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Update to sagemath 8.5.

Browse source 
Also:
- Bundle ipython again; Fedora version is too far ahead.  Also have to bundle
  prompt_toolkit since Fedora version is too far ahead of bundled ipython.
- Drop LANGUAGES variable setting, now ignored by the sagemath build system.
- Drop unused SAGE_CBLAS variable from /usr/bin/sage.
- Do not force the C locale when launching sagemath.
- Allow the user to override SAGE_DEBUG in /usr/bin/sage.
- Add -ecm, -giac, and -latte patches to fix interactions with external tools.
- Add -sigfpe patch from upstream.
This commit is contained in:
Jerry James 2019-01-17 19:27:08 -07:00
parent eaa777c690
commit 55beead27c
31 changed files with 674 additions and 684 deletions
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74
sagemath.spec
View file

@ -4,7 +4,7 @@
%global _python_bytecompile_extra 0
%bcond_with bundled_pexpect
%bcond_with bundled_ipython
%bcond_without bundled_ipython
%bcond_without bundled_ipywidgets
%bcond_without bundled_thebe
%bcond_without bundled_threejs
@ -45,6 +45,7 @@
%global graphs_pkg graphs-20161026
%if %{with bundled_ipython}
%global ipython_pkg ipython-5.8.0
%global prompt_tookit_pkg prompt_toolkit-1.0.15
%endif
%if %{with bundled_ipywidgets}
%global ipywidgets_pkg ipywidgets-7.2.0
@ -54,7 +55,7 @@
%endif
%global polytopes_db_pkg polytopes_db-20170220
%global rubiks_pkg rubiks-20070912
%global sagenb_pkg sagenb-1.0.3
%global sagenb_pkg sagenb-1.1.1
%global sagenb_export_pkg sagenb_export-3.2
%global sagetex_pkg sagetex-3.0
%global Sphinx_pkg Sphinx-1.7.6
@ -72,7 +73,7 @@
# Spkg equivalents of required rpms; we pretend they are installed as spkgs.
# The version numbers shown are those of the latest released spkg, if the Fedora
# version is not behind.
%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.8.6new2 gmp-6.1.2 gmpy2-2.1.0a1 lrslib-062+autotools-2017-03-03 qepcad-B.1.71 saclib-2.2.7 sirocco-2.0 surf-1.0.6-gcc6
%global SAGE_REQUIRED_PKGS 4ti2-1.6.7 cbc-2.9.4 CoCoALib-0.99564 cryptominisat-5.0.1 gap_packages-4.8.6new2.p0 gmp-6.1.2 gmpy2-2.1.0a4.p0 lrslib-062+autotools-2017-03-03 qepcad-B.1.71 saclib-2.2.7 sirocco-2.0 surf-1.0.6-gcc6
%global SAGE_ROOT %{_libdir}/sagemath
%global SAGE_LOCAL %{SAGE_ROOT}/local
@ -85,7 +86,7 @@
Name: sagemath
Summary: A free open-source mathematics software system
Version: 8.4
Version: 8.5
Release: 1%{?dist}
# The file ${SAGE_ROOT}/COPYING.txt is the upstream license breakdown file
# Additionally, every $files section has a comment with the license name
@ -97,6 +98,12 @@ Source1: gprc.expect
# Follow maxima's ExclusiveArch
ExclusiveArch: aarch64 %{arm} %{ix86} x86_64 ppc sparcv9
# Fix ecm interact() command
Patch0: %{name}-ecm.patch
# Adapt a giac doctest to recent versions of giac
Patch1: %{name}-giac.patch
# Set of patches to work with system wide packages
Patch2: %{name}-scripts.patch
@ -148,7 +155,6 @@ Patch13: %{name}-nauty.patch
# remove the buildroot path from Cython output
Patch14: %{name}-buildroot.patch
# correct path to Lfunction include
# update c++ standard to fix FTBFS
Patch15: %{name}-lcalc.patch
@ -186,7 +192,11 @@ Patch25: %{name}-includes.patch
# Use openblas
Patch26: %{name}-openblas.patch
BuildRequires: gdb
# Fix paths to latte-integrale binaries
Patch27: %{name}-latte.patch
# Upstream fixes for random SIGFPEs due to ecl messing with the fp state
Patch28: %{name}-sigfpe.patch
BuildRequires: 4ti2
BuildRequires: arb-devel
@ -217,6 +227,7 @@ BuildRequires: gap-pkg-toric
BuildRequires: gc-devel
BuildRequires: gcc-c++
BuildRequires: gd-devel
BuildRequires: gdb
BuildRequires: gfan
BuildRequires: giac-devel
BuildRequires: glpk-devel
@ -297,7 +308,6 @@ BuildRequires: python3dist(pexpect)
%endif
BuildRequires: python3dist(pickleshare)
BuildRequires: python3dist(pip)
BuildRequires: python3dist(prompt-toolkit)
BuildRequires: python3dist(pkgconfig)
BuildRequires: python3dist(psutil)
BuildRequires: python3dist(ptyprocess)
@ -398,7 +408,7 @@ Requires: python3dist(matplotlib)
Requires: python3dist(networkx)
Requires: python3dist(notebook)
%if %{with bundled_ipython}
Requires: python3dist(path)
Requires: python3dist(path.py)
%endif
Requires: python3dist(pathlib2)
%if %{without bundled_pexpect}
@ -406,7 +416,6 @@ Requires: python3dist(pexpect)
%endif
Requires: python3dist(pickleshare)
Requires: python3dist(pillow)
Requires: python3dist(prompt-toolkit)
Requires: python3dist(psutil)
Requires: python3dist(ptyprocess)
Requires: python3dist(pycryptosat)
@ -422,7 +431,7 @@ Requires: python3dist(sphinx)
Requires: python3dist(sympy)
Requires: python3dist(twisted)
%if %{with bundled_ipython}
Requires: python3dist(zmq)
Requires: python3dist(pyzmq)
%endif
Requires: python3dist(zodb3)
Requires: qepcad-B
@ -461,6 +470,7 @@ Requires: %{name}%{?_isa} = %{version}-%{release}
Obsoletes: %{name}-devel < 6.8-1
%if %{with bundled_ipython}
Provides: bundled(ipython) = %(cut -d- -f2- <<< %{ipython_pkg})
Provides: bundled(prompt_toolkit) = %(cut -d- -f2- <<< %{prompt_tookit_pkg})
%endif
%if %{with bundled_ipywidgets}
Provides: bundled(ipywidgets) = %(cut -d- -f2- <<< %{ipywidgets_pkg})
@ -733,6 +743,11 @@ pushd build/pkgs/ipython
tar zxf ../../../upstream/%{ipython_pkg}.tar.gz
mv %{ipython_pkg} src
popd
pushd build/pkgs/prompt_toolkit
tar zxf ../../../upstream/%{prompt_tookit_pkg}.tar.gz
mv %{prompt_tookit_pkg} src
popd
%endif
%if %{with bundled_ipywidgets}
@ -823,6 +838,8 @@ pushd build/pkgs/widgetsnbextension
popd
%endif
%patch0
%patch1
%patch2
%patch3
%patch4
@ -853,6 +870,8 @@ popd
%patch24
%patch25
%patch26
%patch27
%patch28
sed -e 's|@@SAGE_ROOT@@|%{SAGE_ROOT}|' \
-e 's|@@SAGE_DOC@@|%{SAGE_DOC}|' \
@ -888,6 +907,7 @@ grep -FrlZ '#!%{_bindir}/env python' | \
xargs -0 sed -i 's,#!%{_bindir}/env python,#!%{__python3},'
grep -FrlZ '#!%{_bindir}/env sage-python23' | \
xargs -0 sed -i 's,#!%{_bindir}/env sage-python23,#!%{__python3},'
grep -FrlZ 'sage-python23' | xargs -0 sed -i 's,sage-python23,#!%{__python3},'
grep -FrlZ '#!%{_bindir}/env' | \
xargs -0 sed -i 's,#!%{_bindir}/env ,#!%{_bindir}/,'
grep -rlZ '#!%{_bindir}/python$' | xargs -0 sed -i 's,#!%{_bindir}/python$,&3,'
@ -956,6 +976,11 @@ pushd build/pkgs/ipython/src
%__python3 setup.py build
%__python3 setup.py install --root %{_builddir}
popd
pushd build/pkgs/prompt_toolkit/src
%__python3 setup.py build
%__python3 setup.py install --root %{_builddir}
popd
%endif
%if %{with bundled_ipywidgets}
@ -1065,8 +1090,8 @@ pushd src/ext
if [ $COUNT -gt 0 ]; then
cp -far $dir $SAGE_ETC
fi
cp -far pari $SAGE_ETC
done
cp -far pari $SAGE_ETC
cp -fa %{SOURCE1} $SAGE_ETC
popd
@ -1236,6 +1261,7 @@ popd
#------------------------------------------------------------------------
%if %{with bundled_ipython}
mv %{_builddir}%{python3_sitelib}/IPython %{buildroot}%{SAGE_PYTHONPATH}
mv %{_builddir}%{python3_sitelib}/prompt_toolkit %{buildroot}%{SAGE_PYTHONPATH}
mv %{_builddir}%{_bindir}/ip* %{buildroot}%{SAGE_LOCAL}/bin
%endif
@ -1271,7 +1297,7 @@ popd
cat > %{buildroot}%{_bindir}/sage << EOF
#!/bin/bash -i
export CUR=\`pwd\`
export CUR=\$PWD
##export DOT_SAGE="\$HOME/.sage"
mkdir -p \$DOT_SAGE/{maxima,sympow,tmp}
export SAGE_TESTDIR=\$DOT_SAGE/tmp
@ -1283,7 +1309,7 @@ export SAGE_ETC="$SAGE_ETC"
export SAGE_SRC="%{buildroot}%{SAGE_SRC}"
##export SAGE_DOC="$SAGE_DOC"
##export SAGE_DOC_SRC="\$SAGE_DOC"
##export SAGE_PKGS="\$SAGE_LOCAL//var/lib/sage/installed"
##export SAGE_PKGS="\$SAGE_LOCAL/var/lib/sage/installed"
module load 4ti2-%{_arch}
module load lrcalc-%{_arch}
module load surf-geometry-%{_arch}
@ -1292,14 +1318,13 @@ export SINGULAR_DATA_DIR=%{_datadir}
export SINGULAR_BIN_DIR=%{_libdir}/Singular
export SINGULAR_SO=%{_libdir}/libSingular-4.1.1.so
##export PYTHONPATH="$SAGE_PYTHONPATH:\$SAGE_LOCAL/bin"
export SAGE_CBLAS=blas
export SAGE_FORTRAN=%{_bindir}/gfortran
export SAGE_FORTRAN_LIB=\`gfortran --print-file-name=libgfortran.so\`
export SYMPOW_DIR="\$DOT_SAGE/sympow"
export LC_ALL=C.UTF-8
export LD_LIBRARY_PATH=\$SAGE_ROOT/lib:\$LD_LIBRARY_PATH
# Required for sage -gdb
export SAGE_DEBUG=no
: \${SAGE_DEBUG:=no}
export SAGE_DEBUG
$SAGE_LOCAL/bin/sage "\$@"
EOF
#------------------------------------------------------------------------
@ -1357,7 +1382,7 @@ pushd src/doc
export SAGE_DOC_SRC=$SAGE_DOC
# python -m sage_setup.docbuild
# Build with an X server running, required by some doc builders
SAGE_NUM_THREADS=2 LANGUAGES="ca de en fr hu it ja pt ru tr" \
SAGE_NUM_THREADS=2 \
xvfb-run -a -n 1 %__python3 -m docbuild --no-pdf-links -k all html -j
rm -f %{buildroot}%{SAGE_SRC}/doc
ln -sf %{SAGE_DOC} %{buildroot}%{SAGE_SRC}/doc
@ -1518,9 +1543,6 @@ chmod +x %{buildroot}%{SAGE_LOCAL}/bin/sage-list-packages
# last install command
rm -fr $DOT_SAGE
########################################################################
%ldconfig_scriptlets core
########################################################################
%files
# GPLv2+
@ -1573,6 +1595,7 @@ rm -fr $DOT_SAGE
%endif
%if %{with bundled_ipython}
%{SAGE_PYTHONPATH}/IPython
%{SAGE_PYTHONPATH}/prompt_toolkit
%endif
%if %{with bundled_ipywidgets}
%{SAGE_PYTHONPATH}/ipywidgets
@ -1793,6 +1816,17 @@ rm -fr $DOT_SAGE
########################################################################
%changelog
* Thu Jan 17 2019 Jerry James <loganjerry@gmail.com> - 8.5-1
- Update to sagemath 8.5
- Bundle ipython again; Fedora version is too far ahead. Also have to bundle
prompt_toolkit since Fedora version is too far ahead of bundled ipython.
- Drop LANGUAGES variable setting, now ignored by the sagemath build system
- Drop unused SAGE_CBLAS variable from /usr/bin/sage
- Do not force the C locale when launching sagemath
- Allow the user to override SAGE_DEBUG in /usr/bin/sage
- Add -ecm, -giac, and -latte patches to fix interactions with external tools
- Add -sigfpe patch from upstream
* Thu Oct 25 2018 Jerry James <loganjerry@gmail.com> - 8.4-1
- Update to sagemath 8.4
- Build for python 3 instead of python 2 due to upcoming python 2 removal