move log output

Author: ErinWeisbart

0.preprocess-sites/0.prefilter-features.py

@@ -26,7 +26,7 @@
 from io_utils import check_if_write
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

0.preprocess-sites/1.process-spots.py

@@ -59,7 +59,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

0.preprocess-sites/2.process-cells.py

@@ -35,7 +35,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

0.preprocess-sites/3.visualize-cell-summary.py

@@ -19,7 +19,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

0.preprocess-sites/4.image-and-segmentation-qc.py

@@ -16,7 +16,7 @@
 from io_utils import check_if_write, read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

1.generate-profiles/0.merge-single-cells.py

@@ -23,7 +23,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

1.generate-profiles/1.aggregate.py

@@ -18,7 +18,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

1.generate-profiles/2.normalize.py

@@ -17,7 +17,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(

1.generate-profiles/3.feature-select.py

@@ -17,7 +17,7 @@
 from io_utils import read_csvs_with_chunksize
 
 # Configure logging
-logfolder = os.path.join(os.path.dirname(os.path.abspath(__file__)), "logs")
+logfolder = os.path.join(os.path.dirname(recipe_path), "logs")
 if not os.path.isdir(logfolder):
     os.mkdir(logfolder)
 logging.basicConfig(