From 73970b7d1a517c0a58bf2d29d96661fbb6e39438 Mon Sep 17 00:00:00 2001
From: Robin <robin.gutzen@live.de>
Date: Fri, 17 Nov 2023 14:07:03 +0100
Subject: [PATCH] adapt relative path import to enable doc build

---
 cobrawap/__main__.py        | 12 ++++++------
 cobrawap/cmd_utils.py       |  9 +++++----
 cobrawap/pipeline/Snakefile |  1 -
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/cobrawap/__main__.py b/cobrawap/__main__.py
index 91d62d5c..8b96579b 100755
--- a/cobrawap/__main__.py
+++ b/cobrawap/__main__.py
@@ -14,13 +14,13 @@
 from pprint import pformat
 from pathlib import Path
 import inspect
-# sys.path.append(str(Path(inspect.getfile(lambda: None)).parent))
+sys.path.append(str(Path(inspect.getfile(lambda: None)).parent))
 sys.path.append(str(Path(inspect.getfile(lambda: None)).parent / 'pipeline'))
-from .cmd_utils import get_setting, set_setting, get_initial_available_stages
-from .cmd_utils import is_profile_name_valid, create_new_configfile 
-from .cmd_utils import input_profile, get_profile, setup_entry_stage 
-from .cmd_utils import working_directory, load_config_file, get_config
-from .cmd_utils import locate_str_in_list, read_stage_output
+from cmd_utils import get_setting, set_setting, get_initial_available_stages
+from cmd_utils import is_profile_name_valid, create_new_configfile 
+from cmd_utils import input_profile, get_profile, setup_entry_stage 
+from cmd_utils import working_directory, load_config_file, get_config
+from cmd_utils import locate_str_in_list, read_stage_output
 log = logging.getLogger()
 logging.basicConfig(level=logging.INFO)
 
diff --git a/cobrawap/cmd_utils.py b/cobrawap/cmd_utils.py
index 2fd95db2..a9481bd6 100644
--- a/cobrawap/cmd_utils.py
+++ b/cobrawap/cmd_utils.py
@@ -5,11 +5,12 @@
 import re
 from string import ascii_lowercase
 import contextlib
+import inspect
 from pathlib import Path
-# sys.path.append(str(Path(__file__).parent / 'pipeline' / 'utils'))
-from .pipeline.utils.snakefile import  get_setting, set_setting, get_config
-from .pipeline.utils.snakefile import load_config_file, locate_str_in_list
-from .pipeline.utils.snakefile import read_stage_output, update_configfile
+sys.path.append(str(Path(inspect.getfile(lambda: None))))
+from pipeline.utils.snakefile import  get_setting, set_setting, get_config
+from pipeline.utils.snakefile import load_config_file, locate_str_in_list
+from pipeline.utils.snakefile import read_stage_output, update_configfile
 log = logging.getLogger()
 logging.basicConfig(level=logging.INFO)
 
diff --git a/cobrawap/pipeline/Snakefile b/cobrawap/pipeline/Snakefile
index accaf420..372dfc7f 100644
--- a/cobrawap/pipeline/Snakefile
+++ b/cobrawap/pipeline/Snakefile
@@ -4,7 +4,6 @@ import yaml
 from pathlib import Path
 import numpy as np
 import inspect
-# sys.path.append(os.getcwd())
 sys.path.append(str(Path(inspect.getfile(lambda: None))))
 from utils.snakefile import create_temp_configs, set_global_configs
 from utils.snakefile import set_stage_inputs, read_stage_output, get_setting