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Accepting request 845455 from home:badshah400:branches:science

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- Update to version 2.3.2.
- Drop patches incorporated upstream:
  * cadabra2-python-modules-location.patch.
  * Fix-linking-of-cadabra-module.patch.
- Split out a separate package - jupyter-cadabra2-kernel - for the new jupyter notebook kernel.
- Fix typo in `ENABLE_SYSTEM_JSONCPP` option passed to `%cmake`.
- Set up but disable building and running tests until issues with the test-suite are sorted out [gh#kpeeters/cadabra2#211, gh#kpeeters/cadabra2#212].

OBS-URL: https://build.opensuse.org/request/show/845455
OBS-URL: https://build.opensuse.org/package/show/science/cadabra2?expand=0&rev=36
This commit is contained in:
Dirk Stoecker 2020-11-05 12:13:55 +00:00 committed by Git OBS Bridge
parent 5232b74e10
commit 8e8d8b85fd
6 changed files with 82 additions and 147 deletions
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26
Fix-linking-of-cadabra-module.patch
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@ -1,26 +0,0 @@
From 4df3e7cba29a9bb25a70badbc9de8aeef3693933 Mon Sep 17 00:00:00 2001
From: Kasper Peeters <kasper.peeters@phi-sci.com>
Date: Fri, 28 Aug 2020 21:12:58 +0100
Subject: [PATCH] Link cadabra2.so to libpython.so if system requires it.
---
core/CMakeLists.txt | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/core/CMakeLists.txt b/core/CMakeLists.txt
index 1d4c9851da..71570db28f 100644
--- a/core/CMakeLists.txt
+++ b/core/CMakeLists.txt
@@ -305,6 +305,11 @@ if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
set_target_properties(cadabra2 PROPERTIES LINK_FLAGS "-undefined dynamic_lookup")
elseif(${CMAKE_SYSTEM_NAME} MATCHES "Windows")
target_link_libraries(cadabra2 PRIVATE ${PYTHON_LIBRARIES})
+elseif(CMAKE_SHARED_LINKER_FLAGS MATCHES ".*-Wl,--no-undefined.*")
+ # Exception for systems that require no undefined symbols present
+ # in shared libraries (e.g. openSUSE).
+ message("-- Linking cadabra2.so to libpython.so because of default linker flags.")
+ target_link_libraries(cadabra2 PRIVATE ${PYTHON_LIBRARIES})
endif()
if(ENABLE_SYSTEM_JSONCPP)

3
cadabra2-2.3.0.tar.gz
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:1ba2dd2c91e6678a49a136c181da4ec424f1cec9a7172cf95fd1b0c04c253217
size 24169861

3
cadabra2-2.3.2.tar.gz Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:a17424f41703e4b5c72d44f2c3057f7ea10375ff4b41bbb1675d665a86a489ca
size 24376316

103
cadabra2-python-modules-location.patch
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@ -1,103 +0,0 @@
Index: cadabra2-2.3.0/CMakeLists.txt
===================================================================
--- cadabra2-2.3.0.orig/CMakeLists.txt
+++ cadabra2-2.3.0/CMakeLists.txt
@@ -231,6 +231,9 @@ endif()
print_header("Configuring Python")
+# NEEDED TO USE CMAKE_INSTALL_FULL<dir>
+include(GNUInstallDirs)
+
if(USE_PYTHON_3)
set(PYTHON_POSTFIX "3")
message(STATUS "Building for use with Python 3 (good!)")
@@ -243,9 +246,17 @@ add_subdirectory(libs/pybind11)
message(STATUS "Found python ${PYTHON_LIBRARIES}")
-# We install the python module in our 'share' path, not in
-# the site-wide path as we used to.
-set(PYTHON_SITE_PATH share/cadabra2/python)
+if(${CMAKE_VERSION} VERSION_LESS 3.12.0)
+ find_package(PythonInterp)
+ set(PYTHON_SITE_PATH ${CMAKE_INSTALL_FULL_LIBDIR}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages)
+else()
+ find_package (Python COMPONENTS Interpreter)
+ set(PYTHON_SITE_PATH ${CMAKE_INSTALL_FULL_LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages)
+endif()
+
+string(REGEX REPLACE "^${CMAKE_INSTALL_PREFIX}" "" PYTHON_SITE_PATH_REL ${PYTHON_SITE_PATH})
+set(PYTHON_SITE_PATH_REL ${PYTHON_SITE_PATH_REL})
+
if(NOT WIN32)
execute_process(
COMMAND ${PYTHON_EXECUTABLE} -c "import site; print (site.getsitepackages()[0]);"
Index: cadabra2-2.3.0/core/cadabra2.in
===================================================================
--- cadabra2-2.3.0.orig/core/cadabra2.in
+++ cadabra2-2.3.0/core/cadabra2.in
@@ -19,10 +19,9 @@ import rlcompleter
import os
# Make sure we can find the cadabra2 python module; is always
-# installed in ../share/cadabra2/python relative to the location
-# of the 'cadabra2' script.
+# installed in PYTHON_SITE_PATH
install_prefix=os.path.realpath(sys.argv[0])
-install_prefix=install_prefix.replace(os.sep+'bin'+os.sep+'cadabra2', os.sep+'share'+os.sep+'cadabra2'+os.sep+'python')
+install_prefix=install_prefix.replace(os.sep+'bin'+os.sep+'cadabra2', '${PYTHON_SITE_PATH_REL}')
# print("Module path ", install_prefix)
sys.path.append(install_prefix)
@@ -256,5 +255,5 @@ if __name__ == '__main__':
# pulling in the right locals/globals
# sh.interact(banner='Info at http://cadabra.phi-sci.com/\nAvailable under the terms of the GNU General Public License v3\n', locals(), globals())
else:
- sh.runsource("import os; import sys; install_prefix=os.path.realpath(sys.argv[0]); install_prefix=install_prefix.replace('/bin/cadabra2','/share/cadabra2/python'); sys.path.append(install_prefix); print('Cadabra @CADABRA_VERSION_MAJOR@.@CADABRA_VERSION_MINOR@.@CADABRA_VERSION_PATCH@ (build @CADABRA_VERSION_BUILD@ dated @CADABRA_VERSION_DATE@)'); print ('Copyright (C) @COPYRIGHT_YEARS@ Kasper Peeters <kasper.peeters@phi-sci.com>'); f=open('${CMAKE_INSTALL_PREFIX}/${PYTHON_SITE_PATH}/cadabra2_defaults.py'); code=compile(f.read(), 'cadabra2_defaults.py', 'exec'); exec(code); f.close(); print('Using SymPy version '+sympy.__version__);")
+ sh.runsource("import os; import sys; install_prefix=os.path.realpath(sys.argv[0]); install_prefix=install_prefix.replace('/bin/cadabra2','${PYTHON_SITE_PATH_REL}'); sys.path.append(install_prefix); print('Cadabra @CADABRA_VERSION_MAJOR@.@CADABRA_VERSION_MINOR@.@CADABRA_VERSION_PATCH@ (build @CADABRA_VERSION_BUILD@ dated @CADABRA_VERSION_DATE@)'); print ('Copyright (C) @COPYRIGHT_YEARS@ Kasper Peeters <kasper.peeters@phi-sci.com>'); f=open('${PYTHON_SITE_PATH}/cadabra2_defaults.py'); code=compile(f.read(), 'cadabra2_defaults.py', 'exec'); exec(code); f.close(); print('Using SymPy version '+sympy.__version__);")
sh.interact(banner='Info at http://cadabra.science/\nAvailable under the terms of the GNU General Public License v3\n')
Index: cadabra2-2.3.0/core/cadabra2-cli.cc
===================================================================
--- cadabra2-2.3.0.orig/core/cadabra2-cli.cc
+++ cadabra2-2.3.0/core/cadabra2-cli.cc
@@ -113,7 +113,7 @@ void Shell::restart()
}
sys = PyImport_ImportModule("sys");
- std::string module_path = cadabra::install_prefix() + "/share/cadabra2/python";
+ std::string module_path = PYTHON_SITE_PATH;
PyObject* module_path_str = PyUnicode_FromString(module_path.c_str());
PyList_Append(PyObject_GetAttrString(sys, "path"), module_path_str);
Py_XDECREF(module_path_str);
@@ -122,7 +122,7 @@ void Shell::restart()
void Shell::interact()
{
// Run cadabra2_defaults.py
- if (!execute_file(cadabra::install_prefix() + "/share/cadabra2/python/cadabra2_defaults.py", false)) {
+ if (!execute_file(std::string(PYTHON_SITE_PATH) + "/cadabra2_defaults.py", false)) {
handle_error();
throw ExitRequest("Error encountered while initializing the interpreter");
}
Index: cadabra2-2.3.0/core/Config.hh.in
===================================================================
--- cadabra2-2.3.0.orig/core/Config.hh.in
+++ cadabra2-2.3.0/core/Config.hh.in
@@ -21,3 +21,4 @@
#define Mathematica_KERNEL_EXECUTABLE "@Mathematica_KERNEL_EXECUTABLE@"
#define PYTHON_SITE_PATH "@PYTHON_SITE_PATH@"
+#define PYTHON_SITE_PATH_REL "@PYTHON_SITE_PATH_REL@"
Index: cadabra2-2.3.0/client_server/Server.cc
===================================================================
--- cadabra2-2.3.0.orig/client_server/Server.cc
+++ cadabra2-2.3.0/client_server/Server.cc
@@ -106,7 +106,7 @@ void Server::init()
// Make the C++ CatchOutput class visible on the Python side.
- auto python_path = cadabra::install_prefix()+"/share/cadabra2/python";
+ auto python_path = std::string(PYTHON_SITE_PATH);
std::string stdOutErr =
"import sys\n"

36
cadabra2.changes
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@ -1,3 +1,39 @@
-------------------------------------------------------------------
Sun Nov 1 09:55:08 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>
- Update to version 2.3.2:
* Fixed bug in pattern matching logic used in
integrate_by_parts.
* Fixed bug which would prevent assignment to node multiplier
from Python.
* Tab-completion on command line and in the notebook.
* Install the cadabra2 python module in a standard location.
* Fixes for the Mathematica scalar backend.
* Make expand_delta much faster when the Kronecker delta is
contracted with objects which have anti-symmetry.
* Make meld work correctly with non/anti-commuting objects.
* Make numbered indices like a1 display with a subscript
automatically a<sub>1</sub>.
* Provide pickle functionality for expressions.
* Fixes for compatibility with newer SymPy versions.
* Added a 'find' function in the notebook, to search input
cells.
* New Jupyter kernel (enabled by default) which does not require
Xeus.
* Various improvements and fixed for handling and display of
Young tableaux.
* Added ExNode::ex() to obtain an Ex object from an ExNode
iterator.
- Drop patches incorporated upstream:
* cadabra2-python-modules-location.patch.
* Fix-linking-of-cadabra-module.patch.
- Split out a separate package - jupyter-cadabra2-kernel - for the
new jupyter notebook kernel.
- Fix typo in `ENABLE_SYSTEM_JSONCPP` option passed to `%cmake`.
- Set up but disable building and running tests until issues with
the test-suite are sorted out [gh#kpeeters/cadabra2#211,
gh#kpeeters/cadabra2#212].
-------------------------------------------------------------------
Fri Aug 28 20:52:48 UTC 2020 - Atri Bhattacharya <badshah400@gmail.com>

58
cadabra2.spec
View File

@ -16,8 +16,10 @@
#
# Tests fails due to the way PYTHONPATH is set up for the test-suite [gh#kpeeters/cadabra2#211, gh#kpeeters/cadabra2#212]
%bcond_with tests
Name: cadabra2
Version: 2.3.0
Version: 2.3.2
Release: 0
Summary: A computer algebra system for solving problems in field theory
License: GPL-3.0-or-later
@ -25,10 +27,6 @@ Group: Productivity/Scientific/Math
URL: https://cadabra.science/
Source0: https://github.com/kpeeters/cadabra2/archive/%{version}.tar.gz#/%{name}-%{version}.tar.gz
Source1: %{name}-gtk.appdata.xml
# PATCH-FIX-UPSTREAM -- https://github.com/kpeeters/cadabra2/commit/4df3e7cba29a9bb25a70badbc9de8aeef3693933 (gh#kpeeters/cadabra2#202)
Patch2: Fix-linking-of-cadabra-module.patch
# PATCH-FIX-UPSTREAM cadabra2-python-modules-location.patch gh#kpeeters/cadabra2#203 badshah400@gmail.com -- Move python modules to standard python modules path
Patch3: cadabra2-python-modules-location.patch
BuildRequires: appstream-glib
BuildRequires: cmake
BuildRequires: doxygen
@ -46,6 +44,7 @@ BuildRequires: libuuid-devel
BuildRequires: pcre-devel
BuildRequires: pkgconfig
BuildRequires: python3-devel
BuildRequires: python3-ipykernel
BuildRequires: python3-matplotlib
BuildRequires: python3-sympy
BuildRequires: update-desktop-files
@ -54,6 +53,11 @@ BuildRequires: pkgconfig(gtkmm-3.0)
BuildRequires: pkgconfig(jsoncpp)
BuildRequires: pkgconfig(sqlite3)
Recommends: %{name}-doc
# SECTION For test
%if %{with tests}
BuildRequires: python3-gmpy2
%endif
# /SECTION
Recommends: %{name}-examples
%description
@ -115,10 +119,20 @@ the solution of problems encountered in field theory.
This package provides html documentation for %{name}.
%package -n jupyter-cadabra2-kernel
Summary: Jupyter kernel for cadabra2
Group: Productivity/Scientific/Math
Requires: %{name} = %{version}
Requires: jupyter-notebook
%description -n jupyter-cadabra2-kernel
Cadabra2 is a computer algebra system (CAS) designed specifically for
the solution of problems encountered in field theory.
This package provides a jupyter kernel for %{name}.
%prep
%setup -q
%patch2 -p1
%patch3 -p1
%autosetup -p1
rm examples/.gitignore
# Remove timestamps from Doxygen HTML files
echo "HTML_TIMESTAMP = NO" >> config/Doxyfile
@ -130,13 +144,13 @@ sed -i "1{/#!\/usr\/bin\/env python/d}" libs/appdirs/cdb_appdirs.py
-DCMAKE_MANDIR:PATH=%{_mandir} \
-DINSTALL_LATEX_DIR:PATH=%{_datadir}/texmf \
-DENABLE_FRONTEND:BOOL=ON \
-DENABLE_SYSTEM_JSONPP:BOOL=ON \
-DENABLE_SYSTEM_JSONCPP:BOOL=ON \
-DENABLE_MATHEMATICA:BOOL=OFF \
-DBUILD_TESTS:BOOL=ON
-DBUILD_TESTS:BOOL=%{?_with_tests:ON}%{!?_with_tests:OFF}
%cmake_build
cd ..
make %{?_smp_mflags} doc
%make_build doc
%install
%cmake_install
@ -152,9 +166,13 @@ sed -E -i "s|^#!/usr/bin/env python3|#!/usr/bin/python3|" %{buildroot}%{_bindir}
mkdir -p %{buildroot}%{_datadir}/texmf/tex/latex/cadabra2/
ln %{buildroot}%{_datadir}/cadabra2/latex/* %{buildroot}%{_datadir}/texmf/tex/latex/cadabra2/
%post -p /sbin/ldconfig
%postun -p /sbin/ldconfig
%if %{with tests}
%check
export PYTHONPATH=%{buildroot}%{python3_sitearch}
export PATH=${PATH}:%{buildroot}%{_bindir}
export PYTHONDONTWRITEBYTECODE=1
%ctest
%endif
%files
%doc README.rst
@ -168,16 +186,26 @@ ln %{buildroot}%{_datadir}/cadabra2/latex/* %{buildroot}%{_datadir}/texmf/tex/la
%{_bindir}/%{name}html
%{_datadir}/%{name}/
%{_datadir}/texmf
%{python3_sitearch}/*
%{python3_sitearch}/cadabra2.so
%{python3_sitearch}/cadabra2_defaults.py
%{python3_sitearch}/cdb_appdirs.py
%{python3_sitearch}/cdb/
%{_mandir}/man1/cadabra*.1%{?ext_man}
%files gui
%license doc/license.txt
%{_bindir}/%{name}-gtk
%{_datadir}/icons/hicolor/*/apps/cadabra2-gtk.*
%{_datadir}/applications/cadabra2-gtk.desktop
%dir %{_datadir}/metainfo
%{_datadir}/metainfo/*.appdata.xml
%files -n jupyter-cadabra2-kernel
%license doc/license.txt
%{python3_sitearch}/cadabra2_jupyter/
%{python3_sitearch}/notebook/
%{_jupyter_kernel_dir}/cadabra2/
%files examples
%doc examples/