bmtool 0.5.7__tar.gz → 0.5.7.2__tar.gz

{bmtool-0.5.7 → bmtool-0.5.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.7
+Version: 0.5.7.2
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -30,6 +30,7 @@ Requires-Dist: questionary
 Requires-Dist: pynmodlt
 Requires-Dist: xarray
 Requires-Dist: fooof
+Requires-Dist: requests
 
 # bmtool
 A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.

{bmtool-0.5.7 → bmtool-0.5.7.2}/bmtool/SLURM.py

@@ -59,7 +59,12 @@ def submit_job(script_path):
 
 
 def send_teams_message(webhook,message):
-    # Message payload
+    """Sends a message to a teams channel or chat
+
+    Args:
+        webhook (str): A microsoft teams webhook
+        message (str): A message to send in the chat/channel
+    """
     message = {
         "text": f"{message}" 
     }
@@ -256,8 +261,11 @@ export OUTPUT_DIR={case_output_dir}
         return True
     
     def check_block_completed(self):
-        # Implement this method to check if all jobs are completed
-        # This should return True only if all jobs are in the COMPLETED state
+        """checks if all the jobs in the block have been completed by slurm
+
+        Returns:
+            bool: True if all block jobs have been ran, false if job is still running
+        """
         for job_id in self.job_ids:
             status = check_job_status(job_id)
             if status != 'COMPLETED': # can add PENDING here for debugging NOT FOR ACTUALLY USING IT 
@@ -266,8 +274,11 @@ export OUTPUT_DIR={case_output_dir}
 
 
     def check_block_running(self):
-        # Implement this method to check if all jobs are completed
-        # This should return True only if all jobs are in the COMPLETED state
+        """checks if a job is running
+
+        Returns:
+            bool: True if jobs are RUNNING false if anything else
+        """
         for job_id in self.job_ids:
             status = check_job_status(job_id)
             if status != 'RUNNING': # 
@@ -283,6 +294,7 @@ class SequentialBlockRunner:
         blocks (list): List of SimulationBlock instances to be run.
         json_editor (seedSweep or multiSweep): Instance of seedSweep to edit JSON file.
         param_values (list): List of values for the parameter to be modified.
+        webhook (str): a microsoft webhook for teams. When used will send teams messages to the hook!
     """
 
     def __init__(self, blocks, json_editor=None, param_values=None, check_interval=200,webhook=None):
@@ -322,9 +334,8 @@ class SequentialBlockRunner:
                 message = f"SIMULATION UPDATE: Block {i} has been submitted! There are {(len(self.blocks)-1)-i} left to be submitted"
                 send_teams_message(self.webhook,message)
 
-            time.sleep(self.check_interval)
             # Wait for the block to complete
-            if i == len(self.blocks): # we want to wait for the last block to be completed not just running
+            if i == len(self.blocks) - 1:  # Corrected index to check the last block
                 while not block.check_block_completed():
                     print(f"Waiting for the last block {i} to complete...")
                     time.sleep(self.check_interval)

{bmtool-0.5.7 → bmtool-0.5.7.2}/bmtool/bmplot.py

@@ -197,7 +197,7 @@ def probability_connection_matrix(config=None,nodes=None,edges=None,title=None,s
 
     return
 
-def convergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=True,method='mean+std',include_gap=True):
+def convergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=True,method='mean+std',include_gap=True,return_dict=None):
     """
     Generates connection plot displaying convergence data
     config: A BMTK simulation config 
@@ -213,9 +213,9 @@ def convergence_connection_matrix(config=None,title=None,sources=None, targets=N
         raise Exception("config not defined")
     if not sources or not targets:
         raise Exception("Sources or targets not defined")
-    return divergence_connection_matrix(config,title ,sources, targets, sids, tids, no_prepend_pop, save_file ,convergence, method,include_gap=include_gap)
+    return divergence_connection_matrix(config,title ,sources, targets, sids, tids, no_prepend_pop, save_file ,convergence, method,include_gap=include_gap,return_dict=return_dict)
 
-def divergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=False,method='mean+std',include_gap=True):
+def divergence_connection_matrix(config=None,title=None,sources=None, targets=None, sids=None, tids=None, no_prepend_pop=False,save_file=None,convergence=False,method='mean+std',include_gap=True,return_dict=None):
     """
     Generates connection plot displaying divergence data
     config: A BMTK simulation config 
@@ -264,8 +264,12 @@ def divergence_connection_matrix(config=None,title=None,sources=None, targets=No
             title = title + "Synaptic Convergence"
         else:
             title = title + "Synaptic Divergence"
-    plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file)
-    return
+    if return_dict:
+        dict = plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file,return_dict=return_dict)
+        return dict
+    else:
+        plot_connection_info(syn_info,data,source_labels,target_labels,title, save_file=save_file)
+        return
 
 def gap_junction_matrix(config=None,title=None,sources=None, targets=None, sids=None,tids=None, no_prepend_pop=False,save_file=None,type='convergence'):
     """
@@ -448,7 +452,7 @@ def edge_histogram_matrix(config=None,sources = None,targets=None,sids=None,tids
     fig.text(0.04, 0.5, 'Source', va='center', rotation='vertical')
     plt.draw()
 
-def plot_connection_info(text, num, source_labels,target_labels, title, syn_info='0', save_file=None):
+def plot_connection_info(text, num, source_labels,target_labels, title, syn_info='0', save_file=None,return_dict=None):
     """
     write about function here
     """
@@ -472,10 +476,12 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
     plt.setp(ax1.get_xticklabels(), rotation=45, ha="right",
             rotation_mode="anchor", size=12, weight = 'semibold')
     
+    graph_dict = {}
     # Loop over data dimensions and create text annotations.
     for i in range(num_source):
         for j in range(num_target):
             edge_info = text[i,j]
+            graph_dict[str(source_labels[i])+'2'+str(target_labels[j])] = edge_info
             if syn_info =='2' or syn_info =='3':
                 if num_source > 8 and num_source <20:
                     fig_text = ax1.text(j, i, edge_info,
@@ -499,7 +505,10 @@ def plot_connection_info(text, num, source_labels,target_labels, title, syn_info
         fig1.show()
     if save_file:
         plt.savefig(save_file)
-    return
+    if return_dict:
+        return graph_dict
+    else:
+        return
 
 def connector_percent_matrix(csv_path: str = None, exclude_shell: bool = True, 
                              exclude_assembly: bool = False, title: str = 'Percent connection matrix') -> None:

{bmtool-0.5.7 → bmtool-0.5.7.2}/bmtool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bmtool
-Version: 0.5.7
+Version: 0.5.7.2
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 
@@ -30,6 +30,7 @@ Requires-Dist: questionary
 Requires-Dist: pynmodlt
 Requires-Dist: xarray
 Requires-Dist: fooof
+Requires-Dist: requests
 
 # bmtool
 A collection of modules to make developing [Neuron](https://www.neuron.yale.edu/neuron/) and [BMTK](https://alleninstitute.github.io/bmtk/) models easier.

{bmtool-0.5.7 → bmtool-0.5.7.2}/bmtool.egg-info/requires.txt

@@ -10,3 +10,4 @@ questionary
 pynmodlt
 xarray
 fooof
+requests

{bmtool-0.5.7 → bmtool-0.5.7.2}/setup.py

@@ -6,7 +6,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name="bmtool",
-    version='0.5.7',
+    version='0.5.7.2',
     author="Neural Engineering Laboratory at the University of Missouri",
     author_email="gregglickert@mail.missouri.edu",
     description="BMTool",
@@ -27,7 +27,8 @@ setup(
         'questionary',
         'pynmodlt',
         'xarray',
-        'fooof'
+        'fooof',
+        'requests'
     ],
     classifiers=[
         'Intended Audience :: Developers',