diff --git a/CMakeLists.txt b/CMakeLists.txt
index a513d76eeafce796d2a48097f9eeb28f54012387..0541457f10b02d28c2bdfb92320db88f63435430 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 ${CMAKE_CURRENT_BINARY_DIR}/python
- COMMENT "Genearating bdist using setup.cmake.py."
- VERBATIM
- )
-
############################ CTEST ######################################
include( CTest )
diff --git a/cmake_modules/FindNumPy.cmake b/cmake_modules/FindNumPy.cmake
index f14142f18652c1081f098319b47bf123329352de..5de7901e56780d191dcbc218685c0204f696c22e 100644
--- a/cmake_modules/FindNumPy.cmake
+++ b/cmake_modules/FindNumPy.cmake
@@ -39,23 +39,15 @@
#============================================================================
# Finding NumPy involves calling the Python interpreter
-if(NumPy_FIND_REQUIRED)
- find_package(PythonInterp REQUIRED)
-else()
- find_package(PythonInterp)
-endif()
-
-if(NOT PYTHONINTERP_FOUND)
- set(NUMPY_FOUND FALSE)
- return()
-endif()
-execute_process(COMMAND "${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 713ade07302e224a9600177fce2952d0a61dc791..adf4176b955dcc0e1c254777f304cbac14233151 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 9d5ad2459ecf94e3a6b8b3d4c68d26b54c6c3475..9cda2b80d81b4ffc20ff77bf0dae656c47763e7c 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 b1761f9957ee37b274fc3fbc6cd50b833356a107..94787ff76ba0bf70554c742c158e19a7ad36f23d 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'] },
+ )