From 33bf735fb61ae5a94a2a531fa14a03632ee7ca42 Mon Sep 17 00:00:00 2001
From: Dilawar Singh <dilawars@ncbs.res.in>
Date: Fri, 2 Mar 2018 16:48:47 +0530
Subject: [PATCH] Squashed 'moose-core/' changes from f1dcea8..f38dc5d
f38dc5d On tumbleweed, cmake returns python3 default but python-numpy is python2 version. Won't fix it. Its a upstream problem.
REVERT: f1dcea8 Install in debian layout in packages. Added option in setup.cfg file Its delicate solution. Added a note.
REVERT: 5a73acb Finally. Needs to write setup.cfg file to make /usr/local and /usr prefix consistent.
REVERT: d7c41e4 bdist_egg is more consistent on both RPM and DEB based systems.
REVERT: be42fd2 Merge commit 'bcf5c52d54409a89f9af1cf08e5d369d9e9e0d7f' into chennapoda
REVERT: d27db9c Do not use -p switch. its not easy to get required info from all linux-distributions.
REVERT: e667953 Fixed message to set in cmake.
REVERT: 8523290 Fixed typo in command.
REVERT: 0b125f6 Fixed typo in cmake file.
REVERT: f3118f0 multiple fix to build system. - dont use python setup.py install . It does not work anymore if --prefix directory is not in PYTHONPATH. - Use python setup.py bdist -d INSTALL_DIR and let cmake unarchive and copy it to desired location. This is much better solution.
REVERT: 03d5899 Use bdist instead of install for creating binay distrution. During installation, untar this to destination.
REVERT: a08658e Tweaks to setup.cmake.py file.
REVERT: c5f1d91 Test on travis.
REVERT: 6b32fde Merge commit '6d651b6013e1093a1cdb2541bb8615bbc3a66021'
REVERT: 324a20c Merge commit 'e0b8959ccefd77195b7eac2edc1db7cdcaa40fe6'
REVERT: 59f6e9e On debian/ubuntu install-layout option is set to deb. [skip ci]
REVERT: 62201d9 Merge commit 'f80ae40d5b1e1b63eb9849b9699d76f33e4f2572'
REVERT: 9b81dfc This fixes moose but a better solution to install pymoose in moose-core must be found.
REVERT: 7e27f80 Merge commit '6f7697fb3256626a6d57bda24ae0a7bb5c0e90cc'
REVERT: 939c734 Merge commit '627f1ce1cc73b0e1f6b4fe9051d3597e3a9113a5'
REVERT: 4775933 Merge commit '7b3c355a04d22f279a88bfae4097e9cf3f62439b'
REVERT: 43c0674 Squashed 'moose-core/' changes from d4417dcffd..2657e3345e (#222)
REVERT: 8c9ad49 Fixed the syntax causing failure.
REVERT: 397efaf Handling MOOSE_VERSION is better way.
git-subtree-dir: moose-core
git-subtree-split: f38dc5d6b2d6a3bcb5439a2f5ba680adad754ec7
---
CMakeLists.txt | 45 ++++-------------------------------
cmake_modules/FindNumPy.cmake | 16 ++++---------
pymoose/CMakeLists.txt | 3 ++-
python/moose/moose_test.py | 3 +--
python/setup.cmake.py | 40 +++++++++++++++----------------
5 files changed, 31 insertions(+), 76 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index a513d76e..0541457f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,7 +1,7 @@
set(CMAKE_LEGACY_CYGWIN_WIN32 0)
cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
-project(pymoose)
+project(moose-core)
if(COMMAND cmake_policy)
cmake_policy(SET CMP0003 NEW)
@@ -245,14 +245,6 @@ if(HDF5_LIBRARY_DIRS)
set_target_properties( libmoose PROPERTIES LINK_FLAGS "-L${HDF5_LIBRARY_DIRS}" )
endif()
-find_package(Termcap)
-find_package(Readline)
-
-if(READLINE_FOUND AND TERMCAP_FOUND)
- add_definitions(-DUSE_READLINE)
- include_directories(${Readline_INCLUDE_DIR})
-endif()
-
# Openmpi
if(WITH_MPI)
find_package(MPI REQUIRED)
@@ -393,7 +385,6 @@ endif()
######################### BUILD PYMOOSE ########################################
add_subdirectory( pymoose )
-
######################### INSTALL ##############################################
if(DEBUG)
@@ -422,25 +413,18 @@ execute_process(
message( STATUS "Platform ${_platform_desc}" )
-# DISTUTILS_EXTRA_ARGS may come of top-level cmake script. On DEBIAN/UBUNTU, it
-# is most likely to be --install-layout=deb .
-set(EXTRA_ARGS "--prefix ${CMAKE_INSTALL_PREFIX} ${DISTUTILS_EXTRA_ARGS}")
+set(EXTRA_ARGS "--prefix ${CMAKE_INSTALL_PREFIX}")
-# On Debian/Ubuntu install using debian layout.
-# NOTE: Also create setup.cfg file which setup prefix and install-layout
-# suitable for DEBIAN systems.
+# On Debian/Ubuntu install using debian layout
if( ${_platform_desc} MATCHES ".*(Ubuntu|Debian).*" )
list( APPEND EXTRA_ARGS "--install-layout=deb" )
- file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/python/setup.cfg
- "[install]\nprefix=/usr\ninstall-layout=deb"
- )
endif( )
# If make is called with sudo, install in system directories. Otherwise use
# --user to install in user home.
install(CODE
"execute_process(
- COMMAND ${PYTHON_EXECUTABLE} setup.cmake.py install -f ${EXTRA_ARGS} ${PYMOOSE_EXTRA_INSTALL_ARGS}
+ COMMAND ${PYTHON_EXECUTABLE} setup.cmake.py install ${EXTRA_ARGS} ${PYMOOSE_EXTRA_INSTALL_ARGS}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python
)"
)
@@ -455,27 +439,6 @@ if(${CMAKE_BUILD_TOOL} MATCHES "make")
)
endif()
-# Target for creating bdist. This is handy for creating bdist for packaging.
-# Save the binary distribution (tar.gz) to PYMOOSE_BDIST_DIR. Note that this
-# target is only useful when creating packages on Open Build Service i.e. if you
-# use this target on distribution X, it may not work on distrbutions other than
-# X. See python-wheels for making portable distributions.
-if(NOT PYMOOSE_BDIST_DIR)
- set(PYMOOSE_BDIST_DIR ${CMAKE_BINARY_DIR}/pymoose_bdist)
-endif( )
-
-# get platform and arch using python.
-# NOTE: creating bdist or bdist_dump uses /usr and /usr/local on rpm and deb
-# based unix respectively. Not a great situation to be in. Need to write a
-# setup.cfg file to fix the prefix in all cases.
-find_package( PythonInterp REQUIRED)
-add_custom_target( bdist
- COMMAND ${PYTHON_EXECUTABLE} setup.cmake.py bdist_dumb -d ${PYMOOSE_BDIST_DIR}
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/python
- COMMENT "Genearating bdist using setup.cmake.py."
- VERBATIM
- )
-
############################ CTEST ######################################
include( CTest )
diff --git a/cmake_modules/FindNumPy.cmake b/cmake_modules/FindNumPy.cmake
index f14142f1..5de7901e 100644
--- a/cmake_modules/FindNumPy.cmake
+++ b/cmake_modules/FindNumPy.cmake
@@ -39,23 +39,15 @@
#============================================================================
# Finding NumPy involves calling the Python interpreter
-if(NumPy_FIND_REQUIRED)
- find_package(PythonInterp REQUIRED)
-else()
- find_package(PythonInterp)
-endif()
-
-if(NOT PYTHONINTERP_FOUND)
- set(NUMPY_FOUND FALSE)
- return()
-endif()
-execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+message( STATUS "Using python ${PYTHON_EXECUTABLE} to locate numpy" )
+execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
"import numpy as n; print(n.__version__); print(n.get_include());"
RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
ERROR_VARIABLE _NUMPY_ERROR_VALUE
- OUTPUT_STRIP_TRAILING_WHITESPACE)
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
if(NumPy_FIND_REQUIRED)
diff --git a/pymoose/CMakeLists.txt b/pymoose/CMakeLists.txt
index 713ade07..adf4176b 100644
--- a/pymoose/CMakeLists.txt
+++ b/pymoose/CMakeLists.txt
@@ -10,10 +10,11 @@ set(PYMOOSE_SRCS
test_moosemodule.cpp
PyRun.cpp
)
-add_library( _moose MODULE ${PYMOOSE_SRCS} )
+add_library( _moose MODULE ${PYMOOSE_SRCS} )
set(PYMOOSE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/python/moose")
+find_package(PythonInterp REQUIRED)
execute_process( COMMAND ${PYTHON_EXECUTABLE} -c
"try: import importlib.machinery; print(importlib.machinery.EXTENSION_SUFFIXES[0])
except Exception: pass"
diff --git a/python/moose/moose_test.py b/python/moose/moose_test.py
index 9d5ad245..9cda2b80 100644
--- a/python/moose/moose_test.py
+++ b/python/moose/moose_test.py
@@ -26,12 +26,11 @@ import logging
from collections import defaultdict
import time
-logfile_ = tempfile.NamedTemporaryFile( )
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
datefmt='%m-%d %H:%M',
- filename = logfile_.name,
+ filename='tests.log',
filemode='w'
)
console = logging.StreamHandler()
diff --git a/python/setup.cmake.py b/python/setup.cmake.py
index b1761f99..94787ff7 100644
--- a/python/setup.cmake.py
+++ b/python/setup.cmake.py
@@ -1,11 +1,10 @@
# -*- coding: utf-8 -*-
-"""
-setup.cmake.py:
+"""setup.py:
+Script to install python targets.
-Script to install python targets by cmake.
+NOTE: This script is to be called by CMake. Not intended to be used standalone.
-DO NOT USE IT DIRECTLY. Only `cmake` build system should use it directly.
"""
__author__ = "Dilawar Singh"
@@ -21,30 +20,33 @@ import os
import sys
try:
- from setuptools import setup
+ from setuptools import setup
except Exception as e:
- from distutils.core import setup
-
+ from distutils.core import setup
-# Read version from VERSION created by cmake file. This file must be present for
-# setup.cmake.py to work perfectly.
script_dir = os.path.dirname( os.path.abspath( __file__ ) )
-version = None
-with open( os.path.join( script_dir, 'VERSION'), 'r' ) as f:
- version = f.read( )
+version = '3.2pre1'
+
+
+try:
+ with open( os.path.join( script_dir, 'VERSION'), 'r' ) as f:
+ version = f.read( )
+except Exception as e:
+ print( 'Failed to read VERSION %s' % e )
+ print( 'Using default %s' % version )
try:
import importlib.machinery
- suffix = importlib.machinery.EXTENSION_SUFFIXES[0]
+ suffix = importlib.machinery.EXTENSION_SUFFIXES[0].split('.')[-1]
except Exception as e:
- print( '[WARN] Failed to determine importlib suffix due to %s' % e )
+ print( '[WARN] Failed to determine importlib suffix' )
suffix = '.so'
setup(
name='pymoose',
version=version,
description='Python scripting interface of MOOSE Simulator (https://moose.ncbs.res.in)',
- author='See AUTHORS.md at https://github.com/BhallaLab/moose',
+ author='MOOSERes',
author_email='bhalla@ncbs.res.in',
maintainer='Dilawar Singh',
maintainer_email='dilawars@ncbs.res.in',
@@ -59,11 +61,9 @@ setup(
, 'moose.chemUtil'
, 'moose.chemMerge'
],
- install_requires = [ 'python-libsbml', 'numpy' ],
+ install_requires = [ 'python-libsbml', 'numpy' ],
package_dir = {
'moose' : 'moose', 'rdesigneur' : 'rdesigneur'
},
- package_data = {
- 'moose' : ['_moose' + suffix, 'neuroml2/schema/NeuroMLCoreDimensions.xml']
- },
- )
+ package_data = { 'moose' : ['_moose' + suffix, 'neuroml2/schema/NeuroMLCoreDimensions.xml'] },
+ )
--
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