From 690b66e1ebb18db96c200160a73651dfd4f14e24 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Wed, 27 Jun 2018 21:57:54 -0700 Subject: gnucash: 3.1-1 -> 3.2 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/gnucash/versions. These checks were done: - built on NixOS - /nix/store/29l8ziil4znyr07dm7f8ki893bqfzqm5-gnucash-3.2/bin/gnc-fq-check passed the binary check. - /nix/store/29l8ziil4znyr07dm7f8ki893bqfzqm5-gnucash-3.2/bin/gnc-fq-helper passed the binary check. - /nix/store/29l8ziil4znyr07dm7f8ki893bqfzqm5-gnucash-3.2/bin/gnc-fq-dump passed the binary check. - /nix/store/29l8ziil4znyr07dm7f8ki893bqfzqm5-gnucash-3.2/bin/gnucash passed the binary check. - /nix/store/29l8ziil4znyr07dm7f8ki893bqfzqm5-gnucash-3.2/bin/.gnucash-wrapped passed the binary check. - 5 of 5 passed binary check by having a zero exit code. - 0 of 5 passed binary check by having the new version present in output. - found 3.2 with grep in /nix/store/29l8ziil4znyr07dm7f8ki893bqfzqm5-gnucash-3.2 - directory tree listing: https://gist.github.com/c6f09b837c81684d4febbc1c369ae53d - du listing: https://gist.github.com/f9960cc6c0b43d70986bb1b51c109a68 --- pkgs/applications/office/gnucash/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/office/gnucash/default.nix b/pkgs/applications/office/gnucash/default.nix index c09d0b3aa39b..63fda1e0e8be 100644 --- a/pkgs/applications/office/gnucash/default.nix +++ b/pkgs/applications/office/gnucash/default.nix @@ -25,11 +25,11 @@ in stdenv.mkDerivation rec { name = "gnucash-${version}"; - version = "3.1-1"; + version = "3.2"; src = fetchurl { url = "mirror://sourceforge/gnucash/${name}.tar.bz2"; - sha256 = "0qfjpmr6hnr0v7l2fi00rilnlyan4kqiyygyidxlpdxqqg76dvx1"; + sha256 = "0li4b6pvlahgh5n9v91yxfgm972a1kky80xw3q1ggl4f2h6b1rb3"; }; nativeBuildInputs = [ pkgconfig makeWrapper cmake gtest ]; -- cgit 1.4.1 From 314eb884ecd22803db4149936a2c95b48ad2f60b Mon Sep 17 00:00:00 2001 From: Théo Zimmermann Date: Fri, 29 Jun 2018 11:10:31 +0200 Subject: coq_8_8: 8.8.0 -> 8.8.1 --- pkgs/applications/science/logic/coq/default.nix | 1 + pkgs/top-level/coq-packages.nix | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 2b35c91d10c4..dbfec66789a3 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -23,6 +23,7 @@ let "8.7.1" = "0gjn59jkbxwrihk8fx9d823wjyjh5m9gvj9l31nv6z6bcqhgdqi8"; "8.7.2" = "0a0657xby8wdq4aqb2xsxp3n7pmc2w4yxjmrb2l4kccs1aqvaj4w"; "8.8.0" = "13a4fka22hdxsjk11mgjb9ffzplfxyxp1sg5v1c8nk1grxlscgw8"; + "8.8.1" = "1hlf58gwazywbmfa48219amid38vqdl94yz21i11b4map6jfwhbk"; }."${version}"; coq-version = builtins.substring 0 3 version; camlp5 = ocamlPackages.camlp5_strict; diff --git a/pkgs/top-level/coq-packages.nix b/pkgs/top-level/coq-packages.nix index 2bc5671e9874..de9b6d38b74f 100644 --- a/pkgs/top-level/coq-packages.nix +++ b/pkgs/top-level/coq-packages.nix @@ -74,7 +74,7 @@ in rec { version = "8.7.2"; }; coq_8_8 = callPackage ../applications/science/logic/coq { - version = "8.8.0"; + version = "8.8.1"; }; coqPackages_8_5 = mkCoqPackages coq_8_5; -- cgit 1.4.1 From 6aa82d647d8596760a51e8e21f848b7d9c5a1adc Mon Sep 17 00:00:00 2001 From: Alexander Krupenkin Date: Fri, 29 Jun 2018 12:53:56 +0300 Subject: parity: 1.10.7 -> 1.10.8 --- pkgs/applications/altcoins/parity/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/altcoins/parity/default.nix b/pkgs/applications/altcoins/parity/default.nix index 707889b23eea..4ee13665d1be 100644 --- a/pkgs/applications/altcoins/parity/default.nix +++ b/pkgs/applications/altcoins/parity/default.nix @@ -1,7 +1,7 @@ let - version = "1.10.7"; - sha256 = "0syhvr4n9zyxhx20xln7sf70ljzj6ab36xjz4710ivnwwz2pjajf"; - cargoSha256 = "0zwk8xv71s7xkwvssh27772qfb23yhq5jlcny617qik6bwpcdh6b"; + version = "1.10.8"; + sha256 = "0q6blsbxn48afqf3cmxvmdlyzvf0cpqcymsjbsk8nyx0zxzf1dpk"; + cargoSha256 = "0rzhabyhprmcg0cdmibbb8zgqf6z4izsdq8m060mppkkv675x0lf"; patches = [ ./patches/vendored-sources-1.10.patch ]; in import ./parity.nix { inherit version sha256 cargoSha256 patches; } -- cgit 1.4.1 From 12cf9f7edad3e110900de037f4aa8cb046ec9029 Mon Sep 17 00:00:00 2001 From: Robert Schütz Date: Fri, 29 Jun 2018 18:57:30 +0200 Subject: khal: pin python-dateutil==2.6.1 --- pkgs/applications/misc/khal/default.nix | 25 ++++++++++++++++++++----- 1 file changed, 20 insertions(+), 5 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/khal/default.nix b/pkgs/applications/misc/khal/default.nix index 60f6deefb010..ede85aeada5a 100644 --- a/pkgs/applications/misc/khal/default.nix +++ b/pkgs/applications/misc/khal/default.nix @@ -1,8 +1,22 @@ -{ stdenv, pkgs, python3Packages }: +{ stdenv, pkgs, python3 }: -with python3Packages; +let + python = python3.override { + packageOverrides = self: super: { -buildPythonApplication rec { + # https://github.com/pimutils/khal/issues/780 + python-dateutil = super.python-dateutil.overridePythonAttrs (oldAttrs: rec { + version = "2.6.1"; + src = oldAttrs.src.override { + inherit version; + sha256 = "891c38b2a02f5bb1be3e4793866c8df49c7d19baabf9c1bad62547e0b4866aca"; + }; + }); + + }; + }; + +in with python.pkgs; buildPythonApplication rec { pname = "khal"; version = "0.9.9"; @@ -29,10 +43,11 @@ buildPythonApplication rec { pkginfo freezegun ]; - buildInputs = [ setuptools_scm pytest pkgs.glibcLocales ]; + nativeBuildInputs = [ setuptools_scm pkgs.glibcLocales ]; + checkInputs = [ pytest ]; checkPhase = '' - # py.test + py.test ''; meta = with stdenv.lib; { -- cgit 1.4.1 From 701ddacfb17e9c2f1c0577ef83059c34f81683ad Mon Sep 17 00:00:00 2001 From: Johannes Frankenau Date: Fri, 29 Jun 2018 20:26:52 +0000 Subject: streamlink: 0.13.0 -> 0.14.2 (#42625) --- pkgs/applications/video/streamlink/default.nix | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/video/streamlink/default.nix b/pkgs/applications/video/streamlink/default.nix index 6885caa7d60e..491e6fcd1648 100644 --- a/pkgs/applications/video/streamlink/default.nix +++ b/pkgs/applications/video/streamlink/default.nix @@ -1,22 +1,16 @@ { stdenv, pythonPackages, fetchFromGitHub, rtmpdump, ffmpeg }: pythonPackages.buildPythonApplication rec { - version = "0.13.0"; + version = "0.14.2"; name = "streamlink-${version}"; src = fetchFromGitHub { owner = "streamlink"; repo = "streamlink"; rev = "${version}"; - sha256 = "17i5j5a69d28abg13md2r2ycxgmd5h1pjy0pgca1zcqaqfq4v05x"; + sha256 = "1njwfy1h8a9n5z6crrfnknlw4ys0bap2jam6ga6njgkd10aly9qr"; }; - postPatch = '' - # Fix failing test. This can be removed after version 0.13.0, see: - # https://github.com/streamlink/streamlink/commit/a27e1a2d8eec6eb23c6e1dc280c6afc1cd0b5b32 - substituteInPlace tests/test_plugin.py --replace "lambda: datetime" "datetime" - ''; - checkInputs = with pythonPackages; [ pytest mock requests-mock freezegun ]; propagatedBuildInputs = (with pythonPackages; [ pycryptodome requests iso-639 iso3166 websocket_client isodate ]) ++ [ rtmpdump ffmpeg ]; -- cgit 1.4.1 From a046d8c873e1f792364a4a9e4e5600613b224003 Mon Sep 17 00:00:00 2001 From: obadz Date: Fri, 29 Jun 2018 21:24:04 +0100 Subject: citrix-receiver: override libidn 1.35 back to 1.34 just for this binary pkg --- .../networking/remote/citrix-receiver/default.nix | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/networking/remote/citrix-receiver/default.nix b/pkgs/applications/networking/remote/citrix-receiver/default.nix index 9190deb990e9..26cc0cb6e707 100644 --- a/pkgs/applications/networking/remote/citrix-receiver/default.nix +++ b/pkgs/applications/networking/remote/citrix-receiver/default.nix @@ -1,5 +1,6 @@ { stdenv , lib +, fetchurl , requireFile , makeWrapper , libredirect @@ -27,6 +28,16 @@ }: let + # In 56e1bdc7f9c (libidn: 1.34 -> 1.35), libidn.so.11 became libidn.so.12. + # Citrix looks for the former so we build version 1.34 to please the binary + libidn_134 = libidn.overrideDerivation (_: rec { + name = "libidn-1.34"; + src = fetchurl { + url = "mirror://gnu/libidn/${name}.tar.gz"; + sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p"; + }; + }); + versionInfo = { "13.4.0" = rec { major = "13"; @@ -160,7 +171,7 @@ let xorg.libXinerama xorg.libXfixes libpng12 - libidn + libidn_134 zlib gtk_engines freetype -- cgit 1.4.1 From 79b33a2c0074e35460c3fffb8e2378e033a9a70b Mon Sep 17 00:00:00 2001 From: obadz Date: Fri, 29 Jun 2018 21:26:24 +0100 Subject: citrix-receiver: 13.9.1 -> 13.10.0 --- .../networking/remote/citrix-receiver/default.nix | 13 ++++++++++++- pkgs/top-level/all-packages.nix | 15 ++++++++------- 2 files changed, 20 insertions(+), 8 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/networking/remote/citrix-receiver/default.nix b/pkgs/applications/networking/remote/citrix-receiver/default.nix index 26cc0cb6e707..489de974aaaf 100644 --- a/pkgs/applications/networking/remote/citrix-receiver/default.nix +++ b/pkgs/applications/networking/remote/citrix-receiver/default.nix @@ -24,7 +24,7 @@ , alsaLib , libidn , zlib -, version ? "13.9.1" +, version ? "13.10.0" }: let @@ -113,6 +113,17 @@ let x86hash = "A93E9770FD10FDD3586A2D47448559EA037265717A7000B9BD2B1DCCE7B0A483"; x64suffix = "6"; x86suffix = "6"; + homepage = https://www.citrix.com/downloads/citrix-receiver/legacy-receiver-for-linux/receiver-for-linux-1391.html; + }; + + "13.10.0" = { + major = "13"; + minor = "10"; + patch = "0"; + x64hash = "7025688C7891374CDA11C92FC0BA2FA8151AEB4C4D31589AD18747FAE943F6EA"; + x86hash = "2DCA3C8EDED11C5D824D579BC3A6B7D531EAEDDCBFB16E91B5702C72CAE9DEE4"; + x64suffix = "20"; + x86suffix = "20"; homepage = https://www.citrix.com/downloads/citrix-receiver/linux/receiver-for-linux-latest.html; }; }; diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index c477767d7072..55d9dc9f2d1d 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -1693,13 +1693,14 @@ with pkgs; ciopfs = callPackage ../tools/filesystems/ciopfs { }; citrix_receiver = callPackage ../applications/networking/remote/citrix-receiver { }; - citrix_receiver_13_9_1 = citrix_receiver.override { version = "13.9.1"; }; - citrix_receiver_13_9_0 = citrix_receiver.override { version = "13.9.0"; }; - citrix_receiver_13_8_0 = citrix_receiver.override { version = "13.8.0"; }; - citrix_receiver_13_7_0 = citrix_receiver.override { version = "13.7.0"; }; - citrix_receiver_13_6_0 = citrix_receiver.override { version = "13.6.0"; }; - citrix_receiver_13_5_0 = citrix_receiver.override { version = "13.5.0"; }; - citrix_receiver_13_4_0 = citrix_receiver.override { version = "13.4.0"; }; + citrix_receiver_13_10_0 = citrix_receiver.override { version = "13.10.0"; }; + citrix_receiver_13_9_1 = citrix_receiver.override { version = "13.9.1"; }; + citrix_receiver_13_9_0 = citrix_receiver.override { version = "13.9.0"; }; + citrix_receiver_13_8_0 = citrix_receiver.override { version = "13.8.0"; }; + citrix_receiver_13_7_0 = citrix_receiver.override { version = "13.7.0"; }; + citrix_receiver_13_6_0 = citrix_receiver.override { version = "13.6.0"; }; + citrix_receiver_13_5_0 = citrix_receiver.override { version = "13.5.0"; }; + citrix_receiver_13_4_0 = citrix_receiver.override { version = "13.4.0"; }; citra = libsForQt5.callPackage ../misc/emulators/citra { }; -- cgit 1.4.1 From b70ccf8a7b9571cc7a6daeb46daee460ada04057 Mon Sep 17 00:00:00 2001 From: aszlig Date: Fri, 29 Jun 2018 22:22:57 +0200 Subject: cbatticon: Fix build by removing -Wno-format This conflicts with -Werror=format-security and the build doesn't have any format security problems, so -Wno-format IMHO shouldn't be there in the first place. Signed-off-by: aszlig Cc: @domenkozar --- pkgs/applications/misc/cbatticon/default.nix | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/cbatticon/default.nix b/pkgs/applications/misc/cbatticon/default.nix index 01511b41b08d..f4ba30080f71 100644 --- a/pkgs/applications/misc/cbatticon/default.nix +++ b/pkgs/applications/misc/cbatticon/default.nix @@ -12,6 +12,10 @@ stdenv.mkDerivation rec { sha256 = "16g26vin1693dbdr9qsnw36fdchx394lp79gvp7gcbw0w1ny9av6"; }; + patchPhase = '' + sed -i -e 's/ -Wno-format//g' Makefile + ''; + makeFlags = "PREFIX=$(out)"; nativeBuildInputs = [ pkgconfig gettext ]; -- cgit 1.4.1 From 827d3d37962bfb4f607bf0be11e691a2c00a33b8 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Fri, 29 Jun 2018 16:12:42 -0700 Subject: chirp: 20180611 -> 20180614 (#42525) Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/chirp-daily/versions. These checks were done: - built on NixOS - Warning: no invocation of /nix/store/gfgi7c2ps023ga27vx6s38y4gkgx1c54-chirp-daily-20180614/bin/.chirpw-wrapped had a zero exit code or showed the expected version - Warning: no invocation of /nix/store/gfgi7c2ps023ga27vx6s38y4gkgx1c54-chirp-daily-20180614/bin/chirpw had a zero exit code or showed the expected version - 0 of 2 passed binary check by having a zero exit code. - 0 of 2 passed binary check by having the new version present in output. - found 20180614 with grep in /nix/store/gfgi7c2ps023ga27vx6s38y4gkgx1c54-chirp-daily-20180614 - directory tree listing: https://gist.github.com/5a739e8fa0584360afb3f692d19e3771 - du listing: https://gist.github.com/e530a387cd61ae6e0b944b372041bd3d --- pkgs/applications/misc/chirp/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/chirp/default.nix b/pkgs/applications/misc/chirp/default.nix index 6dc7a5f7dd2d..16f63cfcd107 100644 --- a/pkgs/applications/misc/chirp/default.nix +++ b/pkgs/applications/misc/chirp/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { name = "chirp-daily-${version}"; - version = "20180611"; + version = "20180614"; src = fetchurl { url = "https://trac.chirp.danplanet.com/chirp_daily/daily-${version}/${name}.tar.gz"; - sha256 = "1569gnbs4jb53n58wdkdjrxx9nrayljn5v0wqacn5zfr87s16zxf"; + sha256 = "011bxd418hrl88rhp6lhja68b2kvnm1b845v41g9qfsagvfmbv3g"; }; nativeBuildInputs = [ makeWrapper ]; -- cgit 1.4.1 From 424835acc87112d114944a529bdea27f2fb24843 Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Mon, 7 May 2018 23:11:31 +0200 Subject: symmetrica: add patches --- .../science/math/symmetrica/default.nix | 23 +++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix index a7212299aa63..6123fd7306d9 100644 --- a/pkgs/applications/science/math/symmetrica/default.nix +++ b/pkgs/applications/science/math/symmetrica/default.nix @@ -1,14 +1,15 @@ -{stdenv, fetchurl}: +{ stdenv +, fetchurl +, fetchpatch +}: stdenv.mkDerivation rec { name = "symmetrica-${version}"; version = "2.0"; - # or fetchFromGitHub(owner,repo,rev) or fetchgit(rev) src = fetchurl { url = "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/SYM2_0_tar.gz"; sha256 = "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz"; name = "symmetrica-2.0.tar.gz"; }; - buildInputs = []; sourceRoot = "."; installPhase = '' mkdir -p "$out"/{lib,share/doc/symmetrica,include/symmetrica} @@ -18,6 +19,22 @@ stdenv.mkDerivation rec { cp *.h "$out/include/symmetrica" cp README *.doc "$out/share/doc/symmetrica" ''; + patches = [ + # don't show banner ("SYMMETRICA VERSION X - STARTING) + # it doesn't contain very much helpful information and a banner is not ideal for a library + (fetchpatch { + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/de.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0df0vqixcfpzny6dkhyj87h8aznz3xn3zfwwlj8pd10bpb90k6gb"; + }) + + # use int32_t and uint32_t for type INT + # see https://trac.sagemath.org/ticket/13413 + (fetchpatch { + name = "fix_64bit_integer_overflow.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/int32.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0p33c85ck4kd453z687ni4bdcqr1pqx2756j7aq11bf63vjz4cyz"; + }) + ]; meta = { inherit version; description = ''A collection of routines for representation theory and combinatorics''; -- cgit 1.4.1 From 17e6b391eb6b524331bce29c01467dc055c8543b Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Tue, 24 Apr 2018 23:53:36 +0200 Subject: sage: 8.1 -> 8.2, use system packages --- pkgs/applications/science/math/sage/README.md | 117 +++ pkgs/applications/science/math/sage/default.nix | 443 +++++------ .../science/math/sage/env-locations.nix | 46 ++ pkgs/applications/science/math/sage/env.patch | 22 - .../science/math/sage/fetch-mirrors.sh | 11 - .../science/math/sage/flask-oldsessions.nix | 36 + .../science/math/sage/flask-openid.nix | 28 + .../applications/science/math/sage/openblas-pc.nix | 18 + .../science/math/sage/patchSageShebangs.sh | 51 -- .../math/sage/patches/dochtml-optional.patch | 127 ++++ .../sage/patches/eclib-regulator-precision.patch | 98 +++ .../patches/matplotlib-normed-deprecated.patch | 12 + .../math/sage/patches/maxima-5.41.0-doctests.patch | 48 ++ .../science/math/sage/patches/numpy-1.14.3.patch | 812 +++++++++++++++++++++ .../science/math/sage/patches/pari-stackwarn.patch | 20 + .../math/sage/patches/python-5755-hotpatch.patch | 28 + .../patches/python3-syntax-without-write.patch | 40 + .../math/sage/patches/revert-269c1e1551285.patch | 14 + .../math/sage/patches/sagenb-sphinx-1.7.patch | 31 + .../science/math/sage/patches/sphinx-1.7.patch | 62 ++ .../math/sage/patches/zn_poly_version.patch | 13 + pkgs/applications/science/math/sage/pybrial.nix | 29 + .../science/math/sage/python-openid.nix | 42 ++ pkgs/applications/science/math/sage/sage-env.nix | 162 ++++ pkgs/applications/science/math/sage/sage-src.nix | 197 +++++ .../science/math/sage/sage-with-env.nix | 129 ++++ .../science/math/sage/sage-wrapper.nix | 41 ++ pkgs/applications/science/math/sage/sage.nix | 32 + pkgs/applications/science/math/sage/sagedoc.nix | 97 +++ pkgs/applications/science/math/sage/sagelib.nix | 139 ++++ pkgs/applications/science/math/sage/sagenb.nix | 49 ++ pkgs/applications/science/math/sage/shebangs.patch | 36 - .../applications/science/math/sage/spkg-giac.patch | 20 - pkgs/applications/science/math/sage/spkg-git.patch | 18 - .../science/math/sage/spkg-python.patch | 13 - .../science/math/sage/spkg-singular.patch | 18 - pkgs/top-level/all-packages.nix | 5 +- 37 files changed, 2693 insertions(+), 411 deletions(-) create mode 100644 pkgs/applications/science/math/sage/README.md create mode 100644 pkgs/applications/science/math/sage/env-locations.nix delete mode 100644 pkgs/applications/science/math/sage/env.patch delete mode 100755 pkgs/applications/science/math/sage/fetch-mirrors.sh create mode 100644 pkgs/applications/science/math/sage/flask-oldsessions.nix create mode 100644 pkgs/applications/science/math/sage/flask-openid.nix create mode 100644 pkgs/applications/science/math/sage/openblas-pc.nix delete mode 100644 pkgs/applications/science/math/sage/patchSageShebangs.sh create mode 100644 pkgs/applications/science/math/sage/patches/dochtml-optional.patch create mode 100644 pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch create mode 100644 pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch create mode 100644 pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch create mode 100644 pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch create mode 100644 pkgs/applications/science/math/sage/patches/pari-stackwarn.patch create mode 100644 pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch create mode 100644 pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch create mode 100644 pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch create mode 100644 pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch create mode 100644 pkgs/applications/science/math/sage/patches/sphinx-1.7.patch create mode 100644 pkgs/applications/science/math/sage/patches/zn_poly_version.patch create mode 100644 pkgs/applications/science/math/sage/pybrial.nix create mode 100644 pkgs/applications/science/math/sage/python-openid.nix create mode 100644 pkgs/applications/science/math/sage/sage-env.nix create mode 100644 pkgs/applications/science/math/sage/sage-src.nix create mode 100644 pkgs/applications/science/math/sage/sage-with-env.nix create mode 100644 pkgs/applications/science/math/sage/sage-wrapper.nix create mode 100644 pkgs/applications/science/math/sage/sage.nix create mode 100644 pkgs/applications/science/math/sage/sagedoc.nix create mode 100644 pkgs/applications/science/math/sage/sagelib.nix create mode 100644 pkgs/applications/science/math/sage/sagenb.nix delete mode 100644 pkgs/applications/science/math/sage/shebangs.patch delete mode 100644 pkgs/applications/science/math/sage/spkg-giac.patch delete mode 100644 pkgs/applications/science/math/sage/spkg-git.patch delete mode 100644 pkgs/applications/science/math/sage/spkg-python.patch delete mode 100644 pkgs/applications/science/math/sage/spkg-singular.patch (limited to 'pkgs/applications') diff --git a/pkgs/applications/science/math/sage/README.md b/pkgs/applications/science/math/sage/README.md new file mode 100644 index 000000000000..46496664f28e --- /dev/null +++ b/pkgs/applications/science/math/sage/README.md @@ -0,0 +1,117 @@ +# 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. Here's a quick overview over the functions of the individual files: + +- `sage-src.nix` + Downloads the source code and applies patches. This makes sure that all the other files work with the same sage source. If you want to apply a patch to sage or update sage to a new version, this is the place to do it. + +- `env-locations.nix` + Creates a bash file that sets a bunch of environment variables telling sage where to find various packages and files. The definitions of those environment variables can be found in the sage source in the `src/env.py` file. This bash file needs to be sourced before sage is started (done in `sage-env.nix` and `sagedoc.nix`). + +- `sage-env.nix` + Sets all environment variables sage needs to run. This includes the package locations defined in `env-locations.nix` as well as the location of sage itself and its various subdirectories. + +- `sagelib.nix` + Defines the main sage package (without setting the necessary environments or running any tests). + +- `sage-with-env.nix` + Wraps sage in the necessary environment. + +- `sage.nix` + Runs sages doctests. + +- `sage-wrapper.nix` + Optionally tells sage where do find the docs. + +- `sagedoc.nix` + Builds and tests the sage html documentation. Can be used for offline documentation viewing as well as the sage `browse_sage_doc` and `search_doc` functions. + +- `sagenb.nix` + The (semi deprecated) sage notebook. + +- `default.nix` + Introduces necessary overrides, defines new packages and ties everything together (returning the `sage` package). + +- `flask-oldsessions.nix`, `flask-openid.nix`, `python-openid.nix` + These are python packages that were rejected from the main nixpkgs tree because they appear unmaintained. They are needed for the (semi-deprecated) sage notebook. Since that notebook is still needed to run the sage doctests, these packages are included but not exposed to the rest of nixpkgs. + +- `pybrial.nix` + pybrial is a dependency of sage. However, pybrial itself also has sage as a dependency. Because of that circular dependency, pybrial is hidden from the rest of nixpkgs (just as the flask packages and python-openid. + +- `openblas-pc.nix` + This creates a `.pc` file to be read by `pkg-config` that allows openblas to take on different roles, like `cblas` or `lapack`. + +## 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 ". 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 ~]$ +[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-`. 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-/ develop +[user@localhost sage]$ +[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-/ +``` + +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-/` 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-/` 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/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 7f101bac147e..4e84a18f4f2a 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -1,230 +1,231 @@ -# TODO -# - consider writing a script to convert spkgs to nix packages, similar to vim -# or cabal2nix. This would allow a more efficient and "cleaner" build, greater -# flexibility and the possibility to select which dependencies to add and which -# to remove. It would also allow to use system packages for some dependencies -# and recompile others (optimized for the system) without recompiling everything. -# - add optdeps: -# - imagemagick -# - texlive full for documentation -# - ... -# - further seperate build outputs. Also maybe run `make doc`. -# Configure flags like --bindir and --libdir oculd also be used for that, see -# ./configure --help`. - -# Other resources: -# - https://wiki.debian.org/DebianScience/Sage -# - https://github.com/cschwan/sage-on-gentoo -# - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath - -{ stdenv -, bash -, fetchurl -, perl -, gfortran6 -, python -, autoreconfHook -, gettext -, which -, texlive -, texinfo -, hevea -, buildDocs ? false -, optimize ? false # optimize sage to the current system (obviously impure) +{ nixpkgs +, withDoc ? false }: -stdenv.mkDerivation rec { - version = "8.1"; - name = "sage-${version}"; - - # Modified version of patchShebangs that patches to the sage-internal version if possible - # and falls back to the system version if not. - patchSageShebangs = ./patchSageShebangs.sh; - src = fetchurl { - # Note that the source is *not* fetched from github, since that doesn't - # the upstream folder with all the source tarballs of the spkgs. - # If those are not present they are fetched at build time, which breaks - # when building in a sandbox (and probably only works if you install the - # latest sage version). - urls = [ - "http://mirrors.mit.edu/sage/src/sage-${version}.tar.gz" - "ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-${version}.tar.gz" - "http://sagemath.polytechnic.edu.na/src/sage-${version}.tar.gz" - "ftp://ftp.sun.ac.za/pub/mirrors/www.sagemath.org/src/sage-${version}.tar.gz" - "http://sagemath.mirror.ac.za/src/sage-${version}.tar.gz" - "https://ftp.leg.uct.ac.za/pub/packages/sage/src/sage-${version}.tar.gz" - "http://mirror.ufs.ac.za/sagemath/src/sage-${version}.tar.gz" - "https://mirrors-usa.go-parts.com/sage/sagemath/src/sage-${version}.tar.gz" - "http://www.cecm.sfu.ca/sage/src/sage-${version}.tar.gz" - "http://files.sagemath.org/src/sage-${version}.tar.gz" - "https://mirrors.xmission.com/sage/src/sage-${version}.tar.gz" - "http://sagemath.c3sl.ufpr.br/src/sage-${version}.tar.gz" - "http://linorg.usp.br/sage/src/sage-${version}.tar.gz" - "http://mirror.hust.edu.cn/sagemath/src/sage-${version}.tar.gz" - "https://ftp.iitm.ac.in/sage/src/sage-${version}.tar.gz" - "http://ftp.kaist.ac.kr/sage/src/sage-${version}.tar.gz" - "https://ftp.riken.jp/sagemath/src/sage-${version}.tar.gz" - "https://mirrors.tuna.tsinghua.edu.cn/sagemath/src/sage-${version}.tar.gz" - "https://mirrors.ustc.edu.cn/sagemath/src/sage-${version}.tar.gz" - "http://ftp.tsukuba.wide.ad.jp/software/sage/src/sage-${version}.tar.gz" - "https://ftp.yz.yamagata-u.ac.jp/pub/math/sage/src/sage-${version}.tar.gz" - "https://mirror.yandex.ru/mirrors/sage.math.washington.edu/src/sage-${version}.tar.gz" - "https://mirror.aarnet.edu.au/pub/sage/src/sage-${version}.tar.gz" - "https://sage.mirror.garr.it/mirrors/sage/src/sage-${version}.tar.gz" - "https://www.mirrorservice.org/sites/www.sagemath.org/src/sage-${version}.tar.gz" - "http://mirror.switch.ch/mirror/sagemath/src/sage-${version}.tar.gz" - "https://mirrors.up.pt/pub/sage/src/sage-${version}.tar.gz" - "http://www-ftp.lip6.fr/pub/math/sagemath/src/sage-${version}.tar.gz" - "http://ftp.ntua.gr/pub/sagemath/src/sage-${version}.tar.gz" - ]; - sha256 = "1cpcs1mr0yii64s152xmxyd450bfzjb22jjj0zh9y3n6g9alzpyq"; +let + inherit (nixpkgs) fetchpatch fetchurl symlinkJoin fetchFromGitHub callPackage nodePackages_8_x; + + # https://trac.sagemath.org/ticket/15980 for tracking of python3 support + python = nixpkgs.python2.override { + packageOverrides = self: super: { + cypari2 = super.cypari2.override { inherit pari; }; + + cysignals = super.cysignals.override { inherit pari; }; + + cvxopt = super.cvxopt.override { inherit glpk; }; + + # https://github.com/sagemath/sagenb/issues/437 + flask-babel = super.flask-babel.overridePythonAttrs (attrs: rec { + version = "0.9"; + src = attrs.src.override { + inherit version; + sha256 = "0k7vk4k54y55ma0nx2k5s0phfqbriwslhy5shh3b0d046q7ibzaa"; + }; + doCheck = false; + }); + + # 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. + flask-oldsessions = self.callPackage ./flask-oldsessions.nix {}; + flask-openid = self.callPackage ./flask-openid.nix {}; + python-openid = self.callPackage ./python-openid.nix {}; + + pybrial = self.callPackage ./pybrial.nix {}; + + sagelib = self.callPackage ./sagelib.nix { + inherit flint ecl pari glpk eclib; + inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; + linbox = nixpkgs.linbox.override { withSage = true; }; + # tracking: https://trac.sagemath.org/ticket/24927 + arb = nixpkgs.arb.overrideAttrs (attrs: rec { + name = "arb-${version}"; + version = "2.12.0"; + doCheck = false; # https://github.com/fredrik-johansson/arb/issues/194 + src = fetchFromGitHub { + owner = "fredrik-johansson"; + repo = attrs.pname; + rev = version; + sha256 = "18bwxlcbqb70cj7l9x6w1h4yghrqfhmbhdby373q8vdrdfx58niq"; + }; + }); + }; + + sagenb = self.callPackage ./sagenb.nix { + mathjax = nodePackages_8_x.mathjax; + }; + + sagedoc = self.callPackage ./sagedoc.nix { + inherit sage-src; + }; + + env-locations = self.callPackage ./env-locations.nix { + inherit pari_data ecl pari; + inherit singular; + three = nodePackages_8_x.three; + mathjax = nodePackages_8_x.mathjax; + }; + + sage-env = self.callPackage ./sage-env.nix { + inherit sage-src python rWrapper openblas-cblas-pc glpk ecl singular eclib pari palp flint pynac pythonEnv; + pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + }; + + sage-with-env = self.callPackage ./sage-with-env.nix { + inherit pari eclib pythonEnv; + inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; + pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig + three = nodePackages_8_x.three; + }; + + sage = self.callPackage ./sage.nix { }; + + sage-wrapper = self.callPackage ./sage-wrapper.nix { + inherit sage-src withDoc; + }; + }; }; - postPatch = '' - substituteAllInPlace src/bin/sage-env - bash=${bash} substituteAllInPlace build/bin/sage-spkg - ''; - - installPhase = '' - # Sage installs during first `make`, `make install` is no-op and just takes time. - ''; - - outputs = [ "out" ] ++ stdenv.lib.optionals (buildDocs) [ "doc" ]; - - buildInputs = [ - bash # needed for the build - perl # needed for the build - python # needed for the build - gfortran6 # needed to build giac, openblas - autoreconfHook # needed to configure sage with prefix - gettext # needed to build the singular spkg - which # needed in configure of mpir - texinfo # needed to build maxima - ] ++ stdenv.lib.optionals(buildDocs) [ - hevea # needed to build the docs of the giac spkg - (texlive.combine { inherit (texlive) - scheme-basic - collection-pstricks # needed by giac - times # font needed by giac - stmaryrd # needed by giac - babel-greek # optional for giac, otherwise throws a bunch of latex command not founds - ; - }) - ]; - - nativeBuildInputs = [ gfortran6 perl which ]; - - patches = [ - # fix usages of /bin/rm - ./spkg-singular.patch - # help python find the crypt library - # patches python3 and indirectly python2, since those installation files are symlinked - ./spkg-python.patch - # fix usages of /usr/bin/perl - ./spkg-git.patch - # fix usages of /bin/cp and add necessary argument to function call - ./spkg-giac.patch - # environment - ./env.patch - # adjust wrapper shebang and patch shebangs after each spkg build - ./shebangs.patch + openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; }; + openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; }; + openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; }; + + sage-src = callPackage ./sage-src.nix {}; + + pythonRuntimeDeps = with python.pkgs; [ + sagelib + pybrial + sagenb + cvxopt + networkx + service-identity + psutil + sympy + fpylll + matplotlib + scipy + ipywidgets + rpy2 + sphinx + typing + pillow ]; - enableParallelBuilding = true; + pythonEnv = python.buildEnv.override { + extraLibs = pythonRuntimeDeps; + ignoreCollisions = true; + } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible + + # needs to be rWrapper, standard "R" doesn't include default packages + rWrapper = nixpkgs.rWrapper.override { + # https://trac.sagemath.org/ticket/25674 + R = nixpkgs.R.overrideAttrs (attrs: rec { + name = "R-3.4.4"; + src = fetchurl { + url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz"; + sha256 = "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk"; + }; + }); + }; - hardeningDisable = [ - "format" # needed to build palp, for lines like `printf(ctime(&_NFL->TIME))` - # TODO could be patched with `sed s|printf(ctime(\(.*\)))|%s... or fixed upstream - ]; + # update causes issues + # https://groups.google.com/forum/#!topic/sage-packaging/cS3v05Q0zso + # https://trac.sagemath.org/ticket/24735 + singular = nixpkgs.singular.overrideAttrs (oldAttrs: { + name = "singular-4.1.0p3"; + src = fetchurl { + url = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/4-1-0/singular-4.1.0p3.tar.gz"; + sha256 = "105zs3zk46b1cps403ap9423rl48824ap5gyrdgmg8fma34680a4"; + }; + }); + + # *not* to confuse with the python package "pynac" + # https://trac.sagemath.org/ticket/24838 (depends on arb update) + pynac = (nixpkgs.pynac.override { inherit singular; }).overrideAttrs (oldAttrs: rec { + name = "pynac-0.7.16"; + src = fetchFromGitHub { + owner = "pynac"; + repo = "pynac"; + rev = name; + sha256 = "106an189sg4rpgzfrmy3699271vg4ddazw9wvh51wx7qnm1v86ik"; + }; + }); + + eclib = nixpkgs.eclib.override { inherit pari; }; + + # 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 = nixpkgs.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-${nixpkgs.palp.version}"; + paths = [ + (nixpkgs.palp.override { dimensions = 4; doSymlink = false; }) + (nixpkgs.palp.override { dimensions = 5; doSymlink = false; }) + (nixpkgs.palp.override { dimensions = 6; doSymlink = true; }) + (nixpkgs.palp.override { dimensions = 11; doSymlink = false; }) + ]; + }; - configureFlags = stdenv.lib.optionals(buildDocs) [ "--docdir=$(doc)" ]; - preConfigure = '' - export SAGE_NUM_THREADS="$NIX_BUILD_CORES" - - export HOME=/tmp/sage-home - export SAGE_ROOT="$PWD" - export SAGE_SRC="$PWD" - - mkdir -p "$HOME" - mkdir -p "$out" - - # we need to keep the source around - dir="$PWD" - cd .. - mv "$dir" "$out/sage-root" - - export SAGE_SPKG_INSTALL_DOCS='no' - cd "$out/sage-root" # build in target dir, since `make` is also `make install` - '' - + stdenv.lib.optionalString (buildDocs) '' - mkdir -p "$doc" - export SAGE_DOC="$doc" - export SAGE_DOCBUILD_OPTS="--no-pdf-links -k" - '' - + stdenv.lib.optionalString (!optimize) '' - export SAGE_FAT_BINARY=yes - ''; - - buildFlags = if (buildDocs) then "doc" else "build"; - - # for reference: http://doc.sagemath.org/html/en/installation/source.html - preBuild = '' - # symlink python to make sure the shebangs are patched to the sage path - # while still being able to use python before building it - # (this is important because otherwise sage will try to install python - # packages globally later on) - ln -s "${python}/bin/python2" $out/bin/python2 - ln -s "$out/bin/python2" $out/bin/python - touch $out/bin/python3 - bash $patchSageShebangs . - ''; - - postBuild = '' - # Clean up - rm -r "$out/sage-root/upstream" # don't keep the sources of all the spkgs - rm -rf "$out/sage-root/src/build" - rm -rf "$out/sage-root/src/autom4te.cache" - rm -rf "$out/sage-root/src/config" - rm -rf "$out/sage-root/src/m4" - rm -rf "$out/sage-root/.git" - rm -r "$out/sage-root/logs" - rm -r "$out"/lib/python*/test - # Fix dependency cycle between out and doc - rm -f "$out/sage-root/config.log" - rm -f "$out/sage-root/config.status" - rm -f "$out/sage-root/build/make/Makefile-auto" - rm -f "$out/sage-home/.sage/gap/libgap-workspace-"* - # Make sure unnessessary packages don't end up in the build closure - find "$out" \ - -iname 'config.log' \ - -delete \ - -or -iname 'Makefile' \ - -delete - rm -f "$out/lib/R/etc/Renviron" - # Make sure all shebangs are properly patched - bash $patchSageShebangs $out - ''; - - # TODO there are some doctest failures, which seem harmless. - # We should figure out a way to fix the failures or ignore only those tests. - doCheck = false; - - checkTarget = "ptestalllong"; # all long tests in parallell - preCheck = '' - export SAGE_TIMEOUT=0 # no timeout - export SAGE_TIMEOUT_LONG=0 # no timeout - ''; - - meta = { - homepage = http://www.sagemath.org; - description = "A free open source mathematics software system"; - # taken from the homepage - longDescription = '' - SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers. - Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. - ''; - license = stdenv.lib.licenses.gpl2Plus; - platforms = ["x86_64-linux" "i686-linux"]; - maintainers = with stdenv.lib.maintainers; [ timokau ]; + # Sage expects those in the same directory. + pari_data = symlinkJoin { + name = "pari_data"; + paths = with nixpkgs; [ + pari-galdata + pari-seadata-small + ]; }; -} + + # https://trac.sagemath.org/ticket/22191 + ecl = nixpkgs.ecl_16_1_2; + + # sage currently uses an unreleased version of pari + pari = (nixpkgs.pari.override { withThread = false; }).overrideAttrs (attrs: rec { + version = "2.10-1280-g88fb5b3"; # on update remove pari-stackwarn patch from `sage-src.nix` + src = fetchurl { + url = "mirror://sageupstream/pari/pari-${version}.tar.gz"; + sha256 = "19gbsm8jqq3hraanbmsvzkbh88iwlqbckzbnga3y76r7k42akn7m"; + }; + }); + + # https://trac.sagemath.org/ticket/24824 + glpk = nixpkgs.glpk.overrideAttrs (attrs: rec { + version = "4.63"; + name = "glpk-${version}"; + src = fetchurl { + url = "mirror://gnu/glpk/${name}.tar.gz"; + sha256 = "1xp7nclmp8inp20968bvvfcwmz3mz03sbm0v3yjz8aqwlpqjfkci"; + }; + patches = (attrs.patches or []) ++ [ + # Alternatively patch sage with debians + # https://sources.debian.org/data/main/s/sagemath/8.1-7/debian/patches/t-version-glpk-4.60-extra-hack-fixes.patch + # The header of that debian patch contains a good description of the issue. The gist of it: + # > If GLPK in Sage causes one error, and this is caught by Sage and recovered from, then + # > later (because upstream GLPK does not clear the "error" flag) Sage will append + # > all subsequent terminal output of GLPK into the error_message string but not + # > actually forward it to the user's terminal. This breaks some doctests. + (fetchpatch { + name = "error_recovery.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/error_recovery.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "0z99z9gd31apb6x5n5n26411qzx0ma3s6dnznc4x61x86bhq31qf"; + }) + + # Allow setting a exact verbosity level (OFF|ERR|ON|ALL|DBG) + (fetchpatch { + name = "exact_verbosity.patch"; + url = "https://git.sagemath.org/sage.git/plain/build/pkgs/glpk/patches/glp_exact_verbosity.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba"; + sha256 = "15gm5i2alqla3m463i1qq6jx6c0ns6lip7njvbhp37pgxg4s9hx8"; + }) + ]; + }); +in + python.pkgs.sage-wrapper // { + doc = python.pkgs.sagedoc; + lib = python.pkgs.sagelib; + } diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix new file mode 100644 index 000000000000..2ed079ab32bc --- /dev/null +++ b/pkgs/applications/science/math/sage/env-locations.nix @@ -0,0 +1,46 @@ +{ stdenv +, writeTextFile +, pari_data +, pari +, singular +, maxima-ecl +, conway_polynomials +, graphs +, elliptic_curves +, polytopes_db +, gap-libgap-compatible +, ecl +, combinatorial_designs +, jmol +, mathjax +, three +, cysignals +}: + +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='${singular}/lib/libSingular.so' + export SINGULAR_EXECUTABLE='${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-libgap-compatible}/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="${jmol}" + export MATHJAX_DIR="${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/pkgs/applications/science/math/sage/env.patch b/pkgs/applications/science/math/sage/env.patch deleted file mode 100644 index a7f8538eac3d..000000000000 --- a/pkgs/applications/science/math/sage/env.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/src/bin/sage-env b/src/bin/sage-env -index ead308f861..ed8db9f9b7 100644 ---- a/src/bin/sage-env -+++ b/src/bin/sage-env -@@ -111,6 +111,8 @@ resolvelinks() { - } - - -+SAGE_ROOT="@out@/sage-root" -+ - # New value for SAGE_ROOT: either SAGE_ROOT (if given) - # or a guessed value based on pwd. - if [ -n "$SAGE_ROOT" ]; then -@@ -185,6 +187,8 @@ fi - export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION - - export SAGE_ROOT="$NEW_SAGE_ROOT" -+export SAGE_LOCAL='@out@/' -+export PYTHONPATH="@out@/lib/python2.7/site-packages:$PYTHONPATH" - - - # sage-env must know where the Sage's script files are. diff --git a/pkgs/applications/science/math/sage/fetch-mirrors.sh b/pkgs/applications/science/math/sage/fetch-mirrors.sh deleted file mode 100755 index a1103e86beb9..000000000000 --- a/pkgs/applications/science/math/sage/fetch-mirrors.sh +++ /dev/null @@ -1,11 +0,0 @@ -#! /usr/bin/env nix-shell -#! nix-shell -i bash -p curl go-pup - -# Fetches a list of all available source mirrors from the sage homepage. -# Note that the list is sorted by country, but fetchurl doesn't offer an option -# to customize mirror preference. - -curl -s http://www.sagemath.org/download-source.html \ - | pup 'table#mirror' \ - | pup 'a attr{href}' \ - | sed -e 's/index\.html/sage-${version}.tar.gz/' diff --git a/pkgs/applications/science/math/sage/flask-oldsessions.nix b/pkgs/applications/science/math/sage/flask-oldsessions.nix new file mode 100644 index 000000000000..85e35736d030 --- /dev/null +++ b/pkgs/applications/science/math/sage/flask-oldsessions.nix @@ -0,0 +1,36 @@ +{ stdenv +, buildPythonPackage +, fetchFromGitHub +, python +, flask +}: + +buildPythonPackage rec { + pname = "Flask-OldSessions"; + version = "0.10"; + + # no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1 + src = fetchFromGitHub { + owner = "mitsuhiko"; + repo = "flask-oldsessions"; + rev = "${version}"; + sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn"; + }; + + propagatedBuildInputs = [ + flask + ]; + + # missing module flask.testsuite, probably assumes an old version of flask + doCheck = false; + checkPhase = '' + ${python.interpreter} run-tests.py + ''; + + meta = with stdenv.lib; { + description = "Provides a session class that works like the one in Flask before 0.10."; + license = licenses.bsd2; + maintainers = with maintainers; [ timokau ]; + homepage = https://github.com/mitsuhiko/flask-oldsessions; + }; +} diff --git a/pkgs/applications/science/math/sage/flask-openid.nix b/pkgs/applications/science/math/sage/flask-openid.nix new file mode 100644 index 000000000000..9043fabd9b4a --- /dev/null +++ b/pkgs/applications/science/math/sage/flask-openid.nix @@ -0,0 +1,28 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, flask +, python-openid +}: + +buildPythonPackage rec { + pname = "Flask-OpenID"; + version = "1.2.5"; + + src = fetchPypi { + inherit pname version; + sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss"; + }; + + propagatedBuildInputs = [ + flask + python-openid + ]; + + meta = with stdenv.lib; { + description = "Adds openid support to flask applications"; + license = licenses.bsd2; + maintainers = with maintainers; [ timokau ]; + homepage = https://pythonhosted.org/Flask-OpenID/; + }; +} diff --git a/pkgs/applications/science/math/sage/openblas-pc.nix b/pkgs/applications/science/math/sage/openblas-pc.nix new file mode 100644 index 000000000000..ba46850bbc61 --- /dev/null +++ b/pkgs/applications/science/math/sage/openblas-pc.nix @@ -0,0 +1,18 @@ +{ stdenv +, openblasCompat +, writeTextFile +, name +}: + +writeTextFile { + name = "openblas-${name}-pc-${openblasCompat.version}"; + destination = "/lib/pkgconfig/${name}.pc"; + text = '' + Name: ${name} + Version: ${openblasCompat.version} + + Description: ${name} for SageMath, provided by the OpenBLAS package. + Cflags: -I${openblasCompat}/include + Libs: -L${openblasCompat}/lib -lopenblas + ''; +} diff --git a/pkgs/applications/science/math/sage/patchSageShebangs.sh b/pkgs/applications/science/math/sage/patchSageShebangs.sh deleted file mode 100644 index 6ddf93af0114..000000000000 --- a/pkgs/applications/science/math/sage/patchSageShebangs.sh +++ /dev/null @@ -1,51 +0,0 @@ -# This is a slightly modified version of nix's default patchShebangs - -dir="$1" - -echo "patching sage internal script interpreter paths in $( readlink -f "$dir")" - -find "$dir" -type f -perm -0100 | while read f; do - if [ "$(head -1 "$f" | head -c+2)" != '#!' ]; then - # missing shebang => not a script - continue - fi - - oldInterpreterLine=$(head -1 "$f" | tail -c+3) - read -r oldPath arg0 args <<< "$oldInterpreterLine" - - if $(echo "$oldPath" | grep -q "/bin/env$"); then - # Check for unsupported 'env' functionality: - # - options: something starting with a '-' - # - environment variables: foo=bar - if $(echo "$arg0" | grep -q -- "^-.*\|.*=.*"); then - echo "unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)" - exit 1 - fi - executable="$arg0" - else - if [ "$oldPath" = "" ]; then - # If no interpreter is specified linux will use /bin/sh. Set - # oldpath="/bin/sh" so that we get /nix/store/.../sh. - oldPath="/bin/sh" - fi - executable="$(basename "$oldPath")" - args="$arg0 $args" - fi - - newPath="$(echo "$out/bin/$executable $args" | sed 's/[[:space:]]*$//')" - if [[ ! -x "$newPath" ]] ; then - newPath="$(command -v "$executable" || true)" - fi - - # Strip trailing whitespace introduced when no arguments are present - newInterpreterLine="$(echo "$newPath $args" | sed 's/[[:space:]]*$//')" - - if [ -n "$oldPath" -a "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ]; then - if [ -n "$newPath" -a "$newPath" != "$oldPath" ]; then - echo "$f: sage interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\"" - # escape the escape chars so that sed doesn't interpret them - escapedInterpreterLine=$(echo "$newInterpreterLine" | sed 's|\\|\\\\|g') - sed -i -e "1 s|.*|#\!$escapedInterpreterLine|" "$f" - fi - fi -done diff --git a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch new file mode 100644 index 000000000000..a51e30312ed9 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch @@ -0,0 +1,127 @@ +diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py +index 25f94f7b7d..9f6139ea4a 100644 +--- a/src/doc/common/conf.py ++++ b/src/doc/common/conf.py +@@ -622,9 +622,9 @@ def call_intersphinx(app, env, node, contnode): + Check that the link from the thematic tutorials to the reference + manual is relative, see :trac:`20118`:: + +- sage: from sage.env import SAGE_DOC +- sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html") +- sage: for line in open(thematic_index).readlines(): ++ sage: from sage.env import SAGE_DOC # optional - dochtml ++ sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html") # optional - dochtml ++ sage: for line in open(thematic_index).readlines(): # optional - dochtml + ....: if "padics" in line: + ....: sys.stdout.write(line) +
  • Introduction to the -adics
    • +diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py +index 4236fd05e0..8e499cbaf7 100644 +--- a/src/sage/doctest/control.py ++++ b/src/sage/doctest/control.py +@@ -87,7 +87,7 @@ class DocTestDefaults(SageObject): + self.sagenb = False + self.long = False + self.warn_long = None +- self.optional = set(['sage']) | auto_optional_tags ++ self.optional = set(['sage', 'dochtml']) | auto_optional_tags + self.randorder = None + self.global_iterations = 1 # sage-runtests default is 0 + self.file_iterations = 1 # sage-runtests default is 0 +@@ -343,7 +343,8 @@ 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 + self.files = args +@@ -741,7 +742,7 @@ 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', 'py3'] ++ ['guava', 'magma'] + + We check that files are skipped appropriately:: + +@@ -968,7 +969,7 @@ class DocTestController(SageObject): + sage: from sage.doctest.control import DocTestDefaults, DocTestController + sage: DC = DocTestController(DocTestDefaults(), []) + sage: DC._optional_tags_string() +- 'sage' ++ 'dochtml,sage' + sage: DC = DocTestController(DocTestDefaults(optional="all,and,some,more"), []) + sage: DC._optional_tags_string() + 'all' +diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py +index 9255aa848f..cc4712d3ec 100644 +--- a/src/sage/misc/sagedoc.py ++++ b/src/sage/misc/sagedoc.py +@@ -18,9 +18,9 @@ TESTS: + Check that argspecs of extension function/methods appear correctly, + see :trac:`12849`:: + +- sage: from sage.env import SAGE_DOC +- sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html') +- sage: with open(docfilename) as fobj: ++ sage: from sage.env import SAGE_DOC # optional - dochtml ++ sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html') # optional - dochtml ++ sage: with open(docfilename) as fobj: # optional - dochtml + ....: for line in fobj: + ....: if "#sage.symbolic.expression.Expression.numerical_approx" in line: + ....: print(line) +@@ -790,11 +790,12 @@ def _search_src_or_doc(what, string, extra1='', extra2='', extra3='', + + :: + +- sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1 ++ sage: from sage.misc.sagedoc import _search_src_or_doc # optional - dochtml ++ sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1 # optional - dochtml + True +- sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # long time (4s on sage.math, 2012) ++ sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # optional - dochtml, long time (4s on sage.math, 2012) + True +- sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False) ++ sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False) # optional - dochtml + True + """ + # process keywords +@@ -1160,9 +1161,9 @@ def search_doc(string, extra1='', extra2='', extra3='', extra4='', + counting the length of ``search_doc('tree', + interact=False).splitlines()`` gives the number of matches. :: + +- sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # long time ++ sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # optional - dochtml, long time + True +- sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # long time ++ sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # optional - dochtml, long time + True + """ + return _search_src_or_doc('doc', string, extra1=extra1, extra2=extra2, +@@ -1332,9 +1333,9 @@ class _sage_doc: + + EXAMPLES:: + +- sage: browse_sage_doc._open("reference", testing=True)[0] # indirect doctest ++ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml, indirect doctest + 'http://localhost:8000/doc/live/reference/index.html' +- sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47] ++ sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47] # optional - dochtml + 'Full MatrixSpace of 3 by 3 sparse matrices over Integer Ring' + """ + def __init__(self): +@@ -1494,9 +1495,9 @@ class _sage_doc: + + EXAMPLES:: + +- sage: browse_sage_doc._open("reference", testing=True)[0] ++ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml + 'http://localhost:8000/doc/live/reference/index.html' +- sage: browse_sage_doc._open("tutorial", testing=True)[1] ++ sage: browse_sage_doc._open("tutorial", testing=True)[1] # optional - dochtml + '.../html/en/tutorial/index.html' + """ + url = self._base_url + os.path.join(name, "index.html") diff --git a/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch b/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch new file mode 100644 index 000000000000..a1464b8fe310 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/eclib-regulator-precision.patch @@ -0,0 +1,98 @@ +diff --git a/src/sage/libs/eclib/interface.py b/src/sage/libs/eclib/interface.py +index f77000c478..9d17d412ae 100644 +--- a/src/sage/libs/eclib/interface.py ++++ b/src/sage/libs/eclib/interface.py +@@ -1014,7 +1014,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 2 will not be done; + ... + Gained index 2 +- New regulator = 93.857300720636393209 ++ New regulator = 93.85730... + (False, 2, '[ ]') + sage: EQ.points() + [[-2, 3, 1], [2707496766203306, 864581029138191, 2969715140223272], [-13422227300, -49322830557, 12167000000]] +@@ -1025,7 +1025,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 3 will not be done; + ... + Gained index 3 +- New regulator = 10.4285889689595992455 ++ New regulator = 10.42858... + (False, 3, '[ ]') + sage: EQ.points() + [[-2, 3, 1], [-14, 25, 8], [-13422227300, -49322830557, 12167000000]] +@@ -1036,7 +1036,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 5 will not be done; + ... + Gained index 5 +- New regulator = 0.417143558758383969818 ++ New regulator = 0.41714... + (False, 5, '[ ]') + sage: EQ.points() + [[-2, 3, 1], [-14, 25, 8], [1, -1, 1]] +@@ -1221,7 +1221,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 2 will not be done; + ... + Gained index 2 +- New regulator = 93.857300720636393209 ++ New regulator = 93.85730... + (False, 2, '[ ]') + sage: EQ + Subgroup of Mordell-Weil group: [[-2:3:1], [2707496766203306:864581029138191:2969715140223272], [-13422227300:-49322830557:12167000000]] +@@ -1235,7 +1235,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 3 will not be done; + ... + Gained index 3 +- New regulator = 10.4285889689595992455 ++ New regulator = 10.42858... + (False, 3, '[ ]') + sage: EQ + Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [-13422227300:-49322830557:12167000000]] +@@ -1249,7 +1249,7 @@ class mwrank_MordellWeil(SageObject): + WARNING: saturation at primes p > 5 will not be done; + ... + Gained index 5 +- New regulator = 0.417143558758383969818 ++ New regulator = 0.41714... + (False, 5, '[ ]') + sage: EQ + Subgroup of Mordell-Weil group: [[-2:3:1], [-14:25:8], [1:-1:1]] +diff --git a/src/sage/libs/eclib/mwrank.pyx b/src/sage/libs/eclib/mwrank.pyx +index a4f89e1ca5..f8a22d2f55 100644 +--- a/src/sage/libs/eclib/mwrank.pyx ++++ b/src/sage/libs/eclib/mwrank.pyx +@@ -1234,9 +1234,9 @@ cdef class _two_descent: + sage: D2.saturate() + Searching for points (bound = 8)...done: + found points which generate a subgroup of rank 3 +- and regulator 0.417143558758383969817119544618093396749810106098479 ++ and regulator 0.41714... + Processing points found during 2-descent...done: +- now regulator = 0.417143558758383969817119544618093396749810106098479 ++ now regulator = 0.41714... + No saturation being done + sage: D2.getbasis() + '[[1:-1:1], [-2:3:1], [-14:25:8]]' +@@ -1281,9 +1281,9 @@ cdef class _two_descent: + sage: D2.saturate() + Searching for points (bound = 8)...done: + found points which generate a subgroup of rank 3 +- and regulator 0.417143558758383969817119544618093396749810106098479 ++ and regulator 0.41714... + Processing points found during 2-descent...done: +- now regulator = 0.417143558758383969817119544618093396749810106098479 ++ now regulator = 0.41714... + No saturation being done + sage: D2.getbasis() + '[[1:-1:1], [-2:3:1], [-14:25:8]]' +@@ -1329,9 +1329,9 @@ cdef class _two_descent: + sage: D2.saturate() + Searching for points (bound = 8)...done: + found points which generate a subgroup of rank 3 +- and regulator 0.417143558758383969817119544618093396749810106098479 ++ and regulator 0.41714... + Processing points found during 2-descent...done: +- now regulator = 0.417143558758383969817119544618093396749810106098479 ++ now regulator = 0.41714... + No saturation being done + sage: D2.getbasis() + '[[1:-1:1], [-2:3:1], [-14:25:8]]' diff --git a/pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch b/pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch new file mode 100644 index 000000000000..41747635cacd --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/matplotlib-normed-deprecated.patch @@ -0,0 +1,12 @@ +diff --git a/src/sage/all.py b/src/sage/all.py +index 14cec431f1..25a35a0522 100644 +--- a/src/sage/all.py ++++ b/src/sage/all.py +@@ -310,6 +310,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0)) + # Ignore all deprecations from IPython etc. + warnings.filterwarnings('ignore', + module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)') ++warnings.filterwarnings('ignore', "The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.") # matplotlib normed deprecation + # However, be sure to keep OUR deprecation warnings + warnings.filterwarnings('default', + '[\s\S]*See http://trac.sagemath.org/[0-9]* for details.') diff --git a/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch b/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch new file mode 100644 index 000000000000..fad434e52ada --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/maxima-5.41.0-doctests.patch @@ -0,0 +1,48 @@ +diff --git a/src/sage/interfaces/maxima_abstract.py b/src/sage/interfaces/maxima_abstract.py +index 961c20aaac..3d601d8939 100644 +--- a/src/sage/interfaces/maxima_abstract.py ++++ b/src/sage/interfaces/maxima_abstract.py +@@ -1743,7 +1743,7 @@ class MaximaAbstractElement(ExtraTabCompletion, InterfaceElement): + sage: y,d = var('y,d') + sage: f = function('f') + sage: latex(maxima(derivative(f(x*y), x))) +- \left(\left.{{{\it \partial}}\over{{\it \partial}\, {\it t_0}}}\,f\left({\it t_0}\right) \right|_{{\it t_0}={\it x}\, {\it y}}\right)\,{\it y} ++ \left(\left.{{{\it \partial}}\over{{\it \partial}\, {\it t}_{0}}}\,f\left({\it t}_{0}\right) \right|_{{\it t}_{0}={\it x}\, {\it y}}\right)\,{\it y} + sage: latex(maxima(derivative(f(x,y,d), d,x,x,y))) + {{{\it \partial}^4}\over{{\it \partial}\,{\it d}\, {\it \partial}\,{\it x}^2\,{\it \partial}\, {\it y}}}\,f\left({\it x} , {\it y} , {\it d}\right) + sage: latex(maxima(d/(d-2))) +diff --git a/src/sage/manifolds/differentiable/metric.py b/src/sage/manifolds/differentiable/metric.py +index 3cd6ad3235..1e18af1a6b 100644 +--- a/src/sage/manifolds/differentiable/metric.py ++++ b/src/sage/manifolds/differentiable/metric.py +@@ -993,7 +993,7 @@ class PseudoRiemannianMetric(TensorField): + 2-dimensional differentiable manifold S^2 + sage: g.riemann()[:] + [[[[0, 0], [0, 0]], [[0, sin(th)^2], [-sin(th)^2, 0]]], +- [[[0, (cos(th)^2 - 1)/sin(th)^2], [1, 0]], [[0, 0], [0, 0]]]] ++ [[[0, -1], [1, 0]], [[0, 0], [0, 0]]]] + + In dimension 2, the Riemann tensor can be expressed entirely in terms of + the Ricci scalar `r`: +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index dfb8751467..27402e54ab 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -7154,7 +7154,7 @@ cdef class Expression(CommutativeRingElement): + sage: ex = lcm(sin(x)^2 - 1, sin(x)^2 + sin(x)); ex + (sin(x)^2 + sin(x))*(sin(x)^2 - 1)/(sin(x) + 1) + sage: ex.simplify_full() +- -cos(x)^2*sin(x) ++ sin(x)^3 - sin(x) + + TESTS: + +@@ -10004,7 +10004,7 @@ cdef class Expression(CommutativeRingElement): + + sage: f=tan(3*x) + sage: f.simplify_trig() +- (4*cos(x)^2 - 1)*sin(x)/(4*cos(x)^3 - 3*cos(x)) ++ -(4*cos(x)^2 - 1)*sin(x)/(4*cos(x)*sin(x)^2 - cos(x)) + sage: f.simplify_trig(False) + sin(3*x)/cos(3*x) + diff --git a/pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch b/pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch new file mode 100644 index 000000000000..5927bc116096 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/numpy-1.14.3.patch @@ -0,0 +1,812 @@ +diff --git a/src/doc/en/faq/faq-usage.rst b/src/doc/en/faq/faq-usage.rst +index 79b4205fd3..9a89bd2136 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 df85cce43d..34ea164be0 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.]], + +- [[ 1., 1., 1.], +- [ 0., 0., 0.], +- [ 1., 1., 1.]], ++ [[1., 1., 1.], ++ [0., 0., 0.], ++ [1., 1., 1.]], + +- [[ 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. ]], + +- [[ 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. ]], + +- [[ 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 61b1003002..4baee9cbbd 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 c37700d14e..49b7298d0b 100644 +--- a/src/sage/finance/time_series.pyx ++++ b/src/sage/finance/time_series.pyx +@@ -109,8 +109,8 @@ 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]) +@@ -2098,14 +2098,14 @@ 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 931a4b41e4..bf33fc483d 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 017c85a96f..33fbb499c5 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 679384c907..d63b295a4c 100644 +--- a/src/sage/functions/other.py ++++ b/src/sage/functions/other.py +@@ -390,7 +390,7 @@ 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:: + +@@ -539,7 +539,7 @@ 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) + +@@ -840,7 +840,7 @@ 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/trig.py b/src/sage/functions/trig.py +index e7e7a311cd..e7ff78a9de 100644 +--- a/src/sage/functions/trig.py ++++ b/src/sage/functions/trig.py +@@ -731,7 +731,7 @@ 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) + +@@ -787,7 +787,7 @@ 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) + +@@ -845,7 +845,7 @@ 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) + +@@ -920,13 +920,13 @@ 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 19a1d37df0..5780dfae1c 100644 +--- a/src/sage/matrix/constructor.pyx ++++ b/src/sage/matrix/constructor.pyx +@@ -494,8 +494,8 @@ class MatrixFactory(object): + [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 48e0a8a97f..1be5d35b19 100644 +--- a/src/sage/matrix/matrix_double_dense.pyx ++++ b/src/sage/matrix/matrix_double_dense.pyx +@@ -2546,7 +2546,7 @@ 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:: + +@@ -3662,8 +3662,8 @@ 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 +@@ -3674,16 +3674,16 @@ 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 c698ba5e97..b743bab354 100644 +--- a/src/sage/matrix/special.py ++++ b/src/sage/matrix/special.py +@@ -705,7 +705,7 @@ 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] +@@ -715,7 +715,7 @@ 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 230f142117..2ab1c0ae68 100644 +--- a/src/sage/modules/free_module_element.pyx ++++ b/src/sage/modules/free_module_element.pyx +@@ -982,7 +982,7 @@ 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 +@@ -993,7 +993,7 @@ 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/numerical/optimize.py b/src/sage/numerical/optimize.py +index 17b5ebb84b..92ce35c502 100644 +--- a/src/sage/numerical/optimize.py ++++ b/src/sage/numerical/optimize.py +@@ -486,9 +486,9 @@ def minimize_constrained(func,cons,x0,gradient=None,algorithm='default', **args) + else: + min = optimize.fmin_tnc(f, x0, approx_grad=True, bounds=cons, messages=0, **args)[0] + elif isinstance(cons[0], function_type) or isinstance(cons[0], Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args) + elif isinstance(cons, function_type) or isinstance(cons, Expression): +- min = optimize.fmin_cobyla(f, x0, cons, iprint=0, **args) ++ min = optimize.fmin_cobyla(f, x0, cons, disp=0, **args) + return vector(RDF, min) + + +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/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) +- ++ 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 f66cd898b9..35995886d5 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 a0bfe080f5..7d95e7a1a8 100644 +--- a/src/sage/rings/rational.pyx ++++ b/src/sage/rings/rational.pyx +@@ -1056,7 +1056,7 @@ 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 4c630867a4..64e2187f5b 100644 +--- a/src/sage/rings/real_mpfr.pyx ++++ b/src/sage/rings/real_mpfr.pyx +@@ -1438,7 +1438,7 @@ 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 3d270ebf9d..1144f168e3 100644 +--- a/src/sage/schemes/elliptic_curves/height.py ++++ b/src/sage/schemes/elliptic_curves/height.py +@@ -1623,18 +1623,18 @@ 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 2dcb0492b9..2b1a06385c 100644 +--- a/src/sage/symbolic/ring.pyx ++++ b/src/sage/symbolic/ring.pyx +@@ -1135,7 +1135,7 @@ 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/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch b/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch new file mode 100644 index 000000000000..49cdfd189b92 --- /dev/null +++ b/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): + + """ + 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/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch b/pkgs/applications/science/math/sage/patches/python-5755-hotpatch.patch new file mode 100644 index 000000000000..1b64f39fe60f --- /dev/null +++ b/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/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch b/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch new file mode 100644 index 000000000000..ff1dcd22acf3 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/python3-syntax-without-write.patch @@ -0,0 +1,40 @@ +diff --git a/src/sage/tests/py3_syntax.py b/src/sage/tests/py3_syntax.py +index e564860b48..86ab3725f9 100644 +--- a/src/sage/tests/py3_syntax.py ++++ b/src/sage/tests/py3_syntax.py +@@ -179,15 +179,30 @@ class Python3SyntaxTest(SortedDirectoryWalkerABC): + sage: py3_syntax = Python3SyntaxTest() + sage: py3_syntax.test(src.name) + Invalid Python 3 syntax found: +- File "...py", line 1 +- print "invalid print statement" +- ^ +- SyntaxError: Missing parentheses in call to 'print' ++ Missing parentheses in call to 'print'... + sage: os.unlink(src.name) + """ ++ ++ # compile all given files in memory, printing all errors ++ # inspired by the py_compile module (but without writing to file) ++ script = """ ++import sys ++import importlib.machinery ++rv = 0 ++for file in sys.argv[1:]: ++ loader = importlib.machinery.SourceFileLoader('', file) ++ source_bytes = loader.get_data(file) ++ try: ++ code = loader.source_to_code(source_bytes, file) ++ except Exception as err: ++ print(err) ++ rv = 1 ++sys.exit(rv) ++""" + cmd = [ + 'python3', +- '-m', 'py_compile' ++ '-c', ++ script, + ] + list(filenames) + process = subprocess.Popen( + cmd, diff --git a/pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch b/pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch new file mode 100644 index 000000000000..b57e48b86dec --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/revert-269c1e1551285.patch @@ -0,0 +1,14 @@ +reverted: +--- b/src/sage/geometry/polyhedron/backend_cdd.py ++++ a/src/sage/geometry/polyhedron/backend_cdd.py +@@ -154,7 +154,9 @@ + ... [0.62, -1.38, 0.38],[0.144, -1.04, 0.04], + ... [0.1309090909, -1.0290909091, 0.04]] + sage: Polyhedron(point_list) ++ Traceback (most recent call last): ++ ... ++ ValueError: *Error: Numerical inconsistency is found. Use the GMP exact arithmetic. +- A 3-dimensional polyhedron in RDF^3 defined as the convex hull of 14 vertices + sage: Polyhedron(point_list, base_ring=QQ) + A 3-dimensional polyhedron in QQ^3 defined as the convex hull of 14 vertices + """ diff --git a/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch b/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch new file mode 100644 index 000000000000..42deef4eab0c --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/sagenb-sphinx-1.7.patch @@ -0,0 +1,31 @@ +From 7419e0246230594ebfd5e7a2fe6b80d67abfc98a Mon Sep 17 00:00:00 2001 +From: Jeroen Demeyer +Date: Tue, 20 Mar 2018 10:40:41 +0100 +Subject: Fix sphinxify doctests + +--- + sagenb/misc/sphinxify.py | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/sagenb/misc/sphinxify.py b/sagenb/misc/sphinxify.py +index 4f76d41..15623d9 100644 +--- a/sagenb/misc/sphinxify.py ++++ b/sagenb/misc/sphinxify.py +@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'): + + sage: from sage.misc.sphinxify import sphinxify + sage: sphinxify('A test') +- '...
    \n \n

    A test

    \n\n\n
    ' ++ '
    \n \n

    A test

    \n\n\n
    ' + sage: sphinxify('**Testing**\n`monospace`') +- '...
    Testing\n\n\n\n
    ' ++ '
    Testing\n\n\n\n
    ' + sage: sphinxify('`x=y`') +- '...
    \n \n

    x=y

    \n\n\n
    ' ++ '
    \n \n

    x=y

    \n\n\n
    ' + sage: sphinxify('`x=y`', format='text') + 'x=y\n' + sage: sphinxify(':math:`x=y`', format='text') +-- +cgit v1.0-1-gd88e + diff --git a/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch b/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch new file mode 100644 index 000000000000..c67b8942e28b --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/sphinx-1.7.patch @@ -0,0 +1,62 @@ +diff --git a/src/bin/sage b/src/bin/sage +index 397f30cbed..3fc473c343 100755 +--- a/src/bin/sage ++++ b/src/bin/sage +@@ -980,8 +980,11 @@ if [ "$1" = '-rsyncdist' -o "$1" = "--rsyncdist" ]; then + fi + + if [ "$1" = "-docbuild" -o "$1" = "--docbuild" ]; then ++ # Redirect stdin from /dev/null. This helps with running TeX which ++ # tends to ask interactive questions if something goes wrong. These ++ # cause the build to hang. If stdin is /dev/null, TeX just aborts. + shift +- exec sage-python23 -m "sage_setup.docbuild" "$@" ++ exec sage-python23 -m sage_setup.docbuild "$@" Introduction to the -adics ++
  • Introduction to the -adics
    • + """ + debug_inf(app, "???? Trying intersphinx for %s"%node['reftarget']) + builder = app.builder +diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py +index 4f76d4113a..8f426b5989 100644 +--- a/src/sage/misc/sphinxify.py ++++ b/src/sage/misc/sphinxify.py +@@ -47,11 +47,11 @@ def sphinxify(docstring, format='html'): + + sage: from sage.misc.sphinxify import sphinxify + sage: sphinxify('A test') +- '...
    \n \n

    A test

    \n\n\n
    ' ++ '
    \n \n

    A test

    \n\n\n
    ' + sage: sphinxify('**Testing**\n`monospace`') +- '...
    Testing\n\n\n\n
    ' ++ '
    Testing\n\n \n

    x=y

    \n\n\n
    ' ++ '
    \n \n

    x=y

    \n\n\n
    ' + sage: sphinxify('`x=y`', format='text') + 'x=y\n' + sage: sphinxify(':math:`x=y`', format='text') +diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py +index fda76a4174..d3413239dd 100644 +--- a/src/sage_setup/docbuild/sphinxbuild.py ++++ b/src/sage_setup/docbuild/sphinxbuild.py +@@ -207,7 +207,7 @@ def runsphinx(): + try: + sys.stdout = SageSphinxLogger(sys.stdout, os.path.basename(output_dir)) + sys.stderr = SageSphinxLogger(sys.stderr, os.path.basename(output_dir)) +- sphinx.cmdline.main(sys.argv) ++ sphinx.cmdline.main(sys.argv[1:]) + finally: + sys.stdout = saved_stdout + sys.stderr = saved_stderr diff --git a/pkgs/applications/science/math/sage/patches/zn_poly_version.patch b/pkgs/applications/science/math/sage/patches/zn_poly_version.patch new file mode 100644 index 000000000000..92ea4303e477 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/zn_poly_version.patch @@ -0,0 +1,13 @@ +diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py +index 7ff4f21675..1d72168833 100644 +--- a/src/sage/misc/package.py ++++ b/src/sage/misc/package.py +@@ -350,7 +350,7 @@ def package_versions(package_type, local=False): + sage: 'gap' in std + True + sage: std['zn_poly'] +- ('0.9.p11', '0.9.p11') ++ ('0.9', '0.9.p11') + """ + return {pkg['name']: (pkg['installed_version'], pkg['remote_version']) for pkg in list_packages(package_type, local=local).values()} + diff --git a/pkgs/applications/science/math/sage/pybrial.nix b/pkgs/applications/science/math/sage/pybrial.nix new file mode 100644 index 000000000000..f5cb39603c32 --- /dev/null +++ b/pkgs/applications/science/math/sage/pybrial.nix @@ -0,0 +1,29 @@ +{ stdenv +, fetchFromGitHub +, buildPythonPackage +}: +# 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 = "1.2.3"; + + # included with BRiAl source + src = fetchFromGitHub { + owner = "BRiAl"; + repo = "BRiAl"; + rev = "${version}"; + sha256 = "0qy4cwy7qrk4zg151cmws5cglaa866z461cnj9wdnalabs7v7qbg"; + }; + + sourceRoot = "source/sage-brial"; + + meta = with stdenv.lib; { + description = "python implementation of BRiAl"; + license = licenses.gpl2; + maintainers = with maintainers; [ timokau ]; + }; +} diff --git a/pkgs/applications/science/math/sage/python-openid.nix b/pkgs/applications/science/math/sage/python-openid.nix new file mode 100644 index 000000000000..184eaf29bdd3 --- /dev/null +++ b/pkgs/applications/science/math/sage/python-openid.nix @@ -0,0 +1,42 @@ +{ 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 = [ + 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 ]; + 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/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix new file mode 100644 index 000000000000..317eb6e16c49 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -0,0 +1,162 @@ +{ stdenv +, lib +, writeTextFile +, python +, sage-src +, sagelib +, env-locations +, gfortran +, bash +, coreutils +, gnused +, gnugrep +, binutils +, pythonEnv +, python3 +, pkg-config +, pari +, gap-libgap-compatible +, libgap +, ecl +, maxima-ecl +, singular +, giac +, palp +, rWrapper +, gfan +, cddlib +, jmol +, tachyon +, glpk +, eclib +, sympow +, nauty +, sqlite +, ppl +, ecm +, lcalc +, rubiks +, flintqs +, openblas-cblas-pc +, flint +, gmp +, mpfr +, pynac +, zlib +, gsl +, ntl +}: + +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-libgap-compatible + libgap + ecl + maxima-ecl + singular + giac + palp + rWrapper + gfan + cddlib + jmol + tachyon + glpk + eclib + sympow + nauty + sqlite + ppl + ecm + lcalc + rubiks + flintqs + ] + )); +in +writeTextFile rec { + name = "sage-env"; + destination = "/${name}"; + text = '' + export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [ + # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case + # for it outside of the tests. However since singular and openblas are runtime dependencies anyways + # and openblas-cblas-pc is tiny, it doesn't really hurt to include. + singular + openblas-cblas-pc + ]) + }' + export SAGE_ROOT='${sage-src}' + export SAGE_LOCAL='@sage-local@' + export SAGE_SHARE='${sagelib}/share' + orig_path="$PATH" + export PATH='${runtimepath}' + + # set dependent vars, like JUPYTER_CONFIG_DIR + source "${sage-src}/src/bin/sage-env" + export PATH="${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:-${sage-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${pkg}/lib") [ + flint + libgap + glpk + gmp + mpfr + pari + pynac + zlib + eclib + gsl + ntl + jmol + sympow + ]) + }' + export CFLAGS='${ + lib.concatStringsSep " " (map (pkg: "-isystem ${pkg}/include") [ + singular + gmp.dev + glpk + flint + libgap + pynac + mpfr.dev + ]) + }' + + export SAGE_LIB='${sagelib}/${python.sitePackages}' + + export SAGE_EXTCODE='${sage-src}/src/ext' + + # for find_library + export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH" + ''; +} diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix new file mode 100644 index 000000000000..44b817944674 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -0,0 +1,197 @@ +{ stdenv +, fetchFromGitHub +, fetchpatch +}: +stdenv.mkDerivation rec { + version = "8.2"; + name = "sage-src-${version}"; + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sage"; + rev = version; + sha256 = "0d7vc16s7dj23an2cb8v5bhbnc6nsw20qhnnxr0xh8qg629027b8"; + }; + + nixPatches = [ + # https://trac.sagemath.org/ticket/25309 + (fetchpatch { + name = "spkg-paths.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69&id=a86151429ccce1ddd085e8090ada8ebdf02f3310"; + sha256 = "1xb9108rzzkdhn71vw44525620d3ww9jv1fph5a77v9y7nf9wgr7"; + }) + (fetchpatch { + name = "maxima-fas.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69"; + sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i"; + }) + + # https://trac.sagemath.org/ticket/25328 + (fetchpatch { + name = "respect-jupyter-path.patch"; + url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=029123097d79f2c67bca2d725c470ef667a88ca2"; + sha256 = "0qw9p541ip0kn2gfvn4i05a06p50f3q46847gqfjjgzxhn62znfw"; + }) + + # 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"; + }) + + # https://trac.sagemath.org/ticket/25357 rebased on 8.2 + ./patches/python3-syntax-without-write.patch + + # https://trac.sagemath.org/ticket/25314 + (fetchpatch { + name = "make-qepcad-test-optional.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=fe294c58bd035ef427e268901d54a6faa0058138"; + sha256 = "003d5baf5c0n5rfg010ijwkwz8kg0s414cxwczs2vhdayxdixbix"; + }) + + # https://trac.sagemath.org/ticket/25316 + ./patches/python-5755-hotpatch.patch + + # https://trac.sagemath.org/ticket/25354 + # https://trac.sagemath.org/ticket/25531 + (fetchpatch { + name = "cysignals-include.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=28778bd25a37c80884d2b24e0683fb2989300cef"; + sha256 = "0fiiiw91pgs8avm9ggj8hb64bhqzl6jcw094d94nhirmh8w2jmc5"; + }) + + # https://trac.sagemath.org/ticket/25315 + (fetchpatch { + name = "find-libraries-in-dyld-library-path.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=20d4593876ce9c6004eac2ab6fd61786d0d96a06"; + sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc"; + }) + + # Pari upstream has since accepted a patch, so this patch won't be necessary once sage updates pari. + # https://trac.sagemath.org/ticket/25312 + ./patches/pari-stackwarn.patch + + # https://trac.sagemath.org/ticket/25311 + ./patches/zn_poly_version.patch + + # https://trac.sagemath.org/ticket/25345 + # (upstream patch doesn't apply on 8.2 source) + ./patches/dochtml-optional.patch + ]; + + packageUpgradePatches = [ + # matplotlib 2.2.2 deprecated `normed` (replaced by `density`). + # This patch only ignores the warning. It would be equally easy to fix it + # (by replacing all mentions of `normed` by `density`), but its better to + # stay close to sage upstream. I didn't open an upstream ticket about it + # because the matplotlib update also requires a new dependency (kiwisolver) + # and I don't want to invest the time to learn how to add it. + ./patches/matplotlib-normed-deprecated.patch + + # Update to 20171219 broke the doctests because of insignificant precision + # changes, make the doctests less fragile. + # I didn't open an upstream ticket because its not entirely clear if + # 20171219 is really "released" yet. It is listed on the github releases + # page, but not marked as "latest release" and the homepage still links to + # the last version. + ./patches/eclib-regulator-precision.patch + + # sphinx 1.6 -> 1.7 upgrade + # https://trac.sagemath.org/ticket/24935 + ./patches/sphinx-1.7.patch + + # https://trac.sagemath.org/ticket/25320 + (fetchpatch { + name = "zero_division_error_formatting.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=f79070ddd09fa0ad6b340b097bd8d690a7aa35f0"; + sha256 = "02wsc3wbp8g8dk5jcjyv18d9v537h3zp5v8lwir46j4na4kj0dlb"; + }) + + # Adapt hashes to new boost version + # https://trac.sagemath.org/ticket/22243 + # (this ticket doesn't only upgrade boost but also avoids this problem in the future) + (fetchpatch { + name = "boost-upgrade.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=a24a9c6b30b93957333a3116196214a931325b69"; + sha256 = "0z3870g2ms2a81vnw08dc2i4k7jr62w8fggvcdwaavgd1wvdxwfl"; + }) + + # gfan 0.6.2 + # https://trac.sagemath.org/ticket/23353 + (fetchpatch { + name = "gfan-update.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=420215fc469cde733ec7a339e59b78ad6eec804c&id=112498a293ea2bf563e41aed35f1aa608f01b349"; + sha256 = "0ga3hkx8cr23dpc919lgvpi5lmy0d728jkq9z6kf0fl9s8g31mxb"; + }) + + # New glpk version has new warnings, filter those out until upstream sage has found a solution + # https://trac.sagemath.org/ticket/24824 + (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; + }) + + # https://trac.sagemath.org/ticket/25329 + (fetchpatch { + name = "dont-check-exact-glpk-version.patch"; + url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=89d068d8d77316bfffa6bf8e9ebf70b3b3b88e5c"; + sha256 = "00knwxs6fmymfgfl0q5kcavmxm9sf90a4r76y35n5s55gj8pl918"; + }) + + # https://trac.sagemath.org/ticket/25355 + (fetchpatch { + name = "maxima-5.41.0.patch"; + url = "https://git.sagemath.org/sage.git/patch/?id=87328023c4739abdf24108038201e3fa9bdfc739"; + sha256 = "0hxi7qr5mfx1bc32r8j7iba4gzd7c6v63asylyf5cbyp86azpb7i"; + }) + + # Update cddlib from 0.94g to 0.94h. + # https://trac.sagemath.org/ticket/25341 (doesn't apply to 8.2 sources) + (fetchpatch { + url = "https://salsa.debian.org/science-team/sagemath/raw/58bbba93a807ca2933ca317501d093a1bb4b84db/debian/patches/u2-version-cddlib-094h.patch"; + sha256 = "0fmw7pzbaxs2dshky6iw9pr8i23p9ih2y2lw661qypdrxh5xw03k"; + stripLen = 1; + }) + ./patches/revert-269c1e1551285.patch + + + # Only formatting changes. + # https://trac.sagemath.org/ticket/25260 + ./patches/numpy-1.14.3.patch + + # https://trac.sagemath.org/ticket/24374 + (fetchpatch { + name = "networkx-2.1.patch"; + url = "https://salsa.debian.org/science-team/sagemath/raw/487df9ae48ca1d93d9b1cb3af8745d31e30fb741/debian/patches/u0-version-networkx-2.1.patch"; + sha256 = "1xxxawygbgxgvlv7b4w8hhzgdnva4rhmgdxaiaa3pwdwln0yc750"; + stripLen = 1; + }) + + ]; + + patches = nixPatches ++ 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 '#!${stdenv.shell} + python "$@"' > build/bin/sage-python23 + + # Do not use sage-env-config (generated by ./configure). + # Instead variables are set manually. + echo '# do nothing' > src/bin/sage-env-config + ''; + + configurePhase = "# do nothing"; + + buildPhase = "# do nothing"; + + installPhase = '' + cp -r . "$out" + ''; +} diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix new file mode 100644 index 000000000000..3d1ebe87c6b7 --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-with-env.nix @@ -0,0 +1,129 @@ +{ stdenv +, lib +, makeWrapper +, sage-env +, sage-src +, sagelib +, sagedoc +, openblasCompat +, openblas-blas-pc +, openblas-cblas-pc +, openblas-lapack-pc +, pkg-config +, three +, singular +, libgap +, gap-libgap-compatible +, gcc +, giac +, maxima-ecl +, pari +, gmp +, gfan +, python2 +, flintqs +, eclib +, ntl +, ecm +, pynac +, pythonEnv +}: + +let + buildInputs = [ + pythonEnv # for patchShebangs + makeWrapper + pkg-config + openblasCompat # lots of segfaults with regular (64 bit) openblas + openblas-blas-pc + openblas-cblas-pc + openblas-lapack-pc + singular + three + pynac + giac + libgap + gap-libgap-compatible + 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 isNull dep 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 = sage-src.version; + name = "sage-with-env-${version}"; + + inherit buildInputs; + + src = sage-src; + + configurePhase = "#do nothing"; + + buildPhase = '' + mkdir installed + for pkg in ${lib.concatStringsSep " " input_names}; do + touch "installed/$pkg" + done + ''; + + 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" + 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" + ''; +} diff --git a/pkgs/applications/science/math/sage/sage-wrapper.nix b/pkgs/applications/science/math/sage/sage-wrapper.nix new file mode 100644 index 000000000000..06b667f426fa --- /dev/null +++ b/pkgs/applications/science/math/sage/sage-wrapper.nix @@ -0,0 +1,41 @@ +{ stdenv +, makeWrapper +, sage +, sage-src +, sagedoc +, withDoc +}: + +stdenv.mkDerivation rec { + version = sage.version; + name = "sage-wrapper-${version}"; + + buildInputs = [ + makeWrapper + ]; + + unpackPhase = "#do nothing"; + configurePhase = "#do nothing"; + buildPhase = "#do nothing"; + + installPhase = '' + mkdir -p "$out/bin" + makeWrapper "${sage}/bin/sage" "$out/bin/sage" \ + --set SAGE_DOC_SRC_OVERRIDE "${sage-src}/src/doc" ${ + stdenv.lib.optionalString withDoc "--set SAGE_DOC_OVERRIDE ${sagedoc}/share/doc/sage" + } + ''; + + doInstallCheck = withDoc; + installCheckPhase = '' + export HOME="$TMPDIR/sage-home" + mkdir -p "$HOME" + "$out/bin/sage" -c 'browse_sage_doc._open("reference", testing=True)' + ''; + + 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/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix new file mode 100644 index 000000000000..b1e5d7278b0f --- /dev/null +++ b/pkgs/applications/science/math/sage/sage.nix @@ -0,0 +1,32 @@ +{ stdenv +, sage-with-env +, makeWrapper +}: + +stdenv.mkDerivation rec { + version = sage-with-env.version; + name = "sage-${version}"; + + buildInputs = [ + makeWrapper + ]; + + unpackPhase = "#do nothing"; + configurePhase = "#do nothing"; + buildPhase = "#do nothing"; + + installPhase = '' + mkdir -p "$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 "$HOME" + + # "--long" tests are in the order of 1h, without "--long" its 1/2h + "$out/bin/sage" -t --nthreads "$NIX_BUILD_CORES" --optional=sage --long --all + ''; +} diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix new file mode 100644 index 000000000000..7b280e9e0280 --- /dev/null +++ b/pkgs/applications/science/math/sage/sagedoc.nix @@ -0,0 +1,97 @@ +{ pkgs +, stdenv +, sage-src +, env-locations +, sage-with-env +, sagelib +, python2 +, psutil +, future +, sphinx +, sagenb +, maxima-ecl +, networkx +, scipy +, sympy +, matplotlib +, pillow +, ipykernel +, jupyter_client +, tachyon +, jmol +, ipywidgets +, typing +, cddlib +, pybrial +}: + +stdenv.mkDerivation rec { + version = sage-src.version; + name = "sagedoc-${version}"; + + + # Building the documentation has many dependencies, because all documented + # modules are imported and because matplotlib is used to produce plots. + buildInputs = [ + sagelib + python2 + psutil + future + sphinx + sagenb + maxima-ecl + networkx + scipy + sympy + matplotlib + pillow + ipykernel + jupyter_client + tachyon + jmol + ipywidgets + typing + cddlib + pybrial + ]; + + unpackPhase = '' + export SAGE_DOC_OVERRIDE="$PWD/share/doc/sage" + export SAGE_DOC_SRC_OVERRIDE="$PWD/docsrc" + + cp -r "${sage-src}/src/doc" "$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" + + ${sage-with-env}/bin/sage -python -m sage_setup.docbuild \ + --mathjax \ + --no-pdf-links \ + all html + ''; + + installPhase = '' + cd "$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 = '' + ${sage-with-env}/bin/sage -t --optional=dochtml --all + ''; +} diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix new file mode 100644 index 000000000000..a053d997bf9a --- /dev/null +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -0,0 +1,139 @@ +{ stdenv +, sage-src +, perl +, buildPythonPackage +, arb +, openblasCompat +, openblas-blas-pc +, openblas-cblas-pc +, openblas-lapack-pc +, brial +, cliquer +, cypari2 +, cysignals +, cython +, ecl +, eclib +, ecm +, flint +, gd +, givaro +, glpk +, gsl +, iml +, jinja2 +, lcalc +, lrcalc +, libgap +, linbox +, m4ri +, m4rie +, libmpc +, mpfi +, ntl +, numpy +, pari +, pkgconfig +, planarity +, ppl +, pynac +, python +, ratpoints +, readline +, rankwidth +, symmetrica +, zn_poly +, fflas-ffpack +, boost +, singular +, pip +, jupyter_core +}: + +buildPythonPackage rec { + format = "other"; + version = sage-src.version; + pname = "sagelib"; + + src = sage-src; + + nativeBuildInputs = [ + iml + perl + openblas-blas-pc + openblas-cblas-pc + openblas-lapack-pc + jupyter_core + ]; + + buildInputs = [ + gd + readline + ]; + + propagatedBuildInputs = [ + cypari2 + jinja2 + numpy + pkgconfig + boost + arb + brial + cliquer + ecl + eclib + ecm + fflas-ffpack + flint + givaro + glpk + gsl + lcalc + libgap + libmpc + linbox + lrcalc + m4ri + m4rie + mpfi + ntl + openblasCompat + pari + planarity + ppl + pynac + rankwidth + ratpoints + singular + symmetrica + zn_poly + pip + cython + cysignals + ]; + + buildPhase = '' + export SAGE_ROOT="$PWD" + export SAGE_LOCAL="$SAGE_ROOT" + export SAGE_SHARE="$SAGE_LOCAL/share" + 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" + + cd src + source bin/sage-dist-helpers + + ${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/pkgs/applications/science/math/sage/sagenb.nix b/pkgs/applications/science/math/sage/sagenb.nix new file mode 100644 index 000000000000..5ab387ebc5e1 --- /dev/null +++ b/pkgs/applications/science/math/sage/sagenb.nix @@ -0,0 +1,49 @@ +# Has a cyclic dependency with sage (not expressed here) and is not useful outside of sage +{ stdenv +, fetchpatch +, python +, buildPythonPackage +, fetchFromGitHub +, mathjax +, twisted +, flask +, flask-oldsessions +, flask-openid +, flask-autoindex +, flask-babel +}: + +buildPythonPackage rec { + pname = "sagenb"; + version = "2018-06-26"; # not 1.0.1 because of new flask syntax + + src = fetchFromGitHub { + owner = "sagemath"; + repo = "sagenb"; + rev = "b360a0172e15501fb0163d02dce713a561fee2af"; + sha256 = "12anydw0v9w23rbc0a94bqmjhjdir9h820c5zdhipw9ccdcc2jlf"; + }; + + 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 = '' + ln -s ${mathjax}/lib/node_modules/mathjax "$out/${python.sitePackages}/mathjax" + ''; +} diff --git a/pkgs/applications/science/math/sage/shebangs.patch b/pkgs/applications/science/math/sage/shebangs.patch deleted file mode 100644 index 96ed5a4bc6c3..000000000000 --- a/pkgs/applications/science/math/sage/shebangs.patch +++ /dev/null @@ -1,36 +0,0 @@ -diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg -index 83e61a7e0d..942ba206c7 100755 ---- a/build/bin/sage-spkg -+++ b/build/bin/sage-spkg -@@ -648,8 +648,12 @@ if ! sage-apply-patches; then - error_msg "Error applying patches" - exit 1 - fi -+ -+@bash@/bin/bash @patchSageShebangs@ . -+ - cd .. - -+ - ################################################################## - # The package has been extracted, prepare for installation - ################################################################## -@@ -671,7 +675,7 @@ write_script_wrapper() { - local tmpscript="$(dirname "$script")/.tmp-${script##*/}" - - cat > "$tmpscript" <<__EOF__ --#!/usr/bin/env bash -+#! @bash@/bin/bash - - export SAGE_ROOT="$SAGE_ROOT" - export SAGE_SRC="$SAGE_SRC" -@@ -833,6 +837,9 @@ if [ "$UNAME" = "CYGWIN" ]; then - sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null - fi - -+@bash@/bin/bash @patchSageShebangs@ . -+@bash@/bin/bash @patchSageShebangs@ "$out/bin" -+ - echo "Successfully installed $PKG_NAME" - - if [ "$SAGE_CHECK" = "yes" ]; then diff --git a/pkgs/applications/science/math/sage/spkg-giac.patch b/pkgs/applications/science/math/sage/spkg-giac.patch deleted file mode 100644 index c79d4422133d..000000000000 --- a/pkgs/applications/science/math/sage/spkg-giac.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff --git a/build/pkgs/giac/spkg-install b/build/pkgs/giac/spkg-install -index bdd8df6cb8..3fd7a3ef8a 100644 ---- a/build/pkgs/giac/spkg-install -+++ b/build/pkgs/giac/spkg-install -@@ -2,6 +2,15 @@ - ## Giac - ########################################### - -+# Fix hardcoded paths, while making sure to only update timestamps of actually -+# changed files (otherwise confuses make) -+grep -rlF '/bin/cp' . | while read file -+do -+ sed -e 's@/bin/cp@cp@g' -i "$file" -+done -+ -+# Fix input parser syntax -+sed -e 's@yylex (&yylval)@yylex (\&yyval, scanner)@gp' -i 'src/src/input_parser.cc' - - if [ "$SAGE_LOCAL" = "" ]; then - echo "SAGE_LOCAL undefined ... exiting"; diff --git a/pkgs/applications/science/math/sage/spkg-git.patch b/pkgs/applications/science/math/sage/spkg-git.patch deleted file mode 100644 index 74f552dd3c36..000000000000 --- a/pkgs/applications/science/math/sage/spkg-git.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/build/pkgs/git/spkg-install b/build/pkgs/git/spkg-install -index 87874de3d8..b0906245fa 100644 ---- a/build/pkgs/git/spkg-install -+++ b/build/pkgs/git/spkg-install -@@ -33,6 +33,13 @@ fi - - cd src - -+# Fix hardcoded paths, while making sure to only update timestamps of actually -+# changed files (otherwise confuses make) -+grep -rlF '/usr/bin/perl' . | while read file -+do -+ sed -e 's@/usr/bin/perl@perl@g' -i "$file" -+done -+ - # We don't want to think about Fink or Macports - export NO_FINK=1 - export NO_DARWIN_PORTS=1 diff --git a/pkgs/applications/science/math/sage/spkg-python.patch b/pkgs/applications/science/math/sage/spkg-python.patch deleted file mode 100644 index e39981b6552a..000000000000 --- a/pkgs/applications/science/math/sage/spkg-python.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/build/pkgs/python3/spkg-build b/build/pkgs/python3/spkg-build -index 56db087ae5..b450703c5f 100644 ---- a/build/pkgs/python3/spkg-build -+++ b/build/pkgs/python3/spkg-build -@@ -27,6 +27,8 @@ fi - export EXTRA_CFLAGS="`testcflags.sh -Wno-unused` $CFLAGS" - unset CFLAGS - -+export LDFLAGS="$LDFLAGS -lcrypt" -+ - if [ "$UNAME" = Darwin ]; then - PYTHON_CONFIGURE="--disable-toolbox-glue $PYTHON_CONFIGURE" - diff --git a/pkgs/applications/science/math/sage/spkg-singular.patch b/pkgs/applications/science/math/sage/spkg-singular.patch deleted file mode 100644 index 606ffcd3ad4e..000000000000 --- a/pkgs/applications/science/math/sage/spkg-singular.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/build/pkgs/singular/spkg-install b/build/pkgs/singular/spkg-install -index 8caafb1699..3c34e6608a 100644 ---- a/build/pkgs/singular/spkg-install -+++ b/build/pkgs/singular/spkg-install -@@ -2,6 +2,13 @@ - ## Singular - ########################################### - -+# Fix hardcoded paths, while making sure to only update timestamps of actually -+# changed files (otherwise confuses make) -+grep -rlF '/bin/rm' . | while read file -+do -+ sed -e 's@/bin/rm@rm@g' -i "$file" -+done -+ - if [ -z "$SAGE_LOCAL" ]; then - echo >&2 "Error: SAGE_LOCAL undefined -- exiting..." - echo >&2 "Maybe run 'sage -sh'?" diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index ab740cbfec61..a13b06c91bfb 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20381,7 +20381,10 @@ with pkgs; petsc = callPackage ../development/libraries/science/math/petsc { }; - sage = callPackage ../applications/science/math/sage { }; + sage = callPackage ../applications/science/math/sage { + nixpkgs = pkgs; + }; + sageWithDoc = sage.override { withDoc = true; }; suitesparse_4_2 = callPackage ../development/libraries/science/math/suitesparse/4.2.nix { }; suitesparse_4_4 = callPackage ../development/libraries/science/math/suitesparse {}; -- cgit 1.4.1 From 1d54dc684116a847cea89d8cc1d6620d06b66f6b Mon Sep 17 00:00:00 2001 From: Ryan Mulligan Date: Fri, 29 Jun 2018 17:18:27 -0700 Subject: treewide: http -> https --- doc/languages-frameworks/python.section.md | 2 +- pkgs/applications/science/astronomy/gravit/default.nix | 2 +- pkgs/development/compilers/polyml/5.6.nix | 2 +- pkgs/development/compilers/polyml/default.nix | 2 +- pkgs/development/compilers/scala/2.11.nix | 2 +- pkgs/development/python-modules/langcodes/default.nix | 2 +- pkgs/development/python-modules/lxml/default.nix | 4 ++-- pkgs/development/python-modules/pymc3/default.nix | 2 +- pkgs/development/python-modules/python3-openid/default.nix | 2 +- pkgs/development/tools/misc/epm/default.nix | 2 +- pkgs/servers/sabnzbd/default.nix | 2 +- pkgs/shells/zsh/oh-my-zsh/default.nix | 2 +- pkgs/tools/security/volatility/default.nix | 2 +- 13 files changed, 14 insertions(+), 14 deletions(-) (limited to 'pkgs/applications') diff --git a/doc/languages-frameworks/python.section.md b/doc/languages-frameworks/python.section.md index 4daf488bb28f..c4a5bb0612c9 100644 --- a/doc/languages-frameworks/python.section.md +++ b/doc/languages-frameworks/python.section.md @@ -328,7 +328,7 @@ when building the bindings and are therefore added as `buildInputs`. meta = { description = "Pythonic binding for the libxml2 and libxslt libraries"; - homepage = http://lxml.de; + homepage = https://lxml.de; license = licenses.bsd3; maintainers = with maintainers; [ sjourdois ]; }; diff --git a/pkgs/applications/science/astronomy/gravit/default.nix b/pkgs/applications/science/astronomy/gravit/default.nix index 9edc6220899e..03d0018f237b 100644 --- a/pkgs/applications/science/astronomy/gravit/default.nix +++ b/pkgs/applications/science/astronomy/gravit/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = { - homepage = http://gravit.slowchop.com; + homepage = https://gravit.slowchop.com; description = "Beautiful OpenGL-based gravity simulator"; license = stdenv.lib.licenses.gpl2; diff --git a/pkgs/development/compilers/polyml/5.6.nix b/pkgs/development/compilers/polyml/5.6.nix index 8b5d14e7f5fb..7f22f4de6244 100644 --- a/pkgs/development/compilers/polyml/5.6.nix +++ b/pkgs/development/compilers/polyml/5.6.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation { longDescription = '' Poly/ML is a full implementation of Standard ML. ''; - homepage = http://www.polyml.org/; + homepage = https://www.polyml.org/; license = stdenv.lib.licenses.lgpl21; platforms = with stdenv.lib.platforms; linux; maintainers = [ #Add your name here! diff --git a/pkgs/development/compilers/polyml/default.nix b/pkgs/development/compilers/polyml/default.nix index de5b85055273..b7feed84c37f 100644 --- a/pkgs/development/compilers/polyml/default.nix +++ b/pkgs/development/compilers/polyml/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { longDescription = '' Poly/ML is a full implementation of Standard ML. ''; - homepage = http://www.polyml.org/; + homepage = https://www.polyml.org/; license = licenses.lgpl21; platforms = with platforms; (linux ++ darwin); maintainers = with maintainers; [ z77z yurrriq ]; diff --git a/pkgs/development/compilers/scala/2.11.nix b/pkgs/development/compilers/scala/2.11.nix index b1100eb8aa9d..a1f803b67193 100644 --- a/pkgs/development/compilers/scala/2.11.nix +++ b/pkgs/development/compilers/scala/2.11.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { Code sizes are typically reduced by a factor of two to three when compared to an equivalent Java application. ''; - homepage = http://www.scala-lang.org/; + homepage = https://www.scala-lang.org/; license = stdenv.lib.licenses.bsd3; platforms = stdenv.lib.platforms.all; branch = "2.11"; diff --git a/pkgs/development/python-modules/langcodes/default.nix b/pkgs/development/python-modules/langcodes/default.nix index d1d25f5407c2..d73940e56a6d 100644 --- a/pkgs/development/python-modules/langcodes/default.nix +++ b/pkgs/development/python-modules/langcodes/default.nix @@ -27,7 +27,7 @@ buildPythonPackage rec { meta = with lib; { description = "A toolkit for working with and comparing the standardized codes for languages, such as ‘en’ for English or ‘es’ for Spanish"; - homepage = http://github.com/LuminosoInsight/langcodes; + homepage = https://github.com/LuminosoInsight/langcodes; license = licenses.mit; maintainers = with maintainers; [ ixxie ]; }; diff --git a/pkgs/development/python-modules/lxml/default.nix b/pkgs/development/python-modules/lxml/default.nix index 9fd050ac35ed..8b321b911ccd 100644 --- a/pkgs/development/python-modules/lxml/default.nix +++ b/pkgs/development/python-modules/lxml/default.nix @@ -20,8 +20,8 @@ buildPythonPackage rec { meta = { description = "Pythonic binding for the libxml2 and libxslt libraries"; - homepage = http://lxml.de; + homepage = https://lxml.de; license = stdenv.lib.licenses.bsd3; maintainers = with stdenv.lib.maintainers; [ sjourdois ]; }; -} \ No newline at end of file +} diff --git a/pkgs/development/python-modules/pymc3/default.nix b/pkgs/development/python-modules/pymc3/default.nix index 015233fba8e6..a0dd6113b750 100644 --- a/pkgs/development/python-modules/pymc3/default.nix +++ b/pkgs/development/python-modules/pymc3/default.nix @@ -57,7 +57,7 @@ buildPythonPackage rec { meta = { description = "Bayesian estimation, particularly using Markov chain Monte Carlo (MCMC)"; - homepage = http://github.com/pymc-devs/pymc3; + homepage = https://github.com/pymc-devs/pymc3; license = lib.licenses.asl20; maintainers = with lib.maintainers; [ ilya-kolpakov ]; }; diff --git a/pkgs/development/python-modules/python3-openid/default.nix b/pkgs/development/python-modules/python3-openid/default.nix index 238c416bc98a..d0b10c42d019 100644 --- a/pkgs/development/python-modules/python3-openid/default.nix +++ b/pkgs/development/python-modules/python3-openid/default.nix @@ -17,7 +17,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "OpenID support for modern servers and consumers"; - homepage = http://github.com/necaris/python3-openid; + homepage = https://github.com/necaris/python3-openid; license = licenses.asl20; }; } diff --git a/pkgs/development/tools/misc/epm/default.nix b/pkgs/development/tools/misc/epm/default.nix index 8d2e67859005..f58d06599650 100644 --- a/pkgs/development/tools/misc/epm/default.nix +++ b/pkgs/development/tools/misc/epm/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "The ESP Package Manager generates distribution archives for a variety of platforms"; - homepage = http://www.msweet.org/projects.php?Z2; + homepage = https://www.msweet.org/projects.php?Z2; license = licenses.gpl2; maintainers = with maintainers; [ pSub ]; platforms = platforms.unix; diff --git a/pkgs/servers/sabnzbd/default.nix b/pkgs/servers/sabnzbd/default.nix index 1b5a8c24424a..b7fddeb854d1 100644 --- a/pkgs/servers/sabnzbd/default.nix +++ b/pkgs/servers/sabnzbd/default.nix @@ -28,7 +28,7 @@ in stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Usenet NZB downloader, par2 repairer and auto extracting server"; - homepage = http://sabnzbd.org; + homepage = https://sabnzbd.org; license = licenses.gpl2Plus; platforms = platforms.linux; maintainers = with stdenv.lib.maintainers; [ fridh ]; diff --git a/pkgs/shells/zsh/oh-my-zsh/default.nix b/pkgs/shells/zsh/oh-my-zsh/default.nix index 1ff9455adece..a11a530bcdb1 100644 --- a/pkgs/shells/zsh/oh-my-zsh/default.nix +++ b/pkgs/shells/zsh/oh-my-zsh/default.nix @@ -66,7 +66,7 @@ stdenv.mkDerivation rec { $ cp -v $(nix-env -q --out-path oh-my-zsh | cut -d' ' -f3)/share/oh-my-zsh/templates/zshrc.zsh-template ~/.zshrc ''; - homepage = "http://ohmyz.sh/"; + homepage = https://ohmyz.sh/; license = licenses.mit; platforms = platforms.all; maintainers = with maintainers; [ scolobb nequissimus ]; diff --git a/pkgs/tools/security/volatility/default.nix b/pkgs/tools/security/volatility/default.nix index 086c82faa4c7..e3b7fb643a26 100644 --- a/pkgs/tools/security/volatility/default.nix +++ b/pkgs/tools/security/volatility/default.nix @@ -14,7 +14,7 @@ pythonPackages.buildPythonApplication rec { propagatedBuildInputs = [ pythonPackages.pycrypto pythonPackages.distorm3 ]; meta = with stdenv.lib; { - homepage = http://www.volatilityfoundation.org/; + homepage = https://www.volatilityfoundation.org/; description = "Advanced memory forensics framework"; maintainers = with maintainers; [ bosu ]; license = stdenv.lib.licenses.gpl2Plus; -- cgit 1.4.1 From c328738a06211e3098084ab852eea45a07e1c1e5 Mon Sep 17 00:00:00 2001 From: Luke Adams Date: Fri, 29 Jun 2018 19:55:24 -0500 Subject: gnuradio: fix hash for 3.7.13.3 --- pkgs/applications/misc/gnuradio/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/gnuradio/default.nix b/pkgs/applications/misc/gnuradio/default.nix index 2710850759b9..2ab704ec98ce 100644 --- a/pkgs/applications/misc/gnuradio/default.nix +++ b/pkgs/applications/misc/gnuradio/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { owner = "gnuradio"; repo = "gnuradio"; rev = "v${version}"; - sha256 = "0fqxn1k41xqd52i5z528zdhkn52i9z5hl6cc75ggdx9iqxhvb3jj"; + sha256 = "1qpa53axqavdv2ykby7rwh7xmhvv964xq1d7rcvbwkry7dngrbib"; fetchSubmodules = true; }; -- cgit 1.4.1 From 99d7805a6f0fe8920af412e750e249256a5d68ce Mon Sep 17 00:00:00 2001 From: aszlig Date: Sat, 30 Jun 2018 02:43:37 +0200 Subject: kmymoney: Fix build with Qt 5.11 It's a really small fix that even could have been done via sed, but I'm using the upstream patch instead so that once a new upstream release comes along we don't forget to drop the patch. The patch is from the upstream commit at: https://cgit.kde.org/kmymoney.git/commit/?id=e5198a902996b27bf9abde0ad24af82d55ab5dc1 Signed-off-by: aszlig --- pkgs/applications/office/kmymoney/default.nix | 8 ++++++++ 1 file changed, 8 insertions(+) (limited to 'pkgs/applications') diff --git a/pkgs/applications/office/kmymoney/default.nix b/pkgs/applications/office/kmymoney/default.nix index 212aaa5fa2c4..7899bf607e54 100644 --- a/pkgs/applications/office/kmymoney/default.nix +++ b/pkgs/applications/office/kmymoney/default.nix @@ -1,4 +1,5 @@ { stdenv, lib, fetchurl, doxygen, extra-cmake-modules, graphviz, kdoctools +, fetchpatch , akonadi, alkimia, aqbanking, gmp, gwenhywfar, kactivities, karchive , kcmutils, kcontacts, kdewebkit, kdiagram, kholidays, kidentitymanagement @@ -20,6 +21,13 @@ stdenv.mkDerivation rec { sha256 = "1c9apnvc07y17pzy4vygry1dai5ass2z7j354lrcppa85b18yvnx"; }; + # Fix build with Qt 5.11. + patches = lib.singleton (fetchpatch { + url = "https://cgit.kde.org/kmymoney.git/patch/?id=" + + "e5198a902996b27bf9abde0ad24af82d55ab5dc1"; + sha256 = "1h2f1xznf7343s26fh94x8n2ci0pijk5j86f24lvghawsw848316"; + }); + # Hidden dependency that wasn't included in CMakeLists.txt: NIX_CFLAGS_COMPILE = "-I${kitemmodels.dev}/include/KF5"; -- cgit 1.4.1 From 408bc4bf96128b15e5e28c9437ab1400997c614a Mon Sep 17 00:00:00 2001 From: Luke Adams Date: Fri, 29 Jun 2018 20:21:06 -0500 Subject: gnuradio: undo ninja (revert to unix make) * ninja generator fails to create response file See https://gitlab.kitware.com/cmake/cmake/issues/17877 --- pkgs/applications/misc/gnuradio/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/gnuradio/default.nix b/pkgs/applications/misc/gnuradio/default.nix index 2ab704ec98ce..0224d5fd68c7 100644 --- a/pkgs/applications/misc/gnuradio/default.nix +++ b/pkgs/applications/misc/gnuradio/default.nix @@ -1,7 +1,7 @@ { stdenv, fetchFromGitHub, writeText, makeWrapper # Dependencies documented @ https://gnuradio.org/doc/doxygen/build_guide.html # => core dependencies -, ninja, cmake, pkgconfig, git, boost, cppunit, fftw +, cmake, pkgconfig, git, boost, cppunit, fftw # => python wrappers # May be able to upgrade to swig3 , python, swig2, numpy, scipy, matplotlib @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ - cmake pkgconfig git makeWrapper cppunit orc ninja + cmake pkgconfig git makeWrapper cppunit orc ]; buildInputs = [ -- cgit 1.4.1 From e1eb55deae501bfc19b49e39f71a582f6a042603 Mon Sep 17 00:00:00 2001 From: Tim Engler Date: Sat, 30 Jun 2018 15:16:10 +0800 Subject: android-studio: added libGL as a dependency Without it, when starting an android emulator in some cases results in the cryptic, "KVM is required to run this AVD. Unknown Error" Fixes #41703 --- pkgs/applications/editors/android-studio/common.nix | 2 ++ 1 file changed, 2 insertions(+) (limited to 'pkgs/applications') diff --git a/pkgs/applications/editors/android-studio/common.nix b/pkgs/applications/editors/android-studio/common.nix index a165fad370ec..8a536bad9c48 100644 --- a/pkgs/applications/editors/android-studio/common.nix +++ b/pkgs/applications/editors/android-studio/common.nix @@ -16,6 +16,7 @@ , fontconfig , freetype , libpulseaudio +, libGL , libX11 , libXext , libXi @@ -97,6 +98,7 @@ let # For Android emulator libpulseaudio libX11 + libGL # For GTKLookAndFeel gtk2 -- cgit 1.4.1 From f6a2869031e8d88a59156d3b624e219af0271b19 Mon Sep 17 00:00:00 2001 From: Luz Date: Sat, 30 Jun 2018 13:56:12 +0200 Subject: librepcb-unstable: 2017-12-29 -> 2018-06-28 (#42786) * Update: 2017-12-29 -> 2018-06-28 * Update libs also to qt5.9 * Add required default font file * Switch back to default Qt version --- .../science/electronics/librepcb/default.nix | 14 ++++++----- .../science/electronics/librepcb/fix-2017-12.patch | 29 ---------------------- 2 files changed, 8 insertions(+), 35 deletions(-) delete mode 100644 pkgs/applications/science/electronics/librepcb/fix-2017-12.patch (limited to 'pkgs/applications') diff --git a/pkgs/applications/science/electronics/librepcb/default.nix b/pkgs/applications/science/electronics/librepcb/default.nix index ea0ebd52b3eb..48afb5bf9dc0 100644 --- a/pkgs/applications/science/electronics/librepcb/default.nix +++ b/pkgs/applications/science/electronics/librepcb/default.nix @@ -2,14 +2,14 @@ stdenv.mkDerivation rec { name = "librepcb-${version}"; - version = "20171229"; + version = "20180628"; src = fetchFromGitHub { owner = "LibrePCB"; repo = "LibrePCB"; fetchSubmodules = true; - rev = "4efb06fa42755abc5e606da4669cc17e8de2f8c6"; - sha256 = "0r33fm1djqpy0dzvnf5gv2dfh5nj2acaxb7w4cn8yxdgrazjf7ak"; + rev = "68577ecf8f39299ef4d81ff964b01c3908d1f10b"; + sha256 = "1ca4q8b8fhp19vq5yi55sq6xlsz14ihw3i0h7rq5fw0kigpjldmz"; }; enableParallelBuilding = true; @@ -18,11 +18,13 @@ stdenv.mkDerivation rec { buildInputs = [ qtbase ]; - # LibrePCB still supports QT below 5.9. But some code lines break the build, so they are removed by this patch so that the software builds. - patches = [ ./fix-2017-12.patch ]; - qmakeFlags = ["-r"]; + postInstall = '' + mkdir -p $out/share/librepcb/fontobene + cp share/librepcb/fontobene/newstroke.bene $out/share/librepcb/fontobene/ + ''; + meta = with stdenv.lib; { description = "A free EDA software to develop printed circuit boards"; homepage = http://librepcb.org/; diff --git a/pkgs/applications/science/electronics/librepcb/fix-2017-12.patch b/pkgs/applications/science/electronics/librepcb/fix-2017-12.patch deleted file mode 100644 index 75fc590ad7fe..000000000000 --- a/pkgs/applications/science/electronics/librepcb/fix-2017-12.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- a/libs/librepcb/common/fileio/serializableobjectlist.h -+++ b/libs/librepcb/common/fileio/serializableobjectlist.h -@@ -374,26 +374,6 @@ - } // namespace librepcb - - /***************************************************************************************** -- * Prevent from using SerializableObjectList in a foreach loop because it always would -- * create a deep copy of the list! You should use C++11 range based for loops instead. -- ****************************************************************************************/ -- --#if (QT_VERSION > QT_VERSION_CHECK(5, 9, 0)) --#define QFOREACHCONTAINER_TEMPLATE QtPrivate::QForeachContainer --#else --#define QFOREACHCONTAINER_TEMPLATE QForeachContainer --#endif -- --template --class QFOREACHCONTAINER_TEMPLATE> { public: -- ~QForeachContainer() = delete; --}; --template --class QFOREACHCONTAINER_TEMPLATE> { public: -- ~QForeachContainer() = delete; --}; -- --/***************************************************************************************** - * End of File - ****************************************************************************************/ - -- cgit 1.4.1 From c9f9ec6f18cb74d03c13cdcca757878feeb89943 Mon Sep 17 00:00:00 2001 From: Meghea Iulian Date: Sat, 30 Jun 2018 14:56:33 +0300 Subject: avocode: 3.0.0 -> 3.1.1 (#42808) --- pkgs/applications/graphics/avocode/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/graphics/avocode/default.nix b/pkgs/applications/graphics/avocode/default.nix index 9f9e965c6a91..fbf6443b91f8 100644 --- a/pkgs/applications/graphics/avocode/default.nix +++ b/pkgs/applications/graphics/avocode/default.nix @@ -5,11 +5,11 @@ stdenv.mkDerivation rec { name = "avocode-${version}"; - version = "3.0.0"; + version = "3.1.1"; src = fetchurl { url = "https://media.avocode.com/download/avocode-app/${version}/avocode-${version}-linux.zip"; - sha256 = "1lm0zzqhnk5gm68l8fkmlkh3gl71f1xw0amy23460a7hm9wcwjr7"; + sha256 = "1qvyc08i3b4rr43ssz78xndm4bx8lz2vigh6w9gd7w367xjf4f5b"; }; libPath = stdenv.lib.makeLibraryPath (with xorg; with gnome2; [ -- cgit 1.4.1 From a276404d44bf6b5c11dc17621bfedfa7d6e8ab9c Mon Sep 17 00:00:00 2001 From: worldofpeace Date: Sat, 30 Jun 2018 13:23:37 +0000 Subject: eolie: 0.9.16 -> 0.9.35 (#42813) --- ...-the-python-path-rather-than-replacing-it.patch | 35 ----------- .../networking/browsers/eolie/default.nix | 70 +++++++++------------- 2 files changed, 28 insertions(+), 77 deletions(-) delete mode 100644 pkgs/applications/networking/browsers/eolie/0001-Extend-the-python-path-rather-than-replacing-it.patch (limited to 'pkgs/applications') diff --git a/pkgs/applications/networking/browsers/eolie/0001-Extend-the-python-path-rather-than-replacing-it.patch b/pkgs/applications/networking/browsers/eolie/0001-Extend-the-python-path-rather-than-replacing-it.patch deleted file mode 100644 index 347fb8e12877..000000000000 --- a/pkgs/applications/networking/browsers/eolie/0001-Extend-the-python-path-rather-than-replacing-it.patch +++ /dev/null @@ -1,35 +0,0 @@ -From b51b63b78c9ff1639f5f65ccfdd54681f1cadc1d Mon Sep 17 00:00:00 2001 -From: Sam Parkinson -Date: Tue, 26 Dec 2017 14:46:27 +1100 -Subject: [PATCH] Extend the python path; rather than replacing it - -Some distros (i.e. NixOS) require the special PYTHONPATH, so that -the web extension has access to the python packages it wants (i.e. gi). - -Previously, the PYTHONPATH was replaced with the web extension path; -meaning it would crash on NixOS. This instead prepends the web -extension path to the PYTHONPATH. ---- - eolie/application.py | 6 +++++- - 1 file changed, 5 insertions(+), 1 deletion(-) - -diff --git a/eolie/application.py b/eolie/application.py -index 3c21542..bed4e55 100644 ---- a/eolie/application.py -+++ b/eolie/application.py -@@ -340,7 +340,11 @@ class Application(Gtk.Application): - self.settings = Settings.new() - - # Init extensions -- GLib.setenv("PYTHONPATH", self.__extension_dir, True) -+ current_path = GLib.getenv("PYTHONPATH") -+ new_path = self.__extension_dir -+ if current_path: -+ new_path = new_path + ':' + current_path -+ GLib.setenv("PYTHONPATH", new_path, True) - - # Create favicon path - if not GLib.file_test(self.__FAVICONS_PATH, GLib.FileTest.IS_DIR): --- -2.15.0 - diff --git a/pkgs/applications/networking/browsers/eolie/default.nix b/pkgs/applications/networking/browsers/eolie/default.nix index 9d4c858298d6..5de6c0d882a3 100644 --- a/pkgs/applications/networking/browsers/eolie/default.nix +++ b/pkgs/applications/networking/browsers/eolie/default.nix @@ -1,67 +1,53 @@ -{ stdenv, fetchgit, intltool, itstool, meson, ninja, pkgconfig, wrapGAppsHook -, glib, glib-networking, gsettings-desktop-schemas, gst_all_1, gtk3, gobjectIntrospection -, gtkspell3, libsecret, python36, python36Packages, webkitgtk }: +{ stdenv, fetchgit, meson, ninja, pkgconfig, wrapGAppsHook +, desktop-file-utils, gobjectIntrospection, python36Packages +, gnome3, gst_all_1, gtkspell3, hunspell }: stdenv.mkDerivation rec { name = "eolie-${version}"; - version = "0.9.16"; + version = "0.9.35"; src = fetchgit { - url = https://gitlab.gnome.org/gnumdk/eolie; - rev = version; - sha256 = "0mvhr6hy4nx7xaq9r9qp5rb0y293kjjryw5ykzb473cr3iwzk25b"; + url = "https://gitlab.gnome.org/World/eolie"; + rev = "refs/tags/${version}"; + fetchSubmodules = true; + sha256 = "0x3p1fgx1fhrnr7vkkpnl34401r6k6xg2mrjff7ncb1k57q522k7"; }; - nativeBuildInputs = [ - intltool - itstool + nativeBuildInputs = with python36Packages; [ + desktop-file-utils + gobjectIntrospection meson ninja pkgconfig wrapGAppsHook - gobjectIntrospection + wrapPython ]; - buildInputs = [ - glib - glib-networking - gsettings-desktop-schemas - gst_all_1.gstreamer - gst_all_1.gst-plugins-base - gst_all_1.gst-plugins-good - gst_all_1.gst-plugins-bad - gst_all_1.gst-plugins-ugly - gst_all_1.gst-libav - gtk3 - gtkspell3 - libsecret - python36 - python36Packages.pygobject3 - python36Packages.pycairo - python36Packages.dateutil - python36Packages.dbus-python - python36Packages.beautifulsoup4 - python36Packages.pycrypto - python36Packages.requests - webkitgtk + buildInputs = [ gtkspell3 hunspell python36Packages.pygobject3 ] ++ (with gnome3; [ + glib glib-networking gsettings_desktop_schemas gtk3 webkitgtk libsecret + ]) ++ (with gst_all_1; [ + gst-libav gst-plugins-base gst-plugins-ugly gstreamer + ]); + + pythonPath = with python36Packages; [ + beautifulsoup4 + pycairo + pygobject3 + python-dateutil ]; - wrapPrefixVariables = [ "PYTHONPATH" ]; + postFixup = "wrapPythonPrograms"; postPatch = '' chmod +x meson_post_install.py # patchShebangs requires executable file patchShebangs meson_post_install.py ''; - patches = [ - ./0001-Extend-the-python-path-rather-than-replacing-it.patch - ]; - meta = with stdenv.lib; { description = "A new GNOME web browser"; - homepage = https://wiki.gnome.org/Apps/Eolie; - license = licenses.gpl3; - maintainers = [ maintainers.samdroid-apps ]; - platforms = platforms.linux; + homepage = https://wiki.gnome.org/Apps/Eolie; + license = licenses.gpl3Plus; + maintainers = with maintainers; [ samdroid-apps worldofpeace ]; + platforms = platforms.linux; }; } -- cgit 1.4.1 From 398dad270a0f23fd6e96c26b5f13805e16fbb66f Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Sat, 30 Jun 2018 17:05:56 +0200 Subject: sage, arb: update sage dependencies arb and pynac Removes the version pinning for arb and pynac by backporting the upstream (sage) package upgrades. This necessitates a new patch for arb, which was however already proposed and accepted upstream. --- pkgs/applications/science/math/sage/default.nix | 22 +- .../science/math/sage/patches/arb-2.13.0.patch | 427 ++++++++++++++++++ .../science/math/sage/patches/pynac-0.7.22.patch | 479 +++++++++++++++++++++ pkgs/applications/science/math/sage/sage-src.nix | 5 + pkgs/development/libraries/arb/default.nix | 10 +- 5 files changed, 921 insertions(+), 22 deletions(-) create mode 100644 pkgs/applications/science/math/sage/patches/arb-2.13.0.patch create mode 100644 pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch (limited to 'pkgs/applications') diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 4e84a18f4f2a..9ad112213ffd 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -39,18 +39,6 @@ let inherit flint ecl pari glpk eclib; inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; linbox = nixpkgs.linbox.override { withSage = true; }; - # tracking: https://trac.sagemath.org/ticket/24927 - arb = nixpkgs.arb.overrideAttrs (attrs: rec { - name = "arb-${version}"; - version = "2.12.0"; - doCheck = false; # https://github.com/fredrik-johansson/arb/issues/194 - src = fetchFromGitHub { - owner = "fredrik-johansson"; - repo = attrs.pname; - rev = version; - sha256 = "18bwxlcbqb70cj7l9x6w1h4yghrqfhmbhdby373q8vdrdfx58niq"; - }; - }); }; sagenb = self.callPackage ./sagenb.nix { @@ -143,15 +131,7 @@ let # *not* to confuse with the python package "pynac" # https://trac.sagemath.org/ticket/24838 (depends on arb update) - pynac = (nixpkgs.pynac.override { inherit singular; }).overrideAttrs (oldAttrs: rec { - name = "pynac-0.7.16"; - src = fetchFromGitHub { - owner = "pynac"; - repo = "pynac"; - rev = name; - sha256 = "106an189sg4rpgzfrmy3699271vg4ddazw9wvh51wx7qnm1v86ik"; - }; - }); + pynac = nixpkgs.pynac.override { inherit singular; }; eclib = nixpkgs.eclib.override { inherit pari; }; diff --git a/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch b/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch new file mode 100644 index 000000000000..a20f1670a256 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/arb-2.13.0.patch @@ -0,0 +1,427 @@ +commit c885927e25b29bd23869e02379c2918da430323e +Author: Timo Kaufmann +Date: Sat Jun 30 02:26:15 2018 +0200 + +diff --git a/build/pkgs/arb/checksums.ini b/build/pkgs/arb/checksums.ini +index 1924ee03c3..9323b97391 100644 +--- a/build/pkgs/arb/checksums.ini ++++ b/build/pkgs/arb/checksums.ini +@@ -1,4 +1,4 @@ + tarball=arb-VERSION.tar.gz +-sha1=27476d0529e48a07d92da90bd0fb80dd18f443e3 +-md5=733285d9705d10b8024e551ffa81952f +-cksum=2391183744 ++sha1=44eda7bf8eaa666c45b1fc2c1b5bd08756d94b58 ++md5=fa24de9fffe4394fb6a7a6792e2ecc5f ++cksum=3689220688 +diff --git a/build/pkgs/arb/package-version.txt b/build/pkgs/arb/package-version.txt +index c8810e9bdb..fb2c0766b7 100644 +--- a/build/pkgs/arb/package-version.txt ++++ b/build/pkgs/arb/package-version.txt +@@ -1 +1 @@ +-2.12.0.p0 ++2.13.0 +diff --git a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch b/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch +deleted file mode 100644 +index 3e5c0e708b..0000000000 +--- a/build/pkgs/arb/patches/arb-pie-hardening-conflict.patch ++++ /dev/null +@@ -1,17 +0,0 @@ +-In newer binutils, ld options -r and -pie conflict. +-Patch due to Jörg-Volker Peetz +-(source : https://groups.google.com/d/msg/sage-devel/TduebNoZuBE/sEULolL0BQAJ), +-packaged by Emmanuel Charpentier +- +-diff -ru arb-2.8.1-orig/Makefile.subdirs arb-2.8.1-new/Makefile.subdirs +---- arb-2.8.1-orig/Makefile.subdirs 2015-12-31 17:30:01.000000000 +0100 +-+++ arb-2.8.1-new/Makefile.subdirs 2016-11-07 18:50:34.540051779 +0100 +-@@ -52,7 +52,7 @@ +- $(QUIET_CC) $(CC) $(CFLAGS) $(INCS) -c $< -o $@ -MMD -MP -MF "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$(BUILD_DIR)/$(MOD_DIR)_$*.d" -MT "$@" +- +- $(MOD_LOBJ): $(LOBJS) +-- $(QUIET_CC) $(CC) $(ABI_FLAG) -Wl,-r $^ -o $@ -nostdlib +-+ $(QUIET_CC) $(CC) $(ABI_FLAG) -r $^ -o $@ -nostdlib +- +- -include $(LOBJS:.lo=.d) +- +diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx +index 70d51e655a..00e7caea2c 100644 +--- a/src/sage/rings/complex_arb.pyx ++++ b/src/sage/rings/complex_arb.pyx +@@ -857,14 +857,14 @@ class ComplexBallField(UniqueRepresentation, Field): + [0.500000000000000 +/- 2.09e-16] + + sage: CBF.integral(lambda x, _: x.gamma(), 1 - CBF(i), 1 + CBF(i)) +- [+/- 3.95e-15] + [1.5723926694981 +/- 4.53e-14]*I ++ [+/- 4...e-15] + [1.5723926694981 +/- 4...e-14]*I + + sage: C = ComplexBallField(100) + sage: C.integral(lambda x, _: x.cos() * x.sin(), 0, 1) + [0.35403670913678559674939205737 +/- 8.89e-30] + + sage: CBF.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) +- [0.34740017266 +/- 6.36e-12] ++ [0.34740017266 +/- 6...e-12] + + sage: C = ComplexBallField(2000) + sage: C.integral(lambda x, _: (x + x.exp()).sin(), 0, 8) # long time +@@ -879,14 +879,14 @@ class ComplexBallField(UniqueRepresentation, Field): + ....: else: + ....: return z.sqrt() + sage: CBF.integral(my_sqrt, -1 + CBF(i), -1 - CBF(i)) +- [+/- 1.14e-14] + [-0.4752076627926 +/- 5.18e-14]*I ++ [+/- 1.14e-14] + [-0.4752076627926 +/- 5...e-14]*I + + Note, though, that proper handling of the ``analytic`` flag is required + even when the path does not touch the branch cut:: + + sage: correct = CBF.integral(my_sqrt, 1, 2); correct + [1.21895141649746 +/- 3.73e-15] +- sage: RBF(integral(sqrt(x), x, 1, 2)) ++ sage: RBF(integral(sqrt(x), x, 1, 2)) # long time + [1.21895141649746 +/- 1.79e-15] + sage: wrong = CBF.integral(lambda z, _: z.sqrt(), 1, 2) # WRONG! + sage: correct - wrong +@@ -915,9 +915,9 @@ class ComplexBallField(UniqueRepresentation, Field): + the integrand is unbounded:: + + sage: CBF.integral(lambda x, _: 1/x, -1, 1) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + sage: CBF.integral(lambda x, _: 1/x, 10^-1000, 1, abs_tol=1e-10) + [2302.5850930 +/- 1.26e-8] + +@@ -928,14 +928,15 @@ class ComplexBallField(UniqueRepresentation, Field): + sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=1e-450) + [2.304377150950e-439 +/- 9.74e-452] + sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, abs_tol=0) +- [2.304377150949e-439 +/- 7.53e-452] +- sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-4, abs_tol=0) +- [2.30438e-439 +/- 3.90e-445] ++ [2.304377150950e-439 +/- 7...e-452] ++ sage: CBF.integral(lambda x, _: x.exp(), -1020, -1010, rel_tol=1e-2, abs_tol=0) ++ [2.30438e-439 +/- 5.94e-445] + +- sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1) +- [+/- 0.644] +- sage: CBF.integral(lambda x, _: x*(1/x).sin(), 0, 1, use_heap=True) +- [0.3785300 +/- 4.32e-8] ++ sage: epsi = CBF(1e-10) ++ sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1) ++ [0.38 +/- 8.54e-3] ++ sage: CBF.integral(lambda x, _: x*(1/x).sin(), epsi, 1, use_heap=True) ++ [0.37853002 +/- 8.73e-9] + + ALGORITHM: + +@@ -951,12 +952,12 @@ class ComplexBallField(UniqueRepresentation, Field): + + sage: i = QuadraticField(-1).gen() + sage: CBF.integral(lambda x, _: (1 + i*x).gamma(), -1, 1) +- [1.5723926694981 +/- 4.53e-14] + [+/- 3.95e-15]*I ++ [1.5723926694981 +/- 4...e-14] + [+/- 4...e-15]*I + +- sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-400) +- [0.459... +/- ...e-4...] ++ sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, rel_tol=1e-300) ++ [0.459... +/- ...e-3...] + sage: CBF.integral(lambda x, _: x.sin(), 0, 100, rel_tol=10) +- [+/- 7.61] ++ [0.138 +/- 5.53e-4] + + sage: ComplexBallField(10000).integral(lambda x, _: x.sin(), 0, 1, abs_tol=1e-400) + [0.459697... +/- ...e-4...] +@@ -2389,9 +2390,9 @@ cdef class ComplexBall(RingElement): + sage: ~CBF(i/3) + [-3.00000000000000 +/- 9.44e-16]*I + sage: ~CBF(0) +- [+/- inf] ++ nan + sage: ~CBF(RIF(10,11)) +- [0.1 +/- 9.53e-3] ++ [0.1 +/- 9.10e-3] + """ + cdef ComplexBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -2512,9 +2513,9 @@ cdef class ComplexBall(RingElement): + sage: CBF(-2, 1)/CBF(1, 1/3) + [-1.500000000000000 +/- 8.83e-16] + [1.500000000000000 +/- 5.64e-16]*I + sage: CBF(2+I)/CBF(0) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + sage: CBF(1)/CBF(0) +- [+/- inf] ++ nan + sage: CBF(1)/CBF(RBF(0, 1.)) + nan + """ +@@ -2543,9 +2544,9 @@ cdef class ComplexBall(RingElement): + sage: CBF(0)^(1/3) + 0 + sage: CBF(0)^(-1) +- [+/- inf] ++ nan + sage: CBF(0)^(-2) +- [+/- inf] + [+/- inf]*I ++ nan + nan*I + + TESTS:: + +@@ -2656,12 +2657,12 @@ cdef class ComplexBall(RingElement): + sage: CBF(1).rising_factorial(5) + 120.0000000000000 + sage: CBF(1/3, 1/2).rising_factorial(300) +- [-3.87949484514e+612 +/- 5.23e+600] + [-3.52042209763e+612 +/- 5.55e+600]*I ++ [-3.87949484514e+612 +/- 5...e+600] + [-3.52042209763e+612 +/- 5...e+600]*I + + sage: CBF(1).rising_factorial(-1) + nan + sage: CBF(1).rising_factorial(2**64) +- [+/- 2.30e+347382171305201370464] ++ [+/- 2.30e+347382171326740403407] + sage: ComplexBallField(128)(1).rising_factorial(2**64) + [2.343691126796861348e+347382171305201285713 +/- 4.71e+347382171305201285694] + sage: CBF(1/2).rising_factorial(CBF(2,3)) +@@ -2700,7 +2701,7 @@ cdef class ComplexBall(RingElement): + [1.000000000000000 +/- 2.83e-16] + [-0.441271200305303 +/- 2.82e-16]*I + + sage: CBF('inf').log() +- nan + nan*I ++ [+/- inf] + sage: CBF(2).log(0) + nan + nan*I + """ +@@ -2808,7 +2809,7 @@ cdef class ComplexBall(RingElement): + sage: CBF(pi/2, 1/10).tan() + [+/- 2.87e-14] + [10.0333111322540 +/- 2.36e-14]*I + sage: CBF(pi/2).tan() +- [+/- inf] ++ nan + """ + cdef ComplexBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -2825,7 +2826,7 @@ cdef class ComplexBall(RingElement): + sage: CBF(pi, 1/10).cot() + [+/- 5.74e-14] + [-10.0333111322540 +/- 2.81e-14]*I + sage: CBF(pi).cot() +- [+/- inf] ++ nan + """ + cdef ComplexBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -3211,9 +3212,9 @@ cdef class ComplexBall(RingElement): + 1.000000000000000*I + + sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2]) +- [0.7871684267473 +/- 7.34e-14] + [0.2749254173721 +/- 9.23e-14]*I ++ [0.7871684267473 +/- 7...e-14] + [0.2749254173721 +/- 9...e-14]*I + sage: CBF(2+3*I).hypergeometric([1/4,1/3],[1/2],regularized=True) +- [0.4441122268685 +/- 3.96e-14] + [0.1551100567338 +/- 5.75e-14]*I ++ [0.4441122268685 +/- 3...e-14] + [0.1551100567338 +/- 5...e-14]*I + + sage: CBF(5).hypergeometric([2,3], [-5]) + nan + nan*I +@@ -4041,9 +4042,9 @@ cdef class ComplexBall(RingElement): + + sage: phi = CBF(1,1) + sage: (CBF.pi()/2).elliptic_e_inc(phi) +- [1.283840957898 +/- 3.23e-13] + [-0.5317843366915 +/- 7.79e-14]*I ++ [1.283840957898 +/- 3...e-13] + [-0.5317843366915 +/- 7...e-14]*I + sage: phi.elliptic_e() +- [1.2838409578982 +/- 5.90e-14] + [-0.5317843366915 +/- 3.35e-14]*I ++ [1.2838409578982 +/- 5...e-14] + [-0.5317843366915 +/- 3...e-14]*I + + sage: phi = CBF(2, 3/7) + sage: (CBF.pi()/2).elliptic_e_inc(phi) +@@ -4312,8 +4313,7 @@ cdef class ComplexBall(RingElement): + sage: CBF(10).laguerre_L(3, 2) + [-6.666666666667 +/- 4.15e-13] + sage: CBF(5,7).laguerre_L(CBF(2,3), CBF(1,-2)) +- [5515.315030271 +/- 4.37e-10] + [-12386.942845271 +/- 5.47e-10]*I +- ++ [5515.315030271 +/- 4...e-10] + [-12386.942845271 +/- 5...e-10]*I + """ + cdef ComplexBall my_n = self._parent.coerce(n) + cdef ComplexBall my_m = self._parent.coerce(m) +@@ -4357,9 +4357,9 @@ cdef class ComplexBall(RingElement): + EXAMPLES:: + + sage: CBF(1/2).legendre_P(5) +- [0.08984375000000000 +/- 4.5...e-18] ++ [0.0898437500000000 +/- 7...e-17] + sage: CBF(1,2).legendre_P(CBF(2,3), CBF(0,1)) +- [0.10996180744364 +/- 7.45e-15] + [0.14312767804055 +/- 8.38e-15]*I ++ [0.10996180744364 +/- 7.12e-15] + [0.14312767804055 +/- 8.07e-15]*I + sage: CBF(-10).legendre_P(5, 325/100) + [-22104403.487377 +/- 6.81e-7] + [53364750.687392 +/- 7.25e-7]*I + sage: CBF(-10).legendre_P(5, 325/100, type=3) +@@ -4393,9 +4393,9 @@ cdef class ComplexBall(RingElement): + sage: CBF(1/2).legendre_Q(5) + [0.55508089057168 +/- 2.79e-15] + sage: CBF(1,2).legendre_Q(CBF(2,3), CBF(0,1)) +- [0.167678710 +/- 4.60e-10] + [-0.161558598 +/- 7.47e-10]*I ++ [0.167678710 +/- 3.91e-10] + [-0.161558598 +/- 6.77e-10]*I + sage: CBF(-10).legendre_Q(5, 325/100) +- [-83825154.36008 +/- 4.94e-6] + [-34721515.80396 +/- 5.40e-6]*I ++ [-83825154.36008 +/- 5.02e-6] + [-34721515.80396 +/- 5.42e-6]*I + sage: CBF(-10).legendre_Q(5, 325/100, type=3) + [-4.797306921692e-6 +/- 6.82e-19] + [-4.797306921692e-6 +/- 6.57e-19]*I + +diff --git a/src/sage/rings/polynomial/polynomial_complex_arb.pyx b/src/sage/rings/polynomial/polynomial_complex_arb.pyx +index c436d4705b..ef611a566b 100644 +--- a/src/sage/rings/polynomial/polynomial_complex_arb.pyx ++++ b/src/sage/rings/polynomial/polynomial_complex_arb.pyx +@@ -543,7 +543,7 @@ cdef class Polynomial_complex_arb(Polynomial): + sage: (1 - x/3).inverse_series_trunc(3) + ([0.1111111111111111 +/- 5.99e-17])*x^2 + ([0.3333333333333333 +/- 7.04e-17])*x + 1.000000000000000 + sage: x.inverse_series_trunc(1) +- [+/- inf] ++ nan + sage: Pol(0).inverse_series_trunc(2) + (nan + nan*I)*x + nan + nan*I + +@@ -671,7 +671,7 @@ cdef class Polynomial_complex_arb(Polynomial): + sage: pol._sqrt_series(2) + ([+/- 7.51e-3] + [+/- 0.501]*I)*x + [+/- 5.01e-3] + [+/- 1.01]*I + sage: x._sqrt_series(2) +- ([+/- inf] + [+/- inf]*I)*x ++ (nan + nan*I)*x + """ + cdef Polynomial_complex_arb res = self._new() + if n < 0: +diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx +index c9f68e38d7..76e3037a9a 100644 +--- a/src/sage/rings/real_arb.pyx ++++ b/src/sage/rings/real_arb.pyx +@@ -161,7 +161,7 @@ values and should be preferred:: + + sage: RBF(NaN) < RBF(infinity) + False +- sage: 1/RBF(0) <= RBF(infinity) ++ sage: RBF(0).add_error(infinity) <= RBF(infinity) + True + + TESTS:: +@@ -252,6 +252,8 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision): + (+infinity, +infinity) + sage: RBF(RIF(-infinity)).endpoints() + (-infinity, -infinity) ++ sage: RBF(RIF(-infinity, infinity)).endpoints() ++ (-infinity, +infinity) + sage: RIF(RBF(infinity)).endpoints() + (+infinity, +infinity) + sage: RIF(RBF(-infinity)).endpoints() +@@ -266,10 +268,11 @@ cdef void mpfi_to_arb(arb_t target, const mpfi_t source, const long precision): + if _do_sig(precision): sig_on() + mpfi_get_left(left, source) + mpfi_get_right(right, source) +- arb_set_interval_mpfr(target, left, right, precision) +- # Work around weakness of arb_set_interval_mpfr(tgt, inf, inf) +- if mpfr_equal_p(left, right): +- mag_zero(arb_radref(target)) ++ if mpfr_inf_p(left) and mpfr_inf_p(right) and mpfr_sgn(left) < 0 < mpfr_sgn(right): ++ # Work around a weakness of arb_set_interval_mpfr(tgt, -inf, inf) ++ arb_zero_pm_inf(target) ++ else: ++ arb_set_interval_mpfr(target, left, right, precision) + if _do_sig(precision): sig_off() + + mpfr_clear(left) +@@ -649,17 +652,15 @@ class RealBallField(UniqueRepresentation, Field): + EXAMPLES:: + + sage: RBF.some_elements() +- [1.000000000000000, +- [0.3333333333333333 +/- 7.04e-17], ++ [0, 1.000000000000000, [0.3333333333333333 +/- 7.04e-17], + [-4.733045976388941e+363922934236666733021124 +/- 3.46e+363922934236666733021108], +- [+/- inf], +- [+/- inf], +- nan] ++ [+/- inf], [+/- inf], [+/- inf], nan] + """ + import sage.symbolic.constants +- return [self(1), self(1)/3, ++ inf = self(sage.rings.infinity.Infinity) ++ return [self(0), self(1), self(1)/3, + -self(2)**(Integer(2)**80), +- self(sage.rings.infinity.Infinity), ~self(0), ++ inf, -inf, self.zero().add_error(inf), + self.element_class(self, sage.symbolic.constants.NotANumber())] + + def _sum_of_products(self, terms): +@@ -881,7 +882,7 @@ class RealBallField(UniqueRepresentation, Field): + sage: RBF.gamma(5) + 24.00000000000000 + sage: RBF.gamma(10**20) +- [+/- 5.92e+1956570551809674821757] ++ [+/- 5.50e+1956570552410610660600] + sage: RBF.gamma(1/3) + [2.678938534707747 +/- 8.99e-16] + sage: RBF.gamma(-5) +@@ -2247,7 +2248,7 @@ cdef class RealBall(RingElement): + sage: inf = RBF(+infinity) + sage: other_inf = RBF(+infinity, 42.r) + sage: neg_inf = RBF(-infinity) +- sage: extended_line = 1/RBF(0) ++ sage: extended_line = RBF(0).add_error(infinity) + sage: exact_nan = inf - inf + sage: exact_nan.mid(), exact_nan.rad() + (NaN, 0.00000000) +@@ -2659,7 +2660,7 @@ cdef class RealBall(RingElement): + sage: ~RBF(5) + [0.2000000000000000 +/- 4.45e-17] + sage: ~RBF(0) +- [+/- inf] ++ nan + sage: RBF(RIF(-0.1,0.1)) + [+/- 0.101] + +@@ -2739,7 +2740,7 @@ cdef class RealBall(RingElement): + sage: RBF(pi)/RBF(e) + [1.155727349790922 +/- 8.43e-16] + sage: RBF(2)/RBF(0) +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -2765,7 +2766,7 @@ cdef class RealBall(RingElement): + sage: RBF(-1)^(1/3) + nan + sage: RBF(0)^(-1) +- [+/- inf] ++ nan + sage: RBF(-e)**RBF(pi) + nan + +@@ -3129,7 +3130,7 @@ cdef class RealBall(RingElement): + sage: RBF(1).tan() + [1.557407724654902 +/- 3.26e-16] + sage: RBF(pi/2).tan() +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -3146,7 +3147,7 @@ cdef class RealBall(RingElement): + sage: RBF(1).cot() + [0.642092615934331 +/- 4.79e-16] + sage: RBF(pi).cot() +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() +@@ -3257,7 +3258,7 @@ cdef class RealBall(RingElement): + sage: RBF(1).coth() + [1.313035285499331 +/- 4.97e-16] + sage: RBF(0).coth() +- [+/- inf] ++ nan + """ + cdef RealBall res = self._new() + if _do_sig(prec(self)): sig_on() diff --git a/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch b/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch new file mode 100644 index 000000000000..22f274d608d4 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/pynac-0.7.22.patch @@ -0,0 +1,479 @@ +diff --git a/src/sage/calculus/calculus.py b/src/sage/calculus/calculus.py +index 3a417d9d5c..fadaadbaf6 100644 +--- a/src/sage/calculus/calculus.py ++++ b/src/sage/calculus/calculus.py +@@ -231,7 +231,7 @@ Another example:: + sage: f(x=3) + arcsinh(1) + sage: f.derivative(x) +- 1/3/sqrt(1/9*x^2 + 1) ++ 1/sqrt(x^2 + 9) + + We compute the length of the parabola from 0 to 2:: + +@@ -1509,8 +1509,8 @@ def laplace(ex, t, s, algorithm='maxima'): + Testing SymPy:: + + sage: laplace(t^n, t, s, algorithm='sympy') +- (s^(-n)*gamma(n + 1)/s, 0, -re(n) < 1) +- ++ (gamma(n + 1)/(s*s^n), 0, -re(n) < 1) ++ + Testing Maxima:: + + sage: laplace(t^n, t, s, algorithm='maxima') +diff --git a/src/sage/functions/hypergeometric.py b/src/sage/functions/hypergeometric.py +index 1fc2db5c94..f3e49b9cdb 100644 +--- a/src/sage/functions/hypergeometric.py ++++ b/src/sage/functions/hypergeometric.py +@@ -34,7 +34,7 @@ Simplification (note that ``simplify_full`` does not yet call + sage: a.simplify_hypergeometric() + 1/((-e^x + 1)^e^x) + sage: a.simplify_hypergeometric(algorithm='sage') +- (-e^x + 1)^(-e^x) ++ 1/((-e^x + 1)^e^x) + + Equality testing:: + +@@ -145,7 +145,7 @@ Series expansions of confluent hypergeometric functions:: + + sage: hypergeometric_M(2, 2, x).series(x, 3) + 1 + 1*x + 1/2*x^2 + Order(x^3) +- sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() ++ sage: hypergeometric_U(2, 2, x).series(x == 3, 100).subs(x=1).n() # known bug (see :trac:`25688`) + 0.403652637676806 + sage: hypergeometric_U(2, 2, 1).n() + 0.403652637676806 +@@ -773,7 +773,7 @@ def closed_form(hyp): + sage: closed_form(hypergeometric([], [], z)) + e^z + sage: closed_form(hypergeometric([a], [], z)) +- (-z + 1)^(-a) ++ 1/((-z + 1)^a) + sage: closed_form(hypergeometric([1, 1, 2], [1, 1], z)) + (z - 1)^(-2) + sage: closed_form(hypergeometric([2, 3], [1], x)) +@@ -1121,7 +1121,7 @@ class Hypergeometric_U(BuiltinFunction): + sage: var('a b z') + (a, b, z) + sage: hypergeometric_U(a, b, z).generalized() +- z^(-a)*hypergeometric((a, a - b + 1), (), -1/z) ++ hypergeometric((a, a - b + 1), (), -1/z)/z^a + sage: hypergeometric_U(1, 3, 1/2).generalized() + 2*hypergeometric((1, -1), (), -2) + sage: hypergeometric_U(3, I, 2).generalized() +diff --git a/src/sage/functions/log.py b/src/sage/functions/log.py +index 75d1bf8060..61968582af 100644 +--- a/src/sage/functions/log.py ++++ b/src/sage/functions/log.py +@@ -518,17 +518,17 @@ class Function_polylog(GinacFunction): + + sage: BF = RealBallField(100) + sage: polylog(2, BF(1/3)) +- [0.36621322997706348761674629766 +/- 4.51e-30] ++ [0.36621322997706348761674629766... +/- ...] + sage: polylog(2, BF(4/3)) +- nan ++ [2.27001825336107090380391448586 +/- 5.64e-30] + [-0.90377988538400159956755721265 +/- 8.39e-30]*I + sage: parent(_) +- Real ball field with 100 bits of precision ++ Complex ball field with 100 bits of precision + sage: polylog(2, CBF(1/3)) +- [0.366213229977063 +/- 5.85e-16] ++ [0.366213229977063 +/- ...] + sage: parent(_) + Complex ball field with 53 bits of precision + sage: polylog(2, CBF(1)) +- [1.644934066848226 +/- 6.59e-16] ++ [1.644934066848226 +/- ...] + sage: parent(_) + Complex ball field with 53 bits of precision + """ +diff --git a/src/sage/functions/trig.py b/src/sage/functions/trig.py +index e7e7a311cd..1f2926d6c9 100644 +--- a/src/sage/functions/trig.py ++++ b/src/sage/functions/trig.py +@@ -529,13 +529,8 @@ class Function_arcsin(GinacFunction): + arcsin + sage: asin(complex(1,1)) + (0.6662394324925152+1.0612750619050357j) +- +- Check that :trac:`22823` is fixed:: +- +- sage: bool(asin(SR(2.1)) == NaN) +- True +- sage: asin(SR(2.1)).is_real() +- False ++ sage: asin(SR(2.1)) ++ 1.57079632679490 - 1.37285914424258*I + """ + GinacFunction.__init__(self, 'arcsin', latex_name=r"\arcsin", + conversions=dict(maxima='asin', sympy='asin', fricas="asin", giac="asin")) +@@ -595,13 +590,8 @@ class Function_arccos(GinacFunction): + arccos + sage: acos(complex(1,1)) + (0.9045568943023814-1.0612750619050357j) +- +- Check that :trac:`22823` is fixed:: +- +- sage: bool(acos(SR(2.1)) == NaN) +- True +- sage: acos(SR(2.1)).is_real() +- False ++ sage: acos(SR(2.1)) ++ 1.37285914424258*I + """ + GinacFunction.__init__(self, 'arccos', latex_name=r"\arccos", + conversions=dict(maxima='acos', sympy='acos', fricas='acos', giac='acos')) +@@ -807,7 +797,7 @@ class Function_arcsec(GinacFunction): + sage: arcsec(2).n(100) + 1.0471975511965977461542144611 + sage: arcsec(1/2).n(100) +- NaN ++ 1.3169578969248167086250463473*I + sage: RDF(arcsec(2)) # abs tol 1e-15 + 1.0471975511965976 + sage: arcsec(1 + I) +@@ -958,7 +948,9 @@ class Function_arctan2(GinacFunction): + sage: atan2(0,0,hold=True) + arctan2(0, 0) + sage: atan2(0,0,hold=True).n() +- NaN ++ Traceback (most recent call last): ++ ... ++ RuntimeError: atan2(): division by zero + + Check if :trac:`10062` is fixed, this was caused by + ``(I*I).is_positive()`` returning ``True``:: +diff --git a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py +index 3b5c8d1729..1c6b73a16c 100644 +--- a/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py ++++ b/src/sage/geometry/hyperbolic_space/hyperbolic_geodesic.py +@@ -1422,8 +1422,10 @@ class HyperbolicGeodesicUHP(HyperbolicGeodesic): + expressions do not generate runtime errors. :: + + sage: g=HyperbolicPlane().UHP().get_geodesic(-1+I,1+I) +- sage: g.midpoint() +- Point in UHP 1/2*(sqrt(2)*e^(1/2*arccosh(3)) - sqrt(2) + (I - 1)*e^(1/2*arccosh(3)) + I - 1)/((1/4*I - 1/4)*sqrt(2)*e^(1/2*arccosh(3)) - (1/4*I - 1/4)*sqrt(2) + 1/2*e^(1/2*arccosh(3)) + 1/2) ++ sage: point = g.midpoint(); point ++ Point in UHP -1/2*(sqrt(2)*... ++ sage: QQbar(point.coordinates()).radical_expression() ++ I*sqrt(2) + + Check that floating points remain floating points + in :meth:`midpoint` :: +diff --git a/src/sage/interfaces/fricas.py b/src/sage/interfaces/fricas.py +index 82aae78e37..8501ea2a18 100644 +--- a/src/sage/interfaces/fricas.py ++++ b/src/sage/interfaces/fricas.py +@@ -1084,14 +1084,14 @@ class FriCASElement(ExpectElement): + 0.451026811796262, + 0.732815101786507, + 0.837981225008390, +- NaN, +- NaN, ++ 1.57079632679490 - 0.467145308103262*I, ++ 0.467145308103262*I, + 1.11976951499863, + 0.451026811796262, + 0.732815101786507, + 0.837981225008390, +- NaN, +- NaN] ++ 1.57079632679490 - 0.467145308103262*I, ++ 0.467145308103262*I] + sage: l = [tanh, sinh, cosh, coth, sech, csch, asinh, acosh, atanh, acoth, asech, acsch, arcsinh, arccosh, arctanh, arccoth, arcsech, arccsch] + sage: [f(x)._fricas_().sage().subs(x=0.9) for f in l] # optional - fricas + [0.716297870199024, +diff --git a/src/sage/libs/pynac/pynac.pyx b/src/sage/libs/pynac/pynac.pyx +index 9e9d8f664b..e3406f007e 100644 +--- a/src/sage/libs/pynac/pynac.pyx ++++ b/src/sage/libs/pynac/pynac.pyx +@@ -1824,7 +1824,7 @@ cdef py_atan2(x, y): + sage: atan2(CC(I), CC(I+1)) + 0.553574358897045 + 0.402359478108525*I + sage: atan2(CBF(I), CBF(I+1)) +- [0.55357435889705 +/- 5.58e-15] + [0.402359478108525 +/- 7.11e-16]*I ++ [0.55357435889705 +/- ...] + [0.402359478108525 +/- ...]*I + + Check that :trac:`23776` is fixed and RDF input gives real output:: + +diff --git a/src/sage/matrix/matrix_symbolic_dense.pyx b/src/sage/matrix/matrix_symbolic_dense.pyx +index 46a15e53eb..7a0beb437b 100644 +--- a/src/sage/matrix/matrix_symbolic_dense.pyx ++++ b/src/sage/matrix/matrix_symbolic_dense.pyx +@@ -200,7 +200,7 @@ cdef class Matrix_symbolic_dense(Matrix_generic_dense): + sage: eval, [evec], mult = es[0] + sage: delta = eval*evec - evec*A + sage: abs(abs(delta)) < 1e-10 +- sqrt(9/25*((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + 9/25*((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10) ++ 3/5*sqrt(((2*sqrt(6) - 3)*(sqrt(6) - 2) + 7*sqrt(6) - 18)^2 + ((sqrt(6) - 2)*(sqrt(6) - 4) + 6*sqrt(6) - 14)^2) < (1.00000000000000e-10) + sage: abs(abs(delta)).n() < 1e-10 + True + +diff --git a/src/sage/modules/matrix_morphism.py b/src/sage/modules/matrix_morphism.py +index 17a1d6e290..03892ceec0 100644 +--- a/src/sage/modules/matrix_morphism.py ++++ b/src/sage/modules/matrix_morphism.py +@@ -214,9 +214,9 @@ class MatrixMorphism_abstract(sage.categories.morphism.Morphism): + sage: f((1, 0)) + Traceback (most recent call last): + ... +- TypeError: Unable to coerce entries (=[1.00000000000000*I, 0.000000000000000]) to coefficients in Real Field with 53 bits of precision ++ TypeError: Unable to coerce entries (=[1.00000000000000*I, 0]) to coefficients in Real Field with 53 bits of precision + sage: f((1, 0), coerce=False) +- (1.00000000000000*I, 0.000000000000000) ++ (1.00000000000000*I, 0) + + """ + if self.domain().is_ambient(): +diff --git a/src/sage/plot/plot.py b/src/sage/plot/plot.py +index 77cdeb8c46..e501e74036 100644 +--- a/src/sage/plot/plot.py ++++ b/src/sage/plot/plot.py +@@ -2061,7 +2061,7 @@ def _plot(funcs, xrange, parametric=False, + plot properly (:trac:`13246`):: + + sage: parametric_plot((x, arcsec(x)), (x, -2, 2)) +- Graphics object consisting of 1 graphics primitive ++ Graphics object consisting of 2 graphics primitives + + """ + from sage.plot.colors import Color +diff --git a/src/sage/repl/display/formatter.py b/src/sage/repl/display/formatter.py +index 8ce2e839d7..948207c95e 100644 +--- a/src/sage/repl/display/formatter.py ++++ b/src/sage/repl/display/formatter.py +@@ -25,11 +25,11 @@ generally, all sage expression as an ASCII art object:: + sage: shell = get_test_shell() + sage: shell.run_cell('%display ascii_art') + sage: shell.run_cell('integral(x^2/pi^x, x)') +- / 2 2 \ -x*log(pi) +- -\x *log (pi) + 2*x*log(pi) + 2/*e +- --------------------------------------------- +- 3 +- log (pi) ++ -x / 2 2 \ ++ -pi *\x *log (pi) + 2*x*log(pi) + 2/ ++ -------------------------------------- ++ 3 ++ log (pi) + sage: shell.run_cell("i = var('i')") + sage: shell.run_cell('sum(i*x^i, i, 0, 10)') + 10 9 8 7 6 5 4 3 2 +diff --git a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +index d8ebbf4f76..8c60f65e99 100644 +--- a/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py ++++ b/src/sage/rings/asymptotic/asymptotics_multivariate_generating_functions.py +@@ -151,8 +151,8 @@ A multiple point example (Example 6.5 of [RaWi2012]_):: + [(x + 2*y - 1, 1), (2*x + y - 1, 1)]) + sage: F1 = decomp[1] + sage: F1.asymptotics(p, alpha, 2) +- (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*((1/3)^(-a)*(1/3)^(-b))^r, +- (1/3)^(-a)*(1/3)^(-b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9) ++ (-3*((2*a^2 - 5*a*b + 2*b^2)*r^2 + (a + b)*r + 3)*(1/((1/3)^a*(1/3)^b))^r, ++ 1/((1/3)^a*(1/3)^b), -3*(2*a^2 - 5*a*b + 2*b^2)*r^2 - 3*(a + b)*r - 9) + sage: alpha = [4, 3] + sage: decomp = F.asymptotic_decomposition(alpha) + sage: F1 = decomp[1] +@@ -2159,7 +2159,7 @@ class FractionWithFactoredDenominator(RingElement): + sage: p = {x: 1/3, y: 1/3} + sage: alpha = (var('a'), var('b')) + sage: F.asymptotics_multiple(p, alpha, 2, var('r')) # long time +- (3*((1/3)^(-a)*(1/3)^(-b))^r*e^(2/3), (1/3)^(-a)*(1/3)^(-b), 3*e^(2/3)) ++ (3*(1/((1/3)^a*(1/3)^b))^r*e^(2/3), 1/((1/3)^a*(1/3)^b), 3*e^(2/3)) + """ + from itertools import product + from sage.calculus.functions import jacobian +diff --git a/src/sage/stats/basic_stats.py b/src/sage/stats/basic_stats.py +index 16a268a02c..5fd244e93b 100644 +--- a/src/sage/stats/basic_stats.py ++++ b/src/sage/stats/basic_stats.py +@@ -183,7 +183,7 @@ def std(v, bias=False): + sage: std([]) + NaN + sage: std([I, sqrt(2), 3/5]) +- sqrt(1/450*(10*sqrt(2) - 5*I - 3)^2 + 1/450*(5*sqrt(2) - 10*I + 3)^2 + 1/450*(5*sqrt(2) + 5*I - 6)^2) ++ 1/15*sqrt(1/2)*sqrt((10*sqrt(2) - 5*I - 3)^2 + (5*sqrt(2) - 10*I + 3)^2 + (5*sqrt(2) + 5*I - 6)^2) + sage: std([RIF(1.0103, 1.0103), RIF(2)]) + 0.6998235813403261? + sage: import numpy +diff --git a/src/sage/symbolic/expression.pyx b/src/sage/symbolic/expression.pyx +index ab4c05de3a..60f0dc549a 100644 +--- a/src/sage/symbolic/expression.pyx ++++ b/src/sage/symbolic/expression.pyx +@@ -622,7 +622,7 @@ cdef class Expression(CommutativeRingElement): + sage: x^(-5) + x^(-5) + sage: x^(-y) +- x^(-y) ++ 1/(x^y) + sage: 2*x^(-1) + 2/x + sage: i*x +@@ -3621,14 +3621,14 @@ cdef class Expression(CommutativeRingElement): + sage: repl_dict = {b_0: b_0, b_3: b_1, b_2: b_3, b_1: b_2} + sage: P = precomp.substitute(repl_dict) + sage: P.expand() +- -2^(-b_0)*2^(-b_2)*2^b_3 - 2^b_0*2^(-b_2)*2^b_3 - +- 2^(-b_0)*2^b_2*2^b_3 + 2^b_0*2^b_2*2^b_3 - 2*2^(-b_0)*2^(-b_2) +- - 2*2^b_0*2^(-b_2) - 2*2^(-b_0)*2^b_2 + 2*2^b_0*2^b_2 + +- 2^(-b_0)*2^b_3 + 2^b_0*2^b_3 + 2^(-b_2)*2^b_3 + 2^b_2*2^b_3 + +- 2*2^(-b_0) + 2*2^b_0 + 2*2^(-b_2) + 2*2^b_2 - 9*2^b_3 - +- 2^(-b_0)*2^(-b_2)/2^b_3 - 2^b_0*2^(-b_2)/2^b_3 - +- 2^(-b_0)*2^b_2/2^b_3 + 2^b_0*2^b_2/2^b_3 + 2^(-b_0)/2^b_3 + +- 2^b_0/2^b_3 + 2^(-b_2)/2^b_3 + 2^b_2/2^b_3 - 9/2^b_3 - 18 ++ 2^b_0*2^b_2*2^b_3 + 2*2^b_0*2^b_2 + 2^b_0*2^b_3 + 2^b_2*2^b_3 + ++ 2*2^b_0 + 2*2^b_2 - 9*2^b_3 + 2^b_0*2^b_2/2^b_3 - ++ 2^b_0*2^b_3/2^b_2 - 2^b_2*2^b_3/2^b_0 - 2*2^b_0/2^b_2 - ++ 2*2^b_2/2^b_0 + 2^b_0/2^b_3 + 2^b_2/2^b_3 + 2^b_3/2^b_0 + ++ 2^b_3/2^b_2 + 2/2^b_0 + 2/2^b_2 - 2^b_0/(2^b_2*2^b_3) - ++ 2^b_2/(2^b_0*2^b_3) - 9/2^b_3 - 2^b_3/(2^b_0*2^b_2) - ++ 2/(2^b_0*2^b_2) + 1/(2^b_0*2^b_3) + 1/(2^b_2*2^b_3) - ++ 1/(2^b_0*2^b_2*2^b_3) - 18 + + sage: _0,b_1,b_2=var('b_0,b_1,b_2') + sage: f = 1/27*b_2^2/(2^b_2)^2 + 1/27*b_1^2/(2^b_1)^2 + \ +@@ -3809,7 +3809,7 @@ cdef class Expression(CommutativeRingElement): + + sage: x = SR.symbol('x', domain='real') + sage: (x^3)^(1/3) +- (x^3)^(1/3) ++ x + sage: (x^4)^(1/4) + abs(x) + sage: (x^8)^(1/4) +@@ -3872,7 +3872,7 @@ cdef class Expression(CommutativeRingElement): + sage: 2^(x/log(2)) + e^x + sage: 2^(-x^2/2/log(2)) +- e^(-1/2*x^2) ++ 1/e^(1/2*x^2) + sage: x^(x/log(x)) + x^(x/log(x)) + sage: assume(x > 0) +@@ -4816,18 +4816,24 @@ cdef class Expression(CommutativeRingElement): + sage: ((x+y)^(x+y)).match(w0^w0) + {$0: x + y} + sage: t = ((a+b)*(a+c)).match((a+w0)*(a+w1)) +- sage: t[w0], t[w1] +- (c, b) ++ sage: set([t[w0], t[w1]]) == set([b, c]) ++ True + sage: ((a+b)*(a+c)).match((w0+b)*(w0+c)) + {$0: a} + sage: t = ((a+b)*(a+c)).match((w0+w1)*(w0+w2)) +- sage: t[w0], t[w1], t[w2] +- (a, c, b) +- sage: print(((a+b)*(a+c)).match((w0+w1)*(w1+w2))) +- None ++ sage: t[w0] ++ a ++ sage: set([t[w1], t[w2]]) == set([b, c]) ++ True ++ sage: t = ((a+b)*(a+c)).match((w0+w1)*(w1+w2)) ++ sage: t[w1] ++ a ++ sage: set([t[w0], t[w2]]) == set([b, c]) ++ True + sage: t = (a*(x+y)+a*z+b).match(a*w0+w1) +- sage: t[w0], t[w1] +- (x + y, a*z + b) ++ sage: s = set([t[w0], t[w1]]) ++ sage: s == set([x+y, a*z+b]) or s == set([z, a*(x+y)+b]) ++ True + sage: print((a+b+c+d+f+g).match(c)) + None + sage: (a+b+c+d+f+g).has(c) +@@ -4836,7 +4842,7 @@ cdef class Expression(CommutativeRingElement): + {$0: a + b + d + f + g} + sage: (a+b+c+d+f+g).match(c+g+w0) + {$0: a + b + d + f} +- sage: (a+b).match(a+b+w0) ++ sage: (a+b).match(a+b+w0) # known bug + {$0: 0} + sage: print((a*b^2).match(a^w0*b^w1)) + None +@@ -5009,7 +5015,7 @@ cdef class Expression(CommutativeRingElement): + a^3 + b^3 + (x + y)^3 + + sage: t.subs(w0 == w0^2) +- (x^2 + y^2)^18 + a^16 + b^16 ++ a^8 + b^8 + (x^2 + y^2)^6 + + sage: t.subs(a == b, b == c) + (x + y)^3 + b^2 + c^2 +@@ -8392,9 +8398,13 @@ cdef class Expression(CommutativeRingElement): + sage: SR(I).arctan2(1) + arctan2(I, 1) + sage: SR(CDF(0,1)).arctan2(1) +- NaN + +infinity*I +- sage: SR(1).arctan2(CDF(0,1)) # known bug +- 0.7853981633974484 - 19.012501686914433*I ++ Traceback (most recent call last): ++ ... ++ ValueError: power::eval(): division by zero ++ sage: SR(1).arctan2(CDF(0,1)) ++ Traceback (most recent call last): ++ ... ++ ValueError: power::eval(): division by zero + + sage: arctan2(0,oo) + 0 +@@ -8656,7 +8666,7 @@ cdef class Expression(CommutativeRingElement): + 1/2*I*pi + sage: SR(1/2).arccosh() + arccosh(1/2) +- sage: SR(CDF(1/2)).arccosh() # rel tol 1e-15 ++ sage: SR(CDF(1/2)).arccosh() # rel tol 1e-15 + 1.0471975511965976*I + sage: maxima('acosh(0.5)') + 1.04719755119659...*%i +@@ -11687,7 +11697,7 @@ cdef class Expression(CommutativeRingElement): + sage: a.solve(t) + [] + sage: b = a.canonicalize_radical(); b +- -23040.0*(-2.0*e^(1800*t) + 25.0*e^(900*t) - 32.0)*e^(-2400*t) ++ (46080.0*e^(1800*t) - 576000.0*e^(900*t) + 737280.0)*e^(-2400*t) + sage: b.solve(t) + [] + sage: b.solve(t, to_poly_solve=True) +@@ -12163,14 +12173,14 @@ cdef class Expression(CommutativeRingElement): + + sage: (n,k,j)=var('n,k,j') + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) ++ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) + sage: assume(j>-1) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) + 1 + sage: forget() + sage: assume(n>=j) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) ++ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) + sage: forget() + sage: assume(j==-1) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +@@ -12178,7 +12188,7 @@ cdef class Expression(CommutativeRingElement): + sage: forget() + sage: assume(j<-1) + sage: sum(binomial(n,k)*binomial(k-1,j)*(-1)**(k-1-j),k,j+1,n) +- -(-1)^(-j)*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) ++ -(-1)^j*sum((-1)^k*binomial(k - 1, j)*binomial(n, k), k, j + 1, n) + sage: forget() + + Check that :trac:`16176` is fixed:: +diff --git a/src/sage/symbolic/relation.py b/src/sage/symbolic/relation.py +index da6f0eef42..4bd65ef572 100644 +--- a/src/sage/symbolic/relation.py ++++ b/src/sage/symbolic/relation.py +@@ -895,7 +895,7 @@ def solve(f, *args, **kwds): + sage: (r[0][x], r[0][y]) + (2*lambert_w(1/2), 1) + sage: solve(-2*x**3 + 4*x**2 - 2*x + 6 > 0, x, algorithm='sympy') +- [x < (1/6*sqrt(77) + 79/54)^(1/3) + 1/9/(1/6*sqrt(77) + 79/54)^(1/3) + 2/3] ++ [x < 1/3*(1/2)^(1/3)*(9*sqrt(77) + 79)^(1/3) + 2/3*(1/2)^(2/3)/(9*sqrt(77) + 79)^(1/3) + 2/3] + sage: solve(sqrt(2*x^2 - 7) - (3 - x),x,algorithm='sympy') + [x == -8, x == 2] + sage: solve(sqrt(2*x + 9) - sqrt(x + 1) - sqrt(x + 4),x,algorithm='sympy') diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 44b817944674..448cdd21605e 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -169,6 +169,11 @@ stdenv.mkDerivation rec { stripLen = 1; }) + # https://trac.sagemath.org/ticket/24927 rebased + ./patches/arb-2.13.0.patch + + # https://trac.sagemath.org/ticket/24838 rebased + ./patches/pynac-0.7.22.patch ]; patches = nixPatches ++ packageUpgradePatches; diff --git a/pkgs/development/libraries/arb/default.nix b/pkgs/development/libraries/arb/default.nix index a59641e99d39..ea70e6454536 100644 --- a/pkgs/development/libraries/arb/default.nix +++ b/pkgs/development/libraries/arb/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, mpir, gmp, mpfr, flint}: +{stdenv, fetchFromGitHub, fetchpatch, mpir, gmp, mpfr, flint}: stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "arb"; @@ -17,6 +17,14 @@ stdenv.mkDerivation rec { "--with-flint=${flint}" ]; doCheck = true; + patches = [ + # https://github.com/fredrik-johansson/arb/pull/210, included in next release + (fetchpatch { + url = "https://patch-diff.githubusercontent.com/raw/fredrik-johansson/arb/pull/210.patch"; + name = "return-exact-zero-where-possible.patch"; + sha256 = "01j9npnpmwh4dla9i05qdn606hy34gy9bz7c9bbsqm7az3n7pxjg"; + }) + ]; meta = { inherit version; description = ''A library for arbitrary-precision interval arithmetic''; -- cgit 1.4.1 From 20dd009f6a089d90aa87c7a1d6415572a705bcd8 Mon Sep 17 00:00:00 2001 From: Jaakko Luttinen Date: Sat, 30 Jun 2018 19:43:28 +0300 Subject: nano-wallet: 12.1 -> 14.2 (#42803) --- pkgs/applications/altcoins/nano-wallet/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/altcoins/nano-wallet/default.nix b/pkgs/applications/altcoins/nano-wallet/default.nix index 8c4722bd9917..a14a40e9cc75 100644 --- a/pkgs/applications/altcoins/nano-wallet/default.nix +++ b/pkgs/applications/altcoins/nano-wallet/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { name = "nano-wallet-${version}"; - version = "12.1"; + version = "14.2"; src = fetchFromGitHub { owner = "nanocurrency"; repo = "raiblocks"; rev = "V${version}"; - sha256 = "10ng7qn6y31s2bjahmpivw2plx90ljjjzb87j3l7zmppsjd2iq03"; + sha256 = "0jbv5a8sz403a1pqcgl32idk6y0z510h7ikjg1dcxla0rsch6ipl"; fetchSubmodules = true; }; -- cgit 1.4.1 From 81c2f270e535fbc2b7dc83c555b0d5625af004f4 Mon Sep 17 00:00:00 2001 From: Tad Fisher Date: Sat, 30 Jun 2018 10:03:17 -0700 Subject: zoom-us: 2.0.123200.0405 -> 2.2.128100.0627 (#42742) --- .../instant-messengers/zoom-us/default.nix | 116 ++++++++------------- .../instant-messengers/zoom-us/update.sh | 7 ++ pkgs/top-level/all-packages.nix | 2 +- 3 files changed, 52 insertions(+), 73 deletions(-) create mode 100755 pkgs/applications/networking/instant-messengers/zoom-us/update.sh (limited to 'pkgs/applications') diff --git a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix index 692a43629355..2f08e8af6c90 100644 --- a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix +++ b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix @@ -1,14 +1,16 @@ -{ stdenv, fetchurl, system, makeWrapper, makeDesktopItem, - alsaLib, dbus, glib, fontconfig, freetype, libpulseaudio, - utillinux, zlib, xorg, udev, sqlite, expat, libv4l, procps, libGL }: +{ stdenv, fetchurl, system, makeWrapper, makeDesktopItem, autoPatchelfHook +, dbus, glib, libGL, libX11, libXfixes, libuuid, libxcb, procps +, qtbase, qtdeclarative, qtlocation, qtquickcontrols2, qtscript +, qtwebchannel, qtwebengine +}: let - version = "2.0.123200.0405"; + version = "2.2.128100.0627"; srcs = { x86_64-linux = fetchurl { url = "https://zoom.us/client/${version}/zoom_x86_64.tar.xz"; - sha256 = "1ifwa2xf5mw1ll2j1f39qd7mpyxpc6xj3650dmlnxf525dsm573z"; + sha256 = "1x98zhs75c22x58zj4vzk8gb9yr7a9hfkbiqhjp5jrvccgz6ncin"; }; }; @@ -17,76 +19,44 @@ in stdenv.mkDerivation { src = srcs.${system}; - nativeBuildInputs = [ makeWrapper ]; + nativeBuildInputs = [ autoPatchelfHook makeWrapper ]; - libPath = stdenv.lib.makeLibraryPath [ - alsaLib - expat - glib - freetype - libGL - libpulseaudio - zlib - dbus - fontconfig - sqlite - utillinux - udev - - xorg.libX11 - xorg.libSM - xorg.libICE - xorg.libxcb - xorg.xcbutilimage - xorg.xcbutilkeysyms - xorg.libXcursor - xorg.libXext - xorg.libXfixes - xorg.libXdamage - xorg.libXtst - xorg.libxshmfence - xorg.libXi - xorg.libXrender - xorg.libXcomposite - xorg.libXScrnSaver - xorg.libXrandr - - stdenv.cc.cc + buildInputs = [ + dbus glib libGL libX11 libXfixes libuuid libxcb qtbase qtdeclarative + qtlocation qtquickcontrols2 qtscript qtwebchannel qtwebengine ]; - installPhase = '' - runHook preInstall - - packagePath=$out/share/zoom-us - mkdir -p $packagePath - mkdir -p $out/bin - cp -ar * $packagePath - - patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" $packagePath/zoom - patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" $packagePath/QtWebEngineProcess - patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" $packagePath/qtdiag - patchelf --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" $packagePath/zopen - # included from https://github.com/NixOS/nixpkgs/commit/fc218766333a05c9352b386e0cbb16e1ae84bf53 - # it works for me without it, but, well... - paxmark m $packagePath/zoom - #paxmark m $packagePath/QtWebEngineProcess # is this what dtzWill talked about? - - # RUNPATH set via patchelf is used only for half of libraries (why?), so wrap it - makeWrapper $packagePath/zoom $out/bin/zoom-us \ - --prefix LD_LIBRARY_PATH : "$packagePath:$libPath" \ - --prefix LD_PRELOAD : "${libv4l}/lib/v4l1compat.so" \ - --prefix PATH : "${procps}/bin" \ - --set QT_PLUGIN_PATH "$packagePath/platforms" \ - --set QT_XKB_CONFIG_ROOT "${xorg.xkeyboardconfig}/share/X11/xkb" \ - --set QTCOMPOSE "${xorg.libX11.out}/share/X11/locale" - - cat > $packagePath/qt.conf < Date: Sat, 30 Jun 2018 22:30:30 +0200 Subject: sage: replace JUPYTER_PATH patch by upstream patch The patch was replaced by a better upstream patch that doesn't mvoe the jupyter dir to the user's home. --- .../science/math/sage/patches/test-in-tmpdir.patch | 31 ++++++++++++++++++++++ pkgs/applications/science/math/sage/sage-src.nix | 9 ++++--- 2 files changed, 37 insertions(+), 3 deletions(-) create mode 100644 pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch (limited to 'pkgs/applications') diff --git a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch new file mode 100644 index 000000000000..febab3702771 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch @@ -0,0 +1,31 @@ +diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py +index aa23c8405d..8a87de0591 100644 +--- a/src/sage/repl/ipython_kernel/install.py ++++ b/src/sage/repl/ipython_kernel/install.py +@@ -112,7 +112,7 @@ class SageKernelSpec(object): + EXAMPLES:: + + sage: from sage.repl.ipython_kernel.install import SageKernelSpec +- sage: spec = SageKernelSpec() ++ sage: spec = SageKernelSpec(prefix = tmp_dir()) + sage: spec.use_local_mathjax() + sage: mathjax = os.path.join(spec.nbextensions_dir, 'mathjax') + sage: os.path.isdir(mathjax) +@@ -129,7 +129,7 @@ class SageKernelSpec(object): + EXAMPLES:: + + sage: from sage.repl.ipython_kernel.install import SageKernelSpec +- sage: spec = SageKernelSpec() ++ sage: spec = SageKernelSpec(prefix = tmp_dir()) + sage: spec.use_local_jsmol() + sage: jsmol = os.path.join(spec.nbextensions_dir, 'jsmol') + sage: os.path.isdir(jsmol) +@@ -146,7 +146,7 @@ class SageKernelSpec(object): + EXAMPLES:: + + sage: from sage.repl.ipython_kernel.install import SageKernelSpec +- sage: spec = SageKernelSpec() ++ sage: spec = SageKernelSpec(prefix = tmp_dir()) + sage: spec.use_local_threejs() + sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs') + sage: os.path.isdir(threejs) diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 448cdd21605e..244a6ea72673 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -27,11 +27,14 @@ stdenv.mkDerivation rec { }) # https://trac.sagemath.org/ticket/25328 + # https://trac.sagemath.org/ticket/25546 + # https://trac.sagemath.org/ticket/25722 (fetchpatch { - name = "respect-jupyter-path.patch"; - url = "https://git.sagemath.org/sage.git/patch?id2=8bdc326ba57d1bb9664f63cf165a9e9920cc1afc&id=029123097d79f2c67bca2d725c470ef667a88ca2"; - sha256 = "0qw9p541ip0kn2gfvn4i05a06p50f3q46847gqfjjgzxhn62znfw"; + name = "install-jupyter-kernel-in-correct-prefix.patch"; + url = "https://git.sagemath.org/sage.git/patch?id=72167b98e3f64326df6b2c78785df25539472fcc"; + sha256 = "0pscnjhm7r2yr2rxnv4kkkq626vwaja720lixa3m3w9rwlxll5a7"; }) + ./patches/test-in-tmpdir.patch # https://trac.sagemath.org/ticket/25358 (fetchpatch { -- cgit 1.4.1 From 693a4ce20973a0a0ff6a15b1f80240ff569ad72a Mon Sep 17 00:00:00 2001 From: Gabriel Ebner Date: Sun, 1 Jul 2018 11:57:58 +0200 Subject: goldendict: 1.5.0.rc2 -> 2018-06-13 fixes build --- pkgs/applications/misc/goldendict/default.nix | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/goldendict/default.nix b/pkgs/applications/misc/goldendict/default.nix index f552a74f4c11..5cb51eefe5d7 100644 --- a/pkgs/applications/misc/goldendict/default.nix +++ b/pkgs/applications/misc/goldendict/default.nix @@ -1,12 +1,14 @@ -{ stdenv, fetchurl, pkgconfig, libXtst, libvorbis, hunspell +{ stdenv, fetchFromGitHub, pkgconfig, libXtst, libvorbis, hunspell , libao, ffmpeg, libeb, lzo, xz, libtiff , qtbase, qtsvg, qtwebkit, qtx11extras, qttools, qmake }: stdenv.mkDerivation rec { - name = "goldendict-1.5.0.rc2"; - src = fetchurl { - url = "https://github.com/goldendict/goldendict/archive/1.5.0-RC2.tar.gz"; - sha256 = "1pizz39l61rbps0wby75fkvzyrah805257j33siqybwhsfiy1kmw"; + name = "goldendict-2018-06-13"; + src = fetchFromGitHub { + owner = "goldendict"; + repo = "goldendict"; + rev = "48e850c7ec11d83cba7499f7fdce377ef3849bbb"; + sha256 = "0i4q4waqjv45hgwillvjik97pg26kwlmz4925djjkx8s6hxgjlq9"; }; nativeBuildInputs = [ pkgconfig qmake ]; @@ -22,6 +24,6 @@ stdenv.mkDerivation rec { description = "A feature-rich dictionary lookup program"; platforms = stdenv.lib.platforms.linux; - maintainers = [ stdenv.lib.maintainers.astsmtl ]; + maintainers = with stdenv.lib.maintainers; [ gebner astsmtl ]; }; } -- cgit 1.4.1 From d1b9bf92237abdcfa449075552510b5c0b4b53d9 Mon Sep 17 00:00:00 2001 From: Tuomas Tynkkynen Date: Sun, 1 Jul 2018 13:36:57 +0300 Subject: sidplayfp: Init at 1.4.3 --- pkgs/applications/audio/sidplayfp/default.nix | 22 ++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 24 insertions(+) create mode 100644 pkgs/applications/audio/sidplayfp/default.nix (limited to 'pkgs/applications') diff --git a/pkgs/applications/audio/sidplayfp/default.nix b/pkgs/applications/audio/sidplayfp/default.nix new file mode 100644 index 000000000000..2495759593cf --- /dev/null +++ b/pkgs/applications/audio/sidplayfp/default.nix @@ -0,0 +1,22 @@ +{ stdenv, fetchurl, pkgconfig, libsidplayfp }: + +stdenv.mkDerivation rec { + version = "1.4.3"; + name = "sidplayfp-${version}"; + + src = fetchurl { + url = "mirror://sourceforge/sidplay-residfp/sidplayfp/1.4/${name}.tar.gz"; + sha256 = "04gqhxs4w0riabp1svgcs6gsxdmbfmrs4kaqr5lifvxjvv03vzsn"; + }; + + nativeBuildInputs = [ pkgconfig ]; + buildInputs = [ libsidplayfp ]; + + meta = with stdenv.lib; { + description = "A SID player using libsidplayfp"; + homepage = https://sourceforge.net/projects/sidplay-residfp/; + license = with licenses; [ gpl2Plus ]; + maintainers = with maintainers; [ dezgeg ]; + platforms = with platforms; linux; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 54978fd37866..6b1219690d7f 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -17424,6 +17424,8 @@ with pkgs; sawfish = callPackage ../applications/window-managers/sawfish { }; + sidplayfp = callPackage ../applications/audio/sidplayfp { }; + sxhkd = callPackage ../applications/window-managers/sxhkd { }; sxhkd-unstable = callPackage ../applications/window-managers/sxhkd/unstable.nix { }; -- cgit 1.4.1 From 179f9c4fd12865a2e5089ce18bd0effd1c048f3a Mon Sep 17 00:00:00 2001 From: aszlig Date: Sun, 1 Jul 2018 19:32:50 +0200 Subject: ledger: Use Boost Python support if applicable Since 772eef91686974b7710081a9a77e5c0e287c25e8 Boost no longer has Python support enabled by default, so depending on whether Ledger has Python support built in we also use either Boost with Python support or without. Tested building with and without Python support and both builds now succeed. Signed-off-by: aszlig Cc: @the-kenny, @jwiegley --- pkgs/applications/office/ledger/default.nix | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/office/ledger/default.nix b/pkgs/applications/office/ledger/default.nix index 9675293cfe57..387a71aa04ee 100644 --- a/pkgs/applications/office/ledger/default.nix +++ b/pkgs/applications/office/ledger/default.nix @@ -13,7 +13,10 @@ stdenv.mkDerivation rec { fetchSubmodules = true; }; - buildInputs = [ boost gmp mpfr libedit python texinfo gnused ]; + buildInputs = [ + (boost.override { enablePython = usePython; }) + gmp mpfr libedit python texinfo gnused + ]; nativeBuildInputs = [ cmake ]; -- cgit 1.4.1 From b916ed31f2d71ccb8a89d2fce21a96b8e4b60689 Mon Sep 17 00:00:00 2001 From: aszlig Date: Sun, 1 Jul 2018 19:38:06 +0200 Subject: twister: Use boost with Python support Since 772eef91686974b7710081a9a77e5c0e287c25e8, Boost by default doesn't support Python anymore, so we need to override it with Python support. Signed-off-by: aszlig --- pkgs/applications/networking/p2p/twister/default.nix | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/networking/p2p/twister/default.nix b/pkgs/applications/networking/p2p/twister/default.nix index d30527ca6093..cce44521a620 100644 --- a/pkgs/applications/networking/p2p/twister/default.nix +++ b/pkgs/applications/networking/p2p/twister/default.nix @@ -13,6 +13,8 @@ let }; }; + boostPython = boost.override { enablePython = true; }; + in stdenv.mkDerivation rec { name = "twister-${version}"; version = "0.9.34"; @@ -29,13 +31,13 @@ in stdenv.mkDerivation rec { "--disable-deprecated-functions" "--enable-tests" "--enable-python-binding" - "--with-boost-libdir=${boost.out}/lib" + "--with-boost-libdir=${boostPython.out}/lib" ]; nativeBuildInputs = [ pkgconfig ]; buildInputs = [ autoconf automake libtool python2 - boost db openssl geoip miniupnpc libiconv + boostPython db openssl geoip miniupnpc libiconv ]; patches = stdenv.lib.singleton (fetchpatch { -- cgit 1.4.1 From a22ba5f05b3fb1acd2ad870262a3583aee471c73 Mon Sep 17 00:00:00 2001 From: Peter Hoeg Date: Mon, 2 Jul 2018 13:38:29 +0800 Subject: krename: 20170610 -> 5.0.0 --- pkgs/applications/misc/krename/default.nix | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) (limited to 'pkgs/applications') diff --git a/pkgs/applications/misc/krename/default.nix b/pkgs/applications/misc/krename/default.nix index e686ec94a4a3..a0a2776ae360 100644 --- a/pkgs/applications/misc/krename/default.nix +++ b/pkgs/applications/misc/krename/default.nix @@ -1,5 +1,5 @@ { - mkDerivation, fetchFromGitHub, lib, + mkDerivation, fetchurl, lib, extra-cmake-modules, kdoctools, wrapGAppsHook, kconfig, kinit, kjsembed, taglib, exiv2, podofo, kcrash @@ -7,15 +7,14 @@ let pname = "krename"; - version = "20170610"; + version = "5.0.0"; + in mkDerivation rec { name = "${pname}-${version}"; - src = fetchFromGitHub { - owner = "KDE"; - repo = "krename"; - rev = "18000edfec52de0b417d575e14eb078b4bd7b2f3"; - sha256 = "0hsrlfrbi42jqqnkcz682c6yrfi3xpl299672knj22074wr6sv0j"; + src = fetchurl { + url = "mirror://kde/stable/${pname}/${version}/src/${name}.tar.xz"; + sha256 = "136j1dkqrhv458rjh5v3vzjhvq6dhz7k79zk6mmx8zvqacc7cq8a"; }; meta = with lib; { -- cgit 1.4.1