bluecellulab 2.6.61__py3-none-any.whl → 2.6.63__py3-none-any.whl

bluecellulab/validation/validation.py

@@ -337,7 +337,7 @@ def rin_test(rin):
     }
 
 
-def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
+def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30., n_processes=None):
     """IV curve should have a positive slope."""
     name = "Simulatable Neuron IV Curve Validation"
     amps, steady_states = compute_plot_iv_curve(
@@ -348,7 +348,9 @@ def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
         show_figure=False,
         save_figure=True,
         output_dir=out_dir,
-        output_fname="iv_curve.pdf")
+        output_fname="iv_curve.pdf",
+        n_processes=n_processes,
+    )
 
     outpath = pathlib.Path(out_dir) / "iv_curve.pdf"
 
@@ -375,7 +377,7 @@ def iv_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
     }
 
 
-def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
+def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30., n_processes=None):
     """FI curve should have a positive slope."""
     name = "Simulatable Neuron FI Curve Validation"
     amps, spike_counts = compute_plot_fi_curve(
@@ -386,7 +388,9 @@ def fi_test(template_params, rheobase, out_dir, spike_threshold_voltage=-30.):
         show_figure=False,
         save_figure=True,
         output_dir=out_dir,
-        output_fname="fi_curve.pdf")
+        output_fname="fi_curve.pdf",
+        n_processes=n_processes,
+    )
 
     outpath = pathlib.Path(out_dir) / "fi_curve.pdf"
 
@@ -448,7 +452,8 @@ def run_validations(
     spike_threshold_voltage=-30,
     v_init=-80.0,
     celsius=34.0,
-    output_dir="./memodel_validation_figures"
+    output_dir="./memodel_validation_figures",
+    n_processes=None,
 ):
     """Run all the validations on the cell.
 
@@ -459,6 +464,9 @@ def run_validations(
         v_init: Initial membrane potential. Default is -80.0 mV.
         celsius: Temperature in Celsius. Default is 34.0.
         output_dir (str): The directory to save the validation figures.
+        n_processes (int, optional): The number of processes to use for parallel execution
+            in IV and FI curves computation. If None or higher than the number of steps,
+            then it will use the number of steps as the number of processes instead.
     """
     out_dir = pathlib.Path(output_dir) / cell_name
     out_dir.mkdir(parents=True, exist_ok=True)
@@ -484,41 +492,68 @@ def run_validations(
     )
 
     logger.debug("Running validations...")
-    # Validation 1: Spiking Test
-    spiking_test_result = spiking_test(
-        cell.template_params, rheobase, out_dir, spike_threshold_voltage
-    )
+    from bluecellulab.utils import NestedPool
+    val_n_processes = n_processes if n_processes is not None else 7
+    with NestedPool(processes=val_n_processes) as pool:
+        # Validation 1: Spiking Test
+        spiking_test_result_future = pool.apply_async(
+            spiking_test,
+            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
+        )
 
-    # Validation 2: Depolarization Block Test
-    depolarization_block_result = depolarization_block_test(
-        cell.template_params, rheobase, out_dir
-    )
+        # Validation 2: Depolarization Block Test
+        depolarization_block_result_future = pool.apply_async(
+            depolarization_block_test,
+            (cell.template_params, rheobase, out_dir)
+        )
 
-    # Validation 3: Backpropagating AP Test
-    bpap_result = bpap_test(cell.template_params, rheobase, out_dir)
+        # Validation 3: Backpropagating AP Test
+        bpap_result_future = pool.apply_async(
+            bpap_test,
+            (cell.template_params, rheobase, out_dir)
+        )
 
-    # Validation 4: Postsynaptic Potential Test
-    # We have to wait for ProbAMPANMDA_EMS to be present in entitycore to implement this test
+        # Validation 4: Postsynaptic Potential Test
+        # We have to wait for ProbAMPANMDA_EMS to be present in entitycore to implement this test
 
-    # Validation 5: AIS Spiking Test
-    ais_spiking_test_result = ais_spiking_test(
-        cell.template_params, rheobase, out_dir, spike_threshold_voltage
-    )
+        # Validation 5: AIS Spiking Test
+        ais_spiking_test_result_future = pool.apply_async(
+            ais_spiking_test,
+            (cell.template_params, rheobase, out_dir, spike_threshold_voltage)
+        )
 
-    # Validation 6: Hyperpolarization Test
-    hyperpolarization_result = hyperpolarization_test(cell.template_params, rheobase, out_dir)
+        # Validation 6: Hyperpolarization Test
+        hyperpolarization_result_future = pool.apply_async(
+            hyperpolarization_test,
+            (cell.template_params, rheobase, out_dir)
+        )
 
-    # Validation 7: Rin Test
-    rin_result = rin_test(rin)
+        # Validation 7: Rin Test
+        rin_result_future = pool.apply_async(
+            rin_test,
+            (rin,)
+        )
 
+        # Validation 10: Thumbnail Test
+        thumbnail_result_future = pool.apply_async(
+            thumbnail_test,
+            (cell.template_params, rheobase, out_dir)
+        )
+
+        spiking_test_result = spiking_test_result_future.get()
+        depolarization_block_result = depolarization_block_result_future.get()
+        bpap_result = bpap_result_future.get()
+        ais_spiking_test_result = ais_spiking_test_result_future.get()
+        hyperpolarization_result = hyperpolarization_result_future.get()
+        rin_result = rin_result_future.get()
+        thumbnail_result = thumbnail_result_future.get()
+
+    # IV and FI tests are outside of nestedpool, because they use multiprocessing internaly
     # Validation 8: IV Test
-    iv_test_result = iv_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
+    iv_test_result = iv_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage, n_processes)
 
     # Validation 9: FI Test
-    fi_test_result = fi_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage)
-
-    # Validation 10: Thumbnail Test
-    thumbnail_result = thumbnail_test(cell.template_params, rheobase, out_dir)
+    fi_test_result = fi_test(cell.template_params, rheobase, out_dir, spike_threshold_voltage, n_processes)
 
     return {
         "memodel_properties": {

{bluecellulab-2.6.61.dist-info → bluecellulab-2.6.63.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bluecellulab
-Version: 2.6.61
+Version: 2.6.63
 Summary: Biologically detailed neural network simulations and analysis.
 Author: Blue Brain Project, EPFL
 License: Apache2.0

{bluecellulab-2.6.61.dist-info → bluecellulab-2.6.63.dist-info}/RECORD

@@ -1,5 +1,5 @@
 bluecellulab/__init__.py,sha256=1d_CKIJLIpon7o13h3lBnV_-33obZEPwa9KDTjlFPD8,880
-bluecellulab/circuit_simulation.py,sha256=N_kMjWykpt_UouvwCp-7g0o0NMd_1jB4IHxWplEvEME,39294
+bluecellulab/circuit_simulation.py,sha256=CryoBSUGc9z6nIAyNzCsyppeSlc_URJX6hZoZPgQI2Q,36807
 bluecellulab/connection.py,sha256=-xT0mU7ppeHI_qjCKj17TtxXVVcUDgBsaMKt9ODmcEU,4640
 bluecellulab/dendrogram.py,sha256=FjS6RZ6xcp5zJoY5d5qv_edqPM13tL2-UANgbZuDBjY,6427
 bluecellulab/exceptions.py,sha256=1lKD92VIyD8cUggAI1SLxeKzj_09Ik_TlHCzPLCvDHg,2379
@@ -15,7 +15,7 @@ bluecellulab/type_aliases.py,sha256=DvgjERv2Ztdw_sW63JrZTQGpJ0x5uMTFB5hcBHDb0WA,
 bluecellulab/utils.py,sha256=0NhwlzyLnSi8kziSfDsQf7pokO4qDkMJVAO33kSX4O0,2227
 bluecellulab/verbosity.py,sha256=T0IgX7DrRo19faxrT4Xzb27gqxzoILQ8FzYKxvUeaPM,1342
 bluecellulab/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bluecellulab/analysis/analysis.py,sha256=O2nKHdVqVuL8SP_Q-FjyaRyHJdJCf0315bNrCTVies4,21611
+bluecellulab/analysis/analysis.py,sha256=W5MBCJthuuA7fFEJRZExONjTEWOhgDbtmTq23Cv7fbc,22449
 bluecellulab/analysis/inject_sequence.py,sha256=bpi_C1oz_G5cZv_CvvZG8SnGYaKIlDsIFHdkOAkDm-E,12666
 bluecellulab/analysis/plotting.py,sha256=PqRoaZz33ULMw8A9YnZXXrxcUd84M_dwlYMTFhG7YT4,3999
 bluecellulab/analysis/utils.py,sha256=eMirP557D11BuedgSqjripDxOq1haIldNbnYNetV1bg,121
@@ -38,7 +38,7 @@ bluecellulab/circuit/__init__.py,sha256=Khpa13nzNvDlDS2JduyoFTukEduEkWCc5ML_JwGp
 bluecellulab/circuit/format.py,sha256=90gWOXg6HK0R9a4WFSnnRH8XezxmzOGk5dRpJHbvbbU,1674
 bluecellulab/circuit/iotools.py,sha256=Q65xYDaiensMtrulC3OLsS2_hcWr_Kje0nXFrAizMMo,1589
 bluecellulab/circuit/node_id.py,sha256=FdoFAGq0_sCyQySOuNI0chdbVr3L8R0w2Y1em5MyIDA,1265
-bluecellulab/circuit/simulation_access.py,sha256=keME58gzLVAPEg2nnWD_bwEm9V2Kjeqyfoj_55GPMCM,7061
+bluecellulab/circuit/simulation_access.py,sha256=8LX5nbKw_Hu7AR3pGLdTFGwehvhaj-r8Mh1q3dVoiVg,7745
 bluecellulab/circuit/synapse_properties.py,sha256=TvUMiXZAAeYo1zKkus3z1EUvrE9QCIQ3Ze-jSnPSJWY,6374
 bluecellulab/circuit/validate.py,sha256=wntnr7oIDyasqD1nM-kqz1NpfWDxBGhx0Ep3e5hHXIw,3593
 bluecellulab/circuit/circuit_access/__init__.py,sha256=sgp6m5kP-pq60V1IFGUiSUR1OW01zdxXNNUJmPA8anI,201
@@ -47,19 +47,26 @@ bluecellulab/circuit/circuit_access/definition.py,sha256=_sUU0DkesGOFW82kS1G9vki
 bluecellulab/circuit/circuit_access/sonata_circuit_access.py,sha256=tADHxVZw4VgZAz2z4NKMUwc0rd_EO40EZggw5fDhnF4,10411
 bluecellulab/circuit/config/__init__.py,sha256=aaoJXRKBJzpxxREo9NxKc-_CCPmVeuR1mcViRXcLrC4,215
 bluecellulab/circuit/config/bluepy_simulation_config.py,sha256=V3eqOzskX7VrMDpl-nMQVEhDg8QWgRmRduyJBii5sgI,6974
-bluecellulab/circuit/config/definition.py,sha256=I1jd4KUX21mw03FEv1aYNsT0UFbDANY3YEPwwKXqe4k,2774
+bluecellulab/circuit/config/definition.py,sha256=cotKRDHOjzZKNgNSrZ29voU-66W8jaGt5yuge1hyv18,2953
 bluecellulab/circuit/config/sections.py,sha256=QRnU44-OFvHxcF1LX4bAEP9dk3I6UKsuPNBbWkdfmRE,7151
-bluecellulab/circuit/config/sonata_simulation_config.py,sha256=BlezWJ3dRNIu0Xs6gocscX5X69u45FSrqBtYWRTdhi4,6936
+bluecellulab/circuit/config/sonata_simulation_config.py,sha256=J1DFqNxIJKAxD1KU_oJV9tigMdpT_Not0Q8SF5q2EeQ,7271
 bluecellulab/hoc/Cell.hoc,sha256=z77qRQG_-afj-RLX0xN6V-K6Duq3bR7vmlDrGWPdh4E,16435
 bluecellulab/hoc/RNGSettings.hoc,sha256=okJBdqlPXET8BrpG1Q31GdaxHfpe3CE0L5P7MAhfQTE,1227
 bluecellulab/hoc/TDistFunc.hoc,sha256=WKX-anvL83xGuGPH9g1oIORB17UM4Pi3-iIXzKO-pUQ,2663
 bluecellulab/hoc/TStim.hoc,sha256=noBJbM_ZqF6T6MEgBeowNzz21I9QeYZ5brGgUvCSm4k,8473
 bluecellulab/hoc/fileUtils.hoc,sha256=LSM7BgyjYVqo2DGSOKvg4W8IIusbsL45JVYK0vgwitU,2539
+bluecellulab/reports/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+bluecellulab/reports/manager.py,sha256=hy54B7AXa46bgjKJ_Ar65_GYIu9C8Zg2fgxIlxSweRE,3284
+bluecellulab/reports/utils.py,sha256=yZPtO0HXs6HPDVOZQbeXlPajnSOqE2Qmx8VufQFJFT0,5557
+bluecellulab/reports/writers/__init__.py,sha256=Q8Y2GC83jseH5QY9IlEQsvaUQIH-BzgqhVjGRWD5j90,826
+bluecellulab/reports/writers/base_writer.py,sha256=P5ramFD2oFIroEBCH1pAscbkfcBIVYFIBg4pVpSP2IU,1042
+bluecellulab/reports/writers/compartment.py,sha256=EwFc2NwqhGEwGShEFOIrpYWRgH4b7qZCwsPvpUxeboU,7212
+bluecellulab/reports/writers/spikes.py,sha256=ycMuoT6f-UbAbC47X9gkG44OQYeAGBQMB2RdJAq3Ykg,2558
 bluecellulab/simulation/__init__.py,sha256=P2ebt0SFw-08J3ihN-LeRn95HeF79tzA-Q0ReLm32dM,214
 bluecellulab/simulation/neuron_globals.py,sha256=iBjhg0-1YMP5LsVdtUDt24PEypkCL6mlyzEBZqoS8xo,4508
 bluecellulab/simulation/parallel.py,sha256=oQ_oV2EKr8gP4yF2Dq8q9MiblDyi89_wBgLzQkLV_U0,1514
-bluecellulab/simulation/report.py,sha256=i_VjwIkDnHHAUk4Tx2F5LhaeBVBctcOzchK_8nG6NFw,10474
-bluecellulab/simulation/simulation.py,sha256=VhftOMYU1Rfrphvud6f0U4kvbUivSviQ5TlVljuTb88,6486
+bluecellulab/simulation/report.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+bluecellulab/simulation/simulation.py,sha256=OfrzeHvLmOV2ptYcGie_fVGrtkDfizLpE6ZyQWVxnIE,6492
 bluecellulab/stimulus/__init__.py,sha256=DgIgVaSyR-URf3JZzvO6j-tjCerzvktuK-ep8pjMRPQ,37
 bluecellulab/stimulus/circuit_stimulus_definitions.py,sha256=h_SqjJ-L3yNxiEO8I6Cy7i-lhfZXjrdCc92dl8bjOog,17229
 bluecellulab/stimulus/factory.py,sha256=4fvVFFjOGHSqBidLe_W1zQozfMEeePXWO6yYCs30-SM,30780
@@ -67,10 +74,10 @@ bluecellulab/stimulus/stimulus.py,sha256=a_hKJUtZmIgjiFjbJf6RzUPokELqn0IHCgIWGw5
 bluecellulab/synapse/__init__.py,sha256=RW8XoAMXOvK7OG1nHl_q8jSEKLj9ZN4oWf2nY9HAwuk,192
 bluecellulab/synapse/synapse_factory.py,sha256=NHwRMYMrnRVm_sHmyKTJ1bdoNmWZNU4UPOGu7FCi-PE,6987
 bluecellulab/synapse/synapse_types.py,sha256=zs_yBvGTH4QrbQF3nEViidyq1WM_ZcTSFdjUxB3khW0,16871
-bluecellulab/validation/validation.py,sha256=vLaOAyCO1qwwQ5Ud9X9NDX3iSsh_2S5tUA9xRmoDHiA,18465
-bluecellulab-2.6.61.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
-bluecellulab-2.6.61.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
-bluecellulab-2.6.61.dist-info/METADATA,sha256=DiUIlPkw6xJkCmmFK2tCHbfeaoY3VdsUAMFsK-iN6BE,8259
-bluecellulab-2.6.61.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-bluecellulab-2.6.61.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
-bluecellulab-2.6.61.dist-info/RECORD,,
+bluecellulab/validation/validation.py,sha256=csy1xKOOWdlo3NYHdknePPxb7KBRTjoUV-81ZmWo2CM,20041
+bluecellulab-2.6.63.dist-info/licenses/AUTHORS.txt,sha256=EDs3H-2HXBojbma10psixk3C2rFiOCTIREi2ZAbXYNQ,179
+bluecellulab-2.6.63.dist-info/licenses/LICENSE,sha256=dAMAR2Sud4Nead1wGFleKiwTZfkTNZbzmuGfcTKb3kg,11335
+bluecellulab-2.6.63.dist-info/METADATA,sha256=J9j4rWRv1plUDoTz99tw1JxhVUNpJq4f1jk6qbLM5p4,8259
+bluecellulab-2.6.63.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+bluecellulab-2.6.63.dist-info/top_level.txt,sha256=VSyEP8w9l3pXdRkyP_goeMwiNA8KWwitfAqUkveJkdQ,13
+bluecellulab-2.6.63.dist-info/RECORD,,