diff options
Diffstat (limited to 'pkgs/applications')
27 files changed, 101 insertions, 706 deletions
diff --git a/pkgs/applications/altcoins/parity/beta.nix b/pkgs/applications/altcoins/parity/beta.nix index fc772246cfc1..b2c9fdfd1eeb 100644 --- a/pkgs/applications/altcoins/parity/beta.nix +++ b/pkgs/applications/altcoins/parity/beta.nix @@ -1,7 +1,9 @@ let - version = "2.0.3"; - sha256 = "1yf3ln4ksk8613kqkpsh16cj8xwx761q6czy57rs8kfh7pgc2pzb"; - cargoSha256 = "1jayk4ngwbg0rv7x1slkl2z46czgy2hnfcxc0dhaz4xpbp2bjqq8"; - patches = [ ./patches/vendored-sources-2.0.patch ]; + version = "2.1.3"; + sha256 = "0il18r229r32jzwsjksp8cc63rp6cf6c0j5dvbfzrnv1zndw0cg3"; + cargoSha256 = "08dyb0lgf66zfq9xmfkhcn6rj070d49dm0rjl3v39sfag6sryz20"; + patches = [ + ./patches/vendored-sources-2.1.patch + ]; in import ./parity.nix { inherit version sha256 cargoSha256 patches; } diff --git a/pkgs/applications/altcoins/parity/default.nix b/pkgs/applications/altcoins/parity/default.nix index 234364e73364..b0286bf65837 100644 --- a/pkgs/applications/altcoins/parity/default.nix +++ b/pkgs/applications/altcoins/parity/default.nix @@ -1,7 +1,7 @@ let - version = "1.11.10"; - sha256 = "15sk6dvc8h1bdm6v7xlq517km0bakb9f13h1n7ixj311vahnmk15"; - cargoSha256 = "0p2idd36cyzp2ax81k533bdma4hz0ws2981qj2s7jnhvmj4941l8"; - patches = [ ./patches/vendored-sources-1.11.patch ]; + version = "2.0.8"; + sha256 = "1bz6dvx8wxhs3g447s62d9091sard2x7w2zd6iy7hf76wg0p73hr"; + cargoSha256 = "0wj93md87fr7a9ag73h0rd9xxqscl0lhbj3g3kvnqrqz9xxajing"; + patches = [ ./patches/vendored-sources-2.0.patch ]; in import ./parity.nix { inherit version sha256 cargoSha256 patches; } diff --git a/pkgs/applications/altcoins/parity/patches/vendored-sources-1.11.patch b/pkgs/applications/altcoins/parity/patches/vendored-sources-2.1.patch index 733f6880ad9d..4af536cdf3cf 100644 --- a/pkgs/applications/altcoins/parity/patches/vendored-sources-1.11.patch +++ b/pkgs/applications/altcoins/parity/patches/vendored-sources-2.1.patch @@ -1,8 +1,8 @@ diff --git a/.cargo/config b/.cargo/config -index 72652ad2f..57c5c2f8f 100644 +index 72652ad2f..3c0eca89a 100644 --- a/.cargo/config +++ b/.cargo/config -@@ -1,3 +1,108 @@ +@@ -1,3 +1,78 @@ [target.x86_64-pc-windows-msvc] # Link the C runtime statically ; https://github.com/paritytech/parity/issues/6643 rustflags = ["-Ctarget-feature=+crt-static"] @@ -12,19 +12,9 @@ index 72652ad2f..57c5c2f8f 100644 +branch = "master" +replace-with = "vendored-sources" + -+[source."https://github.com/js-dist-paritytech/parity-master-1-10-shell.git"] -+git = "https://github.com/js-dist-paritytech/parity-master-1-10-shell.git" -+rev = "bd25b41cd642c6b822d820dded3aa601a29aa079" -+replace-with = "vendored-sources" -+ -+[source."https://github.com/js-dist-paritytech/parity-master-1-10-wallet.git"] -+git = "https://github.com/js-dist-paritytech/parity-master-1-10-wallet.git" -+rev = "4b6f112412716cd05123d32eeb7fda448288a6c6" -+replace-with = "vendored-sources" -+ +[source."https://github.com/nikvolf/parity-tokio-ipc"] +git = "https://github.com/nikvolf/parity-tokio-ipc" -+branch = "master" ++rev = "7c9bbe3bc45d8e72a92b0951acc877da228abd50" +replace-with = "vendored-sources" + +[source."https://github.com/nikvolf/tokio-named-pipes"] @@ -32,16 +22,6 @@ index 72652ad2f..57c5c2f8f 100644 +branch = "master" +replace-with = "vendored-sources" + -+[source."https://github.com/parity-js/dapp-wallet.git"] -+git = "https://github.com/parity-js/dapp-wallet.git" -+rev = "65deb02e7c007a0fd8aab0c089c93e3fd1de6f87" -+replace-with = "vendored-sources" -+ -+[source."https://github.com/parity-js/shell.git"] -+git = "https://github.com/parity-js/shell.git" -+rev = "eecaadcb9e421bce31e91680d14a20bbd38f92a2" -+replace-with = "vendored-sources" -+ +[source."https://github.com/paritytech/app-dirs-rs"] +git = "https://github.com/paritytech/app-dirs-rs" +branch = "master" @@ -87,21 +67,11 @@ index 72652ad2f..57c5c2f8f 100644 +branch = "master" +replace-with = "vendored-sources" + -+[source."https://github.com/paritytech/rust-rocksdb"] -+git = "https://github.com/paritytech/rust-rocksdb" -+branch = "master" -+replace-with = "vendored-sources" -+ +[source."https://github.com/paritytech/rust-secp256k1"] +git = "https://github.com/paritytech/rust-secp256k1" +branch = "master" +replace-with = "vendored-sources" + -+[source."https://github.com/paritytech/rust-snappy"] -+git = "https://github.com/paritytech/rust-snappy" -+branch = "master" -+replace-with = "vendored-sources" -+ +[source."https://github.com/paritytech/trezor-sys"] +git = "https://github.com/paritytech/trezor-sys" +branch = "master" diff --git a/pkgs/applications/audio/lollypop/default.nix b/pkgs/applications/audio/lollypop/default.nix index ec9122406993..e999672f4ab3 100644 --- a/pkgs/applications/audio/lollypop/default.nix +++ b/pkgs/applications/audio/lollypop/default.nix @@ -4,7 +4,7 @@ , gobjectIntrospection, wrapGAppsHook }: python3.pkgs.buildPythonApplication rec { - version = "0.9.604"; + version = "0.9.605"; name = "lollypop-${version}"; format = "other"; @@ -14,7 +14,7 @@ python3.pkgs.buildPythonApplication rec { url = "https://gitlab.gnome.org/World/lollypop"; rev = "refs/tags/${version}"; fetchSubmodules = true; - sha256 = "0pfljs5q0xzqll6dybslin4nr7w18bn1yi0xn79vh44zn3l0r8q4"; + sha256 = "10d9k7ssh4snrrjy1hb3y39by6175493cmn50aq88xby2mdy3p74"; }; nativeBuildInputs = with python3.pkgs; [ diff --git a/pkgs/applications/audio/mixxx/default.nix b/pkgs/applications/audio/mixxx/default.nix index 28e29850606a..a5582f908fc0 100644 --- a/pkgs/applications/audio/mixxx/default.nix +++ b/pkgs/applications/audio/mixxx/default.nix @@ -1,6 +1,7 @@ { stdenv, fetchFromGitHub, makeWrapper, chromaprint, fetchpatch , fftw, flac, faad2, glibcLocales, mp4v2 , libid3tag, libmad, libopus, libshout, libsndfile, libusb1, libvorbis +, opusfile , pkgconfig, portaudio, portmidi, protobuf, qt4, rubberband, scons, sqlite , taglib, upower, vampSDK }: @@ -20,7 +21,7 @@ stdenv.mkDerivation rec { buildInputs = [ chromaprint fftw flac faad2 glibcLocales mp4v2 libid3tag libmad libopus libshout libsndfile - libusb1 libvorbis pkgconfig portaudio portmidi protobuf qt4 + libusb1 libvorbis opusfile pkgconfig portaudio portmidi protobuf qt4 rubberband scons sqlite taglib upower vampSDK ]; @@ -28,6 +29,7 @@ stdenv.mkDerivation rec { "build=release" "qtdir=${qt4}" "faad=1" + "opus=1" ]; buildPhase = '' diff --git a/pkgs/applications/audio/radiotray-ng/default.nix b/pkgs/applications/audio/radiotray-ng/default.nix index 82bc42143c67..6f7ce9048c4c 100644 --- a/pkgs/applications/audio/radiotray-ng/default.nix +++ b/pkgs/applications/audio/radiotray-ng/default.nix @@ -40,13 +40,13 @@ let in stdenv.mkDerivation rec { name = "radiotray-ng-${version}"; - version = "0.2.3"; + version = "0.2.4"; src = fetchFromGitHub { owner = "ebruck"; repo = "radiotray-ng"; rev = "v${version}"; - sha256 = "1sq7bc0dswv3vv56w527z268ib0pyhdxyf25388vnj1fv0c146wc"; + sha256 = "1jk80fv8ivwdx7waivls0mczn0rx4wv0fy7a28k77m88i5gkfgyw"; }; nativeBuildInputs = [ cmake pkgconfig wrapGAppsHook makeWrapper ]; diff --git a/pkgs/applications/editors/vscode/default.nix b/pkgs/applications/editors/vscode/default.nix index b8a717fc0e70..8d5dca0a3454 100644 --- a/pkgs/applications/editors/vscode/default.nix +++ b/pkgs/applications/editors/vscode/default.nix @@ -2,7 +2,7 @@ gtk2, wrapGAppsHook, libXScrnSaver, libxkbfile, libsecret }: let - version = "1.28.0"; + version = "1.28.2"; channel = "stable"; plat = { @@ -12,9 +12,9 @@ let }.${stdenv.hostPlatform.system}; sha256 = { - "i686-linux" = "0f54py00lmw96x47nk823gwxxc9kr9haaa821ggi974ycr54af0y"; - "x86_64-linux" = "07bbzm1159k2gkajj6z7dsr0kmadd5gx721w92r252i5hcwg5sx4"; - "x86_64-darwin" = "019cl2rswls3gwwa8y70cllc4jnd8xj0y2m9rvg2rz695snp6rcm"; + "i686-linux" = "13zgx80qzq1wvss3byh56rvp2bdxywc4xmhhljsqrxf17g86g2zr"; + "x86_64-linux" = "1z50hkr9mcf76hlr1jb80nbvpxbpm2bh0l63yh9yqpalmz66xbfy"; + "x86_64-darwin" = "0n7lavpylg1q89qa64z4z1v7pgmwb2kidc57cgpvjnhjg8idys33"; }.${stdenv.hostPlatform.system}; archive_fmt = if stdenv.hostPlatform.system == "x86_64-darwin" then "zip" else "tar.gz"; diff --git a/pkgs/applications/graphics/openimageio/default.nix b/pkgs/applications/graphics/openimageio/default.nix index bc669e9e1a01..1980f470435b 100644 --- a/pkgs/applications/graphics/openimageio/default.nix +++ b/pkgs/applications/graphics/openimageio/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { name = "openimageio-${version}"; - version = "1.8.14"; + version = "1.8.15"; src = fetchFromGitHub { owner = "OpenImageIO"; repo = "oiio"; rev = "Release-${version}"; - sha256 = "07axn7bziy9h5jawpwcchag0nkczivaajsw69mxgmr508gw9r0xn"; + sha256 = "0fbl5rzmip5q155lfsr07n65dnhww1kw97masps1i1x40gq15czx"; }; outputs = [ "bin" "out" "dev" "doc" ]; diff --git a/pkgs/applications/misc/gpxsee/default.nix b/pkgs/applications/misc/gpxsee/default.nix index 2f61ba683f3f..d2427d95c19d 100644 --- a/pkgs/applications/misc/gpxsee/default.nix +++ b/pkgs/applications/misc/gpxsee/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "gpxsee-${version}"; - version = "5.18"; + version = "6.2"; src = fetchFromGitHub { owner = "tumic0"; repo = "GPXSee"; rev = version; - sha256 = "0dl10fr881b8fwf2yj14bd6gagb8hm0s46q18y2y56rw98nk4vrq"; + sha256 = "13hd6n5mzkk4nx9v9dwg8vvixr73zjba72h6vmxvz9fmywc4rs5p"; }; nativeBuildInputs = [ qmake ]; diff --git a/pkgs/applications/networking/browsers/chromium/default.nix b/pkgs/applications/networking/browsers/chromium/default.nix index 51618a479d42..686e8fadec34 100644 --- a/pkgs/applications/networking/browsers/chromium/default.nix +++ b/pkgs/applications/networking/browsers/chromium/default.nix @@ -18,6 +18,8 @@ let callPackage = newScope chromium; chromium = { + inherit stdenv; + upstream-info = (callPackage ./update.nix {}).getChannel channel; mkChromiumDerivation = callPackage ./common.nix { diff --git a/pkgs/applications/networking/browsers/eolie/default.nix b/pkgs/applications/networking/browsers/eolie/default.nix index 1f7ed9732bc7..91b1099bfb86 100644 --- a/pkgs/applications/networking/browsers/eolie/default.nix +++ b/pkgs/applications/networking/browsers/eolie/default.nix @@ -5,7 +5,7 @@ python3.pkgs.buildPythonApplication rec { name = "eolie-${version}"; - version = "0.9.41"; + version = "0.9.45"; format = "other"; doCheck = false; @@ -14,7 +14,7 @@ python3.pkgs.buildPythonApplication rec { url = "https://gitlab.gnome.org/World/eolie"; rev = "refs/tags/${version}"; fetchSubmodules = true; - sha256 = "0qrbgyzhvh96d7h2rcz04m7am6av30pcvb3fwlrjx0c402rslsx8"; + sha256 = "0x6f2qqqxpjf28mqxs4jlrz2z8wa9nvb9h24nf8qwmzavjjbraqg"; }; nativeBuildInputs = [ diff --git a/pkgs/applications/networking/remote/remmina/default.nix b/pkgs/applications/networking/remote/remmina/default.nix index 96aa037d35bf..e823977db204 100644 --- a/pkgs/applications/networking/remote/remmina/default.nix +++ b/pkgs/applications/networking/remote/remmina/default.nix @@ -1,16 +1,18 @@ { stdenv, fetchFromGitLab, cmake, pkgconfig, wrapGAppsHook -, glib, gtk3, gettext, libxkbfile, libgnome-keyring, libX11 +, glib, gtk3, gettext, libxkbfile, libX11 , freerdp, libssh, libgcrypt, gnutls, makeDesktopItem -, pcre, webkitgtk, libdbusmenu-gtk3, libappindicator-gtk3 +, pcre, libdbusmenu-gtk3, libappindicator-gtk3 , libvncserver, libpthreadstubs, libXdmcp, libxkbcommon -, libsecret, spice-protocol, spice-gtk, epoxy, at-spi2-core +, libsecret, libsoup, spice-protocol, spice-gtk, epoxy, at-spi2-core , openssl, gsettings-desktop-schemas, json-glib # The themes here are soft dependencies; only icons are missing without them. , hicolor-icon-theme, adwaita-icon-theme +, gnomeSupport ? true, libgnome-keyring }: +with stdenv.lib; + let - version = "1.2.32"; desktopItem = makeDesktopItem { name = "remmina"; @@ -22,8 +24,9 @@ let categories = "GTK;GNOME;X-GNOME-NetworkSettings;Network;"; }; -in stdenv.mkDerivation { +in stdenv.mkDerivation rec { name = "remmina-${version}"; + version = "1.2.32"; src = fetchFromGitLab { owner = "Remmina"; @@ -33,13 +36,21 @@ in stdenv.mkDerivation { }; nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ cmake wrapGAppsHook gsettings-desktop-schemas - glib gtk3 gettext libxkbfile libgnome-keyring libX11 - freerdp libssh libgcrypt gnutls - pcre webkitgtk libdbusmenu-gtk3 libappindicator-gtk3 - libvncserver libpthreadstubs libXdmcp libxkbcommon - libsecret spice-protocol spice-gtk epoxy at-spi2-core - openssl hicolor-icon-theme adwaita-icon-theme json-glib ]; + buildInputs = [ + cmake wrapGAppsHook gsettings-desktop-schemas + glib gtk3 gettext libxkbfile libX11 + freerdp libssh libgcrypt gnutls + pcre libdbusmenu-gtk3 libappindicator-gtk3 + libvncserver libpthreadstubs libXdmcp libxkbcommon + libsecret libsoup spice-protocol spice-gtk epoxy at-spi2-core + openssl hicolor-icon-theme adwaita-icon-theme json-glib + ] + ++ optional gnomeSupport libgnome-keyring; + + preConfigure = optionalString (!gnomeSupport) '' + substituteInPlace CMakeLists.txt \ + --replace "add_subdirectory(remmina-plugins-gnome)" "" + ''; cmakeFlags = [ "-DWITH_VTE=OFF" @@ -62,7 +73,7 @@ in stdenv.mkDerivation { cp ${desktopItem}/share/applications/* $out/share/applications ''; - meta = with stdenv.lib; { + meta = { license = stdenv.lib.licenses.gpl2; homepage = https://gitlab.com/Remmina/Remmina; description = "Remote desktop client written in GTK+"; diff --git a/pkgs/applications/networking/sync/rclone/browser.nix b/pkgs/applications/networking/sync/rclone/browser.nix new file mode 100644 index 000000000000..4325c8ea88ae --- /dev/null +++ b/pkgs/applications/networking/sync/rclone/browser.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchFromGitHub, cmake, qtbase }: + +stdenv.mkDerivation rec { + name = "rclone-browser-${version}"; + version = "1.2"; + + src = fetchFromGitHub { + owner = "mmozeiko"; + repo = "RcloneBrowser"; + rev = version; + sha256 = "1ldradd5c606mfkh46y4mhcvf9kbjhamw0gahksp9w43h5dh3ir7"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ qtbase ]; + + meta = with stdenv.lib; { + inherit (src.meta) homepage; + description = "Graphical Frontend to Rclone written in Qt"; + license = licenses.unlicense; + platforms = platforms.linux; + maintainers = with maintainers; [ dotlambda ]; + }; +} diff --git a/pkgs/applications/networking/znc/default.nix b/pkgs/applications/networking/znc/default.nix index ca5624d5b73f..861e7d24275d 100644 --- a/pkgs/applications/networking/znc/default.nix +++ b/pkgs/applications/networking/znc/default.nix @@ -3,6 +3,7 @@ , withPython ? false, python3 , withTcl ? false, tcl , withCyrus ? true, cyrus_sasl +, withUnicode ? true, icu }: with stdenv.lib; @@ -22,7 +23,8 @@ stdenv.mkDerivation rec { ++ optional withPerl perl ++ optional withPython python3 ++ optional withTcl tcl - ++ optional withCyrus cyrus_sasl; + ++ optional withCyrus cyrus_sasl + ++ optional withUnicode icu; configureFlags = [ (stdenv.lib.enableFeature withPerl "perl") diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index e4f0cb8d0b1a..3f664006cd0f 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "gtkwave-${version}"; - version = "3.3.94"; + version = "3.3.95"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${name}.tar.gz"; - sha256 = "1v14sdd4lykly6szal6ky79b0s5pv6f1xifk5mkqkg5bkpjq71fg"; + sha256 = "1999wnipah1ncvjzjf95pfdrvgq1kd6hli8xlaj2hfjka8pamfaf"; }; nativeBuildInputs = [ pkgconfig ]; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 23f1ff85edf0..040d722f9410 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -37,6 +37,8 @@ self = stdenv.mkDerivation { passthru = { inherit coq-version; + inherit ocamlPackages; + # For compatibility inherit (ocamlPackages) ocaml camlp5 findlib num; emacsBufferSetup = pkgs: '' ; Propagate coq paths to children diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix index 1ccc365498ce..58609e856c3b 100644 --- a/pkgs/applications/science/logic/why3/default.nix +++ b/pkgs/applications/science/logic/why3/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "why3-${version}"; - version = "1.0.0"; + version = "1.1.0"; src = fetchurl { - url = https://gforge.inria.fr/frs/download.php/file/37604/why3-1.0.0.tar.gz; - sha256 = "18h00diw1c051v7ya0lv09ns5630qi9savwffx0652mcc4b4qpxn"; + url = https://gforge.inria.fr/frs/download.php/file/37767/why3-1.1.0.tar.gz; + sha256 = "199ziq8mv3r24y3dd1n2r8k2gy09p7kdyyhkg9qn1vzfd2fxwzc1"; }; buildInputs = (with ocamlPackages; [ diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix index 288ffd6e0e1a..098ce3925cf3 100644 --- a/pkgs/applications/science/math/sage/env-locations.nix +++ b/pkgs/applications/science/math/sage/env-locations.nix @@ -38,6 +38,7 @@ writeTextFile rec { export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs" export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona" export JMOL_DIR="${jmol}" + export JSMOL_DIR="${jmol}/share/jsmol" export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax" export THREEJS_DIR="${three}/lib/node_modules/three" export SAGE_INCLUDE_DIRECTORIES="${cysignals}/lib/python2.7/site-packages" diff --git a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch deleted file mode 100644 index a51e30312ed9..000000000000 --- a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch +++ /dev/null @@ -1,127 +0,0 @@ -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) - <li><a class="reference external" href="../reference/padics/sage/rings/padics/tutorial.html#sage-rings-padics-tutorial" title="(in Sage Reference Manual: p-Adics ...)"><span>Introduction to the -adics</span></a></li> -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-20180710.patch b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch index d06e1e6cedf2..986ae42aeb62 100644 --- a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch +++ b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch @@ -14,27 +14,3 @@ index 4417b59276..ae57ca2991 100644 """ global instances try: -diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp -index 5fd5693b53..d12468faa8 100644 ---- a/src/sage/libs/eclib/wrap.cpp -+++ b/src/sage/libs/eclib/wrap.cpp -@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose) - - - int mw_process(struct Curvedata* curve, struct mw* m, -- const struct bigint* x, const struct bigint* y, -- const struct bigint* z, int sat) -+ const bigint* x, const bigint* y, -+ const bigint* z, int sat) - { - Point P(*curve, *x, *y, *z); - if (!P.isvalid()) -@@ -188,7 +188,7 @@ int mw_rank(struct mw* m) - } - - /* Returns index and unsat long array, which user must deallocate */ --int mw_saturate(struct mw* m, struct bigint* index, char** unsat, -+int mw_saturate(struct mw* m, bigint* index, char** unsat, - long sat_bd, int odd_primes_only) - { - vector<long> v; diff --git a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch b/pkgs/applications/science/math/sage/patches/pari-no-threads.patch deleted file mode 100644 index 13b47dbdd31b..000000000000 --- a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/src/sage/libs/pari/__init__.py b/src/sage/libs/pari/__init__.py -index e451766474..77eda66097 100644 ---- a/src/sage/libs/pari/__init__.py -+++ b/src/sage/libs/pari/__init__.py -@@ -205,6 +205,13 @@ def _get_pari_instance(): - # messages in Sage. - P.default("debugmem", 0) - -+ # Make sure pari doesn't use threads, regardless of how it was compiled. -+ # Threads cause some doctest failures (memory issues). Those could probably -+ # be solved without disabling threads. But that would require figuring out -+ # some sensible values for `threadsizemax`. See -+ # https://pari.math.u-bordeaux.fr/dochtml/html/GP_defaults.html -+ P.default("nbthreads", 1) -+ - return P - - pari = _get_pari_instance() diff --git a/pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch b/pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch deleted file mode 100644 index 4c8df92904ed..000000000000 --- a/pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch +++ /dev/null @@ -1,274 +0,0 @@ -diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py -index 9d65c9fa6c..a028bbe719 100644 ---- a/src/sage/interfaces/singular.py -+++ b/src/sage/interfaces/singular.py -@@ -654,7 +654,7 @@ class Singular(ExtraTabCompletion, Expect): - - s = Expect.eval(self, x, **kwds) - -- if s.find("error") != -1 or s.find("Segment fault") != -1: -+ if s.find("error occurred") != -1 or s.find("Segment fault") != -1: - raise SingularError('Singular error:\n%s'%s) - - if get_verbose() > 0: -@@ -1079,7 +1079,7 @@ class Singular(ExtraTabCompletion, Expect): - sage: S = singular.ring('real', '(a,b)', 'lp') - sage: singular.current_ring() - polynomial ring, over a field, global ordering -- // coefficients: float -+ // coefficients: Float() - // number of vars : 2 - // block 1 : ordering lp - // : names a b -@@ -1157,7 +1157,7 @@ class Singular(ExtraTabCompletion, Expect): - sage: singular._tab_completion() - ['exteriorPower', - ... -- 'flintZ'] -+ 'crossprod'] - """ - p = re.compile("// *([a-z0-9A-Z_]*).*") #compiles regular expression - proclist = self.eval("listvar(proc)").splitlines() -@@ -1183,7 +1183,7 @@ class Singular(ExtraTabCompletion, Expect): - EXAMPLES:: - - sage: singular.version() -- "Singular ... version 4.1.0 ... -+ "Singular ... version 4... - """ - return singular_version() - -@@ -1562,7 +1562,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): - elif charstr[0] in ['0', 'QQ']: - from sage.all import QQ - br = QQ -- elif charstr[0]=='real': -+ elif charstr[0].startswith('Float'): - from sage.all import RealField, ceil, log - prec = singular.eval('ringlist(basering)[1][2][1]') - br = RealField(ceil((ZZ(prec)+1)/log(2,10))) -@@ -1750,7 +1750,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): - - # Singular 4 puts parentheses around floats and sign outside them - charstr = self.parent().eval('charstr(basering)').split(',',1) -- if charstr[0] in ['real', 'complex']: -+ if charstr[0]=='complex' or charstr[0].startswith('Float'): - for i in range(coeff_start, 2 * coeff_start): - singular_poly_list[i] = singular_poly_list[i].replace('(','').replace(')','') - -@@ -1992,7 +1992,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): - sage: S = singular.ring('real', '(a,b)', 'lp') - sage: singular.current_ring() - polynomial ring, over a field, global ordering -- // coefficients: float -+ // coefficients: Float() - // number of vars : 2 - // block 1 : ordering lp - // : names a b -@@ -2072,7 +2072,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement): - sage: R._tab_completion() - ['exteriorPower', - ... -- 'flintZ'] -+ 'crossprod'] - """ - return self.parent()._tab_completion() - -@@ -2358,7 +2358,7 @@ def singular_version(): - EXAMPLES:: - - sage: singular.version() -- "Singular ... version 4.1.0 ... -+ "Singular ... version 4... - """ - return singular.eval('system("--version");') - -diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd -index 4b658c4807..d863740419 100644 ---- a/src/sage/libs/singular/decl.pxd -+++ b/src/sage/libs/singular/decl.pxd -@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h": - - int n_NumberOfParameters(const n_Procs_s* r) - -- ctypedef struct poly "polyrec": -+ ctypedef struct poly "spolyrec": - poly *next - number *coef - unsigned long exp[1] -@@ -630,9 +630,13 @@ cdef extern from "singular/Singular/libsingular.h": - # return p*q, destroys p and q - poly *p_Mult_q(poly *p, poly *q, ring *r) - -+ # polynomial division, ignoring the rest -+ # via singclap_pdivide resp. idLift, destroys p,q -+ poly *p_Divide(poly *p, poly *q, ring *r) -+ - # divide monomial p by monomial q, p,q const - -- poly *pDivide(poly *p,poly *q) -+ poly *pMDivide(poly *p,poly *q) - - # return the i-th power of p; p destroyed, requires global ring - -diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -index 2a8d9ae021..aeff53af6c 100644 ---- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -+++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx -@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport ( - n_IsUnit, n_Invers, - p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q, - p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup, -- omFree, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, -- pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, -+ omFree, pMDivide, p_Divide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy, -+ pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy, - p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete, - p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize, - idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD, -@@ -1693,8 +1693,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base): - if not g._poly: - raise ZeroDivisionError - -- if r!=currRing: rChangeCurrRing(r) # pDivide -- res = pDivide(f._poly, g._poly) -+ if r!=currRing: rChangeCurrRing(r) # pMDivide -+ res = pMDivide(f._poly, g._poly) - if coeff: - if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): - n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) -@@ -1853,8 +1853,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base): - and (<MPolynomial_libsingular>g) \ - and g.parent() is self \ - and p_LmDivisibleBy((<MPolynomial_libsingular>g)._poly, m, r): -- if r!=currRing: rChangeCurrRing(r) # pDivide -- flt = pDivide(f._poly, (<MPolynomial_libsingular>g)._poly) -+ if r!=currRing: rChangeCurrRing(r) # pMDivide -+ flt = pMDivide(f._poly, (<MPolynomial_libsingular>g)._poly) - #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<MPolynomial_libsingular>g)._poly, r), r), r) - p_SetCoeff(flt, n_Init(1, r), r) - return new_MP(self,flt), g -@@ -4023,16 +4023,6 @@ cdef class MPolynomial_libsingular(MPolynomial): - Traceback (most recent call last): - ... - NotImplementedError: Division of multivariate polynomials over non fields by non-monomials not implemented. -- -- TESTS:: -- -- sage: P.<x,y> = ZZ[] -- sage: p = 3*(-x^8*y^2 - x*y^9 + 6*x^8*y + 17*x^2*y^6 - x^3*y^2) -- sage: q = 7*(x^2 + x*y + y^2 + 1) -- sage: p*q//q == p -- True -- sage: p*q//p == q -- True - """ - cdef MPolynomialRing_libsingular parent = self._parent - cdef ring *r = self._parent_ring -@@ -4052,13 +4042,18 @@ cdef class MPolynomial_libsingular(MPolynomial): - _right = <MPolynomial_libsingular>right - - if r.cf.type != n_unknown: -+ if r.cf.type == n_Z: -+ P = parent.change_ring(RationalField()) -+ f = P(self)//P(right) -+ CM = list(f) -+ return parent(sum([c.floor()*m for c,m in CM])) - if _right.is_monomial(): - p = _self._poly - quo = p_ISet(0,r) -- if r != currRing: rChangeCurrRing(r) # pDivide -+ if r != currRing: rChangeCurrRing(r) # pMDivide - while p: - if p_DivisibleBy(_right._poly, p, r): -- temp = pDivide(p, _right._poly) -+ temp = pMDivide(p, _right._poly) - p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r) - quo = p_Add_q(quo, temp, r) - p = pNext(p) -@@ -4794,6 +4789,8 @@ cdef class MPolynomial_libsingular(MPolynomial): - sage: p = -x*y + x*z + 54*x - 2 - sage: (5*p^2).lcm(3*p) == 15*p^2 - True -+ sage: lcm(2*x,2*x*y) -+ 2*x*y - """ - cdef ring *_ring = self._parent_ring - cdef poly *ret -@@ -4821,9 +4818,7 @@ cdef class MPolynomial_libsingular(MPolynomial): - if _ring!=currRing: rChangeCurrRing(_ring) # singclap_gcd - gcd = singclap_gcd(p_Copy(self._poly, _ring), p_Copy(_g._poly, _ring), _ring ) - prod = pp_Mult_qq(self._poly, _g._poly, _ring) -- ret = singclap_pdivide(prod , gcd , _ring) -- p_Delete(&prod, _ring) -- p_Delete(&gcd, _ring) -+ ret = p_Divide(prod, gcd, _ring) - if count >= 20: - sig_off() - return new_MP(self._parent, ret) -@@ -4866,7 +4861,7 @@ cdef class MPolynomial_libsingular(MPolynomial): - sage: f.quo_rem(y) - (2*x^2, x + 1) - sage: f.quo_rem(3*x) -- (2*x*y + 1, -4*x^2*y - 2*x + 1) -+ (0, 2*x^2*y + x + 1) - - TESTS:: - -@@ -4888,7 +4883,7 @@ cdef class MPolynomial_libsingular(MPolynomial): - if right.is_zero(): - raise ZeroDivisionError - -- if not self._parent._base.is_field() and not is_IntegerRing(self._parent._base): -+ if not self._parent._base.is_field(): - py_quo = self//right - py_rem = self - right*py_quo - return py_quo, py_rem -diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx -index d5439f7f08..ad20ebcca0 100644 ---- a/src/sage/rings/polynomial/plural.pyx -+++ b/src/sage/rings/polynomial/plural.pyx -@@ -998,7 +998,7 @@ cdef class NCPolynomialRing_plural(Ring): - if not g._poly: - raise ZeroDivisionError - -- res = pDivide(f._poly,g._poly) -+ res = pMDivide(f._poly,g._poly) - if coeff: - if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf): - n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf) -@@ -1193,7 +1193,7 @@ cdef class NCPolynomialRing_plural(Ring): - if isinstance(g, NCPolynomial_plural) \ - and (<NCPolynomial_plural>g) \ - and p_LmDivisibleBy((<NCPolynomial_plural>g)._poly, m, r): -- flt = pDivide(f._poly, (<NCPolynomial_plural>g)._poly) -+ flt = pMDivide(f._poly, (<NCPolynomial_plural>g)._poly) - #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((<NCPolynomial_plural>g)._poly, r), r), r) - p_SetCoeff(flt, n_Init(1, r), r) - return new_NCP(self,flt), g -diff --git a/src/sage/rings/polynomial/polynomial_singular_interface.py b/src/sage/rings/polynomial/polynomial_singular_interface.py -index 9331169f8b..f753610fd3 100644 ---- a/src/sage/rings/polynomial/polynomial_singular_interface.py -+++ b/src/sage/rings/polynomial/polynomial_singular_interface.py -@@ -81,8 +81,8 @@ class PolynomialRing_singular_repr: - sage: R.<x,y> = PolynomialRing(CC) - sage: singular(R) - polynomial ring, over a field, global ordering -- // coefficients: float[I](complex:15 digits, additional 0 digits)/(I^2+1) -- // number of vars : 2 -+ // coefficients: real[I](complex:15 digits, additional 0 digits)/(I^2+1) -+ // number of vars : 2 - // block 1 : ordering dp - // : names x y - // block 2 : ordering C -@@ -90,8 +90,8 @@ class PolynomialRing_singular_repr: - sage: R.<x,y> = PolynomialRing(RealField(100)) - sage: singular(R) - polynomial ring, over a field, global ordering -- // coefficients: float -- // number of vars : 2 -+ // coefficients: Float() -+ // number of vars : 2 - // block 1 : ordering dp - // : names x y - // block 2 : ordering C diff --git a/pkgs/applications/science/math/sage/patches/spkg-scripts.patch b/pkgs/applications/science/math/sage/patches/spkg-scripts.patch deleted file mode 100644 index 4d37998b288b..000000000000 --- a/pkgs/applications/science/math/sage/patches/spkg-scripts.patch +++ /dev/null @@ -1,46 +0,0 @@ -commit f02714d4aea80e17cb8df62bab75d7c1a1b61a8e -Author: Timo Kaufmann <timokau@zoho.com> -Date: Mon Jul 9 18:26:18 2018 +0200 - - Don't attempt to create dirs when showing pkg info - - The script dir cannot be assumed to be writeable after installation. - -diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg -index f3e02aeae5..190d558ad1 100755 ---- a/build/bin/sage-spkg -+++ b/build/bin/sage-spkg -@@ -167,14 +167,6 @@ if [ -z "$SAGE_BUILD_DIR" ]; then - export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build" - fi - --for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS"; do -- mkdir -p "$dir" -- if [ $? -ne 0 ]; then -- error_msg "Error creating directory $dir" -- exit 1 -- fi --done -- - - # Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid - # trouble with setuptools / easy_install (cf. #10192, #10176): -@@ -563,11 +555,13 @@ fi - # Setup directories - ################################################################## - --mkdir -p "$SAGE_BUILD_DIR" --if [ $? -ne 0 ]; then -- error_msg "Error creating directory $SAGE_BUILD_DIR" -- exit 1 --fi -+for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS" "$SAGE_BUILD_DIR"; do -+ mkdir -p "$dir" -+ if [ $? -ne 0 ]; then -+ error_msg "Error creating directory $dir" -+ exit 1 -+ fi -+done - - # Trac #5852: check write permissions - if [ ! -w "$SAGE_BUILD_DIR" ]; then diff --git a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch deleted file mode 100644 index febab3702771..000000000000 --- a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch +++ /dev/null @@ -1,31 +0,0 @@ -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 f74da33f4026..f217a7a0caed 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -3,35 +3,17 @@ , fetchpatch }: stdenv.mkDerivation rec { - version = "8.3"; + version = "8.4"; name = "sage-src-${version}"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "0mbm99m5xry21xpi4q3q96gx392liwbifywf5awvl0j85a7rkfyx"; + sha256 = "0gips1hagiz9m7s21bg5as8hrrm2x5k47h1bsq0pc46iplfwmv2d"; }; nixPatches = [ - # https://trac.sagemath.org/ticket/25809 - ./patches/spkg-scripts.patch - - # 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/25722 - ./patches/test-in-tmpdir.patch - # https://trac.sagemath.org/ticket/25358 (fetchpatch { name = "safe-directory-test-without-patch.patch"; @@ -45,46 +27,9 @@ stdenv.mkDerivation rec { # https://trac.sagemath.org/ticket/25316 # https://github.com/python/cpython/pull/7476 ./patches/python-5755-hotpatch.patch - - # 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"; - }) - - # https://trac.sagemath.org/ticket/25345 - # (upstream patch doesn't apply on 8.2 source) - ./patches/dochtml-optional.patch - - # work with pari with threads enabled at compile time (disable them at runtime) - # https://trac.sagemath.org/ticket/26002 - ./patches/pari-no-threads.patch ]; packageUpgradePatches = [ - (fetchpatch { - name = "cypari2-1.2.1.patch"; - url = "https://git.sagemath.org/sage.git/patch/?h=62fe6eb15111327d930336d4252d5b23cbb22ab9"; - sha256 = "1xax7vvs8h4xip16xcsp47xdb6lig6f2r3pl8cksvlz8lhgbyxh2"; - }) - - # 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 - # New glpk version has new warnings, filter those out until upstream sage has found a solution # https://trac.sagemath.org/ticket/24824 ./patches/pari-stackwarn.patch # not actually necessary since tha pari upgrade, but necessary for the glpk patch to apply @@ -94,66 +39,15 @@ stdenv.mkDerivation rec { stripLen = 1; }) - (fetchpatch { - name = "matplotlib-2.2.2"; - url = "https://git.sagemath.org/sage.git/patch?id=0d6244ed53b71aba861ce3d683d33e542c0bf0b0"; - sha256 = "15x4cadxxlsdfh2sblgagqjj6ir13fgdzixxnwnvzln60saahb34"; - }) - - (fetchpatch { - name = "scipy-1.1.0"; - url = "https://git.sagemath.org/sage.git/patch?id=e0db968a51678b34ebd8d34906c7042900272378"; - sha256 = "0kq5zxqphhrmavrmg830wdr7hwp1bkzdqlf3jfqfr8r8xq12qwf7"; - }) - # https://trac.sagemath.org/ticket/25260 ./patches/numpy-1.15.1.patch - # https://trac.sagemath.org/ticket/25862 - ./patches/eclib-20180710.patch - - # https://trac.sagemath.org/ticket/24735 - ./patches/singular-4.1.1p2.patch - - # https://trac.sagemath.org/ticket/25567 and dependency #25635 - (fetchpatch { - name = "pari-upgrade-dependency.patch"; - url = "https://git.sagemath.org/sage.git/patch/?id=6995e7cae1b3476ad0145f8dfc897cf91f0c3c4d"; - sha256 = "1dvhabl1c9pwd9xkjvbjjg15mvb14b24p1f3cby1mlqk34d4lrs6"; - }) - (fetchpatch { - name = "pari-2.11.0.patch"; - url = "https://git.sagemath.org/sage.git/patch/?id=7af4748cab37d651eaa88be501db88f4a5ffc584"; - sha256 = "13f740ly3c19gcmhjngiycvmc3mcfj61y00i6jv0wmfgpm2z3ank"; - }) - # ntl upgrade (fetchpatch { name = "lcalc-c++11.patch"; url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa"; sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb"; }) - - # cddlib 0.94i -> 0.94j - (fetchpatch { - name = "cddlib-0.94j.patch"; - url = "https://git.sagemath.org/sage.git/patch/?id=2ab1546b3e21d1d0ab3b4fcd58576848b3a2d888"; - sha256 = "1c5gnasq7y9xxj762bn79bis0zi8d9bgg7jzlf64ifixsrc5cymb"; - }) - - # arb 2.13.0 -> 2.14.0 - (fetchpatch { - name = "arb-2.14.0.patch"; - url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta0&id=8bef4fd2876a61969b516fe4eb3b8ad7cc076c5e"; - sha256 = "00p3hfsfn3w2vxgd9fjd23mz7xfxjfravf8ysjxkyd657jbkpjmk"; - }) - - # https://trac.sagemath.org/ticket/26117 - (fetchpatch { - name = "sympy-1.2.patch"; - url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta2&id=d94a0a3a3fb4aec05a6f4d95166d90c284f05c36"; - sha256 = "0an2xl1pp3jg36kgg2m1vb7sns7rprk1h3d0qy1gxwdab6i7qnvi"; - }) ]; patches = nixPatches ++ packageUpgradePatches ++ [ diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index abcefba5e260..d26f5dad724e 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -47,6 +47,8 @@ , singular , pip , jupyter_core +, libhomfly +, libbraiding }: buildPythonPackage rec { @@ -109,6 +111,8 @@ buildPythonPackage rec { pip cython cysignals + libhomfly + libbraiding ]; buildPhase = '' diff --git a/pkgs/applications/science/misc/sasview/default.nix b/pkgs/applications/science/misc/sasview/default.nix index bad29df9dc88..ed6fa3ae886b 100644 --- a/pkgs/applications/science/misc/sasview/default.nix +++ b/pkgs/applications/science/misc/sasview/default.nix @@ -17,7 +17,7 @@ in python.pkgs.buildPythonApplication rec { pname = "sasview"; - version = "unstable-2018-05-05"; + version = "4.2.0"; checkInputs = with python.pkgs; [ pytest @@ -60,8 +60,8 @@ python.pkgs.buildPythonApplication rec { src = fetchFromGitHub { owner = "SasView"; repo = "sasview"; - rev = "de431924d0ddf73cfb952df88bd6661181947019"; - sha256 = "01bk0i0g65yzyq16n1a61rgjna8rrc2i51x2ndf1z7khb1fl16vg"; + rev = "v${version}"; + sha256 = "0k3486h46k6406h0vla8h68fd78wh3dcaq5w6f12jh6g4cjxv9qa"; }; patches = [ ./pyparsing-fix.patch ./local_config.patch ]; |