Merge pull request #85 from pymc-devs/fix-84

doc/tutorial/debug_faq.txt

@@ -607,7 +607,7 @@ Breakpoint during Theano function execution
 -------------------------------------------
 
 You can set a breakpoint during the execution of a Theano function with
-:class:`PdbBreakpoint <tests.breakpoint.PdbBreakpoint>`.
-:class:`PdbBreakpoint <tests.breakpoint.PdbBreakpoint>` automatically
+:class:`PdbBreakpoint <theano.breakpoint.PdbBreakpoint>`.
+:class:`PdbBreakpoint <theano.breakpoint.PdbBreakpoint>` automatically
 detects available debuggers and uses the first available in the following order:
 `pudb`, `ipdb`, or `pdb`.

setup.cfg

 [flake8]
 ignore=E501,E123,E133,FI12,FI14,FI15,FI50,FI51,FI53,W503,W504,E203,C901,E231,E741
 per-file-ignores =
-    theano/sparse/sandbox/truedot.py:F401
     theano/sparse/sandbox/sp2.py:F401
     tests/sparse/test_basic.py:E402
     tests/sparse/test_opt.py:E402

tests/gpuarray/test_basic_ops.py

@@ -32,7 +32,7 @@ from theano.gpuarray.subtensor import GpuSubtensor
 
 from tests import unittest_tools as utt
 from tests.gpuarray.config import mode_with_gpu, mode_without_gpu, test_ctx_name
-from tests.theano.tensor.test_basic import (
+from tests.tensor.test_basic import (
     rand,
     safe_make_node,
     TestAlloc,

tests/gpuarray/test_gemmcorr.py

@@ -9,11 +9,11 @@ from theano.gpuarray.blas import GpuCorrMM, GpuCorrMM_gradWeights, GpuCorrMM_gra
 
 from tests import unittest_tools as utt
 from tests.gpuarray.config import mode_with_gpu, mode_without_gpu, ref_cast
-from tests.theano.tensor.nnet.test_abstract_conv import (
+from tests.tensor.nnet.test_abstract_conv import (
     TestGroupedConvNoOptim,
     TestUnsharedConv,
 )
-from tests.tensor.nnet.theano.test_abstract_conv import (
+from tests.tensor.nnet.test_abstract_conv import (
     TestAsymmetricPadding,
     TestCausalConv,
 )

tests/gpuarray/test_opt.py

@@ -9,6 +9,7 @@ import theano.tensor.slinalg as slinalg
 from theano import tensor
 from theano.gof.opt import check_stack_trace
 from theano.tensor.nnet import abstract_conv
+from theano.breakpoint import PdbBreakpoint
 from theano.gpuarray import basic_ops
 from theano.gpuarray.type import GpuArrayType, gpuarray_shared_constructor, get_context
 from theano.gpuarray.basic_ops import (
@@ -34,7 +35,6 @@ from theano.gpuarray.linalg import GpuCusolverSolve, cusolver_available, GpuChol
 
 from tests import unittest_tools as utt, test_ifelse
 from tests.tensor import test_basic
-from tests.breakpoint import PdbBreakpoint
 from tests.gpuarray.config import mode_with_gpu, mode_without_gpu, test_ctx_name
 
 

tests/gpuarray/test_type.py

@@ -15,7 +15,7 @@ from tests.gpuarray.config import test_ctx_name
 from tests.gpuarray.test_basic_ops import rand_gpuarray
 
 # Disabled for now
-# from tests.theano.tensor.test_sharedvar import makeSharedTester
+# from tests.tensor.test_sharedvar import makeSharedTester
 
 
 def test_deep_copy():

tests/test_breakpoint.py

@@ -3,8 +3,9 @@ import numpy as np
 import theano
 import theano.tensor as T
 
+from theano.breakpoint import PdbBreakpoint
+
 from tests import unittest_tools as utt
-from tests.breakpoint import PdbBreakpoint
 
 
 class TestPdbBreakpoint(utt.InferShapeTester):

tests/unittest_tools.py

@@ -12,9 +12,9 @@ from functools import wraps
 from copy import copy, deepcopy
 
 from six import integer_types
-from six.moves import StringIO
 
 from theano import config
+from theano.compile.debugmode import str_diagnostic
 
 
 _logger = logging.getLogger("tests.unittest_tools")
@@ -282,71 +282,6 @@ class InferShapeTester:
             assert np.all(out.shape == shape), (out.shape, shape)
 
 
-def str_diagnostic(expected, value, rtol, atol):
-    """Return a pretty multiline string representating the cause
-    of the exception"""
-    sio = StringIO()
-
-    try:
-        ssio = StringIO()
-        print("           : shape, dtype, strides, min, max, n_inf, n_nan:", file=ssio)
-        print("  Expected :", end=" ", file=ssio)
-        print(expected.shape, end=" ", file=ssio)
-        print(expected.dtype, end=" ", file=ssio)
-        print(expected.strides, end=" ", file=ssio)
-        print(expected.min(), end=" ", file=ssio)
-        print(expected.max(), end=" ", file=ssio)
-        print(np.isinf(expected).sum(), end=" ", file=ssio)
-        print(np.isnan(expected).sum(), end=" ", file=ssio)
-        # only if all succeeds to we add anything to sio
-        print(ssio.getvalue(), file=sio)
-    except Exception:
-        pass
-    try:
-        ssio = StringIO()
-        print("  Value    :", end=" ", file=ssio)
-        print(value.shape, end=" ", file=ssio)
-        print(value.dtype, end=" ", file=ssio)
-        print(value.strides, end=" ", file=ssio)
-        print(value.min(), end=" ", file=ssio)
-        print(value.max(), end=" ", file=ssio)
-        print(np.isinf(value).sum(), end=" ", file=ssio)
-        print(np.isnan(value).sum(), end=" ", file=ssio)
-        # only if all succeeds to we add anything to sio
-        print(ssio.getvalue(), file=sio)
-    except Exception:
-        pass
-
-    print("  expected    :", expected, file=sio)
-    print("  value    :", value, file=sio)
-
-    try:
-        ov = np.asarray(expected)
-        nv = np.asarray(value)
-        ssio = StringIO()
-        absdiff = np.absolute(nv - ov)
-        print("  Max Abs Diff: ", np.max(absdiff), file=ssio)
-        print("  Mean Abs Diff: ", np.mean(absdiff), file=ssio)
-        print("  Median Abs Diff: ", np.median(absdiff), file=ssio)
-        print("  Std Abs Diff: ", np.std(absdiff), file=ssio)
-        reldiff = np.absolute(nv - ov) / np.absolute(ov)
-        print("  Max Rel Diff: ", np.max(reldiff), file=ssio)
-        print("  Mean Rel Diff: ", np.mean(reldiff), file=ssio)
-        print("  Median Rel Diff: ", np.median(reldiff), file=ssio)
-        print("  Std Rel Diff: ", np.std(reldiff), file=ssio)
-        # only if all succeeds to we add anything to sio
-        print(ssio.getvalue(), file=sio)
-    except Exception:
-        pass
-    atol_, rtol_ = T.basic._get_atol_rtol(expected, value)
-    if rtol is not None:
-        rtol_ = rtol
-    if atol is not None:
-        atol_ = atol
-    print("  rtol, atol:", rtol_, atol_, file=sio)
-    return sio.getvalue()
-
-
 class WrongValue(Exception):
     def __init__(self, expected_val, val, rtol, atol):
         Exception.__init__(self)  # to be compatible with python2.4

theano/__init__.py

@@ -165,10 +165,6 @@ from theano.updates import OrderedUpdates
 
 from theano.gradient import Rop, Lop, grad, subgraph_grad
 
-# This need to be before the init of GPU, as it add config variable
-# needed during that phase.
-import tests
-
 if (
     config.device.startswith("cuda")
     or config.device.startswith("opencl")

tests/breakpoint.py → theano/breakpoint.py

@@ -36,7 +36,7 @@ class PdbBreakpoint(Op):
 
         import theano
         import theano.tensor as T
-        from tests.breakpoint import PdbBreakpoint
+        from theano.breakpoint import PdbBreakpoint
 
         input = T.fvector()
         target = T.fvector()

theano/compile/debugmode.py

@@ -157,10 +157,7 @@ class BadThunkOutput(DebugModeError):
         print("  thunk1  :", self.thunk1, file=sio)
         print("  thunk2  :", self.thunk2, file=sio)
 
-        # Don't import it at the top of the file to prevent circular import.
-        import tests.unittest_tools as utt
-
-        print(utt.str_diagnostic(self.val1, self.val2, None, None), file=sio)
+        print(str_diagnostic(self.val1, self.val2, None, None), file=sio)
         ret = sio.getvalue()
         return ret
 
@@ -382,6 +379,71 @@ class InvalidValueError(DebugModeError):
 ########################
 
 
+def str_diagnostic(expected, value, rtol, atol):
+    """Return a pretty multiline string representating the cause
+    of the exception"""
+    sio = StringIO()
+
+    try:
+        ssio = StringIO()
+        print("           : shape, dtype, strides, min, max, n_inf, n_nan:", file=ssio)
+        print("  Expected :", end=" ", file=ssio)
+        print(expected.shape, end=" ", file=ssio)
+        print(expected.dtype, end=" ", file=ssio)
+        print(expected.strides, end=" ", file=ssio)
+        print(expected.min(), end=" ", file=ssio)
+        print(expected.max(), end=" ", file=ssio)
+        print(np.isinf(expected).sum(), end=" ", file=ssio)
+        print(np.isnan(expected).sum(), end=" ", file=ssio)
+        # only if all succeeds to we add anything to sio
+        print(ssio.getvalue(), file=sio)
+    except Exception:
+        pass
+    try:
+        ssio = StringIO()
+        print("  Value    :", end=" ", file=ssio)
+        print(value.shape, end=" ", file=ssio)
+        print(value.dtype, end=" ", file=ssio)
+        print(value.strides, end=" ", file=ssio)
+        print(value.min(), end=" ", file=ssio)
+        print(value.max(), end=" ", file=ssio)
+        print(np.isinf(value).sum(), end=" ", file=ssio)
+        print(np.isnan(value).sum(), end=" ", file=ssio)
+        # only if all succeeds to we add anything to sio
+        print(ssio.getvalue(), file=sio)
+    except Exception:
+        pass
+
+    print("  expected    :", expected, file=sio)
+    print("  value    :", value, file=sio)
+
+    try:
+        ov = np.asarray(expected)
+        nv = np.asarray(value)
+        ssio = StringIO()
+        absdiff = np.absolute(nv - ov)
+        print("  Max Abs Diff: ", np.max(absdiff), file=ssio)
+        print("  Mean Abs Diff: ", np.mean(absdiff), file=ssio)
+        print("  Median Abs Diff: ", np.median(absdiff), file=ssio)
+        print("  Std Abs Diff: ", np.std(absdiff), file=ssio)
+        reldiff = np.absolute(nv - ov) / np.absolute(ov)
+        print("  Max Rel Diff: ", np.max(reldiff), file=ssio)
+        print("  Mean Rel Diff: ", np.mean(reldiff), file=ssio)
+        print("  Median Rel Diff: ", np.median(reldiff), file=ssio)
+        print("  Std Rel Diff: ", np.std(reldiff), file=ssio)
+        # only if all succeeds to we add anything to sio
+        print(ssio.getvalue(), file=sio)
+    except Exception:
+        pass
+    atol_, rtol_ = theano.tensor.basic._get_atol_rtol(expected, value)
+    if rtol is not None:
+        rtol_ = rtol
+    if atol is not None:
+        atol_ = atol
+    print("  rtol, atol:", rtol_, atol_, file=sio)
+    return sio.getvalue()
+
+
 def char_from_number(number):
     """
     Converts number to string by rendering it in base 26 using

theano/gpuarray/opt.py

@@ -51,7 +51,7 @@ import theano.tensor.signal.pool as pool
 import theano.tensor.slinalg as slinalg
 from collections import Counter
 
-from tests.breakpoint import PdbBreakpoint
+from theano.breakpoint import PdbBreakpoint
 
 from .type import (
     GpuArrayType,

theano/sandbox/cuda/__init__.py

-import pytest
-
-pytest.skip(
-    "You are importing theano.sandbox.cuda. This is the old GPU back-end and "
-    "is removed from Theano. Use Theano 0.9 to use it. Even better, "
-    "transition to the new GPU back-end! See "
-    "https://github.com/Theano/Theano/wiki/Converting-to-the-new-gpu-back-end%28gpuarray%29",
-    allow_module_level=True,
-)

theano/sparse/sandbox/truedot.py

-import theano
-import numpy as np
-import scipy.sparse as sp
-
-from theano import sparse
-from theano import gof, tensor, compile
-
-from theano.sparse.basic import (
-    _is_sparse_variable,
-    _is_dense_variable,
-    as_sparse_variable,
-    _is_sparse,
-    _mtypes,
-    _mtype_to_str,
-)
-from theano.sparse import SparseType, dense_from_sparse, transpose
-
-from tests import unittest_tools as utt
-from tests.sparse.test_basic import eval_outputs
-from tests.theano.sparse.test_basic import sparse_random_inputs
-
-# To maintain compatibility
-from theano.sparse.basic import TrueDot, true_dot