From a5bcef23a737c01225ae8d8fe3166e5223cfc8cd Mon Sep 17 00:00:00 2001 From: xaxi Date: Thu, 9 Jan 2025 13:35:59 +0100 Subject: [PATCH] fantasia lowercase --- README.md | 2 +- docker-compose.yml | 2 +- docs/source/conf.py | 2 +- {FANTASIA => fantasia}/README.md | 0 {FANTASIA => fantasia}/__init__.py | 0 {FANTASIA => fantasia}/config.yaml | 4 ++-- {FANTASIA => fantasia}/constants.yaml | 0 {FANTASIA => fantasia}/main.py | 14 +++++++------- {FANTASIA => fantasia}/src/__init__.py | 0 {FANTASIA => fantasia}/src/embedder.py | 0 {FANTASIA => fantasia}/src/helpers.py | 0 {FANTASIA => fantasia}/src/lookup.py | 0 12 files changed, 12 insertions(+), 12 deletions(-) rename {FANTASIA => fantasia}/README.md (100%) rename {FANTASIA => fantasia}/__init__.py (100%) rename {FANTASIA => fantasia}/config.yaml (93%) rename {FANTASIA => fantasia}/constants.yaml (100%) rename {FANTASIA => fantasia}/main.py (82%) rename {FANTASIA => fantasia}/src/__init__.py (100%) rename {FANTASIA => fantasia}/src/embedder.py (100%) rename {FANTASIA => fantasia}/src/helpers.py (100%) rename {FANTASIA => fantasia}/src/lookup.py (100%) diff --git a/README.md b/README.md index ef2195a..2ae3c7e 100644 --- a/README.md +++ b/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 ``` --- diff --git a/docker-compose.yml b/docker-compose.yml index 90a3e10..e3da97d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,7 +6,7 @@ services: app: build: dockerfile: Dockerfile - container_name: FANTASIA + container_name: fantasia depends_on: pgvectorsql: condition: service_healthy diff --git a/docs/source/conf.py b/docs/source/conf.py index 5f7978b..5018436 100644 --- a/docs/source/conf.py +++ b/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' diff --git a/FANTASIA/README.md b/fantasia/README.md similarity index 100% rename from FANTASIA/README.md rename to fantasia/README.md diff --git a/FANTASIA/__init__.py b/fantasia/__init__.py similarity index 100% rename from FANTASIA/__init__.py rename to fantasia/__init__.py diff --git a/FANTASIA/config.yaml b/fantasia/config.yaml similarity index 93% rename from FANTASIA/config.yaml rename to fantasia/config.yaml index 6a7c463..453c817 100644 --- a/FANTASIA/config.yaml +++ b/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" diff --git a/FANTASIA/constants.yaml b/fantasia/constants.yaml similarity index 100% rename from FANTASIA/constants.yaml rename to fantasia/constants.yaml diff --git a/FANTASIA/main.py b/fantasia/main.py similarity index 82% rename from FANTASIA/main.py rename to fantasia/main.py index cb2549c..36bb1e9 100644 --- a/FANTASIA/main.py +++ b/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() @@ -57,9 +57,9 @@ 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() @@ -67,7 +67,7 @@ def wait_forever(): 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() diff --git a/FANTASIA/src/__init__.py b/fantasia/src/__init__.py similarity index 100% rename from FANTASIA/src/__init__.py rename to fantasia/src/__init__.py diff --git a/FANTASIA/src/embedder.py b/fantasia/src/embedder.py similarity index 100% rename from FANTASIA/src/embedder.py rename to fantasia/src/embedder.py diff --git a/FANTASIA/src/helpers.py b/fantasia/src/helpers.py similarity index 100% rename from FANTASIA/src/helpers.py rename to fantasia/src/helpers.py diff --git a/FANTASIA/src/lookup.py b/fantasia/src/lookup.py similarity index 100% rename from FANTASIA/src/lookup.py rename to fantasia/src/lookup.py