removing old commented code from plot

citrus/cli.py

@@ -1,50 +1,6 @@
 """CITRUS command line interface.
 
-See CITRUS/doc/CLI.md for more information.
-
-This tool can be used to run the simulation based on either:
-
-	1. A single configuration JSON file that specifies paths to genotype
-		data files.
-		
-		CITRUS_sim -c <path_to_config_file> 
-		
-	2. A single configuration JSON file and a list of paths to genotype
-		data files. The list of paths must be the same length as the
-		number of input source files in the configuration file (i.e. 
-		the length of the list under the 'input' key in the JSON). Any
-		paths in the configuration file will be ignored. The -g or
-		--genotype_files flag can be used to specify the paths to the
-		genotype files.
-		
-		CITRUS_sim -c <path_to_config_file> -g <path_to_genotype_file> \\
-			<path_to_genotype_file> ...
-			
-		CITRUS_sim -c <path_to_config_file> -g <path_to_genotype_file>
-
-Output:
-
-	If no additional flags are provided, output will be written to the
-	current working directory. The output will be a CSV file (output.csv)
-	containing sample IDs and all corresponding values from the simulation,
-	and a JSON file (sim_config.json) containing the simulation configuration
-	(including any random selections made by nodes).
-
-	If the -o or --output_dir flag is provided, if the directory does not
-	exist it will be created, and the output files will be saved to it. By
-	default the output files will be named output.csv and sim_config.json,
-	but these can be changed with the -f or --output_file_name and -j or
-	--output_config_json flags, respectively.
-
-	Output file will by default be a comma seperated CSV file. Use -t or
-	--tsv flag to instead save as a tab seperated TSV file.
-
-Example Usage:
-
-	CITRUS_sim -c config.json -o sim_results/output_dir
-
-	CITRUS_sim -c config.json -g genotype_file_1 genotype_file_2 \\
-		-o sim_results/output_dir -t -f my_output.tsv -j my_sim_config.json
+See CITRUS/doc/CLI.md and individual tools for more information.
 """
 
 import click
@@ -54,6 +10,9 @@
 def citrus():
 	pass
 
+"""
+citrus simulate
+"""
 @citrus.command(no_args_is_help=True)
 @click.option(
 	'-c', '--config_file', 
@@ -147,6 +106,9 @@ def simulate(
 		sep="\t" if tsv else ","
 	)
 
+"""
+citrus plot
+"""
 @citrus.command(no_args_is_help=True)
 @click.option(
 	'-c', '--config_file', 
@@ -183,6 +145,9 @@ def plot(config_file: str, out: str, format: str):
 	# Create a plot of the model
 	plot.visualize(input_spec=config, filename=out, img_format=format)
 
+"""
+citrus shap
+"""
 @citrus.command(no_args_is_help=True)
 @click.option(
 	'-c', '--config_file', 

pheno_sim/plot.py

@@ -162,68 +162,4 @@ def plot_graph_with_legend(sim_nodes, filename, img_format):
 	y_offset = (img.height - legend.height) // 2
 	combined.paste(legend, (img.width, y_offset))
 
-	combined.save(filename + '.' + img_format)
-
-
-# if __name__ == '__main__':
-
-# 	# dev
-# 	input_spec = '../benchmarking_mlcb/pheno_sim/sim_configs/xor_pheno_1.json'
-# 	filename = '../benchmarking_mlcb/pheno_sim/sim_configs/xor_pheno_1'
-# 	img_format = 'png'
-
-# 	# Generate sim object
-# 	sim = PhenoSimulation.from_JSON_file(input_spec)
-
-# 	# Add input nodes
-# 	sim_nodes = dict()
-
-# 	for input_source in sim.input_runner.input_sources:
-# 		for input_node in input_source.input_nodes:
-# 			sim_nodes[input_node.alias] = CITRUSNode(
-# 				alias=input_node.alias,
-# 				node_type='input',
-# 				class_name=type(input_node).__name__
-# 			)
-
-# 	# Add operator nodes
-# 	for sim_step in sim.simulation_steps:
-# 		step_alias = sim_step.alias
-# 		step_inputs = sim_step.inputs
-
-# 		if isinstance(step_inputs, str):
-# 			step_inputs = [step_inputs]
-# 		elif isinstance(step_inputs, dict):
-# 			step_inputs = list(step_inputs.values())
-
-# 		if isinstance(sim_step, AbstractBaseCombineFunctionNode):
-# 			step_type = 'combine'
-# 		else:
-# 			step_type = 'trans'
-
-# 		sim_nodes[step_alias] = CITRUSNode(
-# 			alias=step_alias,
-# 			inputs=step_inputs,
-# 			node_type=step_type,
-# 			class_name=type(sim_step).__name__
-# 		)
-
-# 	# Identify nodes that are of type 'combine'.
-# 	combine_nodes = [node for node in sim_nodes.values() if node.node_type == 'combine']
-
-# 	# For each combine node, identify its ancestors.
-# 	all_ancestor_nodes = set()
-# 	for combine_node in combine_nodes:
-# 		all_ancestor_nodes.update(get_ancestor_nodes(combine_node, sim_nodes))
-
-# 	# Change the node_type of ancestor nodes which are of type 'trans' to 'cis'.
-# 	for ancestor_node_alias in all_ancestor_nodes:
-# 		if sim_nodes[ancestor_node_alias].node_type == 'trans':
-# 			sim_nodes[ancestor_node_alias].node_type = 'cis'
-
-# 	# Print nodes
-# 	for k,v in sim_nodes.items():
-# 		print(f"{k}:\n\t{str(v)}")
-
-# 	# Plot the graph
-# 	plot_graph_with_legend(sim_nodes, filename, img_format)
+	combined.save(filename + '.' + img_format)