Use a quicker to run cell in the sscx example to speed up tests (#26)

emodelrunner/version.py

@@ -15,5 +15,5 @@
 # limitations under the License.
 
 
-VERSION = "1.0.13"
+VERSION = "1.0.14"
 __version__ = VERSION

examples/sscx_sample_dir/config/config_allsteps.ini

@@ -1,17 +1,48 @@
+[Synapses]
+add_synapses = False
+seed = 846515
+rng_settings_mode = Random123
+hoc_synapse_template_name = hoc_synapses
+
+[Paths]
+prot_path = config/protocols/allsteps.json
+features_path = config/features/cADpyr_L4PC.json
+unoptimized_params_path = config/params/pyr.json
+memodel_dir = .
+output_dir = %(memodel_dir)s/python_recordings
+params_path = %(memodel_dir)s/config/params/final.json
+units_path = %(memodel_dir)s/config/features/units.json
+templates_dir = %(memodel_dir)s/templates
+cell_template_path = %(templates_dir)s/cell_template_neurodamus.jinja2
+run_hoc_template_path = %(templates_dir)s/run_hoc.jinja2
+createsimulation_template_path = %(templates_dir)s/createsimulation.jinja2
+synapses_template_path = %(templates_dir)s/synapses.jinja2
+replace_axon_hoc_path = %(templates_dir)s/replace_axon_hoc.hoc
+syn_dir_for_hoc = %(memodel_dir)s/synapses
+syn_dir = %(memodel_dir)s/synapses
+syn_data_file = synapses.tsv
+syn_conf_file = synconf.txt
+syn_hoc_file = synapses.hoc
+syn_mtype_map = mtype_map.tsv
+simul_hoc_file = createsimulation.hoc
+cell_hoc_file = cell.hoc
+run_hoc_file = run.hoc
+morph_path = morphology/dend-C231296A-P4B2_axon-C200897C-P2_-_Scale_x1.000_y0.975_z1.000.asc
+
+[Morphology]
+mtype = _
+do_replace_axon = True
+
 [Cell]
 celsius = 34
 v_init = -80
-emodel = cADpyr_L5TPC
-gid = 4138379
-
-[Morphology]
-mtype = L5TPCa
+emodel = cADpyr_L4UPC
+gid = 2571167
 
 [Sim]
 dt = 0.025
+cvode_active = False
+
+[Protocol]
+apical_point_isec = 22
 
-[Paths]
-morph_path = morphology/dend-C270999B-P3_axon-C060110A3_-_Scale_x1.000_y0.950_z1.000.asc
-prot_path = config/protocols/allsteps.json
-features_path = config/features/cADpyr_L5PC.json
-unoptimized_params_path = config/params/pyr.json

examples/sscx_sample_dir/config/config_factsheets.ini

@@ -1,17 +1,48 @@
-[Cell]
-celsius = 34
-v_init = -70
-emodel = cADpyr_L5TPC
-gid = 4138379
+[Synapses]
+add_synapses = False
+seed = 846515
+rng_settings_mode = Random123
+hoc_synapse_template_name = hoc_synapses
+
+[Paths]
+prot_path = config/protocols/RmpRiTau.json
+features_path = config/features/cADpyr_L4PC.json
+unoptimized_params_path = config/params/pyr.json
+memodel_dir = .
+output_dir = %(memodel_dir)s/python_recordings
+params_path = %(memodel_dir)s/config/params/final.json
+units_path = %(memodel_dir)s/config/features/units.json
+templates_dir = %(memodel_dir)s/templates
+cell_template_path = %(templates_dir)s/cell_template_neurodamus.jinja2
+run_hoc_template_path = %(templates_dir)s/run_hoc.jinja2
+createsimulation_template_path = %(templates_dir)s/createsimulation.jinja2
+synapses_template_path = %(templates_dir)s/synapses.jinja2
+replace_axon_hoc_path = %(templates_dir)s/replace_axon_hoc.hoc
+syn_dir_for_hoc = %(memodel_dir)s/synapses
+syn_dir = %(memodel_dir)s/synapses
+syn_data_file = synapses.tsv
+syn_conf_file = synconf.txt
+syn_hoc_file = synapses.hoc
+syn_mtype_map = mtype_map.tsv
+simul_hoc_file = createsimulation.hoc
+cell_hoc_file = cell.hoc
+run_hoc_file = run.hoc
+morph_path = morphology/dend-C231296A-P4B2_axon-C200897C-P2_-_Scale_x1.000_y0.975_z1.000.asc
 
 [Morphology]
-mtype = L5TPCa
+mtype = _
+do_replace_axon = True
+
+[Cell]
+celsius = 34
+v_init = -80
+emodel = cADpyr_L4UPC
+gid = 2571167
 
 [Sim]
 dt = 0.025
+cvode_active = False
+
+[Protocol]
+apical_point_isec = 22
 
-[Paths]
-morph_path = morphology/dend-C270999B-P3_axon-C060110A3_-_Scale_x1.000_y0.950_z1.000.asc
-prot_path = config/protocols/RmpRiTau.json
-features_path = config/features/cADpyr_L5PC.json
-unoptimized_params_path = config/params/pyr.json

examples/sscx_sample_dir/config/config_multiprotocols.ini

@@ -1,26 +1,47 @@
-[Protocol]
-apical_point_isec=14
-
-[Sim]
-dt=0.025
-cvode_active=False
-
 [Synapses]
-add_synapses=True
-seed=846515
-rng_settings_mode=Random123
+add_synapses = True
+seed = 846515
+rng_settings_mode = Random123
+hoc_synapse_template_name = hoc_synapses
+
+[Paths]
+prot_path = config/protocols/multiprotocols.json
+features_path = config/features/cADpyr_L4PC.json
+unoptimized_params_path = config/params/pyr.json
+memodel_dir = .
+output_dir = %(memodel_dir)s/python_recordings
+params_path = %(memodel_dir)s/config/params/final.json
+units_path = %(memodel_dir)s/config/features/units.json
+templates_dir = %(memodel_dir)s/templates
+cell_template_path = %(templates_dir)s/cell_template_neurodamus.jinja2
+run_hoc_template_path = %(templates_dir)s/run_hoc.jinja2
+createsimulation_template_path = %(templates_dir)s/createsimulation.jinja2
+synapses_template_path = %(templates_dir)s/synapses.jinja2
+replace_axon_hoc_path = %(templates_dir)s/replace_axon_hoc.hoc
+syn_dir_for_hoc = %(memodel_dir)s/synapses
+syn_dir = %(memodel_dir)s/synapses
+syn_data_file = synapses.tsv
+syn_conf_file = synconf.txt
+syn_hoc_file = synapses.hoc
+syn_mtype_map = mtype_map.tsv
+simul_hoc_file = createsimulation.hoc
+cell_hoc_file = cell.hoc
+run_hoc_file = run.hoc
+morph_path = morphology/dend-C231296A-P4B2_axon-C200897C-P2_-_Scale_x1.000_y0.975_z1.000.asc
 
 [Morphology]
-mtype = L5TPCa
+mtype = _
+do_replace_axon = True
 
 [Cell]
 celsius = 34
 v_init = -80
-emodel = cADpyr_L5TPC
-gid = 4138379
+emodel = cADpyr_L4UPC
+gid = 2571167
 
-[Paths]
-morph_path = morphology/dend-C270999B-P3_axon-C060110A3_-_Scale_x1.000_y0.950_z1.000.asc
-prot_path = config/protocols/multiprotocols.json
-features_path = config/features/cADpyr_L5PC.json
-unoptimized_params_path = config/params/pyr.json
+[Sim]
+dt = 0.025
+cvode_active = False
+
+[Protocol]
+apical_point_isec = 22

examples/sscx_sample_dir/config/config_recipe_protocols.ini

@@ -1,20 +1,48 @@
-[Protocol]
-apical_point_isec=14
+[Synapses]
+add_synapses = False
+seed = 846515
+rng_settings_mode = Random123
+hoc_synapse_template_name = hoc_synapses
+
+[Paths]
+features_path = config/features/cADpyr_L4PC.json
+unoptimized_params_path = config/params/pyr.json
+prot_path = config/protocols/cADpyr_L4PC.json
+memodel_dir = .
+output_dir = %(memodel_dir)s/python_recordings
+params_path = %(memodel_dir)s/config/params/final.json
+units_path = %(memodel_dir)s/config/features/units.json
+templates_dir = %(memodel_dir)s/templates
+cell_template_path = %(templates_dir)s/cell_template_neurodamus.jinja2
+run_hoc_template_path = %(templates_dir)s/run_hoc.jinja2
+createsimulation_template_path = %(templates_dir)s/createsimulation.jinja2
+synapses_template_path = %(templates_dir)s/synapses.jinja2
+replace_axon_hoc_path = %(templates_dir)s/replace_axon_hoc.hoc
+syn_dir_for_hoc = %(memodel_dir)s/synapses
+syn_dir = %(memodel_dir)s/synapses
+syn_data_file = synapses.tsv
+syn_conf_file = synconf.txt
+syn_hoc_file = synapses.hoc
+syn_mtype_map = mtype_map.tsv
+simul_hoc_file = createsimulation.hoc
+cell_hoc_file = cell.hoc
+run_hoc_file = run.hoc
+morph_path = morphology/dend-C231296A-P4B2_axon-C200897C-P2_-_Scale_x1.000_y0.975_z1.000.asc
+
+[Morphology]
+mtype = _
+do_replace_axon = True
 
 [Cell]
 celsius = 34
 v_init = -80
-emodel = cADpyr_L5TPC
-gid = 4138379
-
-[Morphology]
-mtype = L5TPCa
+emodel = cADpyr_L4UPC
+gid = 2571167
 
 [Sim]
 dt = 0.025
+cvode_active = False
+
+[Protocol]
+apical_point_isec = 22
 
-[Paths]
-morph_path = morphology/dend-C270999B-P3_axon-C060110A3_-_Scale_x1.000_y0.950_z1.000.asc
-prot_path = config/protocols/cADpyr_L5PC.json
-features_path = config/features/cADpyr_L5PC.json
-unoptimized_params_path = config/params/pyr.json

examples/sscx_sample_dir/config/config_singlestep.ini

@@ -1,17 +1,48 @@
+[Synapses]
+add_synapses = False
+seed = 846515
+rng_settings_mode = Random123
+hoc_synapse_template_name = hoc_synapses
+
+[Paths]
+prot_path = config/protocols/singlestep.json
+features_path = config/features/cADpyr_L4PC.json
+unoptimized_params_path = config/params/pyr.json
+memodel_dir = .
+output_dir = %(memodel_dir)s/python_recordings
+params_path = %(memodel_dir)s/config/params/final.json
+units_path = %(memodel_dir)s/config/features/units.json
+templates_dir = %(memodel_dir)s/templates
+cell_template_path = %(templates_dir)s/cell_template_neurodamus.jinja2
+run_hoc_template_path = %(templates_dir)s/run_hoc.jinja2
+createsimulation_template_path = %(templates_dir)s/createsimulation.jinja2
+synapses_template_path = %(templates_dir)s/synapses.jinja2
+replace_axon_hoc_path = %(templates_dir)s/replace_axon_hoc.hoc
+syn_dir_for_hoc = %(memodel_dir)s/synapses
+syn_dir = %(memodel_dir)s/synapses
+syn_data_file = synapses.tsv
+syn_conf_file = synconf.txt
+syn_hoc_file = synapses.hoc
+syn_mtype_map = mtype_map.tsv
+simul_hoc_file = createsimulation.hoc
+cell_hoc_file = cell.hoc
+run_hoc_file = run.hoc
+morph_path = morphology/dend-C231296A-P4B2_axon-C200897C-P2_-_Scale_x1.000_y0.975_z1.000.asc
+
+[Morphology]
+mtype = _
+do_replace_axon = True
+
 [Cell]
 celsius = 34
 v_init = -80
-emodel = cADpyr_L5TPC
-gid = 4138379
-
-[Morphology]
-mtype = L5TPCa
+emodel = cADpyr_L4UPC
+gid = 2571167
 
 [Sim]
 dt = 0.025
+cvode_active = False
+
+[Protocol]
+apical_point_isec = 22
 
-[Paths]
-morph_path = morphology/dend-C270999B-P3_axon-C060110A3_-_Scale_x1.000_y0.950_z1.000.asc
-prot_path = config/protocols/singlestep.json
-features_path = config/features/cADpyr_L5PC.json
-unoptimized_params_path = config/params/pyr.json

examples/sscx_sample_dir/config/config_synapses.ini

@@ -1,23 +1,48 @@
-[Sim]
-dt=0.025
-cvode_active=False
-
 [Synapses]
-add_synapses=True
-seed=846515
-rng_settings_mode=Random123
+add_synapses = True
+seed = 846515
+rng_settings_mode = Random123
+hoc_synapse_template_name = hoc_synapses
+
+[Paths]
+prot_path = config/protocols/synapses.json
+features_path = config/features/cADpyr_L4PC.json
+unoptimized_params_path = config/params/pyr.json
+memodel_dir = .
+output_dir = %(memodel_dir)s/python_recordings
+params_path = %(memodel_dir)s/config/params/final.json
+units_path = %(memodel_dir)s/config/features/units.json
+templates_dir = %(memodel_dir)s/templates
+cell_template_path = %(templates_dir)s/cell_template_neurodamus.jinja2
+run_hoc_template_path = %(templates_dir)s/run_hoc.jinja2
+createsimulation_template_path = %(templates_dir)s/createsimulation.jinja2
+synapses_template_path = %(templates_dir)s/synapses.jinja2
+replace_axon_hoc_path = %(templates_dir)s/replace_axon_hoc.hoc
+syn_dir_for_hoc = %(memodel_dir)s/synapses
+syn_dir = %(memodel_dir)s/synapses
+syn_data_file = synapses.tsv
+syn_conf_file = synconf.txt
+syn_hoc_file = synapses.hoc
+syn_mtype_map = mtype_map.tsv
+simul_hoc_file = createsimulation.hoc
+cell_hoc_file = cell.hoc
+run_hoc_file = run.hoc
+morph_path = morphology/dend-C231296A-P4B2_axon-C200897C-P2_-_Scale_x1.000_y0.975_z1.000.asc
 
 [Morphology]
-mtype = L5TPCa
+mtype = _
+do_replace_axon = True
 
 [Cell]
 celsius = 34
 v_init = -80
-emodel = cADpyr_L5TPC
-gid = 4138379
+emodel = cADpyr_L4UPC
+gid = 2571167
+
+[Sim]
+dt = 0.025
+cvode_active = False
+
+[Protocol]
+apical_point_isec = 22
 
-[Paths]
-morph_path = morphology/dend-C270999B-P3_axon-C060110A3_-_Scale_x1.000_y0.950_z1.000.asc
-prot_path = config/protocols/synapses.json
-features_path = config/features/cADpyr_L5PC.json
-unoptimized_params_path = config/params/pyr.json