fantasia lowercase

README.md

@@ -23,7 +23,7 @@ FANTASIA (Functional ANnoTAtion based on embedding space SImilArity) is a pipeli
 To install FANTASIA, ensure you have Python 3.8+ installed and use the following commands:
 
 ```bash
-pip install FANTASIA
+pip install fantasia
 ```
 
 ---

docker-compose.yml

@@ -6,7 +6,7 @@ services:
   app:
     build:
       dockerfile: Dockerfile
-    container_name: FANTASIA
+    container_name: fantasia
     depends_on:
       pgvectorsql:
         condition: service_healthy

docs/source/conf.py

@@ -8,7 +8,7 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'FANTASIA'
+project = 'fantasia'
 copyright = '2024, frapercan'
 author = 'frapercan'
 

FANTASIA/config.yaml → fantasia/config.yaml

@@ -17,7 +17,7 @@ embeddings_url: "https://zenodo.org/records/14546346/files/embeddings.tar?downlo
 embeddings_path: ~/fantasia/dumps/
 
 
-# FANTASIA
+# fantasia
 fantasia_input_fasta: ~/fantasia/input/zinc.fasta
 fantasia_output_h5: ~/fantasia/embeddings/
 fantasia_output_csv: ~/fantasia/results/
@@ -41,6 +41,6 @@ topgo?: True
 
 
 
-constants: "./FANTASIA/constants.yaml"
+constants: "./fantasia/constants.yaml"
 
 

FANTASIA/main.py → fantasia/main.py

@@ -6,9 +6,9 @@
 from datetime import datetime
 import protein_metamorphisms_is.sql.model.model  # noqa: F401
 from protein_metamorphisms_is.helpers.config.yaml import read_yaml_config
-from FANTASIA.src.helpers import download_embeddings, load_dump_to_db
-from FANTASIA.src.embedder import SequenceEmbedder
-from FANTASIA.src.lookup import EmbeddingLookUp
+from fantasia.src.helpers import download_embeddings, load_dump_to_db
+from fantasia.src.embedder import SequenceEmbedder
+from fantasia.src.lookup import EmbeddingLookUp
 
 
 def initialize(config_path):
@@ -37,7 +37,7 @@ def run_pipeline(config_path, fasta_path=None):
     if fasta_path:
         conf["fantasia_input_fasta"] = fasta_path
 
-    # Ejecutar el pipeline de FANTASIA
+    # Ejecutar el pipeline de fantasia
     current_date = datetime.now().strftime("%Y%m%d%H%M%S")
     embedder = SequenceEmbedder(conf, current_date)
     embedder.start()
@@ -57,17 +57,17 @@ def wait_forever():
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="FANTASIA: Command Handler")
+    parser = argparse.ArgumentParser(description="fantasia: Command Handler")
     parser.add_argument("command", type=str, nargs="?", default=None, help="Command to execute: initialize or run")
-    parser.add_argument("--config", type=str, default="./FANTASIA/config.yaml", help="Path to the configuration YAML file.")
+    parser.add_argument("--config", type=str, default="./fantasia/config.yaml", help="Path to the configuration YAML file.")
     parser.add_argument("--fasta", type=str, help="Path to the input FASTA file.")
     args = parser.parse_args()
 
     if args.command == "initialize":
         print("Initializing embeddings and database...")
         initialize(args.config)
     elif args.command == "run":
-        print("Running the FANTASIA pipeline...")
+        print("Running the fantasia pipeline...")
         run_pipeline(config_path=args.config, fasta_path=args.fasta)
     elif args.command is None:
         wait_forever()