Merge pull request #64 from tahiri-lab/update-cli

Refactor CLI to handle help command and following clig.dev guidelines

.gitignore

@@ -33,3 +33,7 @@ aphylogeo/bin/*.fasta
 
 #Output
 *.dnd
+
+#Ignore process files
+datasets/example/geneticTrees.json
+result.csv

Makefile

@@ -1,5 +1,5 @@
 aPhylogeo:
-	python aphylogeo/main.py
+	python aphylogeo/main.py run
 
 .PHONY: clean
 

aphylogeo/main.py

@@ -1,3 +1,5 @@
+import sys
+
 import pandas as pd
 import time
 from aphylogeo.alignement import AlignSequences
@@ -21,17 +23,23 @@
                               \/__/
 """  # https://patorjk.com/software/taag/#p=display&f=Larry%203D&t=aphylogeo%20
 
-app = typer.Typer(invoke_without_command=True)
+app = typer.Typer(
+    invoke_without_command=False,
+    help="A tool for processing climatic and genetic data to generate phylogenetic trees.",
+    callback=lambda: typer.echo(typer.style(titleCard, fg=typer.colors.GREEN))
+)
 
 @app.command()
 def climate_pipeline(
         file_name: str = typer.Option(Params.PARAMETER_KEYS["file_name"], help="The name of the file containing the climatic data."),
         output: str = typer.Option("./datasets/example/climaticTrees.nwk", help="The name of the file to save the climatic trees."),
     ):
     """
-    This function is used to run the climatic pipeline that creates the climatic trees.
+    Run the climatic pipeline that process the climatic trees.
+
     Args:
         file_name (str): The name of the file containing the climatic data.
+        output (str): The name of the file to save the climatic trees.
     """
     Params.load_from_file()
 
@@ -49,9 +57,11 @@ def genetic_pipeline(
         output: str = typer.Option("./datasets/example/geneticTrees.json", help="The name of the file to save the genetic trees."),
     ):
     """
-    This function is used to run the genetic pipeline that creates the genetic trees.
+    Run the genetic pipeline that process the genetic trees.
+
     Args:
         reference_gene_filepath (str): The path to the reference gene file.
+        output (str): The name of the file to save the genetic trees.
     """
     Params.load_from_file()
 
@@ -72,12 +82,20 @@ def genetic_pipeline(
     except Exception as e:
         print(f"Error saving the file: {e}")
 
-@app.callback()
-def main(
+@app.command()
+def run(
     climatic_tree: str = typer.Option(None, help="The name of the file containing the climatic trees."),
     genetic_tree: str = typer.Option(None, help="The name of the file containing the genetic trees."),
+    output: str = typer.Option("./results/output.csv", help="The name of the file to save the output."),
 ):
+    """
+    Run the pipelines and process the trees and phylogeographic analyses.
 
+    Args:
+        climatic_tree (str): The name of the file containing the climatic trees.
+        genetic_tree (str): The name of the file containing the genetic trees.
+        output (str): The name of the file to save the output.
+    """
     # geneticTrees = GeneticTrees.load_trees_from_file("./results/geneticTreesTest.json")
     # loaded_seq_alignment = Alignment.load_from_json("./results/aligned_sequences.json")
 
@@ -93,8 +111,6 @@ def main(
         trees = GeneticTrees(trees_dict=geneticTrees, format="newick")
     else:
 
-        typer.echo(typer.style(titleCard, fg=typer.colors.GREEN))
-
         sequenceFile = utils.loadSequenceFile(Params.reference_gene_filepath)
         align_sequence = AlignSequences(sequenceFile)
 
@@ -115,14 +131,15 @@ def main(
         climatic_data = pd.read_csv(Params.file_name)
         climaticTrees = utils.climaticPipeline(climatic_data)
 
-    utils.filterResults(climaticTrees, geneticTrees, climatic_data)
+    filtered_results = utils.filterResults(climaticTrees, geneticTrees, climatic_data)
+
+    utils.writeOutputFile(filtered_results, output)
 
     # save results
     if alignements is not None:
         alignements.save_to_json(f"./results/aligned_{Params.reference_gene_file}.json")
 
     trees.save_trees_to_json("./results/geneticTrees.json")
 
-
 if __name__ == "__main__":
     app()

aphylogeo/utils.py

@@ -462,17 +462,19 @@ def getData(leavesName, dist, index, climaticList, bootstrap, genetic, csv_data,
                     return [reference_gene_filename, climaticList[index], leave, genetic, str(bootstrap), str(round(dist, 2))]
 
 
-def writeOutputFile(data):
+def writeOutputFile(data, output_file):
     """
     Write the datas from data list into a new csv file
 
     :param data: The list containing the final data.
+    :param output_file: Output csv filepath for the results.
     :type data: list
+    :type output_file: String
     """
     print("Writing the output file")
     directory = os.path.abspath("./results")
     os.makedirs(directory, exist_ok=True)
-    with open("./results/output.csv", "w", encoding="UTF8") as f:
+    with open(output_file, "w", encoding="UTF8") as f:
         writer = csv_writer(f)
         writer.writerow(header())
         for i in range(len(data)):
@@ -498,8 +500,8 @@ def filterResults(
     :param create_file: Whether to create a file or not. Default is True.
     :type create_file: bool
     
-    :return: The final data in a dictionary format.
-    :rtype: dict
+    :return: The final data in a list format.
+    :rtype: list
     """
 
     # Create a list of the tree if the bootstrap is superior to the
@@ -606,10 +608,10 @@ def filterResults(
             else:
                 raise ValueError("Invalid distance method")
 
-    if create_file:
-        # We write the datas into an output csv file
-        writeOutputFile(data)
-    return format_to_csv(data)
+    # if create_file:
+    #     # We write the datas into an output csv file
+    #     writeOutputFile(data, Params.output_file)
+    return data
 
 
 def format_to_csv(data):