Merge branch 'develop' of https://github.com/wmayner/pyphi into develop

Makefile

@@ -1,4 +1,3 @@
-
 .PHONY: test docs dist
 
 src = pyphi
@@ -17,6 +16,9 @@ coverage:
 	coverage html
 	open htmlcov/index.html
 
+lint:
+	pylint $(src)
+
 watch-tests:
 	watchmedo shell-command \
 		--command='make coverage' \

pyphi/compute/parallel.py

@@ -30,10 +30,9 @@ def get_num_processes():
             'Invalid NUMBER_OF_CORES; value may not be 0.')
 
     if config.NUMBER_OF_CORES > cpu_count:
-        raise ValueError(
-            'Invalid NUMBER_OF_CORES; value must be less than or '
-            'equal to the available number of cores ({} for this '
-            'system).'.format(cpu_count))
+        log.info('Requesting {} cores; only {} available'.format(
+            config.NUMBER_OF_CORES, cpu_count))
+        return cpu_count
 
     if config.NUMBER_OF_CORES < 0:
         num = cpu_count + config.NUMBER_OF_CORES + 1

pyphi/memory.py

@@ -19,23 +19,24 @@ def cache(ignore=None):
     """Decorator for memoizing a function using either the filesystem or a
     database.
     """
+    def decorator(func):
+        # Initialize both cached versions
+        joblib_cached = constants.joblib_memory.cache(func, ignore=ignore)
+        db_cached = DbMemoizedFunc(func, ignore)
 
-    def joblib_decorator(func):
-        if func.__name__ == '_sia' and not config.CACHE_SIAS:
-            return func
-        return constants.joblib_memory.cache(func, ignore=ignore)
-
-    def db_decorator(func):
-        if func.__name__ == '_sia' and not config.CACHE_SIAS:
-            return func
-        return DbMemoizedFunc(func, ignore)
-
-    if config.CACHING_BACKEND == 'fs':
-        # Decorate the function with the filesystem memoizer.
-        return joblib_decorator
-    if config.CACHING_BACKEND == 'db':
-        # Decorate the function with the database memoizer.
-        return db_decorator
+        @functools.wraps(func)
+        def wrapper(*args, **kwargs):
+            """Dynamically choose the cache at call-time, not at import."""
+            if func.__name__ == '_sia' and not config.CACHE_SIAS:
+                f = func
+            elif config.CACHING_BACKEND == 'fs':
+                f = joblib_cached
+            elif config.CACHING_BACKEND == 'db':
+                f = db_cached
+            return f(*args, **kwargs)
+
+        return wrapper
+    return decorator
 
 
 class DbMemoizedFunc:

pyphi/utils.py

@@ -7,12 +7,12 @@
 external use.
 """
 
-import functools
 import hashlib
 import os
 from itertools import chain, combinations, product
 from time import time
 
+import decorator
 import numpy as np
 from scipy.misc import comb
 
@@ -201,17 +201,17 @@ def get_path(i):  # pylint: disable=missing-docstring
     return [np.load(get_path(i)) for i in range(num)]
 
 
-def time_annotated(func):
+# Using ``decorator`` preserves the function signature of the wrapped function,
+# allowing joblib to properly introspect the function arguments.
+@decorator.decorator
+def time_annotated(func, *args, **kwargs):
     """Annotate the decorated function or method with the total execution
     time.
 
     The result is annotated with a `time` attribute.
     """
-    @functools.wraps(func)
-    def wrapper(*args, **kwargs):
-        start = time()
-        result = func(*args, **kwargs)
-        end = time()
-        result.time = round(end - start, config.PRECISION)
-        return result
-    return wrapper
+    start = time()
+    result = func(*args, **kwargs)
+    end = time()
+    result.time = round(end - start, config.PRECISION)
+    return result

setup.py

@@ -15,6 +15,7 @@
     exec(f.read(), about)
 
 install_requires = [
+    'decorator >=4.0.0',
     'joblib >=0.8.0',
     'numpy >=1.11.0',
     'psutil >=2.1.1',

test/test_parallel.py

@@ -31,10 +31,9 @@ def test_num_processes():
         with pytest.raises(ValueError):
             parallel.get_num_processes()
 
-    # Requesting too many cores
+    # Requesting more cores than available
     with config.override(NUMBER_OF_CORES=3):
-        with pytest.raises(ValueError):
-            parallel.get_num_processes()
+        assert parallel.get_num_processes() == 2
 
     # Ok
     with config.override(NUMBER_OF_CORES=1):