Merge pull request #1179 from Daetalus/numpy_update_2

Remove numpy submodule

.gitmodules

@@ -31,9 +31,6 @@
 [submodule "build_deps/jemalloc"]
 	path = build_deps/jemalloc
 	url = git://github.com/jemalloc/jemalloc.git
-[submodule "test/lib/numpy"]
-	path = test/lib/numpy
-	url = https://github.com/numpy/numpy
 [submodule "test/lib/decorator"]
 	path = test/lib/decorator
 	url = https://github.com/micheles/decorator

test/integration/numpy_patch.patch

 diff --git a/numpy/core/src/multiarray/compiled_base.c b/numpy/core/src/multiarray/compiled_base.c
-index 8ffeeda..5d43aab 100644
+index b9db3bb..2d24efc 100644
 --- a/numpy/core/src/multiarray/compiled_base.c
 +++ b/numpy/core/src/multiarray/compiled_base.c
-@@ -1336,13 +1336,13 @@ arr_add_docstring(PyObject *NPY_UNUSED(dummy), PyObject *args)
+@@ -1337,13 +1337,13 @@ arr_add_docstring(PyObject *NPY_UNUSED(dummy), PyObject *args)
          _ADDDOC(Type, new->tp_doc, new->tp_name);
      }
      else if (_TESTDOC2(MemberDescr)) {
 -        _ADDDOC(MemberDescr, new->d_member->doc, new->d_member->name);
-+        //_ADDDOC(MemberDescr, new->d_member->doc, new->d_member->name);
++        /* _ADDDOC(MemberDescr, new->d_member->doc, new->d_member->name); */
      }
      else if (_TESTDOC2(GetSetDescr)) {
 -        _ADDDOC(GetSetDescr, new->d_getset->doc, new->d_getset->name);
-+        //_ADDDOC(GetSetDescr, new->d_getset->doc, new->d_getset->name);
++        /* _ADDDOC(GetSetDescr, new->d_getset->doc, new->d_getset->name); */
      }
      else if (_TESTDOC2(MethodDescr)) {
 -        _ADDDOC(MethodDescr, new->d_method->ml_doc, new->d_method->ml_name);
-+        //_ADDDOC(MethodDescr, new->d_method->ml_doc, new->d_method->ml_name);
++        /* _ADDDOC(MethodDescr, new->d_method->ml_doc, new->d_method->ml_name); */
      }
      else {
          PyObject *doc_attr;
-diff --git a/numpy/core/src/multiarray/descriptor.c b/numpy/core/src/multiarray/descriptor.c
-index d025901..27c8718 100644
---- a/numpy/core/src/multiarray/descriptor.c
-+++ b/numpy/core/src/multiarray/descriptor.c
-@@ -1051,6 +1051,11 @@ _convert_from_dict(PyObject *obj, int align)
-                         "with align=True",
-                         (int)offset, (int)newdescr->alignment);
-                 ret = NPY_FAIL;
-+
-+                // Pyston change: we don't deal well with execution continuing
-+                // after an exception has been set. Subsequent calls to GetItem and
-+                // such happen with the exception set (PyErr_Occurred() == true).
-+                goto fail;
-             }
-             else if (offset + newdescr->elsize > totalsize) {
-                 totalsize = offset + newdescr->elsize;
-@@ -1079,6 +1084,11 @@ _convert_from_dict(PyObject *obj, int align)
-             PyErr_SetString(PyExc_ValueError,
-                     "field names must be strings");
-             ret = NPY_FAIL;
-+
-+            // Pyston change: we don't deal well with execution continuing
-+            // after an exception has been set. Subsequent calls to GetItem and
-+            // such happen with the exception set (PyErr_Occurred() == true).
-+            goto fail;
-         }
- 
-         /* Insert into dictionary */
-@@ -1086,6 +1096,11 @@ _convert_from_dict(PyObject *obj, int align)
-             PyErr_SetString(PyExc_ValueError,
-                     "name already used as a name or title");
-             ret = NPY_FAIL;
-+
-+            // Pyston change: we don't deal well with execution continuing
-+            // after an exception has been set. Subsequent calls to GetItem and
-+            // such happen with the exception set (PyErr_Occurred() == true).
-+            goto fail;
-         }
-         PyDict_SetItem(fields, name, tup);
-         Py_DECREF(name);
-@@ -1099,6 +1114,11 @@ _convert_from_dict(PyObject *obj, int align)
-                     PyErr_SetString(PyExc_ValueError,
-                             "title already used as a name or title.");
-                     ret=NPY_FAIL;
-+
-+                    // Pyston change: we don't deal well with execution continuing
-+                    // after an exception has been set. Subsequent calls to GetItem and
-+                    // such happen with the exception set (PyErr_Occurred() == true).
-+                    goto fail;
-                 }
-                 PyDict_SetItem(fields, title, tup);
-             }
-diff --git a/numpy/core/tests/test_records.py b/numpy/core/tests/test_records.py
-index 7a18f29..a8d4e4b 100644
---- a/numpy/core/tests/test_records.py
-+++ b/numpy/core/tests/test_records.py
-@@ -12,7 +12,7 @@ from numpy.testing import (
-     assert_array_almost_equal, assert_raises
+diff --git a/setup.py b/setup.py
+index cc8f3c1..d3f89f6 100755
+--- a/setup.py
++++ b/setup.py
+@@ -352,6 +352,7 @@ def setup_package():
+         platforms = ["Windows", "Linux", "Solaris", "Mac OS-X", "Unix"],
+         test_suite='nose.collector',
+         cmdclass={"sdist": sdist_checked},
++        zip_safe=False,
      )
  
--
-+"""
- class TestFromrecords(TestCase):
-     def test_fromrecords(self):
-         r = np.rec.fromrecords([[456, 'dbe', 1.2], [2, 'de', 1.3]],
-@@ -294,6 +294,6 @@ def test_find_duplicate():
- 
-     l3 = [2, 2, 1, 4, 1, 6, 2, 3]
-     assert_(np.rec.find_duplicate(l3) == [2, 1])
--
-+"""
- if __name__ == "__main__":
-     run_module_suite()
-diff --git a/numpy/lib/tests/test_io.py b/numpy/lib/tests/test_io.py
-index f4ce678..56f5cd9 100644
---- a/numpy/lib/tests/test_io.py
-+++ b/numpy/lib/tests/test_io.py
-@@ -885,7 +885,8 @@ class Testfromregex(TestCase):
- 
- #####--------------------------------------------------------------------------
- 
--
-+# Pyston: these don't work, segfault, not sure why
-+"""
- class TestFromTxt(TestCase):
-     #
-     def test_record(self):
-@@ -1822,6 +1823,7 @@ M   33  21.99
-         assert_allclose(test['f0'], 73786976294838206464.)
-         assert_equal(test['f1'], 17179869184)
-         assert_equal(test['f2'], 1024)
-+"""
- 
- def test_gzip_load():
-     a = np.random.random((5, 5))
-diff --git a/numpy/ma/tests/test_core.py b/numpy/ma/tests/test_core.py
-index d3ec704..d68ffb0 100644
---- a/numpy/ma/tests/test_core.py
-+++ b/numpy/ma/tests/test_core.py
-@@ -1433,7 +1433,12 @@ class TestMaskedArrayAttributes(TestCase):
-         def assign():
-             m = np.ma.array(a)
-             m.dtype = np.dtype('f8')
--        assert_raises(ValueError, assign)
-+
-+        # Pyston: Some weirdness here with a jitted frame calling a C function
-+# that raises an exception in C-style, and the exception is still set as we
-+# return from the jitted function, causing an assertion to be triggered. Also,
-+# this happens with a with context catching the exception and stuff. I have no idea.
-+#assert_raises(ValueError, assign)
- 
-         b = a.view(dtype='f4', type=np.ma.MaskedArray)  # raises?
-         assert_equal(b.dtype, np.dtype('f4'))
-diff --git a/numpy/ma/tests/test_regression.py b/numpy/ma/tests/test_regression.py
-index dba74d3..23cfeed 100644
---- a/numpy/ma/tests/test_regression.py
-+++ b/numpy/ma/tests/test_regression.py
-@@ -35,7 +35,8 @@ class TestRegression(TestCase):
-         a[2, 0] = np.ma.masked
-         b = np.zeros((4, 2))
-         a*b
--        b*a
-+        # Pyston: commented out for now, causes assertion to be triggered.
-+        # b*a
- 
-     def test_masked_array_repeat(self, level=rlevel):
-         # Ticket #271
+     if "--force" in sys.argv:

test/integration/numpy_test.py

@@ -60,7 +60,7 @@ if not os.path.exists(ENV_NAME) or os.stat(sys.executable).st_mtime > os.stat(EN
 SRC_DIR = ENV_NAME
 PYTHON_EXE = os.path.abspath(ENV_NAME + "/bin/python")
 CYTHON_DIR = os.path.abspath(os.path.join(SRC_DIR, "Cython-0.22"))
-NUMPY_DIR = os.path.dirname(__file__) + "/../lib/numpy"
+NUMPY_DIR = os.path.abspath(os.path.join(SRC_DIR, "numpy"))
 
 print_progress_header("Setting up Cython...")
 if not os.path.exists(CYTHON_DIR):
@@ -82,21 +82,32 @@ if not os.path.exists(CYTHON_DIR):
 else:
     print ">>> Cython already installed."
 
-print_progress_header("Patching NumPy...")
 NUMPY_PATCH_FILE = os.path.abspath(os.path.join(os.path.dirname(__file__), "numpy_patch.patch"))
+
+print_progress_header("Cloning up NumPy...")
+if not os.path.exists(NUMPY_DIR):
+    url = "https://github.com/numpy/numpy"
+    subprocess.check_call(["git", "clone", "--branch", "v1.11.0", url], cwd=SRC_DIR)
+else:
+    print ">>> NumPy already installed."
+
+PATCH_FILE = os.path.abspath(os.path.join(os.path.dirname(__file__), "numpy_patch.patch"))
+
+print_progress_header("Patching NumPy...")
+subprocess.check_call(["patch", "-p1", "--input=" + PATCH_FILE], cwd=NUMPY_DIR)
+
 try:
-    cmd = ["patch", "-p1", "--forward", "-i", NUMPY_PATCH_FILE, "-d", NUMPY_DIR]
-    subprocess.check_output(cmd, stderr=subprocess.STDOUT)
-except subprocess.CalledProcessError as e:
-    print e.output
-    if "Reversed (or previously applied) patch detected!  Skipping patch" not in e.output:
-        raise e
-
-print_progress_header("Setting up NumPy...")
-subprocess.check_call([PYTHON_EXE, "setup.py", "build"], cwd=NUMPY_DIR)
-
-print_progress_header("Installing NumPy...")
-subprocess.check_call([PYTHON_EXE, "setup.py", "install"], cwd=NUMPY_DIR)
+    env = os.environ
+    CYTHON_BIN_DIR = os.path.abspath(os.path.join(ENV_NAME + "/bin"))
+    env["PATH"] = CYTHON_BIN_DIR + ":" + env["PATH"]
+
+    print_progress_header("Setting up NumPy...")
+    subprocess.check_call([PYTHON_EXE, "setup.py", "build"], cwd=NUMPY_DIR, env=env)
+
+    print_progress_header("Installing NumPy...")
+    subprocess.check_call([PYTHON_EXE, "setup.py", "install"], cwd=NUMPY_DIR, env=env)
+except:
+    subprocess.check_call(["rm", "-rf", NUMPY_DIR])
 
 # From Wikipedia
 script = """

numpy @ e4d4b45d

-Subproject commit e4d4b45d26813899c66e112365896aabbb7b19fa