From 395bc7a9b4bd3693119370b0f39506816e5762c5 Mon Sep 17 00:00:00 2001
From: alsmith <asmith151@outlook.com>
Date: Tue, 9 Apr 2024 14:12:24 +0100
Subject: [PATCH] Refactor logging verbosity in cli_pipeline function

---
 seqnado/cli.py    | 15 ++++++++++++++-
 seqnado/design.py |  3 ---
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/seqnado/cli.py b/seqnado/cli.py
index dfc0711e..95c7e2c7 100644
--- a/seqnado/cli.py
+++ b/seqnado/cli.py
@@ -53,7 +53,6 @@ def cli_design(method, files, output="design.csv"):
     """
     import pathlib
     from seqnado.design import Design, DesignIP, FastqFile, FastqFileIP
-    from loguru import logger    
     
     if not files:
         potential_file_locations = [
@@ -116,6 +115,12 @@ def cli_design(method, files, output="design.csv"):
     is_flag=True,
     help="Remove symlinks created by previous runs. Useful for re-running pipeline after misconfiguration.",
 )
+@click.option(
+    "-v",
+    "--verbose",
+    is_flag=True,
+    help="Increase logging verbosity",
+)
 @click.argument("pipeline_options", nargs=-1, type=click.UNPROCESSED)
 def cli_pipeline(
     method,
@@ -123,6 +128,7 @@ def cli_pipeline(
     help=False,
     preset="local",
     version=False,
+    verbose=False,
     clean_symlinks=False,
 ):
     """Runs the data processing pipeline"""
@@ -137,6 +143,13 @@ def cli_pipeline(
         _version = version("seqnado")
         print(f"SeqNado version {_version}")
         sys.exit(0)
+    
+    if verbose:
+        logger.remove()
+        logger.add(sys.stderr, level="DEBUG")
+    else:
+        logger.remove()
+        logger.add(sys.stderr, level="INFO")
 
     pipeline_options, cores = extract_cores_from_options(pipeline_options)
 
diff --git a/seqnado/design.py b/seqnado/design.py
index 42183296..f6355f80 100644
--- a/seqnado/design.py
+++ b/seqnado/design.py
@@ -10,9 +10,6 @@
 from pydantic import BaseModel, Field, computed_field, field_validator
 from snakemake.io import expand
 
-logger.add(sink=sys.stderr, level="WARNING")
-
-
 def is_path(path: Optional[Union[str, pathlib.Path]]) -> Optional[pathlib.Path]:
     if isinstance(path, str):
         p = pathlib.Path(path)