Dauer add

.github/workflows/non_omv.yml

@@ -2,9 +2,9 @@ name: Non-OMV-tests
 
 on:
   push:
-    branches: [ main, development, experimental, ow* ]
+    branches: [ main, development, experimental, ow*, feature/* ]
   pull_request:
-    branches: [ main, development, experimental, ow* ]
+    branches: [ main, development, experimental, ow*, feature/* ]
 
 jobs:
   build:
@@ -39,6 +39,10 @@ jobs:
         pip list
 
 
+    - name: Run pytest
+      run: |
+        pytest -vs
+
     - name: Run quick test script
       run: |
         ./test.sh -q

.gitignore

@@ -17,6 +17,7 @@ __pycache__
 /docs/assets/Bentley*
 /docs/assets/Randi*
 /docs/assets/WormNeuro*
+/docs/assets/Yin*
 
 /docs/*Cook*data*.md
 /docs/*Varshney*data*.md
@@ -28,6 +29,7 @@ __pycache__
 /docs/*Randi*data*.md
 /docs/*WormNeuro*data*.md
 /docs/*Ripo*data*.md
+/docs/*Yin*data*.md
 
 /docs/.DS_Store
 /docs/assets/RipollSanchez*

cect/Analysis.py

@@ -6,9 +6,10 @@
 
 def test_bilaterals():
     from cect.White_whole import get_instance
+
     # from cect.VarshneyDataReader import get_instance
 
-    """
+    """from cect.TestDataReader import get_instance
     from cect.Cook2020DataReader import get_instance
     from cect.WormNeuroAtlasFuncReader import get_instance
     from cect.RipollSanchezDataReader import get_instance
@@ -24,7 +25,6 @@ def test_bilaterals():
     from cect.Cook2019MaleReader import get_instance
     from cect.Cook2019HermReader import get_instance
     from cect.WitvlietDataReader8 import get_instance
-    from cect.TestDataReader import get_instance
     from cect.SpreadsheetDataReader import get_instance
     from cect.BrittinDataReader import get_instance
     from cect.WormNeuroAtlasMAReader import get_instance

cect/CellInfo.py

@@ -99,10 +99,10 @@ def load_individual_neuron_info():
     cell_info = {}
     with open(filename) as csvfile:
         reader = csv.reader(csvfile, delimiter=";")
-        print(reader)
+        # print(reader)
 
         for row in reader:
-            print(", ".join(row))
+            print_(", ".join(row))
             if not row[0].startswith("#"):
                 cell_info[row[0]] = (row[1].strip(), row[2].strip(), row[3].strip())
 

cect/Comparison.py

@@ -36,6 +36,7 @@
     "RipollSanchezShortRange": "RipollSanchezShortRange_data",
     "RipollSanchezMidRange": "RipollSanchezMidRange_data",
     "RipollSanchezLongRange": "RipollSanchezLongRange_data",
+    "Yin2024": "Yin2024_data",
     "Test": "Test_data",
     "SSData": "SSData_data",
     "UpdSSData": "UpdSSData_data",
@@ -202,6 +203,8 @@ def generate_comparison_page(quick: bool, color_table=True, dataset_pages=True):
             "RipollSanchez_2023",
         ]
 
+    readers["Yin2024"] = ["cect.Yin2024DataReader", "Yin_2024"]
+
     if not quick:
         readers["SSData"] = ["cect.SpreadsheetDataReader", None]
         readers["UpdSSData"] = ["cect.UpdatedSpreadsheetDataReader", None]
@@ -582,7 +585,7 @@ def generate_comparison_page(quick: bool, color_table=True, dataset_pages=True):
                 .replace("Sanchez", " Sanchez et al. 2023 ")
                 .replace("tley", "tley et al.")
                 .replace("Cook", "Cook et al.")
-                .replace("ttin", "ttin et al.")
+                .replace("in", "in et al.")
                 .replace("19", "19 ")
                 .replace("liet", "liet ")
                 .replace("MA", "Monoamin.")

cect/ConnectomeDataset.py

@@ -102,7 +102,10 @@ def to_networkx_graph(self, synclass, view=None):
         return Gn
 
     def add_connection_info(
-        self, conn: ConnectionInfo, check_overwritten_connections: bool = False
+        self,
+        conn: ConnectionInfo,
+        check_overwritten_connections: bool = True,
+        append_existing_connections=False,
     ):
         if self.verbose:
             print_("----   Adding: %s" % conn)
@@ -138,17 +141,23 @@ def add_connection_info(
                 "Preexisting connection (%i conns already) at (%i,%i) - %s..."
                 % (len(self.connection_infos), pre_index, post_index, conn)
             )
+
             if conn_array[pre_index, post_index] != conn.number:
                 info = (
-                    " *** Existing connection at (%i,%i), was: %s, setting to: %s"
+                    "     *** Existing connection at (%i,%i), was: %s, changing to: %s (appending: %s)"
                     % (
                         pre_index,
                         post_index,
                         conn_array[pre_index, post_index],
                         conn.number,
+                        append_existing_connections,
                     )
                 )
-                if check_overwritten_connections:
+
+                if append_existing_connections:
+                    conn_array[pre_index, post_index] += conn.number
+
+                elif check_overwritten_connections:
                     raise Exception(info)
                 else:
                     print_(info)
@@ -161,7 +170,7 @@ def add_connection_info(
                 % (pre_index, post_index, self.nodes, conn_array)
             )
 
-    def read_data(self):
+    def _read_data(self):
         return self.get_neuron_to_neuron_conns()
 
     def get_neuron_to_neuron_conns(self):
@@ -174,7 +183,7 @@ def get_neuron_to_neuron_conns(self):
                 neuron_conns.append(conn_info)
         return list(neurons), neuron_conns
 
-    def read_muscle_data(self):
+    def _read_muscle_data(self):
         return self.get_neuron_to_muscle_conns()
 
     def get_neuron_to_muscle_conns(self):
@@ -730,7 +739,6 @@ def get_node_size(node_set):
                     thickness=15,
                     title="Node Connections",
                     xanchor="left",
-                    titleside="right",
                 ),
                 line_width=1,
             ),
@@ -1095,26 +1103,27 @@ def connection_number_plot(self, synclass):  # Todo: get better name
     print(pprint.pprint(nx.node_link_data(G)))
 
     # from cect.ConnectomeView import NEURONS_VIEW as view
-    # from cect.ConnectomeView import RAW_VIEW as view
+    from cect.ConnectomeView import RAW_VIEW as view
     # from cect.ConnectomeView import ESCAPE_VIEW as view
 
     # from cect.ConnectomeView import SOCIAL_VIEW as view
     # from cect.ConnectomeView import SOCIAL_VIEW as view
     # from cect.ConnectomeView import COOK_FIG3_VIEW as view
-    from cect.ConnectomeView import PEP_HUBS_VIEW as view
+    # from cect.ConnectomeView import PEP_HUBS_VIEW as view
 
     # from cect.White_whole import get_instance
-    from cect.BrittinDataReader import get_instance
+    # from cect.BrittinDataReader import get_instance
     # from cect.WitvlietDataReader8 import get_instance
     # from cect.Cook2019HermReader import get_instance
+    from cect.Yin2024DataReader import get_instance
 
     synclass = "Chemical Inh"
     synclass = "Chemical Exc"
 
     # synclass = "Acetylcholine"
-    # synclass = "Chemical"
+    synclass = "Chemical"
     # synclass = "Electrical"
-    synclass = "Contact"
+    # synclass = "Contact"
     # from cect.TestDataReader import get_instance
 
     cds = get_instance()

cect/ConnectomeReader.py

@@ -89,7 +89,7 @@ def check_cells(cells):
             missing_preferred.remove(c)
 
     if False:
-        print(
+        print_(
             "Of these %i cells:\n  %i in preferred: %s\n  %i not in preferred: %s\n  %i missing preferred: %s\n  %i muscles: %s"
             % (
                 len(cells),

cect/ConnectomeView.py

@@ -510,7 +510,6 @@ def get_index_of_cell(self, cell):
     RAW_VIEW,
     NEURONS_VIEW,
     PHARYNX_VIEW,
-    NONPHARYNGEAL_NEURONS_HERM_VIEW,
     SOCIAL_VIEW,
     ESCAPE_VIEW,
     COOK_FIG3_VIEW,

cect/Cook2019DataReader.py

@@ -144,6 +144,12 @@ def __init__(self, sex):
         for conn in conns:
             self.add_connection_info(conn)
 
+    def read_data(self):
+        return self._read_data()
+
+    def read_muscle_data(self):
+        return self._read_muscle_data()
+
     def read_all_data(self):
         """
         Returns:

cect/Cook2019HermReader.py

@@ -17,18 +17,18 @@ def get_instance():
     return Cook2019DataReader("Hermaphodite")
 
 
-my_instance = get_instance()
-
+"""
 read_data = my_instance.read_data
-read_muscle_data = my_instance.read_muscle_data
+read_muscle_data = my_instance.read_muscle_data"""
 
 READER_DESCRIPTION = (
     """Data extracted from %s for neuronal connectivity of hermaphrodite"""
-    % get_dataset_source_on_github(my_instance.filename.split("/")[-1])
+    % get_dataset_source_on_github(Cook2019DataReader.filename.split("/")[-1])
 )
 
 
 def main1():
+    my_instance = get_instance()
     cells, neuron_conns = my_instance.read_data()
     neurons2muscles, muscles, muscle_conns = my_instance.read_muscle_data()
     analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)

cect/Cook2019MaleReader.py

@@ -10,20 +10,20 @@ def get_instance():
     return Cook2019DataReader("Male")
 
 
-my_instance = get_instance()
-
+"""
 read_data = my_instance.read_data
-read_muscle_data = my_instance.read_muscle_data
+read_muscle_data = my_instance.read_muscle_data"""
 
 READER_DESCRIPTION = (
     """Data extracted from %s for neuronal connectivity of male"""
-    % get_dataset_source_on_github(my_instance.filename.split("/")[-1])
+    % get_dataset_source_on_github(Cook2019DataReader.filename.split("/")[-1])
 )
 
 
 def main1():
-    cells, neuron_conns = read_data()
-    neurons2muscles, muscles, muscle_conns = read_muscle_data()
+    my_instance = get_instance()
+    cells, neuron_conns = my_instance.read_data()
+    neurons2muscles, muscles, muscle_conns = my_instance.read_muscle_data()
     analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)
 
 

cect/Cook2020DataReader.py

@@ -45,7 +45,7 @@ def __init__(self):
 
         cells, neuron_conns = self.read_data()
         for conn in neuron_conns:
-            self.add_connection_info(conn)
+            self.add_connection_info(conn, check_overwritten_connections=False)
 
     def read_data(self):
         """

cect/RipollSanchezDataReader.py

@@ -27,16 +27,20 @@ def standardise_cell_name(cell):
     return cell
 
 
+def get_filename(model):
+    spreadsheet_location = os.path.dirname(os.path.abspath(__file__)) + "/data/"
+    filename = "%s01022024_neuropeptide_connectome_%s.csv" % (
+        spreadsheet_location,
+        model,
+    )
+    return filename
+
+
 class RipollSanchezDataReader(ConnectomeDataset):
     verbose = False
 
     def __init__(self, model):
-        spreadsheet_location = os.path.dirname(os.path.abspath(__file__)) + "/data/"
-
-        self.filename = "%s01022024_neuropeptide_connectome_%s.csv" % (
-            spreadsheet_location,
-            model,
-        )
+        self.filename = get_filename(model)
 
         ConnectomeDataset.__init__(self)
 
@@ -51,7 +55,7 @@ def read_data(self):
         with open(self.filename) as csvfile:
             data = list(csv.reader(csvfile))
 
-        print_("Opened the CSV file: " + self.filename)
+        print_("Opened up the CSV file: " + self.filename)
 
         for i in range(1, len(data)):
             pre_cell = standardise_cell_name(data[0][i])
@@ -86,10 +90,9 @@ def get_instance():
     return RipollSanchezDataReader("short_range_model")
 
 
-my_instance = get_instance()
-
+"""
 read_data = my_instance.read_data
-read_muscle_data = my_instance.read_muscle_data
+read_muscle_data = my_instance.read_muscle_data"""
 
 
 def load_hub_info():
@@ -123,6 +126,8 @@ def load_hub_info():
 
 
 def main():
+    print("Testing...")
+
     tdr_instance = RipollSanchezDataReader("short_range_model")
 
     cells, neuron_conns = tdr_instance.read_data()
@@ -162,5 +167,5 @@ def main():
 
 
 if __name__ == "__main__":
-    # main()
+    main()
     load_hub_info()

cect/RipollSanchezLongRangeReader.py

@@ -7,35 +7,37 @@
 ############################################################
 
 
-from cect.RipollSanchezDataReader import RipollSanchezDataReader
+from cect.RipollSanchezDataReader import RipollSanchezDataReader, get_filename
 from cect.ConnectomeDataset import get_dataset_source_on_github
 from cect.ConnectomeReader import analyse_connections
 
+MODEL = "long_range_model"
+
 
 def get_instance():
     """Uses ``RipollSanchezDataReader`` to load data on the long range model of neuropedtidergic connectome
 
     Returns:
         RipollSanchezDataReader: The initialised connectome reader
     """
-    return RipollSanchezDataReader("long_range_model")
-
+    return RipollSanchezDataReader(MODEL)
 
-my_instance = get_instance()
 
+"""
 read_data = my_instance.read_data
-read_muscle_data = my_instance.read_muscle_data
+read_muscle_data = my_instance.read_muscle_data"""
 
 
 READER_DESCRIPTION = (
     """Data extracted from %s for long range model of neuropedtidergic connectome"""
-    % get_dataset_source_on_github(my_instance.filename.split("/")[-1])
+    % get_dataset_source_on_github(get_filename(MODEL).split("/")[-1])
 )
 
 
 def main1():
-    cells, neuron_conns = read_data()
-    neurons2muscles, muscles, muscle_conns = read_muscle_data()
+    my_instance = get_instance()
+    cells, neuron_conns = my_instance.read_data()
+    neurons2muscles, muscles, muscle_conns = my_instance.read_muscle_data()
 
     analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns)