Merge branch 'lapack-imports' into master.

Review at scipy#358.

Author: Ralf Gommers

doc/API.rst.txt

@@ -104,6 +104,9 @@ change is made.
 
 * scipy.linalg
 
+  - scipy.linalg.blas
+  - scipy.linalg.lapack
+
 * scipy.misc
 
 * scipy.ndimage

doc/release/0.12.0-notes.rst

@@ -43,7 +43,6 @@ exactly the same interface as KDTree, and can be used as a drop-in replacement.
 -------------------------------
 A callback mechanism was added to L-BFGS-B and TNC minimization solvers.
 
-
 Complex error functions in ``scipy.special``
 --------------------------------------------
 The computation of special functions related to the error function now uses a
@@ -63,10 +62,27 @@ Evaluation of orthogonal polynomials (the ``eval_*`` routines) in now
 faster in ``scipy.special``, and their ``out=`` argument functions
 properly.
 
+Documented BLAS and LAPACK low-level interfaces
+-----------------------------------------------
+The modules `scipy.linalg.blas` and `scipy.linalg.lapack` can be used
+to access low-level BLAS and LAPACK functions.
+
 
 Deprecated features
 ===================
 
+`scipy.lib.lapack`
+------------------
+The module `scipy.lib.lapack` is deprecated. You can use
+`scipy.linalg.lapack` instead. The module `scipy.lib.blas` was
+deprecated earlier in Scipy 0.10.0.
+
+`fblas` and `cblas`
+-------------------
+Accessing the modules `scipy.linalg.fblas`, `cblas`, `flapack`,
+`clapack` is deprecated. Instead, use the modules
+`scipy.linalg.lapack` and `scipy.linalg.blas`.
+
 
 Backwards incompatible changes
 ==============================

doc/source/linalg.blas.rst

@@ -0,0 +1 @@
+.. automodule:: scipy.linalg.blas

doc/source/linalg.lapack.rst

@@ -0,0 +1 @@
+.. automodule:: scipy.linalg.lapack

doc/source/linalg.rst

@@ -1 +1,7 @@
 .. automodule:: scipy.linalg
+
+.. toctree::
+   :hidden:
+
+   linalg.blas
+   linalg.lapack

scipy/lib/blas/__init__.py

@@ -2,6 +2,8 @@
 Wrappers to BLAS library
 ========================
 
+NOTE: this module is deprecated -- use scipy.linalg.blas instead!
+
 fblas -- wrappers for Fortran [*] BLAS routines
 cblas -- wrappers for ATLAS BLAS routines
 get_blas_funcs -- query for wrapper functions.
@@ -88,6 +90,15 @@
 
 from numpy import deprecate
 
+@deprecate(old_name="scipy.lib.blas", new_name="scipy.linalg.blas")
+def _deprecated():
+    pass
+try:
+    _deprecated()
+except DeprecationWarning, e:
+    # don't fail import if DeprecationWarnings raise error -- works around
+    # the situation with Numpy's test framework
+    pass
 
 _use_force_cblas = 1
 if hasattr(cblas,'empty_module'):

scipy/lib/lapack/__init__.py

@@ -2,6 +2,8 @@
 Wrappers to LAPACK library
 ==========================
 
+NOTE: this module is deprecated -- use scipy.linalg.lapack instead!
+
   flapack -- wrappers for Fortran [*] LAPACK routines
   clapack -- wrappers for ATLAS LAPACK routines
   calc_lwork -- calculate optimal lwork parameters
@@ -137,17 +139,27 @@
 
 __all__ = ['get_lapack_funcs','calc_lwork','flapack','clapack']
 
+from numpy import deprecate
 
 import calc_lwork
 
 # The following ensures that possibly missing flavor (C or Fortran) is
 # replaced with the available one. If none is available, exception
 # is raised at the first attempt to use the resources.
 
+@deprecate(old_name="scipy.lib.lapack", new_name="scipy.linalg.lapack")
+def _deprecated():
+    pass
+try:
+    _deprecated()
+except DeprecationWarning, e:
+    # don't fail import if DeprecationWarnings raise error -- works around
+    # the situation with Numpy's test framework
+    pass
+
 import flapack
 import clapack
 
-
 _use_force_clapack = 1
 if hasattr(clapack,'empty_module'):
     clapack = flapack
@@ -159,7 +171,7 @@
 _type_conv = {'f':'s', 'd':'d', 'F':'c', 'D':'z'} # 'd' will be default for 'i',..
 _inv_type_conv = {'s':'f','d':'d','c':'F','z':'D'}
 
-
+@deprecate
 def get_lapack_funcs(names,arrays=(),debug=0,force_clapack=1):
     """Return available LAPACK function objects with names.
     arrays are used to determine the optimal prefix of

scipy/linalg/__init__.py

@@ -126,6 +126,18 @@
    toeplitz - Toeplitz matrix
    tri - Construct a matrix filled with ones at and below a given diagonal
 
+Low-level routines
+==================
+
+.. autosummary::
+   :toctree: generated/
+
+   get_blas_funcs
+   get_lapack_funcs
+   find_best_blas_type
+   scipy.linalg.blas
+   scipy.linalg.lapack
+
 """
 
 from linalg_version import linalg_version as __version__
@@ -141,6 +153,7 @@
 from decomp_schur import *
 from matfuncs import *
 from blas import *
+from lapack import *
 from special_matrices import *
 from _solvers import *
 

scipy/linalg/basic.py

@@ -356,31 +356,18 @@ def inv(a, overwrite_a=False, check_finite=True):
 ##         if info<0: raise ValueError,\
 ##            'illegal value in %d-th argument of internal inv.getrf|getri'%(-info)
     getrf, getri = get_lapack_funcs(('getrf','getri'), (a1,))
-    #XXX: C ATLAS versions of getrf/i have rowmajor=1, this could be
-    #     exploited for further optimization. But it will be probably
-    #     a mess. So, a good testing site is required before trying
-    #     to do that.
-    if getrf.module_name[:7] == 'clapack' != getri.module_name[:7]:
-        # ATLAS 3.2.1 has getrf but not getri.
-        lu, piv, info = getrf(np.transpose(a1), rowmajor=0,
-                                                overwrite_a=overwrite_a)
-        lu = np.transpose(lu)
-    else:
-        lu, piv, info = getrf(a1, overwrite_a=overwrite_a)
+    lu, piv, info = getrf(a1, overwrite_a=overwrite_a)
     if info == 0:
-        if getri.module_name[:7] == 'flapack':
-            lwork = calc_lwork.getri(getri.prefix, a1.shape[0])
-            lwork = lwork[1]
-            # XXX: the following line fixes curious SEGFAULT when
-            # benchmarking 500x500 matrix inverse. This seems to
-            # be a bug in LAPACK ?getri routine because if lwork is
-            # minimal (when using lwork[0] instead of lwork[1]) then
-            # all tests pass. Further investigation is required if
-            # more such SEGFAULTs occur.
-            lwork = int(1.01 * lwork)
-            inv_a, info = getri(lu, piv, lwork=lwork, overwrite_lu=1)
-        else: # clapack
-            inv_a, info = getri(lu, piv, overwrite_lu=1)
+        lwork = calc_lwork.getri(getri.typecode, a1.shape[0])
+        lwork = lwork[1]
+        # XXX: the following line fixes curious SEGFAULT when
+        # benchmarking 500x500 matrix inverse. This seems to
+        # be a bug in LAPACK ?getri routine because if lwork is
+        # minimal (when using lwork[0] instead of lwork[1]) then
+        # all tests pass. Further investigation is required if
+        # more such SEGFAULTs occur.
+        lwork = int(1.01 * lwork)
+        inv_a, info = getri(lu, piv, lwork=lwork, overwrite_lu=1)
     if info > 0:
         raise LinAlgError("singular matrix")
     if info < 0:
@@ -531,16 +518,14 @@ def lstsq(a, b, cond=None, overwrite_a=False, overwrite_b=False,
 
     overwrite_a = overwrite_a or _datacopied(a1, a)
     overwrite_b = overwrite_b or _datacopied(b1, b)
-    if gelss.module_name[:7] == 'flapack':
-        # get optimal work array
-        work = gelss(a1, b1, lwork=-1)[4]
-        lwork = work[0].real.astype(np.int)
-        v, x, s, rank, work, info = gelss(
-            a1, b1, cond=cond, lwork=lwork, overwrite_a=overwrite_a,
-            overwrite_b=overwrite_b)
 
-    else:
-        raise NotImplementedError('calling gelss from %s' % gelss.module_name)
+    # get optimal work array
+    work = gelss(a1, b1, lwork=-1)[4]
+    lwork = work[0].real.astype(np.int)
+    v, x, s, rank, work, info = gelss(
+        a1, b1, cond=cond, lwork=lwork, overwrite_a=overwrite_a,
+        overwrite_b=overwrite_b)
+
     if info > 0:
         raise LinAlgError("SVD did not converge in Linear Least Squares")
     if info < 0:

scipy/linalg/bento.info

@@ -1,17 +1,17 @@
 HookFile: bscript
 
 Library:
-    Extension: fblas
+    Extension: _fblas
         Sources:
             fblas.pyf.src,
             src/fblaswrap.f
-    Extension: cblas
+    Extension: _cblas
         Sources:
             generic_cblas.pyf
-    Extension: flapack
+    Extension: _flapack
         Sources:
             flapack.pyf.src
-    Extension: clapack
+    Extension: _clapack
         Sources:
             generic_clapack.pyf
     Extension: _flinalg