From 21b16d73afb1e08222435bd256b0cad448049224 Mon Sep 17 00:00:00 2001 From: ErinWeisbart Date: Tue, 7 Dec 2021 09:55:25 -0800 Subject: [PATCH] move log output --- 0.preprocess-sites/0.prefilter-features.py | 2 +- 0.preprocess-sites/1.process-spots.py | 2 +- 0.preprocess-sites/2.process-cells.py | 2 +- 0.preprocess-sites/3.visualize-cell-summary.py | 2 +- 0.preprocess-sites/4.image-and-segmentation-qc.py | 2 +- 1.generate-profiles/0.merge-single-cells.py | 2 +- 1.generate-profiles/1.aggregate.py | 2 +- 1.generate-profiles/2.normalize.py | 2 +- 1.generate-profiles/3.feature-select.py | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/0.preprocess-sites/0.prefilter-features.py b/0.preprocess-sites/0.prefilter-features.py index 04177e8..431cfa0 100644 --- a/0.preprocess-sites/0.prefilter-features.py +++ b/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( diff --git a/0.preprocess-sites/1.process-spots.py b/0.preprocess-sites/1.process-spots.py index b1393a1..94fea7e 100644 --- a/0.preprocess-sites/1.process-spots.py +++ b/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( diff --git a/0.preprocess-sites/2.process-cells.py b/0.preprocess-sites/2.process-cells.py index 57f1bd3..bb10915 100644 --- a/0.preprocess-sites/2.process-cells.py +++ b/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( diff --git a/0.preprocess-sites/3.visualize-cell-summary.py b/0.preprocess-sites/3.visualize-cell-summary.py index e821017..f906cd1 100644 --- a/0.preprocess-sites/3.visualize-cell-summary.py +++ b/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( diff --git a/0.preprocess-sites/4.image-and-segmentation-qc.py b/0.preprocess-sites/4.image-and-segmentation-qc.py index 8e8412d..d82a540 100644 --- a/0.preprocess-sites/4.image-and-segmentation-qc.py +++ b/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( diff --git a/1.generate-profiles/0.merge-single-cells.py b/1.generate-profiles/0.merge-single-cells.py index 0dcf83c..6b9c2c5 100644 --- a/1.generate-profiles/0.merge-single-cells.py +++ b/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( diff --git a/1.generate-profiles/1.aggregate.py b/1.generate-profiles/1.aggregate.py index 6a6f639..29691f8 100644 --- a/1.generate-profiles/1.aggregate.py +++ b/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( diff --git a/1.generate-profiles/2.normalize.py b/1.generate-profiles/2.normalize.py index e05e986..ad9f664 100644 --- a/1.generate-profiles/2.normalize.py +++ b/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( diff --git a/1.generate-profiles/3.feature-select.py b/1.generate-profiles/3.feature-select.py index a950374..71594a5 100644 --- a/1.generate-profiles/3.feature-select.py +++ b/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(