Add more verbosity for thalamus protocols (#86)

* set default CLI verbosity to 1, logger.INFO

* add extra verbosity with progress bars to thalamus RatSSCxMainProtocol

* update unit test: test_get_parser_args

* fix unit test: test_get_parser_args

* update argparse to store int for verbosity with default=1

emodelrunner/parsing_utilities.py

@@ -30,7 +30,7 @@ def get_parser_args():
         default=None,
         help="the path to the config file.",
     )
-    parser.add_argument("-v", "--verbose", action="count", dest="verbosity", default=0)
+    parser.add_argument("-v", "--verbose", type=int, dest="verbosity", default=1)
     return parser.parse_args()
 
 

emodelrunner/protocols/thalamus_protocols.py

@@ -20,7 +20,9 @@
 import copy
 import logging
 import numpy as np
+
 from bluepyopt import ephys
+from tqdm import tqdm
 
 from emodelrunner.protocols.protocols_func import CurrentOutputKeyMixin
 
@@ -124,12 +126,14 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
         cell_model.freeze(param_values)
 
         # Find resting membrane potential
+        logger.info("Running RMP protocol")
         rmp_response = self.rmp_protocol.run(cell_model, {}, sim=sim)
         responses.update(rmp_response)
         rmp = self.rmp_efeature.calculate_feature(rmp_response)
 
         # Find Rin and holding current
         if hasattr(self, "rinhold_protocol_dep"):
+            logger.info("Running Rinhold protocol (depolarizing)")
             rinhold_response_dep = self.rinhold_protocol_dep.run(
                 cell_model, {}, sim=sim, rmp=rmp
             )
@@ -138,6 +142,7 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
             rin_dep = self.rin_efeature_dep.calculate_feature(rinhold_response_dep)
             responses.update(rinhold_response_dep)
 
+        logger.info("Running Rinhold protocol (hyperpolarizing)")
         rinhold_response_hyp = self.rinhold_protocol_hyp.run(
             cell_model, {}, sim=sim, rmp=rmp
         )
@@ -148,6 +153,7 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
             responses.update(rinhold_response_hyp)
 
             if hasattr(self, "thdetect_protocol_dep"):
+                logger.info("Running threshold detection protocol (depolarizing)")
                 responses.update(
                     self.thdetect_protocol_dep.run(
                         cell_model,
@@ -159,6 +165,7 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
                     )
                 )
 
+            logger.info("Running threshold detection protocol (hyperpolarizing)")
             responses.update(
                 self.thdetect_protocol_hyp.run(
                     cell_model,
@@ -180,13 +187,15 @@ def run(self, cell_model, param_values, sim=None, isolate=None):
 
     def _run_pre_protocols(self, cell_model, sim, responses):
         """Runs the pre_protocols and updates responses dict."""
-        for pre_protocol in self.pre_protocols:
+        logger.info("Running pre-protocols")
+        for pre_protocol in tqdm(self.pre_protocols):
             response = pre_protocol.run(cell_model, {}, sim=sim)
             responses.update(response)
 
     def _run_other_protocols(self, cell_model, sim, responses):
         """Runs the other_protocols and updates responses dict."""
-        for other_protocol in self.other_protocols:
+        logger.info("Running other protocols")
+        for other_protocol in tqdm(self.other_protocols):
             response = other_protocol.run(cell_model, {}, sim=sim)
             responses.update(response)
 

emodelrunner/run.py

@@ -31,10 +31,6 @@
 
 logger = logging.getLogger(__name__)
 
-# if logger.level is unset, then set it to INFO
-if logger.level == logging.NOTSET:
-    logger.setLevel(logging.INFO)
-
 
 def main(config_path):
     """Main.

emodelrunner/run_pairsim.py

@@ -31,9 +31,6 @@
 
 # Configure logger
 logger = logging.getLogger(__name__)
-# if logger.level is unset, then set it to INFO
-if logger.level == logging.NOTSET:
-    logger.setLevel(logging.INFO)
 
 
 def run(

emodelrunner/run_synplas.py

@@ -31,9 +31,6 @@
 
 # Configure logger
 logger = logging.getLogger(__name__)
-# if logger.level is unset, then set it to INFO
-if logger.level == logging.NOTSET:
-    logger.setLevel(logging.INFO)
 
 
 # taken from glusynapse.simulation.simulator

setup.py

@@ -50,6 +50,7 @@
         "schema",
         "Pebble>=4.3.10",
         "importlib_metadata; python_version<'3.8'",
+        "tqdm>=4.65.0",
     ],
     packages=find_packages(exclude=["tests"]),
     python_requires=">=3.7",

tests/unit_tests/test_parsing_utilities.py

@@ -28,25 +28,25 @@ def test_get_parser_args():
     args = get_parser_args()
 
     assert args.config_path == "mock/config/path"
-    assert args.verbosity == 0
+    assert args.verbosity == 1
 
     # --verbose case
-    sys.argv = "run.py --config_path mock/config/path --verbose".split()
+    sys.argv = "run.py --config_path mock/config/path --verbose=0".split()
     args = get_parser_args()
 
-    assert args.verbosity == 1
+    assert args.verbosity == 0
 
     # -v case
-    sys.argv = "run.py --config_path mock/config/path -v".split()
+    sys.argv = "run.py --config_path mock/config/path -v=2".split()
     args = get_parser_args()
 
-    assert args.verbosity == 1
+    assert args.verbosity == 2
 
-    # -vv case
-    sys.argv = "run.py --config_path mock/config/path -vv".split()
+    # space separated case
+    sys.argv = "run.py --config_path mock/config/path --verbose 3".split()
     args = get_parser_args()
 
-    assert args.verbosity == 2
+    assert args.verbosity == 3
 
 
 @patch("logging.basicConfig")