Merge pull request #2143 from nouiz/log

bin/theano-cache

@@ -8,7 +8,6 @@ from theano import config
 from theano.gof.cc import get_module_cache
 
 _logger = logging.getLogger('theano.bin.theano-cache')
-_logger.setLevel(logging.WARN)
 
 
 def print_help(exit_status):

bin/theano-nose

@@ -18,7 +18,6 @@ disable that plugin.
 
 import logging
 _logger = logging.getLogger('theano.bin.theano-nose')
-_logger.setLevel(logging.WARN)
 
 import os
 import nose

theano/compile/debugmode.py

@@ -97,7 +97,6 @@ AddConfigVar('DebugMode.check_preallocated_output_ndim',
 
 import logging
 _logger = logging.getLogger("theano.compile.debugmode")
-_logger.setLevel(logging.WARNING)
 
 
 # Filter to avoid duplicating optimization warnings
@@ -757,7 +756,6 @@ def _check_viewmap(node, storage_map):
 
         good_alias, bad_alias = {}, {}
         outstorage = storage_map[onode][0]
-        instorage_id = [id(storage_map[i][0]) for i in node.inputs]
 
         # first find out which input it aliases
         view_map = getattr(node.op, 'view_map', {})
@@ -869,8 +867,6 @@ def _find_bad_optimizations0(order, reasons, r_vals):
     for i, node in enumerate(order):
         for new_r in node.outputs:
             for reason, r, old_graph_str, new_graph_str in reasons[new_r]:
-                problem = False
-
                 #check if the value for new_r doesn't match the value for r
                 new_r_val = r_vals[new_r]
                 r_val = r_vals[r]
@@ -1553,7 +1549,6 @@ class _Linker(gof.link.LocalLinker):
             # don't do this ugly hacky way of setting the
             # filter_checks_isfinite
             from theano.tensor import TensorType  # to set filter_check_isfinite
-            from theano import tests  # for config.unittests.rseed
         fgraph = self.fgraph
         input_storage_ = input_storage
         output_storage_ = output_storage
@@ -1707,8 +1702,6 @@ class _Linker(gof.link.LocalLinker):
                                          if r.owner is None]
 
             try:
-                equiv_vals = {}
-                problematic = set()
                 # r_vals are the true values associated with each
                 # variable in the graph they should not change during
                 # the evaluation of this function, even when the graph
@@ -2266,7 +2259,6 @@ class _Maker(FunctionMaker):  # inheritance buys a few helper functions
                                     "default for a SymbolicInputKit.")
                 input_storage.append(default.storage)
                 default = None
-                required = False
             elif isinstance(input, SymbolicInputKit):
                 # If the input is a SymbolicInputKit, it represents more than
                 # one storage unit. The indices and subinputs lists represent

theano/gof/cc.py

@@ -70,7 +70,6 @@ from theano.gof import cmodule
 
 import logging
 _logger = logging.getLogger("theano.gof.cc")
-_logger.setLevel(logging.WARN)
 
 from theano.gof.callcache import CallCache
 

theano/gof/cmodule.py

@@ -68,7 +68,6 @@ AddConfigVar('cmodule.preload_cache',
              in_c_key=False)
 
 _logger = logging.getLogger("theano.gof.cmodule")
-_logger.setLevel(logging.WARNING)
 
 METH_VARARGS = "METH_VARARGS"
 METH_NOARGS = "METH_NOARGS"

theano/gof/compilelock.py

@@ -11,8 +11,10 @@ import logging
 from theano import config
 
 _logger = logging.getLogger("theano.gof.compilelock")
-# INFO will show the the messages "Refreshing lock" message
-_logger.setLevel(logging.INFO)
+# If the user provided a logging level, we don't want to override it.
+if _logger.level == logging.NOTSET:
+    # INFO will show the the messages "Refreshing lock" message
+    _logger.setLevel(logging.INFO)
 
 # In seconds, time that a process will wait before deciding to override an
 # existing lock. An override only happens when the existing lock is held by

theano/misc/hooks/check_whitespace.py

@@ -10,7 +10,14 @@ import sys
 import tabnanny
 import tokenize
 
-import argparse
+try:
+    import argparse
+except ImportError:
+    raise ImportError(
+        "check_whitespace.py need Python module argparse introduced in"
+        " Python 2.7. It is available in pypi for compatibility."
+        " You can install it with this command 'pip install argparse'")
+
 import reindent
 from theano.compat.six import StringIO
 

theano/misc/nose_pr.py

-#!/usr/bin/env python
-"""
-This is a script for testing pull requests for Theano. It merges the pull
-request with current master, installs and tests on all available versions of
-Python, and posts the results to Gist if any tests fail.
-
-It is copied from ipython
-
-Usage:
-    python test_pr.py 1657
-"""
-from __future__ import print_function
-
-import errno
-from glob import glob
-import io
-import json
-import os
-import pickle
-import re
-import requests
-import shutil
-import time
-from subprocess import (call, check_call, check_output,
-                        PIPE, STDOUT, CalledProcessError)
-import sys
-
-import gh_api
-
-basedir = os.path.join(os.path.expanduser("~"), ".theano_pr_tests")
-repodir = os.path.join(basedir, "Theano")
-ipy_repository = 'git://github.com/Theano/Theano.git'
-ipy_http_repository = 'http://github.com/Theano/Theano.git'
-gh_project = "Theano/Theano"
-
-supported_pythons = ['python2.6', 'python2.7', 'python3.1', 'python3.2']
-supported_pythons = ['python2.7']
-unavailable_pythons = []
-
-
-def available_python_versions():
-    """Get the executable names of available versions of Python on the system.
-    """
-    del unavailable_pythons[:]
-    for py in supported_pythons:
-        try:
-            check_call([py, '-c', 'import nose'], stdout=PIPE)
-            yield py
-        except (OSError, CalledProcessError):
-            unavailable_pythons.append(py)
-
-venvs = []
-
-
-def setup():
-    """Prepare the repository and virtualenvs."""
-    global venvs
-
-    try:
-        os.mkdir(basedir)
-    except OSError, e:
-        if e.errno != errno.EEXIST:
-            raise
-    os.chdir(basedir)
-
-    # Delete virtualenvs and recreate
-    for venv in glob('venv-*'):
-        shutil.rmtree(venv)
-    for py in available_python_versions():
-        check_call(['virtualenv', '-p', py,
-             '--system-site-packages', 'venv-%s' % py])
-        venvs.append((py, 'venv-%s' % py))
-
-    # Check out and update the repository
-    if not os.path.exists('Theano'):
-        try:
-            check_call(['git', 'clone', ipy_repository])
-        except CalledProcessError:
-            check_call(['git', 'clone', ipy_http_repository])
-    os.chdir(repodir)
-    check_call(['git', 'checkout', 'master'])
-    try:
-        check_call(['git', 'pull', ipy_repository, 'master'])
-    except CalledProcessError:
-        check_call(['git', 'pull', ipy_http_repository, 'master'])
-    os.chdir(basedir)
-
-missing_libs_re = re.compile(r"Tools and libraries NOT available at test"
-                             r" time:\n\s*(.*?)\n")
-
-
-def get_missing_libraries(log):
-    m = missing_libs_re.search(log)
-    if m:
-        return m.group(1)
-
-
-def get_branch(repo, branch, owner, mergeable):
-    os.chdir(repodir)
-    if mergeable:
-        merged_branch = "%s-%s" % (owner, branch)
-        # Delete the branch first
-        call(['git', 'branch', '-D', merged_branch])
-        check_call(['git', 'checkout', '-b', merged_branch])
-        check_call(['git', 'pull', '--no-ff', '--no-commit', repo, branch])
-        check_call(['git', 'commit', '-m', "merge %s/%s" % (repo, branch)])
-    else:
-        # Fetch the branch without merging it.
-        check_call(['git', 'fetch', repo, branch])
-        check_call(['git', 'checkout', 'FETCH_HEAD'])
-    os.chdir(basedir)
-
-
-def run_tests(venv):
-    py = os.path.join(basedir, venv, 'bin', 'python')
-    print(py)
-    os.chdir(repodir)
-    # cleanup build-dir
-    if os.path.exists('build'):
-        shutil.rmtree('build')
-    check_call([py, 'setup.py', 'install'])
-    os.chdir(basedir)
-
-    # Environment variables:
-    orig_path = os.environ["PATH"]
-    os.environ["PATH"] = os.path.join(basedir, venv,
-                                      'bin') + ':' + os.environ["PATH"]
-    os.environ.pop("PYTHONPATH", None)
-    iptest = os.path.join(basedir, venv, 'bin', 'theano-test')
-#    if not os.path.exists(iptest):
-#        iptest = os.path.join(basedir, venv, 'bin', 'iptest3')
-
-    print("\nRunning tests, this typically takes a few minutes...")
-    try:
-
-        return True, check_output([iptest], stderr=STDOUT).decode('utf-8')
-    except CalledProcessError, e:
-        return False, e.output.decode('utf-8')
-    finally:
-        # Restore $PATH
-        os.environ["PATH"] = orig_path
-
-
-def markdown_format(pr, results_urls, unavailable_pythons):
-    def format_result(py, passed, gist_url, missing_libraries):
-        s = "* %s: " % py
-        if passed:
-            s += "OK"
-        else:
-            s += "Failed, log at %s" % gist_url
-        if missing_libraries:
-            s += " (libraries not available: " + missing_libraries + ")"
-        return s
-
-    if pr['mergeable']:
-        com = pr['head']['sha'][:7] + " merged into master"
-    else:
-        com = pr['head']['sha'][:7] + " (can't merge cleanly)"
-    lines = ["**Test results for commit %s**" % com,
-             "Platform: " + sys.platform,
-             ""] + \
-            [format_result(*r) for r in results_urls] + \
-            ["",
-             "Not available for testing: " + ", ".join(unavailable_pythons)]
-    return "\n".join(lines)
-
-
-def post_results_comment(pr, results, num,
-                         unavailable_pythons=unavailable_pythons):
-    body = markdown_format(pr, results, unavailable_pythons)
-    gh_api.post_issue_comment(gh_project, num, body)
-
-
-def print_results(pr, results_urls, unavailable_pythons=unavailable_pythons):
-    print("\n")
-    if pr['mergeable']:
-        print("**Test results for commit %s merged into master**" %
-             pr['head']['sha'][:7])
-    else:
-        print(
-            "**Test results for commit %s (can't merge cleanly)**" %
-            pr['head']['sha'][:7])
-    print("Platform:", sys.platform)
-    for py, passed, gist_url, missing_libraries in results_urls:
-        if passed:
-            print(py, ":", "OK")
-        else:
-            print(py, ":", "Failed")
-            print("    Test log:", gist_url)
-        if missing_libraries:
-            print("    Libraries not available:", missing_libraries)
-    print("Not available for testing:", ", ".join(unavailable_pythons))
-
-
-def dump_results(num, results, pr):
-    f = open(os.path.join(basedir, 'lastresults.pkl'), 'wb')
-    try:
-        pickle.dump((num, results, pr, unavailable_pythons), f)
-    finally:
-        f.close()
-
-
-def load_results():
-    f = open(os.path.join(basedir, 'lastresults.pkl'), 'rb')
-    try:
-        ret = pickle.load(f)
-    finally:
-        f.close()
-    return ret
-
-
-def save_logs(results, pr):
-    results_paths = []
-    for py, passed, log, missing_libraries in results:
-        if passed:
-            results_paths.append((py, passed, None, missing_libraries))
-        else:
-
-            result_locn = os.path.abspath(os.path.join('venv-%s' % py,
-                                        pr['head']['sha'][:7] + ".log"))
-            f = io.open(result_locn, 'w', encoding='utf-8')
-            try:
-                f.write(log)
-            finally:
-                f.close()
-
-            results_paths.append((py, False, result_locn, missing_libraries))
-
-    return results_paths
-
-
-def post_logs(results):
-    results_urls = []
-    for py, passed, log, missing_libraries in results:
-        if passed:
-            results_urls.append((py, passed, None, missing_libraries))
-        else:
-            result_locn = gh_api.post_gist(log, description='Theano test log',
-                                            filename="results.log", auth=True)
-            results_urls.append((py, False, result_locn, missing_libraries))
-
-    return results_urls
-
-
-def test_pr(num, post_results=True):
-    # Get Github authorisation first, so that the user is prompted
-    # straight away if their login is needed.
-    if post_results:
-        gh_api.get_auth_token()
-
-    setup()
-    pr = gh_api.get_pull_request(gh_project, num)
-    get_branch(repo=pr['head']['repo']['clone_url'],
-                 branch=pr['head']['ref'],
-                 owner=pr['head']['repo']['owner']['login'],
-                 mergeable=pr['mergeable'],
-              )
-
-    results = []
-    for py, venv in venvs:
-        tic = time.time()
-        passed, log = run_tests(venv)
-        elapsed = int(time.time() - tic)
-        print("Ran tests with %s in %is" % (py, elapsed))
-        missing_libraries = get_missing_libraries(log)
-        if passed:
-            results.append((py, True, None, missing_libraries))
-        else:
-            results.append((py, False, log, missing_libraries))
-
-    dump_results(num, results, pr)
-
-    results_paths = save_logs(results, pr)
-    print_results(pr, results_paths)
-
-    if post_results:
-        results_urls = post_logs(results)
-        post_results_comment(pr, results_urls, num)
-        print("(Posted to Github)")
-    else:
-        post_script = os.path.join(os.path.dirname(sys.argv[0]),
-             "post_pr_test.py")
-        print("To post the results to Github, run", post_script)
-
-
-if __name__ == '__main__':
-    import argparse
-    parser = argparse.ArgumentParser(description="Test an Theano pull request")
-    parser.add_argument('-p', '--publish', action='store_true',
-                        help="Publish the results to Github")
-    parser.add_argument('number', type=int, help="The pull request number")
-
-    args = parser.parse_args()
-    test_pr(args.number, post_results=args.publish)

theano/sandbox/cuda/__init__.py

@@ -16,7 +16,6 @@ import nvcc_compiler
 
 _logger_name = 'theano.sandbox.cuda'
 _logger = logging.getLogger(_logger_name)
-_logger.setLevel(logging.WARNING)
 
 AddConfigVar('pycuda.init',
         """If True, always initialize PyCUDA when Theano want to

theano/sandbox/cuda/basic_ops.py

@@ -9,6 +9,7 @@ import theano
 from theano import gof, Type, Apply
 from theano import tensor, scalar, config
 from theano.compat.six import StringIO
+from theano.gradient import grad_undefined
 from theano.scalar import Scalar
 
 scal = scalar # somewhere scalar gets reassigned to be a function
@@ -31,8 +32,6 @@ from theano.sandbox.cuda.elemwise import NaiveAlgo
 
 _logger_name = 'theano.sandbox.cuda.basic_ops'
 _logger = logging.getLogger(_logger_name)
-_logger.setLevel(logging.INFO)
-_logger.addHandler(logging.StreamHandler())  # TO REMOVE
 
 
 def as_cuda_ndarray_variable(x):

theano/sandbox/cuda/elemwise.py

@@ -7,21 +7,19 @@ that ndim is 0 as with all scalar type.
 """
 
 
-import copy, logging, sys
+import logging
 
 import numpy
 
 from theano.scalar.basic import upgrade_to_float_no_complex, complex_types
 from theano.scalar.basic_scipy import Erfinv
 from theano.compat.six import StringIO
-from theano import Apply, Constant, Op, Type, Variable
-from theano import gof, scalar, tensor
+from theano import Apply
+from theano import gof, scalar
 
 
 _logger_name = 'theano.sandbox.cuda.elemwise'
 _logger = logging.getLogger(_logger_name)
-_logger.setLevel(logging.INFO)
-_logger.addHandler(logging.StreamHandler()) #TO REMOVE
 
 
 def _logical_scalar(x):
@@ -432,7 +430,6 @@ class NaiveAlgo(object):
         return sio.getvalue()
 
     def c_src_kernel_Ccontiguous(self, node, nodename):
-        nd = node.outputs[0].type.ndim
         sio = StringIO()
         #print 'C_SRC_KERNEL', sio.getvalue()
 

theano/sandbox/cuda/nvcc_compiler.py

-import commands
 import distutils
 import logging
 import os
-import re
 import subprocess
 import sys
 import warnings
@@ -19,7 +17,6 @@ from theano.gof.python25 import any
 from theano.misc.windows import output_subprocess_Popen
 
 _logger = logging.getLogger("theano.sandbox.cuda.nvcc_compiler")
-_logger.setLevel(logging.WARN)
 
 from theano.configparser import (config, AddConfigVar, StrParam,
                                  BoolParam, ConfigParam)
@@ -246,7 +243,6 @@ class NVCC_compiler(object):
             preargs = list(preargs)
         if sys.platform != 'win32':
             preargs.append('-fPIC')
-        no_opt = False
         cuda_root = config.cuda.root
 
         #The include dirs gived by the user should have precedence over

theano/sandbox/gpuarray/__init__.py

@@ -7,7 +7,6 @@ from theano.compile import optdb
 
 _logger_name = 'theano.sandbox.gpuarray'
 _logger = logging.getLogger(_logger_name)
-_logger.setLevel(logging.WARNING)
 
 error = _logger.error
 info = _logger.info

theano/scan_module/numpy_api_changes.diff

@@ -25,7 +25,7 @@ index aaebb43..2d06b29 100644
   * cdef inline object get_array_base(ndarray arr):
   */
 -  __pyx_v_arr->base = __pyx_v_baseptr;
-+#if NPY_API < 0x00000007
++#if NPY_API_VERSION < 0x00000007
 +  PyArray_BASE(__pyx_v_arr) = __pyx_v_baseptr;
 +#else
 +  PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_baseptr);

theano/scan_module/scan_perform.c

@@ -7156,7 +7156,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a
  * 
  * cdef inline object get_array_base(ndarray arr):
  */
-#if NPY_API < 0x00000007
+#if NPY_API_VERSION < 0x00000007
   PyArray_BASE(__pyx_v_arr) = __pyx_v_baseptr;
 #else
   PyArray_SetBaseObject(__pyx_v_arr, __pyx_v_baseptr);

theano/scan_module/scan_perform_ext.py

@@ -2,6 +2,7 @@ import errno
 import logging
 import os
 import sys
+import warnings
 
 import numpy
 
@@ -13,7 +14,6 @@ from theano.gof import cmodule
 
 
 _logger = logging.getLogger('theano.scan_module.scan_perform')
-_logger.setLevel(logging.WARN)
 
 
 version = 0.283  # must match constant returned in function get_version()

theano/tensor/blas_headers.py

@@ -12,7 +12,6 @@ from theano import config
 from theano.gof.cmodule import GCC_compiler
 
 _logger = logging.getLogger('theano.tensor.blas')
-#_logger.setLevel(logging.INFO)
 
 
 def detect_macos_sdot_bug():