add option to set temporary directory (#139)

* add option to set temporary directory in pyndl.ndl.ndl

pyndl/__init__.py

@@ -17,7 +17,7 @@
 __author__ = ('Konstantin Sering, Marc Weitz, '
               'David-Elias Künstle, Lennard Schneider')
 __author_email__ = '[email protected]'
-__version__ = '0.4.1'
+__version__ = '0.4.2'
 __license__ = 'MIT'
 __description__ = ('Naive discriminative learning implements learning and '
                    'classification models based on the Rescorla-Wagner '

pyndl/ndl.py

@@ -56,7 +56,7 @@ def events_from_file(event_path):
 def ndl(events, alpha, betas, lambda_=1.0, *,
         method='openmp', weights=None,
         number_of_threads=8, len_sublists=10, remove_duplicates=None,
-        verbose=False):
+        verbose=False, temporary_directory=None):
     """
     Calculate the weights for all_outcomes over all events in event_file
     given by the files path.
@@ -89,6 +89,10 @@ def ndl(events, alpha, betas, lambda_=1.0, *,
         preferred!)
     verbose : bool
         print some output if True.
+    temporary_directory : str
+        path to directory to use for storing temporary files created;
+        if none is provided, the operating system's default will
+        be used (/tmp on unix)
 
     Returns
     -------
@@ -155,7 +159,7 @@ def ndl(events, alpha, betas, lambda_=1.0, *,
 
     beta1, beta2 = betas
 
-    with tempfile.TemporaryDirectory(prefix="pyndl") as binary_path:
+    with tempfile.TemporaryDirectory(prefix="pyndl", dir=temporary_directory) as binary_path:
         number_events = preprocess.create_binary_event_files(events, binary_path, cue_map,
                                                              outcome_map, overwrite=True,
                                                              number_of_processes=number_of_threads,

tests/test_ndl.py

@@ -124,6 +124,9 @@ def test_exceptions():
         ndl.ndl(FILE_PATH_SIMPLE, ALPHA, BETAS, remove_duplicates="magic")
         assert e_info == "remove_duplicates must be None, True or False"
 
+    with pytest.raises(FileNotFoundError, match="No such file or directory") as e_info:
+        ndl.ndl(FILE_PATH_SIMPLE, ALPHA, BETAS, temporary_directory="./magic")
+
 
 def test_continue_learning_dict():
     events_simple = pd.read_csv(FILE_PATH_SIMPLE, sep="\t")
@@ -217,6 +220,11 @@ def test_return_values(result_dict_ndl, result_dict_ndl_data_array, result_ndl_t
     assert isinstance(result_ndl_threading, xr.DataArray)
 
 
+def test_provide_temporary_directory():
+    with tempfile.TemporaryDirectory(dir=TMP_PATH) as temporary_directory:
+        ndl.ndl(FILE_PATH_SIMPLE, ALPHA, BETAS, temporary_directory=temporary_directory)
+
+
 # Test internal consistency
 
 def test_dict_ndl_vs_ndl_threading(result_dict_ndl, result_ndl_threading):