From 0f008ab93382d74103badd888ef35d51a271ce0c Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 3 Sep 2024 10:44:12 +0100 Subject: [PATCH] More formatting --- c302/__init__.py | 1 + c302/backers.py | 4 +--- c302/c302_info.py | 12 +++++------ c302/c302_utils.py | 54 +++++++++++++++++++++++++--------------------- test.sh | 2 ++ 5 files changed, 39 insertions(+), 34 deletions(-) diff --git a/c302/__init__.py b/c302/__init__.py index 1c4171c6..7fd9add6 100755 --- a/c302/__init__.py +++ b/c302/__init__.py @@ -79,6 +79,7 @@ def load_data_reader(data_reader="SpreadsheetDataReader"): reader (obj): The data reader object """ return importlib.import_module("c302.%s" % data_reader) + # return importlib.import_module("cect.%s" % data_reader) def get_str_from_expnotation(num): diff --git a/c302/backers.py b/c302/backers.py index 7635a0a9..5556fa9a 100644 --- a/c302/backers.py +++ b/c302/backers.py @@ -41,9 +41,7 @@ def get_adopted_cell_names(root=os.path.dirname(os.path.abspath(__file__)) + "/d info += "----------\n\n" info += "Adopted name: **" + name + "**\n\n\n" i = 0 - search_file = open( - "../examples/c302_A_Full.nml", "r" - ) + search_file = open("../examples/c302_A_Full.nml", "r") for line in search_file: i += 1 if 'tag="OpenWormBackerAssignedName" value="%s"' % name in line: diff --git a/c302/c302_info.py b/c302/c302_info.py index e6ad0cbe..550a78d7 100644 --- a/c302/c302_info.py +++ b/c302/c302_info.py @@ -27,13 +27,13 @@ def generate_c302_info(nml_doc, verbose=False): for c in cp.continuous_connection_instance_ws: if "inh" in c.post_component: - cc_inh_conns[cp.presynaptic_population][ - cp.postsynaptic_population - ] = float(c.weight) + cc_inh_conns[cp.presynaptic_population][cp.postsynaptic_population] = ( + float(c.weight) + ) else: - cc_exc_conns[cp.presynaptic_population][ - cp.postsynaptic_population - ] = float(c.weight) + cc_exc_conns[cp.presynaptic_population][cp.postsynaptic_population] = ( + float(c.weight) + ) gj_conns = {} for ep in net.electrical_projections: diff --git a/c302/c302_utils.py b/c302/c302_utils.py index d50b1927..bc2a0d4f 100644 --- a/c302/c302_utils.py +++ b/c302/c302_utils.py @@ -483,13 +483,13 @@ def generate_conn_matrix( for c in cp.continuous_connection_instance_ws: if "inh" in c.post_component: - cc_inh_conns[cp.presynaptic_population][ - cp.postsynaptic_population - ] = float(c.weight) + cc_inh_conns[cp.presynaptic_population][cp.postsynaptic_population] = ( + float(c.weight) + ) else: - cc_exc_conns[cp.presynaptic_population][ - cp.postsynaptic_population - ] = float(c.weight) + cc_exc_conns[cp.presynaptic_population][cp.postsynaptic_population] = ( + float(c.weight) + ) gj_conns = {} for ep in net.electrical_projections: @@ -546,13 +546,13 @@ def generate_conn_matrix( "Exc Conn %s -> %s: %s" % (pre, post, cc_exc_conns[pre][post]), verbose ) if post in all_neurons: - data_exc_n[ - all_neurons.index(pre), all_neurons.index(post) - ] = cc_exc_conns[pre][post] + data_exc_n[all_neurons.index(pre), all_neurons.index(post)] = ( + cc_exc_conns[pre][post] + ) else: - data_exc_m[ - all_neurons.index(pre), all_muscles.index(post) - ] = cc_exc_conns[pre][post] + data_exc_m[all_neurons.index(pre), all_muscles.index(post)] = ( + cc_exc_conns[pre][post] + ) if pre in all_muscles: raise Exception("Unexpected...") @@ -562,13 +562,13 @@ def generate_conn_matrix( "Inh Conn %s -> %s: %s" % (pre, post, cc_inh_conns[pre][post]), verbose ) if post in all_neurons: - data_inh_n[ - all_neurons.index(pre), all_neurons.index(post) - ] = cc_inh_conns[pre][post] + data_inh_n[all_neurons.index(pre), all_neurons.index(post)] = ( + cc_inh_conns[pre][post] + ) else: - data_inh_m[ - all_neurons.index(pre), all_muscles.index(post) - ] = cc_inh_conns[pre][post] + data_inh_m[all_neurons.index(pre), all_muscles.index(post)] = ( + cc_inh_conns[pre][post] + ) if pre in all_muscles: raise Exception("Unexpected...") @@ -652,13 +652,13 @@ def generate_conn_matrix( and post in all_neurons ): if pre in all_neurons: - data_n_m[ - all_neurons.index(pre), all_muscles.index(post) - ] = gj_conns[pre][post] + data_n_m[all_neurons.index(pre), all_muscles.index(post)] = ( + gj_conns[pre][post] + ) else: - data_n_m[ - all_muscles.index(pre), all_neurons.index(post) - ] = gj_conns[pre][post] + data_n_m[all_muscles.index(pre), all_neurons.index(post)] = ( + gj_conns[pre][post] + ) neuron_muscle = True elif pre in all_muscles and post in all_muscles: muscle_muscle = True @@ -736,7 +736,7 @@ def generate_conn_matrix( colormap = None if "-phar" in sys.argv: - configs = ["c302_C0_Pharyngeal.net.nml"] + configs = ["c302_C1_Pharyngeal.net.nml"] elif "-osc" in sys.argv: configs = ["c302_C1_Oscillator.net.nml"] @@ -744,6 +744,10 @@ def generate_conn_matrix( elif "-soc" in sys.argv: configs = ["c302_C1_Social.net.nml"] + elif "-syns" in sys.argv: + configs = ["c302_C1_Syns.net.nml"] + figsize = (10, 10) + elif "-musc" in sys.argv: configs = ["c302_C1_Muscles.net.nml"] figsize = (10, 10) diff --git a/test.sh b/test.sh index f6919554..367452f6 100755 --- a/test.sh +++ b/test.sh @@ -1,5 +1,7 @@ set -ex +pip install . + ## Test readers python -m c302.SpreadsheetDataReader