Merge branch 't/29785/move_extension_options_from_src_module_list_py_…

…to__distutils___directives_in_the_individual_files__part_3__get_rid_of_uname_specific_' into t/29847/install_sage_setup_with_pip__move_sage_include_directories__cython_aliases_from_sage_env_to_sage_setup

src/sage/algebras/quatalg/quaternion_algebra_cython.pyx

@@ -1,3 +1,5 @@
+# distutils: language = c++
+# distutils: libraries = gmp m ntl
 """
 Optimized Cython code needed by quaternion algebras
 

src/sage/algebras/quatalg/quaternion_algebra_element.pyx

@@ -1,3 +1,5 @@
+# distutils: language = c++
+# distutils: libraries = gmp m ntl
 """
 Elements of Quaternion Algebras
 

src/sage/env.py

@@ -381,47 +381,46 @@ def cython_aliases():
         {...}
         sage: sorted(cython_aliases().keys())
         ['ARB_LIBRARY',
-         'FFLASFFPACK_CFLAGS',
-         'FFLASFFPACK_INCDIR',
-         'FFLASFFPACK_LIBDIR',
-         'FFLASFFPACK_LIBEXTRA',
-         'FFLASFFPACK_LIBRARIES',
-         'GIVARO_CFLAGS',
-         'GIVARO_INCDIR',
-         'GIVARO_LIBDIR',
-         'GIVARO_LIBEXTRA',
-         'GIVARO_LIBRARIES',
-         'GSL_CFLAGS',
-         'GSL_INCDIR',
-         'GSL_LIBDIR',
-         'GSL_LIBEXTRA',
-         'GSL_LIBRARIES',
-         'LINBOX_CFLAGS',
-         'LINBOX_INCDIR',
-         'LINBOX_LIBDIR',
-         'LINBOX_LIBEXTRA',
-         'LINBOX_LIBRARIES',
-         'SINGULAR_CFLAGS',
-         'SINGULAR_INCDIR',
-         'SINGULAR_LIBDIR',
-         'SINGULAR_LIBEXTRA',
-         'SINGULAR_LIBRARIES']
+         'CBLAS_CFLAGS',
+         ...,
+         'ZLIB_LIBRARIES']
     """
     import pkgconfig
 
     aliases = {}
 
-    for lib in ['fflas-ffpack', 'givaro', 'gsl', 'linbox', 'Singular']:
+    for lib in ['fflas-ffpack', 'givaro', 'gsl', 'linbox', 'Singular',
+                'libpng', 'gdlib', 'm4ri', 'zlib', 'cblas', 'lapack']:
         var = lib.upper().replace("-", "") + "_"
-        aliases[var + "CFLAGS"] = pkgconfig.cflags(lib).split()
-        pc = pkgconfig.parse(lib)
+        if lib == 'zlib':
+            aliases[var + "CFLAGS"] = ""
+            try:
+                pc = pkgconfig.parse('zlib')
+            except pkgconfig.PackageNotFoundError:
+                from collections import defaultdict
+                pc = defaultdict(list, {'libraries': ['z']})
+        else:
+            aliases[var + "CFLAGS"] = pkgconfig.cflags(lib).split()
+            pc = pkgconfig.parse(lib)
         # INCDIR should be redundant because the -I options are also
         # passed in CFLAGS
         aliases[var + "INCDIR"] = pc['include_dirs']
         aliases[var + "LIBDIR"] = pc['library_dirs']
         aliases[var + "LIBEXTRA"] = list(filter(lambda s: not s.startswith(('-l','-L')), pkgconfig.libs(lib).split()))
         aliases[var + "LIBRARIES"] = pc['libraries']
 
+    # uname-specific flags
+    UNAME = os.uname()
+
+    def uname_specific(name, value, alternative):
+        if name in UNAME[0]:
+            return value
+        else:
+            return alternative
+
+    aliases["LINUX_NOEXECSTACK"] = uname_specific("Linux", ["-Wl,-z,noexecstack"],
+                                                  [])
+
     # LinBox needs special care because it actually requires C++11 with
     # GNU extensions: -std=c++11 does not work, you need -std=gnu++11
     # (this is true at least with GCC 7.2.0).
@@ -432,4 +431,14 @@ def cython_aliases():
     # fflas-ffpack and fflas-ffpack does add such a C++11 flag.
     aliases["LINBOX_CFLAGS"].append("-std=gnu++11")
     aliases["ARB_LIBRARY"] = ARB_LIBRARY
+
+    # TODO: Remove Cygwin hack by installing a suitable cblas.pc
+    if os.path.exists('/usr/lib/libblas.dll.a'):
+        aliases["CBLAS_LIBS"] = ['gslcblas']
+
+    try:
+        aliases["M4RI_CFLAGS"].remove("-pedantic")
+    except ValueError:
+        pass
+
     return aliases

src/sage/geometry/polyhedron/combinatorial_polyhedron/combinatorial_face.pyx

@@ -1,3 +1,7 @@
+# distutils: depends = sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc
+# distutils: language = c++
+# distutils: extra_compile_args = -std=c++11
+
 r"""
 Combinatorial face of a polyhedron
 

src/sage/geometry/polyhedron/combinatorial_polyhedron/face_iterator.pyx

@@ -1,3 +1,7 @@
+# distutils: depends = sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc
+# distutils: language = c++
+# distutils: extra_compile_args = -std=c++11
+
 r"""
 Face iterator for polyhedra
 

src/sage/geometry/polyhedron/combinatorial_polyhedron/list_of_faces.pyx

@@ -1,3 +1,7 @@
+# distutils: depends = sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc
+# distutils: language = c++
+# distutils: extra_compile_args = -std=c++11
+
 r"""
 List of faces
 

src/sage/geometry/polyhedron/combinatorial_polyhedron/polyhedron_face_lattice.pyx

@@ -1,3 +1,7 @@
+# distutils: depends = sage/geometry/polyhedron/combinatorial_polyhedron/bit_vector_operations.cc
+# distutils: language = c++
+# distutils: extra_compile_args = -std=c++11
+
 r"""
 PolyhedronFaceLattice
 

src/sage/geometry/triangulation/base.pyx

@@ -1,3 +1,7 @@
+# distutils: sources = sage/geometry/triangulation/functions.cc sage/geometry/triangulation/data.cc sage/geometry/triangulation/triangulations.cc
+# distutils: depends = sage/geometry/triangulation/functions.h sage/geometry/triangulation/data.h sage/geometry/triangulation/triangulations.h
+# distutils: language = c++
+
 r"""
 Base classes for triangulations
 

src/sage/libs/libecm.pyx

@@ -1,3 +1,5 @@
+# distutils: libraries = ecm
+# distutils: extra_link_args = LINUX_NOEXECSTACK
 r"""
 The Elliptic Curve Method for Integer Factorization (ECM)
 

src/sage/libs/ntl/convert.pyx

@@ -1,4 +1,7 @@
 # distutils: depends = NTL/ZZ.h
+# distutils: libraries = ntl gmp
+# distutils: language = c++
+
 """
 Conversion between NTL's ``ZZ`` and various other types
 """

src/sage/libs/ntl/error.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp
+# distutils: language = c++
+
 """
 NTL error handler
 

src/sage/libs/ntl/ntl_GF2.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2007 Martin Albrecht <[email protected]>
 #

src/sage/libs/ntl/ntl_GF2E.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #       Copyright (C) 2007 Martin Albrecht <[email protected]>

src/sage/libs/ntl/ntl_GF2EContext.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_GF2EX.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_GF2X.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 # ****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #       Copyright (C) 2007 Martin Albrecht <[email protected]>

src/sage/libs/ntl/ntl_ZZ.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_ZZX.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_ZZ_p.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_ZZ_pContext.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_ZZ_pE.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_ZZ_pEContext.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_ZZ_pEX.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 """
 Wrapper for NTL's polynomials over finite ring extensions of $\Z / p\Z.$
 

src/sage/libs/ntl/ntl_ZZ_pX.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 # ****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_lzz_p.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 """
 ntl_lzz_p.pyx
 

src/sage/libs/ntl/ntl_lzz_pContext.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_lzz_pX.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 """
 ntl_lzz_pX.pyx
 

src/sage/libs/ntl/ntl_mat_GF2.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 """
 Matrices over the $\GF{2}$ via NTL
 

src/sage/libs/ntl/ntl_mat_GF2E.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/libs/ntl/ntl_mat_ZZ.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = ntl gmp m
+# distutils: language = c++
+
 #*****************************************************************************
 #       Copyright (C) 2005 William Stein <[email protected]>
 #

src/sage/modular/modsym/apply.pyx

@@ -1,3 +1,5 @@
+# distutils: extra_compile_args = -D_XPG6
+
 """
 Monomial expansion of `(aX + bY)^i (cX + dY)^{j-i}`
 """

src/sage/modular/modsym/heilbronn.pyx

@@ -1,3 +1,5 @@
+# distutils: extra_compile_args = -D_XPG6
+
 """
 Heilbronn matrix computation
 """

src/sage/modular/modsym/p1list.pyx

@@ -1,3 +1,6 @@
+# distutils: libraries = gmp zn_poly
+# distutils: extra_compile_args = -D_XPG6
+
 r"""
 Lists of Manin symbols (elements of `\mathbb{P}^1(\ZZ/N\ZZ)`) over `\QQ`
 """

src/sage/modular/pollack_stevens/dist.pyx

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+# distutils: libraries = gmp zn_poly
+# distutils: extra_compile_args = -D_XPG6
 """
 `p`-adic distributions spaces
 

src/sage/modules/vector_mod2_dense.pyx

@@ -1,3 +1,8 @@
+# distutils: libraries = M4RI_LIBRARIES GDLIB_LIBRARIES LIBPNG_LIBRARIES
+# distutils: library_dirs = M4RI_LIBDIR GDLIB_LIBDIR LIBPNG_LIBDIR
+# distutils: include_dirs = M4RI_INCDIR GDLIB_INCDIR LIBPNG_INCDIR
+# distutils: extra_compile_args = M4RI_CFLAGS
+
 """
 Vectors with elements in GF(2)
 

src/sage/schemes/elliptic_curves/descent_two_isogeny.pyx

@@ -1,3 +1,5 @@
+# distutils: libraries = ratpoints
+
 r"""
 Descent on elliptic curves over `\QQ` with a 2-isogeny
 """

src/sage/schemes/hyperelliptic_curves/hypellfrob.pyx

@@ -1,3 +1,9 @@
+# distutils: language = c++
+# distutils: sources = sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.cpp sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.cpp sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.cpp
+# distutils: depends = sage/schemes/hyperelliptic_curves/hypellfrob/hypellfrob.h sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_ntl.h sage/schemes/hyperelliptic_curves/hypellfrob/recurrences_zn_poly.h
+# distutils: include_dirs = sage/libs/ntl/ sage/schemes/hyperelliptic_curves/hypellfrob/
+# distutils: libraries = gmp ntl zn_poly
+
 r"""
 Frobenius on Monsky-Washnitzer cohomology of a hyperelliptic curve over a
 largish prime finite field

src/sage/stats/distributions/discrete_gaussian_integer.pyx

@@ -1,4 +1,9 @@
 # -*- coding: utf-8 -*-
+#
+# distutils: sources = sage/stats/distributions/dgs_gauss_mp.c sage/stats/distributions/dgs_gauss_dp.c sage/stats/distributions/dgs_bern.c
+# distutils: depends = sage/stats/distributions/dgs_gauss.h sage/stats/distributions/dgs_bern.h sage/stats/distributions/dgs_misc.h
+# distutils: extra_compile_args = -D_XOPEN_SOURCE=600
+
 r"""
 Discrete Gaussian Samplers over the Integers
 

src/sage/structure/element.pyx

@@ -1,3 +1,9 @@
+# Compile this with -Os because it works around a bug with
+# GCC-4.7.3 + Cython 0.19 on Itanium, see Trac #14452. Moreover, it
+# actually results in faster code than -O3.
+#
+# distutils: extra_compile_args = -Os
+
 r"""
 Elements
 

src/sage/tests/stl_vector.pyx

@@ -1,3 +1,5 @@
+# distutils: language = c++
+
 """
 Example of a class wrapping an STL vector