Index: setup.py =================================================================== RCS file: /home/repository/biopython/biopython/setup.py,v retrieving revision 1.115 diff -u -r1.115 setup.py --- setup.py 10 Oct 2006 03:53:34 -0000 1.115 +++ setup.py 14 Mar 2007 15:45:10 -0000 @@ -76,8 +76,6 @@ dependencies = [ ("mxTextTools", is_mxTextTools_installed, 1, "http://www.egenix.com/files/python/eGenix-mx-Extensions.html"), - ("Numerical Python", is_Numpy_installed, 0, - "http://numpy.sourceforge.net/"), ("Reportlab", is_reportlab_installed, 0, "http://www.reportlab.org/downloads.html"), ] @@ -127,10 +125,40 @@ ["Bio/KDTree/KDTree.cpp", "Bio/KDTree/KDTree.swig.cpp"], libraries=["stdc++"], + include_dirs=arrayobject_h_include, + define_macros=[(NUMPY_CHOICE, None)], language="c++")) - - return 1 + return check_numpy() + + +def check_numpy(): + """Return whether the installation should continue.""" + choice = None + print "Testing for Numeric: " + if is_Numeric_installed(): + print "found." + choice = "Numeric" + else: + print "not found." + print "Testing for NumPy: " + if is_NumPy_installed(): + print "found." + choice = "numpy" + else: + print "not found." + if choice is None: + print """ + These packages are optional, which means they are only used in a few + specialized modules in Biopython. You probably don't need this if you + are unsure. You can ignore this requirement, and install it later if + you see ImportErrors.""" + print "You can find both Numeric and NumPy at http://numpy.sourceforge.net/" + + if not get_yes_or_no("Do you want to continue this installation?", True): + return False + return True + class install_biopython(install): """Override the standard install to check for dependencies. @@ -152,8 +180,8 @@ # it automatically. if not is_Martel_installed(): self.packages.append("Martel") - # Add software that requires Numpy to be installed. - if is_Numpy_installed(): + # Add software that requires Numeric or NumPy to be installed. + if is_NumPy_installed() or is_Numeric_installed(): self.packages.extend(NUMPY_PACKAGES) build_py.run(self) @@ -181,8 +209,8 @@ def run(self): if not check_dependencies_once(): return - # add software that requires NumPy to install - if is_Numpy_installed(): + # Add software that requires Numeric or NumPy to be installed. + if is_NumPy_installed() or is_Numeric_installed(): self.extensions.extend(NUMPY_EXTENSIONS) build_ext.run(self) @@ -305,9 +333,12 @@ return 1 return can_import("mx.TextTools") -def is_Numpy_installed(): +def is_Numeric_installed(): return can_import("Numeric") +def is_NumPy_installed(): + return can_import("numpy") + def is_reportlab_installed(): return can_import("reportlab") @@ -401,7 +432,7 @@ 'Bio.WWW', ] -# packages that require Numeric Python +# packages that require Numerical Python NUMPY_PACKAGES = [ 'Bio.Affy', 'Bio.Cluster', @@ -453,12 +484,29 @@ ), ] -# extensions that require numeric python +# Extensions that require Numeric or NumPy +if can_import("numpy"): + import numpy + arrayobject_h_include = [numpy.get_include()] + NUMPY_CHOICE = "NUMPY" +else: + arrayobject_h_include = [] + if can_import("Numeric"): + NUMPY_CHOICE = "NUMERIC" + else: + NUMPY_CHOICE = "NONE" + NUMPY_EXTENSIONS = [ + Extension('Bio.numpy_selector', + ['Bio/numpy_selector.c'], + include_dirs= arrayobject_h_include, + define_macros=[(NUMPY_CHOICE, None)] + ), Extension('Bio.Cluster.cluster', ['Bio/Cluster/clustermodule.c', 'Bio/Cluster/cluster.c'], - include_dirs=["Bio/Cluster"] + include_dirs=["Bio/Cluster"] + arrayobject_h_include, + define_macros=[(NUMPY_CHOICE, None)] ), # CplusplusExtension('Bio.Affy._cel', # The file parser in celmodule.cc was # ['Bio/Affy/celmodule.cc'], # replaced by a scanner/consumer in Index: Bio/LogisticRegression.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/LogisticRegression.py,v retrieving revision 1.4 diff -u -r1.4 LogisticRegression.py --- Bio/LogisticRegression.py 3 Feb 2007 17:22:44 -0000 1.4 +++ Bio/LogisticRegression.py 14 Mar 2007 15:45:10 -0000 @@ -14,8 +14,8 @@ classify Classify an observation into a class. """ try: - from Numeric import * - from LinearAlgebra import * # inverse + from Bio.numpy_wrapper import * + from Bio.linear_algebra_wrapper import * # inverse except ImportError, x: raise ImportError, "This module requires Numeric (precursor to NumPy) with the LinearAlgebra lib" Index: Bio/MarkovModel.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/MarkovModel.py,v retrieving revision 1.2 diff -u -r1.2 MarkovModel.py --- Bio/MarkovModel.py 21 Mar 2004 16:56:53 -0000 1.2 +++ Bio/MarkovModel.py 14 Mar 2007 15:45:10 -0000 @@ -17,8 +17,8 @@ """ import math -from Numeric import * -import RandomArray +from Bio.numpy_wrapper import * +from Bio.random_array_wrapper import seed, random import StringIO # StringIO is in Numeric's namespace, so import this after. @@ -26,7 +26,7 @@ #RandomArray.seed(0, 0) # use 0 for debugging -RandomArray.seed() +seed() VERY_SMALL_NUMBER = 1E-300 LOG0 = log(VERY_SMALL_NUMBER) @@ -173,12 +173,15 @@ pseudo_initial=None, pseudo_transition=None, pseudo_emission=None, update_fn=None): # Returns (p_initial, p_transition, p_emission) - p_initial = _safe_copy_and_check(p_initial, (N,)) or \ - _random_norm(N) - p_transition = _safe_copy_and_check(p_transition, (N,N)) or \ - _random_norm((N,N)) - p_emission = _safe_copy_and_check(p_emission, (N,M)) or \ - _random_norm((N,M)) + p_initial = _safe_copy_and_check(p_initial, (N,)) + if alltrue(p_initial == 0): + p_initial == _random_norm(N) + p_transition = _safe_copy_and_check(p_transition, (N,N)) + if alltrue(p_transition.flat == 0): + p_transition == _random_norm((N,N)) + p_emission = _safe_copy_and_check(p_emission, (N,M)) + if alltrue(p_emission.flat == 0): + p_emission = _random_norm((N,M)) # Do all the calculations in log space to avoid underflows. lp_initial, lp_transition, lp_emission = map( @@ -504,7 +507,7 @@ return _normalize(matrix) def _random_norm(shape): - matrix = asarray(RandomArray.random(shape), MATCODE) + matrix = asarray(random(shape), MATCODE) return _normalize(matrix) def _copy_and_check(matrix, desired_shape): Index: Bio/MaxEntropy.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/MaxEntropy.py,v retrieving revision 1.4 diff -u -r1.4 MaxEntropy.py --- Bio/MaxEntropy.py 21 Mar 2004 16:56:53 -0000 1.4 +++ Bio/MaxEntropy.py 14 Mar 2007 15:45:10 -0000 @@ -13,7 +13,7 @@ """ import math -from Numeric import * +from Bio.numpy_wrapper import * from Bio import listfns # XXX typecodes for Numeric Index: Bio/NaiveBayes.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/NaiveBayes.py,v retrieving revision 1.4 diff -u -r1.4 NaiveBayes.py --- Bio/NaiveBayes.py 3 Feb 2007 17:33:58 -0000 1.4 +++ Bio/NaiveBayes.py 14 Mar 2007 15:45:10 -0000 @@ -30,7 +30,7 @@ # use objects try: - from Numeric import * + from Bio.numpy_wrapper import * except ImportError, x: raise ImportError, "This module requires Numeric (precursor to NumPy)" Index: Bio/cMarkovModelmodule.c =================================================================== RCS file: /home/repository/biopython/biopython/Bio/cMarkovModelmodule.c,v retrieving revision 1.2 diff -u -r1.2 cMarkovModelmodule.c --- Bio/cMarkovModelmodule.c 27 Nov 2002 01:38:13 -0000 1.2 +++ Bio/cMarkovModelmodule.c 14 Mar 2007 15:45:10 -0000 @@ -9,6 +9,8 @@ #include "Python.h" #include "csupport.h" +void initcMarkovModel(void); +static PyObject *cMarkovModel__logadd(PyObject *self, PyObject *args); /* Functions in this module. */ Index: Bio/distance.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/distance.py,v retrieving revision 1.4 diff -u -r1.4 distance.py --- Bio/distance.py 3 Feb 2007 17:22:44 -0000 1.4 +++ Bio/distance.py 14 Mar 2007 15:45:10 -0000 @@ -9,7 +9,7 @@ # XXX cosine distance import math try: - from Numeric import * + from Bio.numpy_wrapper import * except ImportError, x: raise ImportError, "This module requires Numeric (precursor to NumPy)" Index: Bio/kNN.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/kNN.py,v retrieving revision 1.4 diff -u -r1.4 kNN.py --- Bio/kNN.py 3 Feb 2007 17:33:58 -0000 1.4 +++ Bio/kNN.py 14 Mar 2007 15:45:10 -0000 @@ -25,7 +25,7 @@ """ try: - from Numeric import * + from Bio.numpy_wrapper import * except ImportError, x: raise ImportError, "This module requires Numeric (precursor to NumPy)" Index: Bio/linear_algebra_wrapper.py =================================================================== RCS file: Bio/linear_algebra_wrapper.py diff -N Bio/linear_algebra_wrapper.py --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ Bio/linear_algebra_wrapper.py 14 Mar 2007 15:45:10 -0000 @@ -0,0 +1,21 @@ +""" +A simple wrapper interface for Numeric and NumPy. + +Sees whether numpy_selector.c was compiled with Numeric or NumPy support, +and imports the appropriate package. + +Date created: 2007-03-05 +Author: Ed Schofield +""" + +import numpy_selector + +choice = numpy_selector.choice() +if choice == "Numeric": + from LinearAlgebra import * +elif choice == "numpy": + from numpy.oldnumeric.linear_algebra import * +else: + raise ImportError, "BioPython was not compiled with support for "\ + "Numeric or NumPy" + Index: Bio/matrix_wrapper.py =================================================================== RCS file: Bio/matrix_wrapper.py diff -N Bio/matrix_wrapper.py --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ Bio/matrix_wrapper.py 14 Mar 2007 15:45:10 -0000 @@ -0,0 +1,21 @@ +""" +A simple wrapper interface for Numeric and NumPy. + +Sees whether numpy_selector.c was compiled with Numeric or NumPy support, +and imports the appropriate package. + +Date created: 2007-03-05 +Author: Ed Schofield +""" + +import numpy_selector + +choice = numpy_selector.choice() +if choice == "Numeric": + from Matrix import * +elif choice == "numpy": + from numpy.oldnumeric.matrix import * +else: + raise ImportError, "BioPython was not compiled with support for "\ + "Numeric or NumPy" + Index: Bio/mlab_wrapper.py =================================================================== RCS file: Bio/mlab_wrapper.py diff -N Bio/mlab_wrapper.py --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ Bio/mlab_wrapper.py 14 Mar 2007 15:45:10 -0000 @@ -0,0 +1,21 @@ +""" +A simple wrapper interface for Numeric and NumPy. + +Sees whether numpy_selector.c was compiled with Numeric or NumPy support, +and imports the appropriate package. + +Date created: 2007-03-05 +Author: Ed Schofield +""" + +import numpy_selector + +choice = numpy_selector.choice() +if choice == "Numeric": + from MLab import * +elif choice == "numpy": + from numpy.oldnumeric.mlab import * +else: + raise ImportError, "BioPython was not compiled with support for "\ + "Numeric or NumPy" + Index: Bio/numpy_selector.c =================================================================== RCS file: Bio/numpy_selector.c diff -N Bio/numpy_selector.c --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ Bio/numpy_selector.c 14 Mar 2007 15:45:10 -0000 @@ -0,0 +1,60 @@ +/* Simple C module that exports the compile-time selection of NumPy or Numeric + * back to Python. This is to prevent breakage if a user compiles BioPython + * against Numeric, then later installs NumPy (or vice versa). + * + * Date created: 2007-03-05 + * Author: Ed Schofield + * License: see LICENSE file in root of BioPython tree + */ + +#include "Python.h" + +static PyObject* choice(PyObject *self, PyObject *args); +PyMODINIT_FUNC initnumpy_selector(void); + +static char numpy_selector__doc__[] = \ + "numpy_selector: a simple C module that exports BioPython's compile-time\n "\ + "selection of NumPy or Numeric back to Python. This is to prevent breakage\n"\ + "if a user compiles BioPython against Numeric, then later installs NumPy\n"\ + "(or vice versa).\n"; + +static char choice__doc__[] = \ + "choice(): returns either 'Numeric' or 'numpy' as a string, indicating\n" + "which array package the BioPython C modules were compiled against.\n"; + +static PyObject* +choice(PyObject *self, PyObject *args) +{ +#ifdef NUMERIC + return Py_BuildValue("s", "Numeric"); +#else +#ifdef NUMPY + return Py_BuildValue("s", "numpy"); +#else + /* neither */ + Py_INCREF(Py_None); + return Py_None; +#endif +#endif +} + + +/* Module functions */ +static PyMethodDef module_methods[] = { + {"choice", choice, METH_VARARGS, choice__doc__}, + {NULL, NULL, 0, NULL} /* Sentinel */ +}; + + +#ifndef PyMODINIT_FUNC /* declarations for shared library import/export */ +#define PyMODINIT_FUNC DL_EXPORT(void) +#endif +PyMODINIT_FUNC +initnumpy_selector(void) +{ + /* Create the module and add the functions */ + (void) Py_InitModule3("numpy_selector", module_methods, + numpy_selector__doc__); +} + + Index: Bio/numpy_wrapper.py =================================================================== RCS file: Bio/numpy_wrapper.py diff -N Bio/numpy_wrapper.py --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ Bio/numpy_wrapper.py 14 Mar 2007 15:45:10 -0000 @@ -0,0 +1,21 @@ +""" +A simple wrapper interface for Numeric and NumPy. + +Sees whether numpy_selector.c was compiled with Numeric or NumPy support, +and imports the appropriate package. + +Date created: 2007-03-05 +Author: Ed Schofield +""" + +from Bio import numpy_selector + +choice = numpy_selector.choice() +if choice == "Numeric": + from Numeric import * +elif choice == "numpy": + from numpy.oldnumeric import * +else: + raise ImportError, "BioPython was not compiled with support for "\ + "Numeric or NumPy" + Index: Bio/random_array_wrapper.py =================================================================== RCS file: Bio/random_array_wrapper.py diff -N Bio/random_array_wrapper.py --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ Bio/random_array_wrapper.py 14 Mar 2007 15:45:10 -0000 @@ -0,0 +1,21 @@ +""" +A simple wrapper interface for Numeric and NumPy. + +Sees whether numpy_selector.c was compiled with Numeric or NumPy support, +and imports the appropriate package. + +Date created: 2007-03-05 +Author: Ed Schofield +""" + +import numpy_selector + +choice = numpy_selector.choice() +if choice == "Numeric": + from RandomArray import * +elif choice == "numpy": + from numpy.oldnumeric.random_array import * +else: + raise ImportError, "BioPython was not compiled with support for "\ + "Numeric or NumPy" + Index: Bio/Affy/CelFile.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Affy/CelFile.py,v retrieving revision 1.3 diff -u -r1.3 CelFile.py --- Bio/Affy/CelFile.py 11 Feb 2005 08:08:30 -0000 1.3 +++ Bio/Affy/CelFile.py 14 Mar 2007 15:45:10 -0000 @@ -16,7 +16,7 @@ # import _cel from Bio.ParserSupport import AbstractConsumer -from Numeric import * +from Bio.numpy_wrapper import * class CelScanner: """Scannner for Affymetrix CEL files. Index: Bio/Affy/celmodule.cc =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Affy/celmodule.cc,v retrieving revision 1.2 diff -u -r1.2 celmodule.cc --- Bio/Affy/celmodule.cc 4 May 2004 16:15:29 -0000 1.2 +++ Bio/Affy/celmodule.cc 14 Mar 2007 15:45:10 -0000 @@ -9,7 +9,12 @@ // #include "Python.h" + +#ifdef NUMERIC #include "Numeric/arrayobject.h" +#else +#include "numpy/arrayobject.h" +#endif using namespace std; Index: Bio/Cluster/__init__.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Cluster/__init__.py,v retrieving revision 1.6 diff -u -r1.6 __init__.py --- Bio/Cluster/__init__.py 19 Jun 2006 19:39:44 -0000 1.6 +++ Bio/Cluster/__init__.py 14 Mar 2007 15:45:10 -0000 @@ -1,4 +1,4 @@ -from Numeric import * +from Bio.numpy_wrapper import * from cluster import * Index: Bio/Cluster/clustermodule.c =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Cluster/clustermodule.c,v retrieving revision 1.15 diff -u -r1.15 clustermodule.c --- Bio/Cluster/clustermodule.c 13 Mar 2007 15:06:05 -0000 1.15 +++ Bio/Cluster/clustermodule.c 14 Mar 2007 15:45:10 -0000 @@ -1,8 +1,24 @@ #include "Python.h" + +#ifdef NUMERIC #include "Numeric/arrayobject.h" +/* The data type used to store the Numeric or NumPy dimensions and strides + * array attributes: */ +typedef int npy_generic_dimension_t; +#define NPY_GENERIC_DIMENSION_FMT "d" + +#else /* Assume NumPy */ + +#include "numpy/arrayobject.h" +typedef npy_intp npy_generic_dimension_t; +#define NPY_GENERIC_DIMENSION_FMT NPY_INTP_FMT +#endif + + #include #include #include + #include "cluster.h" static char buffer[512]; @@ -21,7 +37,7 @@ /* Takes the Python object from the argument list, and finds the microarray * data set. In case of an error, the array is DECREF'ed and set to NULL. */ { int i, j; - int nrows, ncols; + npy_generic_dimension_t nrows, ncols; double** data = NULL; if(!PyArray_Check (object)) /* Try to convert object to a 2D double array */ { *array = (PyArrayObject*) PyArray_FromObject(object, PyArray_DOUBLE, 2, 2); @@ -84,7 +100,7 @@ free_data(PyArrayObject* array, double** data) { if(data[0]!=(double*)(array->data)) { int i; - const int nrows = array->dimensions[0]; + const npy_generic_dimension_t nrows = array->dimensions[0]; for (i=0; idimensions[0] != nrows) /* Checking number of rows */ { sprintf(message, - "mask has incorrect number of rows (%d expected %d)", + "mask has incorrect number of rows (%" NPY_GENERIC_DIMENSION_FMT \ + ", expected %" NPY_GENERIC_DIMENSION_FMT ")", \ (*array)->dimensions[0], nrows); PyErr_SetString (PyExc_ValueError, buffer); Py_DECREF((PyObject*)*array); @@ -147,7 +164,8 @@ /* no checking on last dimension of expected size 1 */ if (ncolumns != 1 && (*array)->dimensions[1] != ncolumns) { sprintf(message, - "mask incorrect number of columns (%d expected %d)", + "mask has incorrect number of columns (%" NPY_GENERIC_DIMENSION_FMT \ + ", expected %" NPY_GENERIC_DIMENSION_FMT ")", (*array)->dimensions[1], ncolumns); PyErr_SetString (PyExc_ValueError, buffer); *array = NULL; @@ -166,7 +184,7 @@ const int colstride = (*array)->strides[1]; for (i=0; i < nrows; i++) { const char* p = p0; - mask[i] = malloc(ncolumns*sizeof(int)); + mask[i] = malloc(ncolumns*sizeof(int*)); for (j=0; j < ncolumns; j++, p+=colstride) mask[i][j] = *((int*)p); p0 += rowstride; } @@ -221,7 +239,7 @@ { /* no checking on last dimension of expected size 1 */ if (ndata!=1 && ndata!=(*array)->dimensions[0]) { sprintf(message, - "weight has incorrect extent (%d expected %d)", + "weight has incorrect extent (%" NPY_GENERIC_DIMENSION_FMT ", expected %d)", (*array)->dimensions[0], ndata); PyErr_SetString (PyExc_ValueError, buffer); Py_DECREF(*array); @@ -311,8 +329,8 @@ if(array->nd == 1) { /* no checking on last dimension of expected size 1 */ if (nitems!=1 && nitems!=array->dimensions[0]) - { sprintf(message, "initialid has incorrect extent (%d expected %d)", - array->dimensions[0], nitems); + { sprintf(message, "initialid has incorrect extent (%" NPY_GENERIC_DIMENSION_FMT \ + ", expected %d)", array->dimensions[0], nitems); PyErr_SetString (PyExc_ValueError, buffer); Py_DECREF((PyObject*) array); Py_DECREF((PyObject*) clusterid); @@ -369,7 +387,7 @@ /* -- clusterid ------------------------------------------------------------- */ static int* -parse_clusterid(PyObject* object, PyArrayObject** array, unsigned int nitems, +parse_clusterid(PyObject* object, PyArrayObject** array, int nitems, int* nclusters) /* This function reads the cluster assignments of all items from object */ { int i; @@ -411,7 +429,7 @@ { /* no checking on last dimension of expected size 1 */ if (nitems!=1 && nitems!=(*array)->dimensions[0]) { sprintf(message, - "clusterid has incorrect extent (%d expected %d)", + "clusterid has incorrect extent (%" NPY_GENERIC_DIMENSION_FMT ", expected %d)", (*array)->dimensions[0], nitems); PyErr_SetString (PyExc_ValueError, buffer); Py_DECREF((PyObject*) (*array)); @@ -549,7 +567,7 @@ break; } if (a->dimensions[0]!=i) - { sprintf (message, "Row %d in the distance matrix has incorrect size (%d, should be %d).", i, a->dimensions[0], i); + { sprintf (message, "Row %d in the distance matrix has incorrect size (%" NPY_GENERIC_DIMENSION_FMT ", should be %d).", i, a->dimensions[0], i); PyErr_SetString(PyExc_ValueError, buffer); break; } @@ -605,7 +623,7 @@ break; } if (a->dimensions[0]!=i) - { sprintf (message, "Row %d in the distance matrix has incorrect size (%d, should be %d).", i, a->dimensions[0], i); + { sprintf (message, "Row %d in the distance matrix has incorrect size (%" NPY_GENERIC_DIMENSION_FMT ", should be %d).", i, a->dimensions[0], i); PyErr_SetString(PyExc_ValueError, buffer); Py_DECREF((PyObject*)a); break; @@ -1305,9 +1323,8 @@ static PyObject* py_kcluster (PyObject* self, PyObject* args, PyObject* keywords) { int NCLUSTERS = 2; - int nrows, ncolumns; - int nitems; - int ndata; + npy_generic_dimension_t nrows, ncolumns; + int nitems, ndata; PyObject* DATA = NULL; PyArrayObject* aDATA = NULL; double** data = NULL; @@ -1700,8 +1717,7 @@ } if (DISTANCEMATRIX==NULL) /* DATA contains gene expression data */ - { int nrows; - int ncolumns; + { npy_generic_dimension_t nrows, ncolumns; int ndata; PyArrayObject* aDATA = NULL; PyArrayObject* aMASK = NULL; @@ -1841,10 +1857,8 @@ static PyObject* py_somcluster (PyObject* self, PyObject* args, PyObject* keywords) -{ int nrows; - int ncolumns; - int nitems; - int ndata; +{ npy_generic_dimension_t nrows, ncolumns; + int nitems, ndata; PyObject* DATA = NULL; PyArrayObject* aDATA = NULL; double** data = NULL; @@ -2304,9 +2318,8 @@ static PyObject* py_clustercentroids(PyObject* self, PyObject* args, PyObject* keywords) -{ int nrows; - int ncolumns; - unsigned int nitems; +{ npy_generic_dimension_t nrows, ncolumns; + int nitems; int nclusters; PyObject* DATA = NULL; PyArrayObject* aDATA = NULL; @@ -2474,7 +2487,8 @@ int TRANSPOSE = 0; char DIST = 'e'; double** distances = NULL; - int nrows, ncolumns, nelements, ndata; + npy_generic_dimension_t nrows, ncolumns; + int nelements, ndata; /* -- Read the input variables ----------------------------------------- */ static char* kwlist[] = { "data", Index: Bio/KDTree/KDTree.i =================================================================== RCS file: /home/repository/biopython/biopython/Bio/KDTree/KDTree.i,v retrieving revision 1.1 diff -u -r1.1 KDTree.i --- Bio/KDTree/KDTree.i 21 Mar 2004 14:37:46 -0000 1.1 +++ Bio/KDTree/KDTree.i 14 Mar 2007 15:45:10 -0000 @@ -4,7 +4,11 @@ %{ #include "KDTree.h" - #include + #ifdef NUMERIC + #include "Numeric/arrayobject.h" + #else + #include "numpy/arrayobject.h" + #endif %} // import_array() call initialises Numpy Index: Bio/KDTree/KDTree.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/KDTree/KDTree.py,v retrieving revision 1.5 diff -u -r1.5 KDTree.py --- Bio/KDTree/KDTree.py 3 Feb 2007 17:05:09 -0000 1.5 +++ Bio/KDTree/KDTree.py 14 Mar 2007 15:45:10 -0000 @@ -8,11 +8,10 @@ """ try: - import Numeric - from Numeric import sum, sqrt - from RandomArray import * + from Bio.numpy_selector import sum, sqrt + from Bio.random_array_wrapper import random except ImportError: - raise ImportError, "This module requires Numeric (precursor to NumPy)" + raise ImportError, "this module requires Numeric or NumPy" import CKDTree @@ -128,16 +127,16 @@ def set_coords(self, coords): """Add the coordinates of the points. - o coords - two dimensional Numeric array of type "f". E.g. if the - points have dimensionality D and there are N points, the coords - array should be NxD dimensional. + o coords - two dimensional Numeric or NumPy array of type "f". + E.g. if the points have dimensionality D and there are N points, + the coords array should be NxD dimensional. """ if min(coords)<=-1e6 or max(coords)>=1e6: raise Exception, "Points should lie between -1e6 and 1e6" if len(coords.shape)!=2 or coords.shape[1]!=self.dim: - raise Exception, "Expected a Nx%i Numeric array" % self.dim + raise Exception, "Expected an Nx%i array" % self.dim if coords.typecode()!="f": - raise Exception, "Expected a Numeric array of type float" + raise Exception, "Expected an array of type float" self.kdt.set_data(coords, coords.shape[0]) self.built=1 @@ -146,17 +145,16 @@ def search(self, center, radius): """Search all points within radius of center. - o center - one dimensional Numeric array of type "f". E.g. if the - points have dimensionality D, the center array should be D - dimensional. - o radius - float>0 + o center - one dimensional Numeric or NumPy array of type "f". + E.g. if the points have dimensionality D, the center array should + be D dimensional. o radius - float>0 """ if not self.built: raise Exception, "No point set specified" if center.shape!=(self.dim,): - raise Exception, "Expected a %i-dimensional Numeric array" % self.dim + raise Exception, "Expected a %i-dimensional array" % self.dim if center.typecode()!="f": - raise Exception, "Expected a Numeric array of type float" + raise Exception, "Expected an array of type float" self.kdt.search_center_radius(center, radius) def get_radii(self): @@ -173,9 +171,9 @@ def get_indices(self): """Return the list of indices. - Return the list of indices after a neighbor search. - The indices refer to the original coords Numeric array. The - coordinates with these indices were within radius of center. + Return the list of indices after a neighbor search. The indices + refer to the original coords array. The coordinates with these + indices were within radius of center. For an index pair, the first index + #ifdef NUMERIC + #include "Numeric/arrayobject.h" + #else + #include "numpy/arrayobject.h" + #endif PyObject *KDTree_get_indices(KDTree *kdtree) Index: Bio/MetaTool/Record.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/MetaTool/Record.py,v retrieving revision 1.4 diff -u -r1.4 Record.py --- Bio/MetaTool/Record.py 21 Jun 2003 02:49:53 -0000 1.4 +++ Bio/MetaTool/Record.py 14 Mar 2007 15:45:11 -0000 @@ -4,7 +4,7 @@ # standard modules import string -import Matrix +# import Matrix # local stuff import Bio.MetaTool Index: Bio/MetaTool/__init__.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/MetaTool/__init__.py,v retrieving revision 1.7 diff -u -r1.7 __init__.py --- Bio/MetaTool/__init__.py 13 May 2004 16:58:34 -0000 1.7 +++ Bio/MetaTool/__init__.py 14 Mar 2007 15:45:11 -0000 @@ -18,7 +18,7 @@ import sgmllib import urlparse import copy -import Matrix +from Bio.matrix_wrapper import Matrix # XML from python 2.0 from xml.sax import handler @@ -224,7 +224,7 @@ def end_stochiometric( self, content ): if( self._vectors != [] ): - self.data.stochiometric.matrix = Matrix.Matrix( self._vectors ) + self.data.stochiometric.matrix = Matrix( self._vectors ) self.data.stochiometric.enzymes = [] for enzyme in self._enzymes: self.data.stochiometric.enzymes.append( enzyme ) @@ -236,7 +236,7 @@ def end_kernel( self, content ): if( self._vectors != [] ): - self.data.kernel.matrix = Matrix.Matrix( self._vectors ) + self.data.kernel.matrix = Matrix( self._vectors ) self.data.kernel.enzymes = [] for enzyme in self._enzymes: self.data.kernel.enzymes.append( enzyme ) @@ -245,7 +245,7 @@ def end_subsets( self, content ): if( self._vectors != [] ): - self.data.subsets.matrix = Matrix.Matrix( self._vectors ) + self.data.subsets.matrix = Matrix( self._vectors ) self.data.subsets.enzymes = [] for enzyme in self._enzymes: self.data.subsets.enzymes.append( enzyme ) @@ -255,7 +255,7 @@ def end_reduced_system( self, content ): if( self._vectors != [] ): - self.data.reduced_system.matrix = Matrix.Matrix( self._vectors[:14] ) + self.data.reduced_system.matrix = Matrix( self._vectors[:14] ) self.data.reduced_system.enzymes = [] for enzyme in self._enzymes: self.data.reduced_system.enzymes.append( enzyme ) @@ -267,7 +267,7 @@ def end_convex_basis( self, content ): if( self._vectors != [] ): - self.data.convex_basis.matrix = Matrix.Matrix( self._vectors ) + self.data.convex_basis.matrix = Matrix( self._vectors ) self.data.convex_basis.enzymes = [] for enzyme in self._enzymes: self.data.convex_basis.enzymes.append( enzyme ) @@ -276,7 +276,7 @@ def end_conservation_relations( self, content ): if( self._vectors != [] ): - self.data.conservation_relations.matrix = Matrix.Matrix( self._vectors ) + self.data.conservation_relations.matrix = Matrix( self._vectors ) self.data.conservation_relations.enzymes = [] for enzyme in self._enzymes: self.data.conservation_relations.enzymes.append( enzyme ) @@ -286,7 +286,7 @@ def end_elementary_modes( self, content ): if( self._vectors != [] ): - self.data.elementary_modes.matrix = Matrix.Matrix( self._vectors ) + self.data.elementary_modes.matrix = Matrix( self._vectors ) self.data.elementary_modes.enzymes = [] for enzyme in self._enzymes: self.data.elementary_modes.enzymes.append( enzyme ) Index: Bio/PDB/Atom.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/Atom.py,v retrieving revision 1.18 diff -u -r1.18 Atom.py --- Bio/PDB/Atom.py 3 Feb 2007 17:23:36 -0000 1.18 +++ Bio/PDB/Atom.py 14 Mar 2007 15:45:11 -0000 @@ -4,7 +4,7 @@ # as part of this package. # Python stuff -from Numeric import array, sum, sqrt, matrixmultiply +from Bio.numpy_wrapper import array, sum, sqrt, dot # My stuff from Entity import DisorderedEntityWrapper @@ -228,7 +228,7 @@ @param tran: the translation vector @type tran: size 3 Numeric array """ - self.coord=matrixmultiply(self.coord, rot)+tran + self.coord=dot(self.coord, rot)+tran def get_vector(self): """ Index: Bio/PDB/Entity.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/Entity.py,v retrieving revision 1.20 diff -u -r1.20 Entity.py --- Bio/PDB/Entity.py 6 Feb 2007 17:13:04 -0000 1.20 +++ Bio/PDB/Entity.py 14 Mar 2007 15:45:11 -0000 @@ -5,7 +5,7 @@ from __future__ import generators -from Numeric import Float0 +from Bio.numpy_wrapper import Float0 from copy import copy from PDBExceptions import PDBConstructionException, PDBException Index: Bio/PDB/FragmentMapper.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/FragmentMapper.py,v retrieving revision 1.9 diff -u -r1.9 FragmentMapper.py --- Bio/PDB/FragmentMapper.py 3 Feb 2007 17:23:36 -0000 1.9 +++ Bio/PDB/FragmentMapper.py 14 Mar 2007 15:45:11 -0000 @@ -3,7 +3,7 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import array, Float0, zeros +from Bio.numpy_wrapper import array, Float0, zeros import os from Bio.SVDSuperimposer import SVDSuperimposer Index: Bio/PDB/MMCIFParser.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/MMCIFParser.py,v retrieving revision 1.4 diff -u -r1.4 MMCIFParser.py --- Bio/PDB/MMCIFParser.py 12 Oct 2006 08:47:37 -0000 1.4 +++ Bio/PDB/MMCIFParser.py 14 Mar 2007 15:45:11 -0000 @@ -5,7 +5,7 @@ #Python stuff from string import atoi, atof, letters -from Numeric import array, Float0 +from Bio.numpy_wrapper import array, Float0 # My stuff from MMCIF2Dict import MMCIF2Dict Index: Bio/PDB/Model.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/Model.py,v retrieving revision 1.7 diff -u -r1.7 Model.py --- Bio/PDB/Model.py 12 Oct 2006 08:47:37 -0000 1.7 +++ Bio/PDB/Model.py 14 Mar 2007 15:45:11 -0000 @@ -3,7 +3,7 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import sqrt, argmin, argmax, sum, power, concatenate, array, Float0 +from Bio.numpy_wrapper import sqrt, argmin, argmax, sum, power, concatenate, array, Float0 import os # My Stuff Index: Bio/PDB/NeighborSearch.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/NeighborSearch.py,v retrieving revision 1.15 diff -u -r1.15 NeighborSearch.py --- Bio/PDB/NeighborSearch.py 3 Feb 2007 17:15:57 -0000 1.15 +++ Bio/PDB/NeighborSearch.py 14 Mar 2007 15:45:11 -0000 @@ -3,7 +3,7 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import array +from Bio.numpy_wrapper import array from Bio.KDTree import * from PDBExceptions import PDBException @@ -123,7 +123,7 @@ if __name__=="__main__": - from RandomArray import * + from Bio.random_array_wrapper import * class Atom: def __init__(self): Index: Bio/PDB/PDBParser.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/PDBParser.py,v retrieving revision 1.20 diff -u -r1.20 PDBParser.py --- Bio/PDB/PDBParser.py 16 Feb 2007 15:26:44 -0000 1.20 +++ Bio/PDB/PDBParser.py 14 Mar 2007 15:45:11 -0000 @@ -6,7 +6,7 @@ # Python stuff import sys from string import split -from Numeric import array, Float0 +from Bio.numpy_wrapper import array, Float0 # My stuff from StructureBuilder import StructureBuilder Index: Bio/PDB/Polypeptide.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/Polypeptide.py,v retrieving revision 1.32 diff -u -r1.32 Polypeptide.py --- Bio/PDB/Polypeptide.py 18 Dec 2006 11:29:53 -0000 1.32 +++ Bio/PDB/Polypeptide.py 14 Mar 2007 15:45:11 -0000 @@ -3,7 +3,7 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import sum +from Bio.numpy_wrapper import sum from types import StringType from Bio.Alphabet import ProteinAlphabet Index: Bio/PDB/ResidueDepth.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/ResidueDepth.py,v retrieving revision 1.8 diff -u -r1.8 ResidueDepth.py --- Bio/PDB/ResidueDepth.py 3 Feb 2007 17:15:57 -0000 1.8 +++ Bio/PDB/ResidueDepth.py 14 Mar 2007 15:45:11 -0000 @@ -6,7 +6,7 @@ # make yield compatible with Python 2.2 from __future__ import generators -from Numeric import array, sum, sqrt +from Bio.numpy_wrapper import array, sum, sqrt import tempfile import os import sys Index: Bio/PDB/Superimposer.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/Superimposer.py,v retrieving revision 1.8 diff -u -r1.8 Superimposer.py --- Bio/PDB/Superimposer.py 12 Oct 2006 08:47:37 -0000 1.8 +++ Bio/PDB/Superimposer.py 14 Mar 2007 15:45:11 -0000 @@ -3,7 +3,7 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import Float0, zeros +from Bio.numpy_wrapper import Float0, zeros from Bio.SVDSuperimposer import SVDSuperimposer from Bio.PDB.PDBExceptions import PDBException @@ -60,7 +60,7 @@ if __name__=="__main__": import sys - from Numeric import * + from Bio.numpy_wrapper import * from Bio.PDB import * Index: Bio/PDB/Vector.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/PDB/Vector.py,v retrieving revision 1.40 diff -u -r1.40 Vector.py --- Bio/PDB/Vector.py 3 Feb 2007 17:15:57 -0000 1.40 +++ Bio/PDB/Vector.py 14 Mar 2007 15:45:11 -0000 @@ -3,11 +3,11 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import array, sum, sqrt, arccos, matrixmultiply, transpose, cos, \ +from Bio.numpy_wrapper import array, sum, sqrt, arccos, dot, transpose, cos, \ sin, zeros, trace from math import acos -from LinearAlgebra import determinant, eigenvectors -from MLab import eye +from Bio.linear_algebra_wrapper import determinant, eigenvectors +from Bio.mlab_wrapper import eye import sys from math import pi @@ -138,7 +138,7 @@ b=pq.get_array() b.shape=(3, 1) i=eye(3) - ref=i-2*matrixmultiply(b, transpose(b)) + ref=i-2*dot(b, transpose(b)) return ref def rotmat(p,q): @@ -158,7 +158,7 @@ @return: rotation matrix that rotates p onto q @rtype: 3x3 Numeric array """ - rot=matrixmultiply(refmat(q, -p), refmat(p, -p)) + rot=dot(refmat(q, -p), refmat(p, -p)) return rot def calc_angle(v1, v2, v3): @@ -301,12 +301,12 @@ def left_multiply(self, matrix): "Return Vector=Matrix x Vector" - a=matrixmultiply(matrix, self._ar) + a=dot(matrix, self._ar) return Vector(a) def right_multiply(self, matrix): "Return Vector=Vector x Matrix" - a=matrixmultiply(self._ar, matrix) + a=dot(self._ar, matrix) return Vector(a) def copy(self): @@ -316,8 +316,8 @@ if __name__=="__main__": from math import pi - from RandomArray import * - from Numeric import * + from Bio.random_array_wrapper import * + from Bio.numpy_wrapper import * v1=Vector(0,0,1) v2=Vector(0,0,0) Index: Bio/SVDSuperimposer/SVDSuperimposer.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/SVDSuperimposer/SVDSuperimposer.py,v retrieving revision 1.2 diff -u -r1.2 SVDSuperimposer.py --- Bio/SVDSuperimposer/SVDSuperimposer.py 19 Mar 2004 21:37:02 -0000 1.2 +++ Bio/SVDSuperimposer/SVDSuperimposer.py 14 Mar 2007 15:45:11 -0000 @@ -3,8 +3,8 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -from Numeric import matrixmultiply, transpose, sum, sqrt -from LinearAlgebra import singular_value_decomposition, determinant +from Bio.numpy_wrapper import dot, transpose, sum, sqrt +from Bio.linear_algebra_wrapper import singular_value_decomposition, determinant class SVDSuperimposer: @@ -77,14 +77,14 @@ coords=coords-av1 reference_coords=reference_coords-av2 # correlation matrix - a=matrixmultiply(transpose(coords), reference_coords) + a=dot(transpose(coords), reference_coords) u, d, vt=singular_value_decomposition(a) - self.rot=transpose(matrixmultiply(transpose(vt), transpose(u))) + self.rot=transpose(dot(transpose(vt), transpose(u))) # check if we have found a reflection if determinant(self.rot)<0: vt[2]=-vt[2] - self.rot=transpose(matrixmultiply(transpose(vt), transpose(u))) - self.tran=av2-matrixmultiply(av1, self.rot) + self.rot=transpose(dot(transpose(vt), transpose(u))) + self.tran=av2-dot(av1, self.rot) def get_transformed(self): "Get the transformed coordinate set." @@ -93,7 +93,7 @@ if self.rot is None: raise Exception, "Nothing superimposed yet." if self.transformed_coords is None: - self.transformed_coords=matrixmultiply(self.coords, self.rot)+self.tran + self.transformed_coords=dot(self.coords, self.rot)+self.tran return self.transformed_coords def get_rotran(self): @@ -120,7 +120,7 @@ if __name__=="__main__": - from Numeric import * + from Bio.numpy_wrapper import * # start with two coordinate sets (Nx3 arrays - Float0) @@ -151,7 +151,7 @@ rot, tran=sup.get_rotran() # rotate y on x - y_on_x1=matrixmultiply(y, rot)+tran + y_on_x1=dot(y, rot)+tran # same thing y_on_x2=sup.get_transformed() Index: Bio/Statistics/lowess.py =================================================================== RCS file: /home/repository/biopython/biopython/Bio/Statistics/lowess.py,v retrieving revision 1.2 diff -u -r1.2 lowess.py --- Bio/Statistics/lowess.py 3 Feb 2007 17:24:32 -0000 1.2 +++ Bio/Statistics/lowess.py 14 Mar 2007 15:45:11 -0000 @@ -11,8 +11,8 @@ """ try: - from Numeric import * - from LinearAlgebra import solve_linear_equations + from Bio.numpy_wrapper import * + from Bio.linear_algebra_wrapper import solve_linear_equations except ImportError, x: raise ImportError, "This module requires Numeric (precursor to NumPy) with the LinearAlgebra and MLab libraries" Index: Doc/install/Installation.html =================================================================== RCS file: /home/repository/biopython/biopython/Doc/install/Installation.html,v retrieving revision 1.9 diff -u -r1.9 Installation.html --- Doc/install/Installation.html 27 Sep 2006 03:50:07 -0000 1.9 +++ Doc/install/Installation.html 14 Mar 2007 15:45:11 -0000 @@ -301,14 +301,18 @@

3.2  Numerical Python

-The Numerical Python distribution (also known an Numeric or Numpy) is a -fast implementation of arrays and associated array functionality. This -is important for a number of Biopython modules that deal with -number processing. The main web site for Numeric is: +The Numerical Python distribution is a fast implementation of arrays and +associated array functionality. This is important for a number of Biopython +modules that deal with array processing. BioPython supports both the older +Numeric package, which is mature but now deprecated, and the newer NumPy +package, which is more efficient and offers new functionality. + +The main web site for both Numeric and NumPy is: http://sourceforge.net/projects/numpy and downloads are available from: http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351.

+

3.2.1  UNIX and Mac OS X systems

Index: Tests/test_Cluster.py =================================================================== RCS file: /home/repository/biopython/biopython/Tests/test_Cluster.py,v retrieving revision 1.6 diff -u -r1.6 test_Cluster.py --- Tests/test_Cluster.py 27 Feb 2007 17:42:00 -0000 1.6 +++ Tests/test_Cluster.py 14 Mar 2007 15:45:11 -0000 @@ -1,4 +1,4 @@ -from Numeric import * +from Bio.numpy_wrapper import * def print_row(data): print "[", Index: Tests/test_MarkovModel.py =================================================================== RCS file: /home/repository/biopython/biopython/Tests/test_MarkovModel.py,v retrieving revision 1.1 diff -u -r1.1 test_MarkovModel.py --- Tests/test_MarkovModel.py 11 Aug 2002 04:38:15 -0000 1.1 +++ Tests/test_MarkovModel.py 14 Mar 2007 15:45:11 -0000 @@ -4,7 +4,7 @@ from operator import truth from Bio import MarkovModel -from Numeric import ones, zeros, log, asarray +from Bio.numpy_wrapper import ones, zeros, log, asarray def print_mm(markov_model): print "STATES: %s" % ' '.join(markov_model.states) Index: Tests/test_SVDSuperimposer.py =================================================================== RCS file: /home/repository/biopython/biopython/Tests/test_SVDSuperimposer.py,v retrieving revision 1.2 diff -u -r1.2 test_SVDSuperimposer.py --- Tests/test_SVDSuperimposer.py 11 Aug 2002 04:23:08 -0000 1.2 +++ Tests/test_SVDSuperimposer.py 14 Mar 2007 15:45:11 -0000 @@ -1,4 +1,4 @@ -from Numeric import * +from Bio.numpy_wrapper import * from Bio.SVDSuperimposer import * @@ -30,7 +30,7 @@ rot, tran=sup.get_rotran() # rotate y on x manually -y_on_x1=matrixmultiply(y, rot)+tran +y_on_x1=dot(y, rot)+tran # same thing y_on_x2=sup.get_transformed()