From dcc05dd1b89e7787ccd706575eb6a0ddb626a0fb Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 22 Feb 2019 16:18:27 +0100
Subject: [PATCH] Removed numpy from requirements
I think the inclusion of numpy headers was related to non used variables
forgotten from an intermediate implementation.
I just removed them. In this manner it is not necessary that numpy is
already installed when plumed extension is compiled.
Numpy would be anyway required to run our test.
---
configure | 5 ++---
configure.ac | 3 +--
macports/PortfilePython.in | 10 ++++++----
python/README.rst | 6 ++----
python/plumed.pyx | 12 +++++++-----
python/setup.py | 11 ++---------
user-doc/Installation.md | 6 ++----
7 files changed, 22 insertions(+), 31 deletions(-)
diff --git a/configure b/configure
index 113b119d9..cafcbc3fd 100755
--- a/configure
+++ b/configure
@@ -8760,8 +8760,8 @@ done
then
{ $as_echo "$as_me:${as_lineno-$LINENO}: Python executable is $PYTHON_BIN" >&5
$as_echo "$as_me: Python executable is $PYTHON_BIN" >&6;}
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking support for required python modules (setuptools, cython, numpy, subprocess, os, shutil)" >&5
-$as_echo_n "checking support for required python modules (setuptools, cython, numpy, subprocess, os, shutil)... " >&6; }
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking support for required python modules (setuptools, cython, subprocess, os, shutil)" >&5
+$as_echo_n "checking support for required python modules (setuptools, cython, subprocess, os, shutil)... " >&6; }
testimport="
from setuptools import setup
from setuptools import Extension
@@ -8770,7 +8770,6 @@ import os
import os.path
import sys
from shutil import copyfile
-import numpy
from Cython.Build import cythonize
"
if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null; then
diff --git a/configure.ac b/configure.ac
index 73a717ce7..582cb0da1 100644
--- a/configure.ac
+++ b/configure.ac
@@ -760,7 +760,7 @@ if test $python == true ; then
if test -n "$PYTHON_BIN"
then
AC_MSG_NOTICE([Python executable is $PYTHON_BIN])
- AC_MSG_CHECKING([support for required python modules (setuptools, cython, numpy, subprocess, os, shutil)])
+ AC_MSG_CHECKING([support for required python modules (setuptools, cython, subprocess, os, shutil)])
testimport="
from setuptools import setup
from setuptools import Extension
@@ -769,7 +769,6 @@ import os
import os.path
import sys
from shutil import copyfile
-import numpy
from Cython.Build import cythonize
"
if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null; then
diff --git a/macports/PortfilePython.in b/macports/PortfilePython.in
index e4a5aad8a..31d990ef6 100644
--- a/macports/PortfilePython.in
+++ b/macports/PortfilePython.in
@@ -41,12 +41,14 @@ if {${name} ne ${subport}} {
build.env-append plumed_default_kernel=${prefix}/lib/libplumedKernel.dylib \
plumed_macports=yes
- depends_build-append port:py${python.version}-cython
+ depends_build-append port:py${python.version}-cython \
+ port:py${python.version}-setuptools
- depends_lib-append port:py${python.version}-numpy \
- path:${prefix}/lib/libplumedKernel.dylib:plumed
+ depends_lib-append path:${prefix}/lib/libplumedKernel.dylib:plumed
+
+ depends_test-append port:py${python.version}-nose \
+ port:py${python.version}-numpy
- depends_test-append port:py${python.version}-nose
test.cmd nosetests-${python.branch}
test.target
test.run yes
diff --git a/python/README.rst b/python/README.rst
index 30a0244b3..1d9f989c2 100644
--- a/python/README.rst
+++ b/python/README.rst
@@ -1,11 +1,8 @@
Python wrappers for plumed
==========================
-Install using the following commands::
+Install using the following command::
- # install dependencies
- python -m pip install numpy
- # install plumed
python -m pip install plumed
WARNING: You will need to also build and install the plumed library (see http://www.plumed.org) and set the environment variable
@@ -16,3 +13,4 @@ WARNING: You will need to also build and install the plumed library (see http://
>>> import plumed
>>> p=plumed.Plumed()
+CHANGES: See the PLUMED documentation.
diff --git a/python/plumed.pyx b/python/plumed.pyx
index 1a897863a..6b3d6ac5a 100644
--- a/python/plumed.pyx
+++ b/python/plumed.pyx
@@ -25,8 +25,12 @@
#
cimport cplumed # This imports information from pxd file - including contents of this file here causes name clashes
-import numpy as np
-cimport numpy as np
+
+try:
+ import numpy as np
+ HAS_NUMPY=True
+except:
+ HAS_NUMPY=False
cdef class Plumed:
cdef cplumed.Plumed c_plumed
@@ -59,8 +63,6 @@ cdef class Plumed:
cdef bytes py_bytes = key.encode()
cdef char* ckey = py_bytes
cdef char* cval
- cdef np.int_t[:] ibuffer
- cdef np.float64_t[:] dbuffer
if val is None :
self.c_plumed.cmd( ckey, NULL )
elif isinstance(val, (int,long) ):
@@ -71,7 +73,7 @@ cdef class Plumed:
if key=="getBias" :
raise ValueError("when using cmd with getBias option value must be a size one ndarray")
self.cmd_float(ckey, val)
- elif isinstance(val, np.ndarray) :
+ elif HAS_NUMPY and isinstance(val, np.ndarray) :
if( val.dtype=="float64" ):
self.cmd_ndarray_real(ckey, val)
elif( val.dtype=="int64" ) :
diff --git a/python/setup.py b/python/setup.py
index 3e9df6f9a..929c3af12 100644
--- a/python/setup.py
+++ b/python/setup.py
@@ -76,18 +76,11 @@ def readme():
with open('README.rst') as f:
return f.read()
-try:
- import numpy
-except:
- print('Error: building ' + plumedname + ' requires numpy. Please install it first with pip install numpy')
- sys.exit(-1)
-
-include_dirs=[numpy.get_include()]
try:
- include_dirs.append(os.environ["plumed_include_dir"])
+ include_dirs=[os.environ["plumed_include_dir"]]
except:
- include_dirs.append(".")
+ include_dirs=["."]
# allow one to force using cython with env var plumed_force_cython=yes
USE_CYTHON = False
diff --git a/user-doc/Installation.md b/user-doc/Installation.md
index 8497f60bc..0b31786b2 100644
--- a/user-doc/Installation.md
+++ b/user-doc/Installation.md
@@ -690,7 +690,7 @@ There are two ways to install Python wrappers.
\subsection installingpython-inside Installing Python wrappers within PLUMED
-If `./configure` finds a `python` executable that also has the modules `numpy` and `cython` available, Python wrappers will be installed within `/prefix/lib/plumed/python`. In order to access them, you should add this directory to the environment variable `PYTHONPATH`. Notice that if your python interpreter has a different name you might have to pass it to `./configure` with `PYTHON_BIN=python3.6`. The whole thing would then be:
+If `./configure` finds a `python` executable that also has the `cython` module available, Python wrappers will be installed within `/prefix/lib/plumed/python`. In order to access them, you should add this directory to the environment variable `PYTHONPATH`. Notice that if your python interpreter has a different name you might have to pass it to `./configure` with `PYTHON_BIN=python3.6`. The whole thing would then be:
````
./configure PYTHON_BIN=python3.6 --prefix=$HOME/opt
@@ -707,7 +707,6 @@ Notice that in this manner you will have to commit to a specific python version
If you use multiple python versions, you might find it easier to install the Python wrappers separately from PLUMED. The simplest way is to do it with `pip`:
````
-pip3.6 install --user numpy
pip3.6 install --user plumed
````
@@ -724,8 +723,7 @@ If you want to install using pip the development version of the wrappers you sho
the following commands:
````
-pip3.6 install --user cython # also cython is required in this case
-pip3.6 install --user numpy
+pip3.6 install --user cython # cython is required in this case
cd plumed2/python
make pip
pip3.6 install --user .
--
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