bmtool 0.6.8.8__py3-none-any.whl → 0.6.9__py3-none-any.whl

bmtool/SLURM.py

@@ -6,6 +6,7 @@ import requests
 import shutil
 import time
 import copy
+import numpy as np
 
 
 def check_job_status(job_id):
@@ -205,12 +206,12 @@ class SimulationBlock:
         case_output_dir = os.path.join(block_output_dir, case_name)  # Create case-specific output folder
         os.makedirs(case_output_dir, exist_ok=True)
 
-        batch_script_path = os.path.join(block_output_dir, 'script.sh')
+        batch_script_path = os.path.join(block_output_dir, f'{case_name}_script.sh')
         additional_commands_str = "\n".join(self.additional_commands)
         # Conditional account linegit
         account_line = f"#SBATCH --account={self.account}\n" if self.account else ""
         env_var_component_path = f"export COMPONENT_PATH={self.component_path}" if self.component_path else ""
-        mem_per_cpu = int(int(self.mem)/int(self.ntasks))
+        mem_per_cpu = int(np.ceil(int(self.mem)/int(self.ntasks))) # do ceil cause more mem is always better then less
 
         # Write the batch script to the file
         with open(batch_script_path, 'w') as script_file:
@@ -333,6 +334,7 @@ def globus_transfer(source_endpoint, dest_endpoint, source_path, dest_path):
     """
     Transfers file using custom globus transfer function. 
     For more info see https://github.com/GregGlickert/transfer-files/blob/main/globus_transfer.sh
+    work in progress still... kinda forgot about this 
     """
     relative_source_path = get_relative_path(source_endpoint, source_path)
     if relative_source_path is None:
@@ -379,7 +381,7 @@ class BlockRunner:
                 source_dir = block.component_path
                 destination_dir = f"{source_dir}{i+1}"
                 block.component_path = destination_dir
-                shutil.copytree(source_dir, destination_dir) # create new components folder 
+                shutil.copytree(source_dir, destination_dir,dirs_exist_ok = True) # create new components folder 
                 print(f"skipping json editing for block {block.block_name}",flush=True)
             else:
                 if len(self.blocks) != len(self.param_values):
@@ -390,7 +392,7 @@ class BlockRunner:
                 destination_dir = f"{source_dir}{i+1}"
                 block.component_path = destination_dir
 
-                shutil.copytree(source_dir, destination_dir) # create new components folder
+                shutil.copytree(source_dir, destination_dir,dirs_exist_ok = True) # create new components folder
                 json_file_path = os.path.join(destination_dir,self.json_file_path)
                 
                 if self.syn_dict == None:
@@ -439,7 +441,7 @@ class BlockRunner:
                 source_dir = block.component_path
                 destination_dir = f"{source_dir}{i+1}"
                 block.component_path = destination_dir
-                shutil.copytree(source_dir, destination_dir) # create new components folder 
+                shutil.copytree(source_dir, destination_dir,dirs_exist_ok = True) # create new components folder 
                 print(f"skipping json editing for block {block.block_name}",flush=True)
             else:
                 if block.component_path == None:
@@ -450,7 +452,7 @@ class BlockRunner:
                 destination_dir = f"{source_dir}{i+1}"
                 block.component_path = destination_dir
 
-                shutil.copytree(source_dir, destination_dir) # create new components folder 
+                shutil.copytree(source_dir, destination_dir,dirs_exist_ok = True) # create new components folder 
                 json_file_path = os.path.join(destination_dir,self.json_file_path)
                 
                 if self.syn_dict == None:

bmtool/analysis/lfp.py

@@ -768,7 +768,6 @@ def cwt_spectrogram_xarray(x, fs, time=None, axis=-1, downsample_fs=None,
     fs: sampling frequency (Hz)
     axis: dimension index of time axis in x
     downsample_fs: downsample to the frequency if specified
-    time_unit: unit of time in seconds
     channel_coords: dictionary of {coordinate name: index} for channels
     cwt_kwargs: keyword arguments for cwt_spectrogram()
     """

{bmtool-0.6.8.8.dist-info → bmtool-0.6.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bmtool
-Version: 0.6.8.8
+Version: 0.6.9
 Summary: BMTool
 Home-page: https://github.com/cyneuro/bmtool
 Download-URL: 

{bmtool-0.6.8.8.dist-info → bmtool-0.6.9.dist-info}/RECORD

@@ -1,4 +1,4 @@
-bmtool/SLURM.py,sha256=umHYGUX2HDlZr6Zo89wQekGrK9mZdAi0rBdCA7a--hE,19904
+bmtool/SLURM.py,sha256=PST_jOD5ZmwbJj15Tgq3UIvdq4FYN4EkPuDt66P8OXU,20136
 bmtool/__init__.py,sha256=ZStTNkAJHJxG7Pwiy5UgCzC4KlhMS5pUNPtUJZVwL_Y,136
 bmtool/__main__.py,sha256=TmFkmDxjZ6250nYD4cgGhn-tbJeEm0u-EMz2ajAN9vE,650
 bmtool/bmplot.py,sha256=ymyrNBctZoglsNA28733mXzM_l4b_3JIchXkQa2V2XE,54099
@@ -9,7 +9,7 @@ bmtool/plot_commands.py,sha256=Tqujyf0c0u8olhiHOMwgUSJXIIE1hgjv6otb25G9cA0,12298
 bmtool/singlecell.py,sha256=XZAT_2n44EhwqVLnk3qur9aO7oJ-10axJZfwPBslM88,27219
 bmtool/synapses.py,sha256=gIkfLhKDG2dHHCVJJoKuQrFn_Qut843bfk_-s97wu6c,54553
 bmtool/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bmtool/analysis/lfp.py,sha256=TfPSLIh2LqbWTRFnYwBMBpfbj6yxyhC7EAQM1e2H4qs,33609
+bmtool/analysis/lfp.py,sha256=KTDMzqhkpTI308sWqoJnbHeCMSFScaJCO4u50Kd4FzA,33570
 bmtool/analysis/spikes.py,sha256=qqJ4zD8xfvSwltlWm_Bhicdngzl6uBqH6Kn5wOMKRc8,11507
 bmtool/debug/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/debug/commands.py,sha256=AwtcR7BUUheM0NxvU1Nu234zCdpobhJv5noX8x5K2vY,583
@@ -19,9 +19,9 @@ bmtool/util/commands.py,sha256=zJF-fiLk0b8LyzHDfvewUyS7iumOxVnj33IkJDzux4M,64396
 bmtool/util/util.py,sha256=00vOAwTVIifCqouBoFoT0lBashl4fCalrk8fhg_Uq4c,56654
 bmtool/util/neuron/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 bmtool/util/neuron/celltuner.py,sha256=xSRpRN6DhPFz4q5buq_W8UmsD7BbUrkzYBEbKVloYss,87194
-bmtool-0.6.8.8.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
-bmtool-0.6.8.8.dist-info/METADATA,sha256=IqLuFdtSCGW_gxwgU8vD543KUj19fP-dhTbeSG_6HNg,20478
-bmtool-0.6.8.8.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-bmtool-0.6.8.8.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
-bmtool-0.6.8.8.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
-bmtool-0.6.8.8.dist-info/RECORD,,
+bmtool-0.6.9.dist-info/licenses/LICENSE,sha256=qrXg2jj6kz5d0EnN11hllcQt2fcWVNumx0xNbV05nyM,1068
+bmtool-0.6.9.dist-info/METADATA,sha256=D2t3-ElmKHpCIuvyafzqlihr6xaeeG-0aabZJXkeXMU,20476
+bmtool-0.6.9.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+bmtool-0.6.9.dist-info/entry_points.txt,sha256=0-BHZ6nUnh0twWw9SXNTiRmKjDnb1VO2DfG_-oprhAc,45
+bmtool-0.6.9.dist-info/top_level.txt,sha256=gpd2Sj-L9tWbuJEd5E8C8S8XkNm5yUE76klUYcM-eWM,7
+bmtool-0.6.9.dist-info/RECORD,,