merging files from master: travis, examples/pipeline, integration-tes…

…t.sh, yass/util.py

.travis.yml

@@ -15,7 +15,6 @@ script:
   - pip install tensorflow
   - make download-test-data
   - make test
-  # this is still broken se we are not running integration tests
   # - make integration-test
   - make docs
 

examples/pipeline/cluster.py

@@ -1,23 +1,25 @@
+import numpy as np
 import logging
 
 import yass
 from yass import preprocess
 from yass import detect
 from yass import cluster
 
+np.random.seed(0)
+
 # configure logging module to get useful information
 logging.basicConfig(level=logging.INFO)
 
 # set yass configuration parameters
-yass.set_config('config_sample.yaml')
+yass.set_config('config_sample.yaml', 'preprocess-example/')
 
 standarized_path, standarized_params, whiten_filter = preprocess.run()
 
-(score, spike_index_clear,
+(spike_index_clear,
  spike_index_all) = detect.run(standarized_path,
                                standarized_params,
                                whiten_filter)
 
 
-spike_train_clear, tmp_loc, vbParam = cluster.run(
-    score, spike_index_clear)
+spike_train_clear, tmp_loc, vbParam = cluster.run(spike_index_clear)

examples/pipeline/deconvolute.py

@@ -1,4 +1,5 @@
 import logging
+import numpy as np
 
 import yass
 from yass import preprocess
@@ -7,22 +8,23 @@
 from yass import templates
 from yass import deconvolute
 
+np.random.seed(0)
+
 # configure logging module to get useful information
 logging.basicConfig(level=logging.INFO)
 
 # set yass configuration parameters
-yass.set_config('config_sample.yaml')
+yass.set_config('config_sample.yaml', 'deconv-example')
 
 standarized_path, standarized_params, whiten_filter = preprocess.run()
 
-(score, spike_index_clear,
+(spike_index_clear,
  spike_index_all) = detect.run(standarized_path,
                                standarized_params,
                                whiten_filter)
 
 
-spike_train_clear, tmp_loc, vbParam = cluster.run(
-    score, spike_index_clear)
+spike_train_clear, tmp_loc, vbParam = cluster.run(spike_index_clear)
 
 (templates_, spike_train,
  groups, idx_good_templates) = templates.run(

examples/pipeline/detect.py

@@ -12,12 +12,12 @@
 logging.basicConfig(level=logging.INFO)
 
 # set yass configuration parameters
-yass.set_config('config_sample.yaml')
+yass.set_config('config_sample.yaml', 'detect-example')
 
 # run preprocessor
 standarized_path, standarized_params, whiten_filter = preprocess.run()
 
 # run detection
-scores, clear, collision = detect.run(standarized_path,
-                                      standarized_params,
-                                      whiten_filter)
+clear, collision = detect.run(standarized_path,
+                              standarized_params,
+                              whiten_filter)

examples/pipeline/preprocess.py

@@ -7,7 +7,7 @@
 logging.basicConfig(level=logging.INFO)
 
 # set yass configuration parameters
-yass.set_config('config_sample.yaml')
+yass.set_config('config_sample.yaml', 'preprocess-example')
 
 # run preprocessor
 standarized_path, standarized_params, whiten_filter = preprocess.run()

examples/pipeline/templates.py

@@ -1,3 +1,4 @@
+import numpy as np
 import logging
 
 import yass
@@ -6,22 +7,23 @@
 from yass import cluster
 from yass import templates
 
+np.random.seed(0)
+
 # configure logging module to get useful information
 logging.basicConfig(level=logging.INFO)
 
 # set yass configuration parameters
-yass.set_config('config_sample.yaml')
+yass.set_config('config_sample.yaml', 'templates-example')
 
 standarized_path, standarized_params, whiten_filter = preprocess.run()
 
-(score, spike_index_clear,
+(spike_index_clear,
  spike_index_all) = detect.run(standarized_path,
                                standarized_params,
                                whiten_filter)
 
 
-spike_train_clear, tmp_loc, vbParam = cluster.run(
-    score, spike_index_clear)
+spike_train_clear, tmp_loc, vbParam = cluster.run(spike_index_clear)
 
 (templates_, spike_train,
  groups, idx_good_templates) = templates.run(

integration-test/integration-test.sh

@@ -9,10 +9,10 @@ cd $DIR/../examples
 
 # run readme examples
 echo "Running config_sample.yaml example"
-yass sort config_sample.yaml
+yass sort config_sample.yaml --clean
 
 echo "Running config_sample_complete.yaml example"
-yass sort config_sample_complete.yaml
+yass sort config_sample_complete.yaml --clean
 
 
 # run examples in examples/pipeline

src/yass/util.py

@@ -506,12 +506,6 @@ def _check_for_files(func):
         def wrapper(*args, **kwargs):
             _kwargs = map_parameters_in_fn_call(args, kwargs, func)
 
-            # if not relative_path exists, just run the function
-            if _kwargs.get(relative_to) is None:
-                logging.debug('No output path was passed, running the '
-                              'function without checking for files...')
-                return func(*args, **kwargs)
-
             if_file_exists = _kwargs['if_file_exists']
 
             if mode == 'extract':
@@ -520,13 +514,13 @@ def wrapper(*args, **kwargs):
             else:
                 names = filenames
 
-            if prepend_root_folder and not os.path.isabs(_kwargs[relative_to]):
+            if relative_to is None:
                 CONFIG = yass.read_config()
-                root_path = Path(CONFIG.data.root_folder, _kwargs[relative_to])
+                root_path = Path(CONFIG.path_to_output_directory)
             else:
                 root_path = Path(_kwargs[relative_to])
 
-            root_path.mkdir(parents=True, exist_ok=True)
+                root_path.mkdir(parents=True, exist_ok=True)
 
             # generate paths for files
             paths = [root_path / f.value for f in names]