From bebec55cb09da7aa8cdd577431b4135edb7b539e Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 20 Nov 2018 13:39:31 +0100
Subject: [PATCH] Improvements to allow for pip install
- renamed script to setup.py
- Use "make pip" to copy required files in this dir for pip
- Use try/except when importing numpy and cython so as to notify the user
- renamed env vars to plumed_xxx so that there is no risk of clashes
Plumed can now also be installed using
cd python
make pip
pip install --user .
make pip is just needed to bring version information and Plumed.h
in this directory. Might be solved differently in MacPorts / Pypi.
---
python/Makefile | 17 ++++++++---
python/{buildPythonInterface.py => setup.py} | 32 ++++++++++++++++----
src/lib/Makefile | 9 +++---
3 files changed, 43 insertions(+), 15 deletions(-)
rename python/{buildPythonInterface.py => setup.py} (73%)
diff --git a/python/Makefile b/python/Makefile
index 072c148ad..488b2e924 100644
--- a/python/Makefile
+++ b/python/Makefile
@@ -3,6 +3,8 @@ ifneq ($(MAKECMDGOALS),clean)
-include ../Makefile.conf
endif
+VERSION = $(shell if test -f ../VERSION ; then grep -v \\\# ../VERSION ; else echo "Unknown" ; fi )
+
.PHONY: all clean install
plumed_compiled := $(wildcard ../src/lib/plumed)
@@ -19,10 +21,11 @@ ifdef python_bin
all:
@echo Building python interface for PLUMED
unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
- program_name=plumed \
- include_dir=../src/wrapper \
- default_kernel="$$PWD/../src/lib/libplumedKernel.$(SOEXT)" \
- $(python_bin) buildPythonInterface.py build_ext -i
+ plumed_program_name=plumed \
+ plumed_version=$(VERSION) \
+ plumed_include_dir=../src/wrapper \
+ plumed_default_kernel="$$PWD/../src/lib/libplumedKernel.$(SOEXT)" \
+ $(python_bin) setup.py build_ext -i
else
@@ -32,5 +35,9 @@ endif
endif
+pip:
+ cp ../src/wrapper/Plumed.h .
+ cp ../VERSION .
+
clean:
- rm -fr *.so plumed.cpp build
+ rm -fr *.so plumed.cpp build Plumed.h VERSION
diff --git a/python/buildPythonInterface.py b/python/setup.py
similarity index 73%
rename from python/buildPythonInterface.py
rename to python/setup.py
index ff7fd60bd..e9f416266 100644
--- a/python/buildPythonInterface.py
+++ b/python/setup.py
@@ -24,27 +24,47 @@
#
from distutils.core import setup
from distutils.extension import Extension
-from Cython.Build import cythonize
-import numpy
import subprocess
import os
+import sys
-plumedname = os.getenv("program_name")
+plumedname = os.getenv("plumed_program_name")
if plumedname is None:
plumedname = "plumed"
-plumedversion = subprocess.check_output(['grep','-v','#','../VERSION']).decode("utf-8")
+plumedversion = os.getenv("plumed_version")
+if plumedversion is None:
+ plumedversion = subprocess.check_output(['grep','-v','#','./VERSION']).decode("utf-8")
print( "Module name " + plumedname )
print( "Version number " + plumedversion )
extra_compile_args=['-D__PLUMED_HAS_DLOPEN','-D__PLUMED_WRAPPER_LINK_RUNTIME=1','-D__PLUMED_WRAPPER_CXX=1','-D__PLUMED_WRAPPER_IMPLEMENTATION=1','-D__PLUMED_WRAPPER_EXTERN=0','-D__PLUMED_WRAPPER_CXX_DEFAULT_INVALID=1']
-defaultkernel=os.getenv("default_kernel")
+defaultkernel=os.getenv("plumed_default_kernel")
if defaultkernel is not None:
extra_compile_args.append("-D__PLUMED_DEFAULT_KERNEL=" + os.path.abspath(defaultkernel))
print( "Hardcoded PLUMED_KERNEL " + os.path.abspath(defaultkernel))
+try:
+ import numpy
+except:
+ print('Error: building ' + plumedname + ' requires numpy. Please install it first with pip install numpy')
+ sys.exit(-1)
+
+try:
+ from Cython.Build import cythonize
+except:
+ print('Error: building ' + plumedname + ' requires cython. Please install it first with pip install cython')
+ sys.exit(-1)
+
+include_dirs=[numpy.get_include()]
+
+try:
+ include_dirs.append(os.environ["plumed_include_dir"])
+except:
+ include_dirs.append(".")
+
setup(
name=plumedname,
version=plumedversion,
@@ -56,7 +76,7 @@ setup(
Extension( name=plumedname,
sources=["plumed.pyx"],
language="c++",
- include_dirs=[os.environ["include_dir"], numpy.get_include()],
+ include_dirs=include_dirs,
extra_compile_args=extra_compile_args
)
])
diff --git a/src/lib/Makefile b/src/lib/Makefile
index 9cb765941..1dc913886 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -313,10 +313,11 @@ ifdef python_bin
cp -pr ../../python install
cd install/python && rm -fr *.so plumed.cpp build && \
unset CXX && unset CC && unset CFLAGS && unset CXXFLAGS && unset LDSHARED && \
- program_name="$(program_name)" \
- include_dir=../../../wrapper \
- default_kernel="$(libdir)/lib$(program_name)Kernel.$(SOEXT)" \
- $(python_bin) buildPythonInterface.py build_ext -i
+ plumed_program_name="$(program_name)" \
+ plumed_version=$(VERSION) \
+ plumed_include_dir=../../../wrapper \
+ plumed_default_kernel="$(libdir)/lib$(program_name)Kernel.$(SOEXT)" \
+ $(python_bin) setup.py build_ext -i
cp -pr install/python "$(DESTDIR)$(libdir)/$(program_name)/"
endif
ifdef BASH_COMPLETION_DIR
--
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