source.tgz"; + sha256 = "0v3hg03lzw4hz28hm45hpv0gyydqz0wav7xvb5n0v0jrm47mrspv"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ gfortran openblas openmpi python3 ]; + + meta = with stdenv.lib; { + description = "A General Environment for the Treatment of Discrete Problems"; + longDescription = '' + GetDP is a free finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions. + The main feature of GetDP is the closeness between the input data defining discrete problems (written by the user in ASCII data files) and the symbolic mathematical expressions of these problems. + ''; + homepage = http://getdp.info/; + license = stdenv.lib.licenses.gpl2Plus; + maintainers = with maintainers; [ wucke13 ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix index c689ae98b7ad..694c621db00b 100644 --- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg , zlib, libGLU_combined, libGLU, xorg }: -let version = "4.0.7"; in +let version = "4.1.3"; in stdenv.mkDerivation { name = "gmsh-${version}"; src = fetchurl { url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "c6572320d0ffdf7d2488e113861bc4bd9c38a29f7fc5b67957f6fbcb63fbdbd5"; + sha256 = "0padylvicyhcm4vqkizpknjfw8qxh39scw3mj5xbs9bs8c442kmx"; }; buildInputs = [ cmake openblasCompat gmm fltk libjpeg zlib libGLU_combined diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix index d4a4133d06e8..be14d1411285 100644 --- a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "gurobi-${version}"; - version = "8.0.1"; + version = "8.1.0"; src = with stdenv.lib; fetchurl { url = "http://packages.gurobi.com/${versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; - sha256 = "0y3lb0mngnyn7ql4s2n8qxnr1d2xcjdpdhpdjdxc4sc8f2w2ih18"; + sha256 = "1yjqbzqnq4jjkjm616d36bgd3rmqr0a1ii17n0prpdjzmdlq63dz"; }; sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix b/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix index 2158021c7548..065360a112d8 100644 --- a/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix +++ b/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix @@ -5,10 +5,10 @@ with lib; l10ns = flip map [ { - version = "11.2.0"; + version = "11.3.0"; lang = "en"; language = "English"; - sha256 = "4a1293cc1c404303aa1cab1bd273c7be151d37ac5ed928fbbb18e9c5ab2d8df9"; + sha256 = "0fcfe208c1eac8448e7be3af0bdb84370b17bd9c5d066c013928c8ee95aed10e"; } { version = "11.2.0"; diff --git a/nixpkgs/pkgs/applications/science/math/pynac/default.nix b/nixpkgs/pkgs/applications/science/math/pynac/default.nix index 9bbb695a331b..032b2ef09643 100644 --- a/nixpkgs/pkgs/applications/science/math/pynac/default.nix +++ b/nixpkgs/pkgs/applications/science/math/pynac/default.nix @@ -9,14 +9,14 @@ }: stdenv.mkDerivation rec { - version = "0.7.22"; + version = "0.7.23"; name = "pynac-${version}"; src = fetchFromGitHub { owner = "pynac"; repo = "pynac"; rev = "pynac-${version}"; - sha256 = "1ribm5vpbgsja4hbca1ckw4ln9kjkv608aaqsvxxvbs4z76ys6yi"; + sha256 = "02yhl8v9l6aj3wl6dk9iacz4hdv08i1d750rxpygjp43nlgvvb2h"; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/sage/default.nix b/nixpkgs/pkgs/applications/science/math/sage/default.nix index 46e60a2b81e4..dfdf210eec04 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/default.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/default.nix @@ -70,7 +70,7 @@ let sage-env = callPackage ./sage-env.nix { sagelib = python.pkgs.sagelib; inherit env-locations; - inherit python rWrapper ecl singular palp flint pynac pythonEnv; + inherit python ecl singular palp flint pynac pythonEnv; pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig }; @@ -124,19 +124,6 @@ let ignoreCollisions = true; } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible - # needs to be rWrapper, standard "R" doesn't include default packages - rWrapper = pkgs.rWrapper.override { - # https://trac.sagemath.org/ticket/25674 - R = pkgs.R.overrideAttrs (attrs: rec { - name = "R-3.4.4"; - doCheck = false; - src = fetchurl { - url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz"; - sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"; - }; - }); - }; - arb = pkgs.arb.override { inherit flint; }; singular = pkgs.singular.override { inherit flint; }; diff --git a/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix b/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix index 9ec8d5cd83e5..8354629cab55 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/env-locations.nix @@ -7,7 +7,7 @@ , graphs , elliptic_curves , polytopes_db -, gap-libgap-compatible +, gap , ecl , combinatorial_designs , jmol @@ -35,7 +35,7 @@ writeTextFile rec { 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-libgap-compatible}/share/gap/build-dir' + 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" 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/numpy-1.15.1.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/numpy-1.15.1.patch deleted file mode 100644 index 9e855ba4ad94..000000000000 --- a/nixpkgs/pkgs/applications/science/math/sage/patches/numpy-1.15.1.patch +++ /dev/null @@ -1,911 +0,0 @@ -diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst -index 2347a1190d..f5b0fe71a4 100644 ---- a/src/doc/en/faq/faq-usage.rst -+++ b/src/doc/en/faq/faq-usage.rst -@@ -338,7 +338,7 @@ ints. For example:: - sage: RealNumber = float; Integer = int - sage: from scipy import stats - sage: stats.ttest_ind(list([1,2,3,4,5]),list([2,3,4,5,.6])) -- Ttest_indResult(statistic=0.076752955645333687, pvalue=0.94070490247380478) -+ Ttest_indResult(statistic=0.0767529..., pvalue=0.940704...) - sage: stats.uniform(0,15).ppf([0.5,0.7]) - array([ 7.5, 10.5]) - -diff --git a/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst b/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst -index 314811c42b..e5f54ec4c2 100644 ---- a/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst -+++ b/src/doc/en/thematic_tutorials/numerical_sage/cvxopt.rst -@@ -48,11 +48,13 @@ we could do the following. - sage: B = numpy.array([1.0]*5) - sage: B.shape=(5,1) - sage: print(B) -- [[ 1.] -- [ 1.] -- [ 1.] -- [ 1.] -- [ 1.]] -+ [[1.] -+ [1.] -+ [1.] -+ [1.] -+ [1.]] -+ -+ - sage: print(A) - [ 2.00e+00 3.00e+00 0 0 0 ] - [ 3.00e+00 0 4.00e+00 0 6.00e+00] -diff --git a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst -index 5b89cd75ee..e50b2ea5d4 100644 ---- a/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst -+++ b/src/doc/en/thematic_tutorials/numerical_sage/numpy.rst -@@ -84,7 +84,7 @@ well as take slices - sage: l[3] - 3.0 - sage: l[3:6] -- array([ 3., 4., 5.]) -+ array([3., 4., 5.]) - - You can do basic arithmetic operations - -@@ -147,11 +147,11 @@ also do matrix vector multiplication, and matrix addition - sage: n = numpy.matrix([[1,2],[3,4]],dtype=float) - sage: v = numpy.array([[1],[2]],dtype=float) - sage: n*v -- matrix([[ 5.], -- [ 11.]]) -+ matrix([[ 5.], -+ [11.]]) - sage: n+n -- matrix([[ 2., 4.], -- [ 6., 8.]]) -+ matrix([[2., 4.], -+ [6., 8.]]) - - If ``n`` was created with :meth:`numpy.array`, then to do matrix vector - multiplication, you would use ``numpy.dot(n,v)``. -@@ -170,11 +170,11 @@ to manipulate - 22., 23., 24.]) - sage: n.shape=(5,5) - sage: n -- array([[ 0., 1., 2., 3., 4.], -- [ 5., 6., 7., 8., 9.], -- [ 10., 11., 12., 13., 14.], -- [ 15., 16., 17., 18., 19.], -- [ 20., 21., 22., 23., 24.]]) -+ array([[ 0., 1., 2., 3., 4.], -+ [ 5., 6., 7., 8., 9.], -+ [10., 11., 12., 13., 14.], -+ [15., 16., 17., 18., 19.], -+ [20., 21., 22., 23., 24.]]) - - This changes the one-dimensional array into a `5\times 5` array. - -@@ -187,8 +187,8 @@ NumPy arrays can be sliced as well - sage: n=numpy.array(range(25),dtype=float) - sage: n.shape=(5,5) - sage: n[2:4,1:3] -- array([[ 11., 12.], -- [ 16., 17.]]) -+ array([[11., 12.], -+ [16., 17.]]) - - It is important to note that the sliced matrices are references to - the original -@@ -224,8 +224,8 @@ Some particularly useful commands are - - sage: x=numpy.arange(0,2,.1,dtype=float) - sage: x -- array([ 0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , -- 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9]) -+ array([0. , 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1. , 1.1, 1.2, -+ 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9]) - - You can see that :meth:`numpy.arange` creates an array of floats increasing by 0.1 - from 0 to 2. There is a useful command :meth:`numpy.r_` that is best explained by example -@@ -240,10 +240,11 @@ from 0 to 2. There is a useful command :meth:`numpy.r_` that is best explained b - sage: Integer=int - sage: n=r_[0.0:5.0] - sage: n -- array([ 0., 1., 2., 3., 4.]) -+ array([0., 1., 2., 3., 4.]) - sage: n=r_[0.0:5.0, [0.0]*5] - sage: n -- array([ 0., 1., 2., 3., 4., 0., 0., 0., 0., 0.]) -+ array([0., 1., 2., 3., 4., 0., 0., 0., 0., 0.]) -+ - - :meth:`numpy.r_` provides a shorthand for constructing NumPy arrays efficiently. - Note in the above ``0.0:5.0`` was shorthand for ``0.0, 1.0, 2.0, 3.0, 4.0``. -@@ -255,7 +256,7 @@ intervals. We can do this as follows - :: - - sage: r_[0.0:5.0:11*j] -- array([ 0. , 0.5, 1. , 1.5, 2. , 2.5, 3. , 3.5, 4. , 4.5, 5. ]) -+ array([0. , 0.5, 1. , 1.5, 2. , 2.5, 3. , 3.5, 4. , 4.5, 5. ]) - - The notation ``0.0:5.0:11*j`` expands to a list of 11 equally space - points between 0 and 5 including both endpoints. Note that ``j`` is the -@@ -287,23 +288,23 @@ an equally spaced grid with `\Delta x = \Delta y = .25` for - sage: y=numpy.r_[0.0:1.0:5*j] - sage: xx,yy= meshgrid(x,y) - sage: xx -- array([[ 0. , 0.25, 0.5 , 0.75, 1. ], -- [ 0. , 0.25, 0.5 , 0.75, 1. ], -- [ 0. , 0.25, 0.5 , 0.75, 1. ], -- [ 0. , 0.25, 0.5 , 0.75, 1. ], -- [ 0. , 0.25, 0.5 , 0.75, 1. ]]) -+ array([[0. , 0.25, 0.5 , 0.75, 1. ], -+ [0. , 0.25, 0.5 , 0.75, 1. ], -+ [0. , 0.25, 0.5 , 0.75, 1. ], -+ [0. , 0.25, 0.5 , 0.75, 1. ], -+ [0. , 0.25, 0.5 , 0.75, 1. ]]) - sage: yy -- array([[ 0. , 0. , 0. , 0. , 0. ], -- [ 0.25, 0.25, 0.25, 0.25, 0.25], -- [ 0.5 , 0.5 , 0.5 , 0.5 , 0.5 ], -- [ 0.75, 0.75, 0.75, 0.75, 0.75], -- [ 1. , 1. , 1. , 1. , 1. ]]) -+ array([[0. , 0. , 0. , 0. , 0. ], -+ [0.25, 0.25, 0.25, 0.25, 0.25], -+ [0.5 , 0.5 , 0.5 , 0.5 , 0.5 ], -+ [0.75, 0.75, 0.75, 0.75, 0.75], -+ [1. , 1. , 1. , 1. , 1. ]]) - sage: f(xx,yy) -- array([[ 0. , 0.0625, 0.25 , 0.5625, 1. ], -- [ 0.0625, 0.125 , 0.3125, 0.625 , 1.0625], -- [ 0.25 , 0.3125, 0.5 , 0.8125, 1.25 ], -- [ 0.5625, 0.625 , 0.8125, 1.125 , 1.5625], -- [ 1. , 1.0625, 1.25 , 1.5625, 2. ]]) -+ array([[0. , 0.0625, 0.25 , 0.5625, 1. ], -+ [0.0625, 0.125 , 0.3125, 0.625 , 1.0625], -+ [0.25 , 0.3125, 0.5 , 0.8125, 1.25 ], -+ [0.5625, 0.625 , 0.8125, 1.125 , 1.5625], -+ [1. , 1.0625, 1.25 , 1.5625, 2. ]]) - - You can see that :meth:`numpy.meshgrid` produces a pair of matrices, here denoted - `xx` and `yy`, such that `(xx[i,j],yy[i,j])` has coordinates -@@ -324,7 +325,7 @@ equation `Ax=b` do - sage: b=numpy.array(range(1,6)) - sage: x=linalg.solve(A,b) - sage: numpy.dot(A,x) -- array([ 1., 2., 3., 4., 5.]) -+ array([1., 2., 3., 4., 5.]) - - This creates a random 5x5 matrix ``A``, and solves `Ax=b` where - ``b=[0.0,1.0,2.0,3.0,4.0]``. There are many other routines in the :mod:`numpy.linalg` -diff --git a/src/sage/calculus/riemann.pyx b/src/sage/calculus/riemann.pyx -index 60f37f7557..4ac3dedf1d 100644 ---- a/src/sage/calculus/riemann.pyx -+++ b/src/sage/calculus/riemann.pyx -@@ -1191,30 +1191,30 @@ cpdef complex_to_spiderweb(np.ndarray[COMPLEX_T, ndim = 2] z_values, - sage: zval = numpy.array([[0, 1, 1000],[.2+.3j,1,-.3j],[0,0,0]],dtype = numpy.complex128) - sage: deriv = numpy.array([[.1]],dtype = numpy.float64) - sage: complex_to_spiderweb(zval, deriv,deriv, 4,4,[0,0,0],1,False,0.001) -- array([[[ 1., 1., 1.], -- [ 1., 1., 1.], -- [ 1., 1., 1.]], -+ array([[[1., 1., 1.], -+ [1., 1., 1.], -+ [1., 1., 1.]], - <BLANKLINE> -- [[ 1., 1., 1.], -- [ 0., 0., 0.], -- [ 1., 1., 1.]], -+ [[1., 1., 1.], -+ [0., 0., 0.], -+ [1., 1., 1.]], - <BLANKLINE> -- [[ 1., 1., 1.], -- [ 1., 1., 1.], -- [ 1., 1., 1.]]]) -+ [[1., 1., 1.], -+ [1., 1., 1.], -+ [1., 1., 1.]]]) - - sage: complex_to_spiderweb(zval, deriv,deriv, 4,4,[0,0,0],1,True,0.001) -- array([[[ 1. , 1. , 1. ], -- [ 1. , 0.05558355, 0.05558355], -- [ 0.17301243, 0. , 0. ]], -+ array([[[1. , 1. , 1. ], -+ [1. , 0.05558355, 0.05558355], -+ [0.17301243, 0. , 0. ]], - <BLANKLINE> -- [[ 1. , 0.96804683, 0.48044583], -- [ 0. , 0. , 0. ], -- [ 0.77351965, 0.5470393 , 1. ]], -+ [[1. , 0.96804683, 0.48044583], -+ [0. , 0. , 0. ], -+ [0.77351965, 0.5470393 , 1. ]], - <BLANKLINE> -- [[ 1. , 1. , 1. ], -- [ 1. , 1. , 1. ], -- [ 1. , 1. , 1. ]]]) -+ [[1. , 1. , 1. ], -+ [1. , 1. , 1. ], -+ [1. , 1. , 1. ]]]) - """ - cdef Py_ssize_t i, j, imax, jmax - cdef FLOAT_T x, y, mag, arg, width, target, precision, dmag, darg -@@ -1279,14 +1279,14 @@ cpdef complex_to_rgb(np.ndarray[COMPLEX_T, ndim = 2] z_values): - sage: from sage.calculus.riemann import complex_to_rgb - sage: import numpy - sage: complex_to_rgb(numpy.array([[0, 1, 1000]], dtype = numpy.complex128)) -- array([[[ 1. , 1. , 1. ], -- [ 1. , 0.05558355, 0.05558355], -- [ 0.17301243, 0. , 0. ]]]) -+ array([[[1. , 1. , 1. ], -+ [1. , 0.05558355, 0.05558355], -+ [0.17301243, 0. , 0. ]]]) - - sage: complex_to_rgb(numpy.array([[0, 1j, 1000j]], dtype = numpy.complex128)) -- array([[[ 1. , 1. , 1. ], -- [ 0.52779177, 1. , 0.05558355], -- [ 0.08650622, 0.17301243, 0. ]]]) -+ array([[[1. , 1. , 1. ], -+ [0.52779177, 1. , 0.05558355], -+ [0.08650622, 0.17301243, 0. ]]]) - - - TESTS:: -diff --git a/src/sage/combinat/fully_packed_loop.py b/src/sage/combinat/fully_packed_loop.py -index 0a9bd61267..d2193cc2d6 100644 ---- a/src/sage/combinat/fully_packed_loop.py -+++ b/src/sage/combinat/fully_packed_loop.py -@@ -72,11 +72,11 @@ def _make_color_list(n, colors=None, color_map=None, randomize=False): - sage: _make_color_list(5, ['blue', 'red']) - ['blue', 'red', 'blue', 'red', 'blue'] - sage: _make_color_list(5, color_map='summer') -- [(0.0, 0.5, 0.40000000000000002), -- (0.25098039215686274, 0.62549019607843137, 0.40000000000000002), -- (0.50196078431372548, 0.75098039215686274, 0.40000000000000002), -- (0.75294117647058822, 0.87647058823529411, 0.40000000000000002), -- (1.0, 1.0, 0.40000000000000002)] -+ [(0.0, 0.5, 0.4), -+ (0.25098039215686274, 0.6254901960784314, 0.4), -+ (0.5019607843137255, 0.7509803921568627, 0.4), -+ (0.7529411764705882, 0.8764705882352941, 0.4), -+ (1.0, 1.0, 0.4)] - sage: _make_color_list(8, ['blue', 'red'], randomize=True) - ['blue', 'blue', 'red', 'blue', 'red', 'red', 'red', 'blue'] - """ -diff --git a/src/sage/finance/time_series.pyx b/src/sage/finance/time_series.pyx -index 28779365df..3ab0282861 100644 ---- a/src/sage/finance/time_series.pyx -+++ b/src/sage/finance/time_series.pyx -@@ -111,8 +111,8 @@ cdef class TimeSeries: - - sage: import numpy - sage: v = numpy.array([[1,2], [3,4]], dtype=float); v -- array([[ 1., 2.], -- [ 3., 4.]]) -+ array([[1., 2.], -+ [3., 4.]]) - sage: finance.TimeSeries(v) - [1.0000, 2.0000, 3.0000, 4.0000] - sage: finance.TimeSeries(v[:,0]) -@@ -2100,14 +2100,14 @@ cdef class TimeSeries: - - sage: w[0] = 20 - sage: w -- array([ 20. , -3. , 4.5, -2. ]) -+ array([20. , -3. , 4.5, -2. ]) - sage: v - [20.0000, -3.0000, 4.5000, -2.0000] - - If you want a separate copy do not give the ``copy=False`` option. :: - - sage: z = v.numpy(); z -- array([ 20. , -3. , 4.5, -2. ]) -+ array([20. , -3. , 4.5, -2. ]) - sage: z[0] = -10 - sage: v - [20.0000, -3.0000, 4.5000, -2.0000] -diff --git a/src/sage/functions/hyperbolic.py b/src/sage/functions/hyperbolic.py -index aff552f450..7a6df931e7 100644 ---- a/src/sage/functions/hyperbolic.py -+++ b/src/sage/functions/hyperbolic.py -@@ -214,7 +214,7 @@ class Function_coth(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2, 5) - sage: coth(a) -- array([ 1.03731472, 1.00496982, 1.00067115]) -+ array([1.03731472, 1.00496982, 1.00067115]) - """ - return 1.0 / tanh(x) - -@@ -267,7 +267,7 @@ class Function_sech(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2, 5) - sage: sech(a) -- array([ 0.26580223, 0.09932793, 0.03661899]) -+ array([0.26580223, 0.09932793, 0.03661899]) - """ - return 1.0 / cosh(x) - -@@ -318,7 +318,7 @@ class Function_csch(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2, 5) - sage: csch(a) -- array([ 0.27572056, 0.09982157, 0.03664357]) -+ array([0.27572056, 0.09982157, 0.03664357]) - """ - return 1.0 / sinh(x) - -@@ -586,7 +586,7 @@ class Function_arccoth(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2,5) - sage: acoth(a) -- array([ 0.54930614, 0.34657359, 0.25541281]) -+ array([0.54930614, 0.34657359, 0.25541281]) - """ - return arctanh(1.0 / x) - -diff --git a/src/sage/functions/orthogonal_polys.py b/src/sage/functions/orthogonal_polys.py -index ed6365bef4..99b8b04dad 100644 ---- a/src/sage/functions/orthogonal_polys.py -+++ b/src/sage/functions/orthogonal_polys.py -@@ -810,12 +810,12 @@ class Func_chebyshev_T(ChebyshevFunction): - sage: z2 = numpy.array([[1,2],[1,2]]) - sage: z3 = numpy.array([1,2,3.]) - sage: chebyshev_T(1,z) -- array([ 1., 2.]) -+ array([1., 2.]) - sage: chebyshev_T(1,z2) -- array([[ 1., 2.], -- [ 1., 2.]]) -+ array([[1., 2.], -+ [1., 2.]]) - sage: chebyshev_T(1,z3) -- array([ 1., 2., 3.]) -+ array([1., 2., 3.]) - sage: chebyshev_T(z,0.1) - array([ 0.1 , -0.98]) - """ -@@ -1095,12 +1095,12 @@ class Func_chebyshev_U(ChebyshevFunction): - sage: z2 = numpy.array([[1,2],[1,2]]) - sage: z3 = numpy.array([1,2,3.]) - sage: chebyshev_U(1,z) -- array([ 2., 4.]) -+ array([2., 4.]) - sage: chebyshev_U(1,z2) -- array([[ 2., 4.], -- [ 2., 4.]]) -+ array([[2., 4.], -+ [2., 4.]]) - sage: chebyshev_U(1,z3) -- array([ 2., 4., 6.]) -+ array([2., 4., 6.]) - sage: chebyshev_U(z,0.1) - array([ 0.2 , -0.96]) - """ -diff --git a/src/sage/functions/other.py b/src/sage/functions/other.py -index 1883daa3e6..9885222817 100644 ---- a/src/sage/functions/other.py -+++ b/src/sage/functions/other.py -@@ -389,7 +389,7 @@ class Function_ceil(BuiltinFunction): - sage: import numpy - sage: a = numpy.linspace(0,2,6) - sage: ceil(a) -- array([ 0., 1., 1., 2., 2., 2.]) -+ array([0., 1., 1., 2., 2., 2.]) - - Test pickling:: - -@@ -553,7 +553,7 @@ class Function_floor(BuiltinFunction): - sage: import numpy - sage: a = numpy.linspace(0,2,6) - sage: floor(a) -- array([ 0., 0., 0., 1., 1., 2.]) -+ array([0., 0., 0., 1., 1., 2.]) - sage: floor(x)._sympy_() - floor(x) - -@@ -869,7 +869,7 @@ def sqrt(x, *args, **kwds): - sage: import numpy - sage: a = numpy.arange(2,5) - sage: sqrt(a) -- array([ 1.41421356, 1.73205081, 2. ]) -+ array([1.41421356, 1.73205081, 2. ]) - """ - if isinstance(x, float): - return math.sqrt(x) -diff --git a/src/sage/functions/spike_function.py b/src/sage/functions/spike_function.py -index 1e021de3fe..56635ca98f 100644 ---- a/src/sage/functions/spike_function.py -+++ b/src/sage/functions/spike_function.py -@@ -157,7 +157,7 @@ class SpikeFunction: - sage: S = spike_function([(-3,4),(-1,1),(2,3)]); S - A spike function with spikes at [-3.0, -1.0, 2.0] - sage: P = S.plot_fft_abs(8) -- sage: p = P[0]; p.ydata -+ sage: p = P[0]; p.ydata # abs tol 1e-8 - [5.0, 5.0, 3.367958691924177, 3.367958691924177, 4.123105625617661, 4.123105625617661, 4.759921664218055, 4.759921664218055] - """ - w = self.vector(samples = samples, xmin=xmin, xmax=xmax) -@@ -176,8 +176,8 @@ class SpikeFunction: - sage: S = spike_function([(-3,4),(-1,1),(2,3)]); S - A spike function with spikes at [-3.0, -1.0, 2.0] - sage: P = S.plot_fft_arg(8) -- sage: p = P[0]; p.ydata -- [0.0, 0.0, -0.211524990023434..., -0.211524990023434..., 0.244978663126864..., 0.244978663126864..., -0.149106180027477..., -0.149106180027477...] -+ sage: p = P[0]; p.ydata # abs tol 1e-8 -+ [0.0, 0.0, -0.211524990023434, -0.211524990023434, 0.244978663126864, 0.244978663126864, -0.149106180027477, -0.149106180027477] - """ - w = self.vector(samples = samples, xmin=xmin, xmax=xmax) - xmin, xmax = self._ranges(xmin, xmax) -diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py -index 501e7ff6b6..5f760912f0 100644 ---- a/src/sage/functions/trig.py -+++ b/src/sage/functions/trig.py -@@ -724,7 +724,7 @@ class Function_arccot(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2, 5) - sage: arccot(a) -- array([ 0.46364761, 0.32175055, 0.24497866]) -+ array([0.46364761, 0.32175055, 0.24497866]) - """ - return math.pi/2 - arctan(x) - -@@ -780,7 +780,7 @@ class Function_arccsc(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2, 5) - sage: arccsc(a) -- array([ 0.52359878, 0.33983691, 0.25268026]) -+ array([0.52359878, 0.33983691, 0.25268026]) - """ - return arcsin(1.0/x) - -@@ -838,7 +838,7 @@ class Function_arcsec(GinacFunction): - sage: import numpy - sage: a = numpy.arange(2, 5) - sage: arcsec(a) -- array([ 1.04719755, 1.23095942, 1.31811607]) -+ array([1.04719755, 1.23095942, 1.31811607]) - """ - return arccos(1.0/x) - -@@ -913,13 +913,13 @@ class Function_arctan2(GinacFunction): - sage: a = numpy.linspace(1, 3, 3) - sage: b = numpy.linspace(3, 6, 3) - sage: atan2(a, b) -- array([ 0.32175055, 0.41822433, 0.46364761]) -+ array([0.32175055, 0.41822433, 0.46364761]) - - sage: atan2(1,a) -- array([ 0.78539816, 0.46364761, 0.32175055]) -+ array([0.78539816, 0.46364761, 0.32175055]) - - sage: atan2(a, 1) -- array([ 0.78539816, 1.10714872, 1.24904577]) -+ array([0.78539816, 1.10714872, 1.24904577]) - - TESTS:: - -diff --git a/src/sage/matrix/constructor.pyx b/src/sage/matrix/constructor.pyx -index 12136f1773..491bf22e62 100644 ---- a/src/sage/matrix/constructor.pyx -+++ b/src/sage/matrix/constructor.pyx -@@ -503,8 +503,8 @@ def matrix(*args, **kwds): - [7 8 9] - Full MatrixSpace of 3 by 3 dense matrices over Integer Ring - sage: n = matrix(QQ, 2, 2, [1, 1/2, 1/3, 1/4]).numpy(); n -- array([[ 1. , 0.5 ], -- [ 0.33333333, 0.25 ]]) -+ array([[1. , 0.5 ], -+ [0.33333333, 0.25 ]]) - sage: matrix(QQ, n) - [ 1 1/2] - [1/3 1/4] -diff --git a/src/sage/matrix/matrix_double_dense.pyx b/src/sage/matrix/matrix_double_dense.pyx -index 66e54a79a4..0498334f4b 100644 ---- a/src/sage/matrix/matrix_double_dense.pyx -+++ b/src/sage/matrix/matrix_double_dense.pyx -@@ -606,6 +606,9 @@ cdef class Matrix_double_dense(Matrix_dense): - [ 3.0 + 9.0*I 4.0 + 16.0*I 5.0 + 25.0*I] - [6.0 + 36.0*I 7.0 + 49.0*I 8.0 + 64.0*I] - sage: B.condition() -+ doctest:warning -+ ... -+ ComplexWarning: Casting complex values to real discards the imaginary part - 203.851798... - sage: B.condition(p='frob') - 203.851798... -@@ -654,9 +657,7 @@ cdef class Matrix_double_dense(Matrix_dense): - True - sage: B = A.change_ring(CDF) - sage: B.condition() -- Traceback (most recent call last): -- ... -- LinAlgError: Singular matrix -+ +Infinity - - Improper values of ``p`` are caught. :: - -@@ -2519,7 +2520,7 @@ cdef class Matrix_double_dense(Matrix_dense): - sage: P.is_unitary(algorithm='orthonormal') - Traceback (most recent call last): - ... -- ValueError: failed to create intent(cache|hide)|optional array-- must have defined dimensions but got (0,) -+ error: ((lwork==-1)||(lwork >= MAX(1,2*n))) failed for 3rd keyword lwork: zgees:lwork=0 - - TESTS:: - -@@ -3635,8 +3636,8 @@ cdef class Matrix_double_dense(Matrix_dense): - [0.0 1.0 2.0] - [3.0 4.0 5.0] - sage: m.numpy() -- array([[ 0., 1., 2.], -- [ 3., 4., 5.]]) -+ array([[0., 1., 2.], -+ [3., 4., 5.]]) - - Alternatively, numpy automatically calls this function (via - the magic :meth:`__array__` method) to convert Sage matrices -@@ -3647,16 +3648,16 @@ cdef class Matrix_double_dense(Matrix_dense): - [0.0 1.0 2.0] - [3.0 4.0 5.0] - sage: numpy.array(m) -- array([[ 0., 1., 2.], -- [ 3., 4., 5.]]) -+ array([[0., 1., 2.], -+ [3., 4., 5.]]) - sage: numpy.array(m).dtype - dtype('float64') - sage: m = matrix(CDF, 2, range(6)); m - [0.0 1.0 2.0] - [3.0 4.0 5.0] - sage: numpy.array(m) -- array([[ 0.+0.j, 1.+0.j, 2.+0.j], -- [ 3.+0.j, 4.+0.j, 5.+0.j]]) -+ array([[0.+0.j, 1.+0.j, 2.+0.j], -+ [3.+0.j, 4.+0.j, 5.+0.j]]) - sage: numpy.array(m).dtype - dtype('complex128') - -diff --git a/src/sage/matrix/special.py b/src/sage/matrix/special.py -index ccbd208810..c3f9a65093 100644 ---- a/src/sage/matrix/special.py -+++ b/src/sage/matrix/special.py -@@ -706,7 +706,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True): - - sage: import numpy - sage: entries = numpy.array([1.2, 5.6]); entries -- array([ 1.2, 5.6]) -+ array([1.2, 5.6]) - sage: A = diagonal_matrix(3, entries); A - [1.2 0.0 0.0] - [0.0 5.6 0.0] -@@ -716,7 +716,7 @@ def diagonal_matrix(arg0=None, arg1=None, arg2=None, sparse=True): - - sage: j = numpy.complex(0,1) - sage: entries = numpy.array([2.0+j, 8.1, 3.4+2.6*j]); entries -- array([ 2.0+1.j , 8.1+0.j , 3.4+2.6j]) -+ array([2. +1.j , 8.1+0.j , 3.4+2.6j]) - sage: A = diagonal_matrix(entries); A - [2.0 + 1.0*I 0.0 0.0] - [ 0.0 8.1 0.0] -diff --git a/src/sage/modules/free_module_element.pyx b/src/sage/modules/free_module_element.pyx -index 37d92c1282..955d083b34 100644 ---- a/src/sage/modules/free_module_element.pyx -+++ b/src/sage/modules/free_module_element.pyx -@@ -988,7 +988,7 @@ cdef class FreeModuleElement(Vector): # abstract base class - sage: v.numpy() - array([1, 2, 5/6], dtype=object) - sage: v.numpy(dtype=float) -- array([ 1. , 2. , 0.83333333]) -+ array([1. , 2. , 0.83333333]) - sage: v.numpy(dtype=int) - array([1, 2, 0]) - sage: import numpy -@@ -999,7 +999,7 @@ cdef class FreeModuleElement(Vector): # abstract base class - be more efficient but may have unintended consequences:: - - sage: v.numpy(dtype=None) -- array([ 1. , 2. , 0.83333333]) -+ array([1. , 2. , 0.83333333]) - - sage: w = vector(ZZ, [0, 1, 2^63 -1]); w - (0, 1, 9223372036854775807) -diff --git a/src/sage/modules/vector_double_dense.pyx b/src/sage/modules/vector_double_dense.pyx -index 39fc2970de..2badf98284 100644 ---- a/src/sage/modules/vector_double_dense.pyx -+++ b/src/sage/modules/vector_double_dense.pyx -@@ -807,13 +807,13 @@ cdef class Vector_double_dense(FreeModuleElement): - - sage: v = vector(CDF,4,range(4)) - sage: v.numpy() -- array([ 0.+0.j, 1.+0.j, 2.+0.j, 3.+0.j]) -+ array([0.+0.j, 1.+0.j, 2.+0.j, 3.+0.j]) - sage: v = vector(CDF,0) - sage: v.numpy() - array([], dtype=complex128) - sage: v = vector(RDF,4,range(4)) - sage: v.numpy() -- array([ 0., 1., 2., 3.]) -+ array([0., 1., 2., 3.]) - sage: v = vector(RDF,0) - sage: v.numpy() - array([], dtype=float64) -@@ -823,11 +823,11 @@ cdef class Vector_double_dense(FreeModuleElement): - sage: import numpy - sage: v = vector(CDF, 3, range(3)) - sage: v.numpy() -- array([ 0.+0.j, 1.+0.j, 2.+0.j]) -+ array([0.+0.j, 1.+0.j, 2.+0.j]) - sage: v.numpy(dtype=numpy.float64) -- array([ 0., 1., 2.]) -+ array([0., 1., 2.]) - sage: v.numpy(dtype=numpy.float32) -- array([ 0., 1., 2.], dtype=float32) -+ array([0., 1., 2.], dtype=float32) - """ - if dtype is None or dtype is self._vector_numpy.dtype: - from copy import copy -diff --git a/src/sage/plot/complex_plot.pyx b/src/sage/plot/complex_plot.pyx -index ad9693da62..758fb709b7 100644 ---- a/src/sage/plot/complex_plot.pyx -+++ b/src/sage/plot/complex_plot.pyx -@@ -61,9 +61,9 @@ cdef inline double mag_to_lightness(double r): - - sage: from sage.plot.complex_plot import complex_to_rgb - sage: complex_to_rgb([[0, 1, 10]]) -- array([[[ 0. , 0. , 0. ], -- [ 0.77172568, 0. , 0. ], -- [ 1. , 0.22134776, 0.22134776]]]) -+ array([[[0. , 0. , 0. ], -+ [0.77172568, 0. , 0. ], -+ [1. , 0.22134776, 0.22134776]]]) - """ - return atan(log(sqrt(r)+1)) * (4/PI) - 1 - -@@ -82,13 +82,13 @@ def complex_to_rgb(z_values): - - sage: from sage.plot.complex_plot import complex_to_rgb - sage: complex_to_rgb([[0, 1, 1000]]) -- array([[[ 0. , 0. , 0. ], -- [ 0.77172568, 0. , 0. ], -- [ 1. , 0.64421177, 0.64421177]]]) -+ array([[[0. , 0. , 0. ], -+ [0.77172568, 0. , 0. ], -+ [1. , 0.64421177, 0.64421177]]]) - sage: complex_to_rgb([[0, 1j, 1000j]]) -- array([[[ 0. , 0. , 0. ], -- [ 0.38586284, 0.77172568, 0. ], -- [ 0.82210588, 1. , 0.64421177]]]) -+ array([[[0. , 0. , 0. ], -+ [0.38586284, 0.77172568, 0. ], -+ [0.82210588, 1. , 0.64421177]]]) - """ - import numpy - cdef unsigned int i, j, imax, jmax -diff --git a/src/sage/plot/histogram.py b/src/sage/plot/histogram.py -index 5d28473731..fc4b2046c0 100644 ---- a/src/sage/plot/histogram.py -+++ b/src/sage/plot/histogram.py -@@ -53,10 +53,17 @@ class Histogram(GraphicPrimitive): - """ - import numpy as np - self.datalist=np.asarray(datalist,dtype=float) -+ if 'normed' in options: -+ from sage.misc.superseded import deprecation -+ deprecation(25260, "the 'normed' option is deprecated. Use 'density' instead.") - if 'linestyle' in options: - from sage.plot.misc import get_matplotlib_linestyle - options['linestyle'] = get_matplotlib_linestyle( - options['linestyle'], return_type='long') -+ if options.get('range', None): -+ # numpy.histogram performs type checks on "range" so this must be -+ # actual floats -+ options['range'] = [float(x) for x in options['range']] - GraphicPrimitive.__init__(self, options) - - def get_minmax_data(self): -@@ -80,10 +87,14 @@ class Histogram(GraphicPrimitive): - {'xmax': 4.0, 'xmin': 0, 'ymax': 2, 'ymin': 0} - - TESTS:: -- - sage: h = histogram([10,3,5], normed=True)[0] -- sage: h.get_minmax_data() # rel tol 1e-15 -- {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.4761904761904765, 'ymin': 0} -+ doctest:warning...: -+ DeprecationWarning: the 'normed' option is deprecated. Use 'density' instead. -+ See https://trac.sagemath.org/25260 for details. -+ sage: h.get_minmax_data() -+ doctest:warning ...: -+ VisibleDeprecationWarning: Passing `normed=True` on non-uniform bins has always been broken, and computes neither the probability density function nor the probability mass function. The result is only correct if the bins are uniform, when density=True will produce the same result anyway. The argument will be removed in a future version of numpy. -+ {'xmax': 10.0, 'xmin': 3.0, 'ymax': 0.476190476190..., 'ymin': 0} - """ - import numpy - -@@ -152,7 +163,7 @@ class Histogram(GraphicPrimitive): - 'rwidth': 'The relative width of the bars as a fraction of the bin width', - 'cumulative': '(True or False) If True, then a histogram is computed in which each bin gives the counts in that bin plus all bins for smaller values. Negative values give a reversed direction of accumulation.', - 'range': 'A list [min, max] which define the range of the histogram. Values outside of this range are treated as outliers and omitted from counts.', -- 'normed': 'Deprecated alias for density', -+ 'normed': 'Deprecated. Use density instead.', - 'density': '(True or False) If True, the counts are normalized to form a probability density. (n/(len(x)*dbin)', - 'weights': 'A sequence of weights the same length as the data list. If supplied, then each value contributes its associated weight to the bin count.', - 'stacked': '(True or False) If True, multiple data are stacked on top of each other.', -@@ -199,7 +210,7 @@ class Histogram(GraphicPrimitive): - subplot.hist(self.datalist.transpose(), **options) - - --@options(aspect_ratio='automatic',align='mid', weights=None, range=None, bins=10, edgecolor='black') -+@options(aspect_ratio='automatic', align='mid', weights=None, range=None, bins=10, edgecolor='black') - def histogram(datalist, **options): - """ - Computes and draws the histogram for list(s) of numerical data. -@@ -231,8 +242,9 @@ def histogram(datalist, **options): - - ``linewidth`` -- (float) width of the lines defining the bars - - ``linestyle`` -- (default: 'solid') Style of the line. One of 'solid' - or '-', 'dashed' or '--', 'dotted' or ':', 'dashdot' or '-.' -- - ``density`` -- (boolean - default: False) If True, the counts are -- normalized to form a probability density. -+ - ``density`` -- (boolean - default: False) If True, the result is the -+ value of the probability density function at the bin, normalized such -+ that the integral over the range is 1. - - ``range`` -- A list [min, max] which define the range of the - histogram. Values outside of this range are treated as outliers and - omitted from counts -diff --git a/src/sage/plot/line.py b/src/sage/plot/line.py -index 23f5e61446..3b1b51d7cf 100644 ---- a/src/sage/plot/line.py -+++ b/src/sage/plot/line.py -@@ -502,14 +502,12 @@ def line2d(points, **options): - from sage.plot.all import Graphics - from sage.plot.plot import xydata_from_point_list - from sage.rings.all import CC, CDF -+ points = list(points) # make sure points is a python list - if points in CC or points in CDF: - pass - else: -- try: -- if not points: -- return Graphics() -- except ValueError: # numpy raises a ValueError if not empty -- pass -+ if len(points) == 0: -+ return Graphics() - xdata, ydata = xydata_from_point_list(points) - g = Graphics() - g._set_extra_kwds(Graphics._extract_kwds_for_show(options)) -diff --git a/src/sage/plot/plot_field.py b/src/sage/plot/plot_field.py -index 0025098a8d..23c80902f3 100644 ---- a/src/sage/plot/plot_field.py -+++ b/src/sage/plot/plot_field.py -@@ -49,9 +49,10 @@ class PlotField(GraphicPrimitive): - sage: r.xpos_array - [0.0, 0.0, 1.0, 1.0] - sage: r.yvec_array -- masked_array(data = [0.0 0.70710678118... 0.70710678118... 0.89442719...], -- mask = [False False False False], -- fill_value = 1e+20) -+ masked_array(data=[0.0, 0.70710678118..., 0.70710678118..., -+ 0.89442719...], -+ mask=[False, False, False, False], -+ fill_value=1e+20) - - TESTS: - -diff --git a/src/sage/plot/streamline_plot.py b/src/sage/plot/streamline_plot.py -index f3da57c370..3806f4b32f 100644 ---- a/src/sage/plot/streamline_plot.py -+++ b/src/sage/plot/streamline_plot.py -@@ -38,16 +38,14 @@ class StreamlinePlot(GraphicPrimitive): - sage: r.options()['plot_points'] - 2 - sage: r.xpos_array -- array([ 0., 1.]) -+ array([0., 1.]) - sage: r.yvec_array -- masked_array(data = -- [[1.0 1.0] -- [0.5403023058681398 0.5403023058681398]], -- mask = -- [[False False] -- [False False]], -- fill_value = 1e+20) -- <BLANKLINE> -+ masked_array( -+ data=[[1.0, 1.0], -+ [0.5403023058681398, 0.5403023058681398]], -+ mask=[[False, False], -+ [False, False]], -+ fill_value=1e+20) - - TESTS: - -diff --git a/src/sage/probability/probability_distribution.pyx b/src/sage/probability/probability_distribution.pyx -index 1b119e323f..3290b00695 100644 ---- a/src/sage/probability/probability_distribution.pyx -+++ b/src/sage/probability/probability_distribution.pyx -@@ -130,7 +130,17 @@ cdef class ProbabilityDistribution: - 0.0, - 1.4650000000000003] - sage: b -- [0.0, 0.20000000000000001, 0.40000000000000002, 0.60000000000000009, 0.80000000000000004, 1.0, 1.2000000000000002, 1.4000000000000001, 1.6000000000000001, 1.8, 2.0] -+ [0.0, -+ 0.2, -+ 0.4, -+ 0.6000000000000001, -+ 0.8, -+ 1.0, -+ 1.2000000000000002, -+ 1.4000000000000001, -+ 1.6, -+ 1.8, -+ 2.0] - """ - import pylab - l = [float(self.get_random_element()) for _ in range(num_samples)] -diff --git a/src/sage/rings/rational.pyx b/src/sage/rings/rational.pyx -index 12ca1b222b..9bad7dae0c 100644 ---- a/src/sage/rings/rational.pyx -+++ b/src/sage/rings/rational.pyx -@@ -1041,7 +1041,7 @@ cdef class Rational(sage.structure.element.FieldElement): - dtype('O') - - sage: numpy.array([1, 1/2, 3/4]) -- array([ 1. , 0.5 , 0.75]) -+ array([1. , 0.5 , 0.75]) - """ - if mpz_cmp_ui(mpq_denref(self.value), 1) == 0: - if mpz_fits_slong_p(mpq_numref(self.value)): -diff --git a/src/sage/rings/real_mpfr.pyx b/src/sage/rings/real_mpfr.pyx -index 9b90c8833e..1ce05b937d 100644 ---- a/src/sage/rings/real_mpfr.pyx -+++ b/src/sage/rings/real_mpfr.pyx -@@ -1439,7 +1439,7 @@ cdef class RealNumber(sage.structure.element.RingElement): - - sage: import numpy - sage: numpy.arange(10.0) -- array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]) -+ array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]) - sage: numpy.array([1.0, 1.1, 1.2]).dtype - dtype('float64') - sage: numpy.array([1.000000000000000000000000000000000000]).dtype -diff --git a/src/sage/schemes/elliptic_curves/height.py b/src/sage/schemes/elliptic_curves/height.py -index de31fe9883..7a33ea6f5b 100644 ---- a/src/sage/schemes/elliptic_curves/height.py -+++ b/src/sage/schemes/elliptic_curves/height.py -@@ -1627,18 +1627,18 @@ class EllipticCurveCanonicalHeight: - even:: - - sage: H.wp_on_grid(v,4) -- array([[ 25.43920182, 5.28760943, 5.28760943, 25.43920182], -- [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], -- [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], -- [ 25.43920182, 5.28760943, 5.28760943, 25.43920182]]) -+ array([[25.43920182, 5.28760943, 5.28760943, 25.43920182], -+ [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], -+ [ 6.05099485, 1.83757786, 1.83757786, 6.05099485], -+ [25.43920182, 5.28760943, 5.28760943, 25.43920182]]) - - The array of values on the half-grid:: - - sage: H.wp_on_grid(v,4,True) -- array([[ 25.43920182, 5.28760943], -- [ 6.05099485, 1.83757786], -- [ 6.05099485, 1.83757786], -- [ 25.43920182, 5.28760943]]) -+ array([[25.43920182, 5.28760943], -+ [ 6.05099485, 1.83757786], -+ [ 6.05099485, 1.83757786], -+ [25.43920182, 5.28760943]]) - """ - tau = self.tau(v) - fk, err = self.fk_intervals(v, 15, CDF) -diff --git a/src/sage/symbolic/ring.pyx b/src/sage/symbolic/ring.pyx -index 9da38002e8..d61e74bf82 100644 ---- a/src/sage/symbolic/ring.pyx -+++ b/src/sage/symbolic/ring.pyx -@@ -1136,7 +1136,7 @@ cdef class NumpyToSRMorphism(Morphism): - sage: cos(numpy.int('2')) - cos(2) - sage: numpy.cos(numpy.int('2')) -- -0.41614683654714241 -+ -0.4161468365471424 - """ - cdef _intermediate_ring - diff --git a/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix b/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix index 184eaf29bdd3..1bfe02f50df1 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/python-openid.nix @@ -20,15 +20,13 @@ buildPythonPackage rec { }; propagatedBuildInputs = [ - django - twill 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 ]; + checkInputs = [ nose django twill ]; checkPhase = '' nosetests ''; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix index c071f8945506..8fd69f62171a 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix @@ -14,8 +14,7 @@ , python3 , pkg-config , pari -, gap-libgap-compatible -, libgap +, gap , ecl , maxima-ecl , singular @@ -70,13 +69,13 @@ let binutils.bintools pkg-config pari - gap-libgap-compatible - libgap + 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 @@ -117,7 +116,7 @@ writeTextFile rec { # set dependent vars, like JUPYTER_CONFIG_DIR source "${sagelib.src}/src/bin/sage-env" - export PATH="${runtimepath}:$orig_path" # sage-env messes with PATH + export PATH="$RUNTIMEPATH_PREFIX:${runtimepath}:$orig_path" # sage-env messes with PATH export SAGE_LOGS="$TMPDIR/sage-logs" export SAGE_DOC="''${SAGE_DOC_OVERRIDE:-doc-placeholder}" @@ -132,7 +131,7 @@ writeTextFile rec { export LDFLAGS='${ lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [ flint - libgap + gap glpk gmp mpfr @@ -152,7 +151,7 @@ writeTextFile rec { gmp.dev glpk flint - libgap + gap pynac mpfr.dev ]) diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix index 5dc73e26a596..5bdd53b37e4f 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix @@ -9,14 +9,14 @@ # all get the same sources with the same patches applied. stdenv.mkDerivation rec { - version = "8.4"; + version = "8.6"; name = "sage-src-${version}"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "0gips1hagiz9m7s21bg5as8hrrm2x5k47h1bsq0pc46iplfwmv2d"; + sha256 = "1vs3pbgbqpg0qnwr018bqsdmm7crgjp310cx8zwh7za3mv1cw5j3"; }; # Patches needed because of particularities of nix or the way this is packaged. @@ -46,6 +46,9 @@ stdenv.mkDerivation rec { # 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 ]; # Patches needed because of package updates. We could just pin the versions of @@ -58,16 +61,18 @@ stdenv.mkDerivation rec { # 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, ...}@args: ( + fetchSageDiff = { base, rev, name ? "sage-diff-${base}-${rev}.patch", ...}@args: ( fetchpatch ({ - url = "https://git.sagemath.org/sage.git/patch?id2=${base}&id=${rev}"; + inherit name; + url = "https://git.sagemath.org/sage.git/rawdiff?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/*" ]; + 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 { @@ -76,45 +81,15 @@ stdenv.mkDerivation rec { stripLen = 1; }) - # https://trac.sagemath.org/ticket/25260 - ./patches/numpy-1.15.1.patch - # https://trac.sagemath.org/ticket/26315 ./patches/giac-1.5.0.patch - # needed for ntl update - # https://trac.sagemath.org/ticket/25532 - (fetchpatch { - name = "lcalc-c++11.patch"; - url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa"; - sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb"; - }) - - (fetchpatch { - name = "cython-0.29.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=f77de1d0e7f90ee12761140500cb8cbbb789ab20"; - sha256 = "14wrpy8jgbnpza1j8a2nx8y2r946y82pll1fv3cn6gpfmm6640l3"; - }) - # https://trac.sagemath.org/ticket/26360 - (fetchpatch { - name = "arb-2.15.1.patch"; - url = "https://git.sagemath.org/sage.git/patch/?id=30cc778d46579bd0c7537ed33e8d7a4f40fd5c31"; - sha256 = "13vc2q799dh745sm59xjjabllfj0sfjzcacf8k59kwj04x755d30"; - }) - - # https://trac.sagemath.org/ticket/26326 - # needs to be split because there is a merge commit in between - (fetchSageDiff { - name = "networkx-2.2-1.patch"; - base = "8.4"; - rev = "68f5ad068184745b38ba6716bf967c8c956c52c5"; - sha256 = "112b5ywdqgyzgvql2jj5ss8la9i8rgnrzs8vigsfzg4shrcgh9p6"; - }) + # https://trac.sagemath.org/ticket/26442 (fetchSageDiff { - name = "networkx-2.2-2.patch"; - base = "626485bbe5f33bf143d6dfba4de9c242f757f59b~1"; - rev = "db10d327ade93711da735a599a67580524e6f7b4"; - sha256 = "09v87id25fa5r9snfn4mv79syhc77jxfawj5aizmdpwdmpgxjk1f"; + name = "cypari2-2.0.3.patch"; + base = "8.6.rc1"; + rev = "cd62d45bcef93fb4f7ed62609a46135e6de07051"; + sha256 = "08l2b9w0rn1zrha6188j72f7737xs126gkgmydjd31baa6367np2"; }) ]; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix index 1f400db18fcb..12433e12fe90 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-tests.nix @@ -3,7 +3,12 @@ , sage-with-env , makeWrapper , files ? null # "null" means run all tests -, longTests ? true # run tests marked as "long time" +, 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: @@ -14,6 +19,7 @@ let 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}/${relpath}"; # paths need to be absolute testFileList = lib.concatStringsSep " " (map relpathToArg files); in @@ -45,7 +51,7 @@ stdenv.mkDerivation rec { export HOME="$TMPDIR/sage-home" mkdir -p "$HOME" - # "--long" tests are in the order of 1h, without "--long" its 1/2h - "sage" -t --timeout=0 --nthreads "$NIX_BUILD_CORES" --optional=sage ${patienceSpecifier} ${testArgs} + echo "Running sage tests with arguments ${timeSpecifier} ${patienceSpecifier} ${testArgs}" + "sage" -t --nthreads "$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 index c5db392f1036..18060f342a92 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix @@ -6,8 +6,7 @@ , pkg-config , three , singular -, libgap -, gap-libgap-compatible +, gap , giac , maxima-ecl , pari @@ -35,8 +34,7 @@ let three pynac giac - libgap - gap-libgap-compatible + gap pari gmp gfan diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage.nix b/nixpkgs/pkgs/applications/science/math/sage/sage.nix index ac255643a348..541b9cb36dc2 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage.nix @@ -54,6 +54,7 @@ stdenv.mkDerivation rec { 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; diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix index 03b1ecd2c0b7..a754a2745098 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix @@ -20,7 +20,7 @@ , jinja2 , lcalc , lrcalc -, libgap +, gap , linbox , m4ri , m4rie @@ -88,7 +88,7 @@ buildPythonPackage rec { glpk gsl lcalc - libgap + gap libmpc linbox lrcalc |