Update CytoTable Environment File (#56)

* fixed minor pathing bugs

* applied pre-commit changes

* update cytotable env file

* removed prefix parameter

* update python version

Author: axiomcura

cytosnake/cli/exec/workflow_exec.py

@@ -61,7 +61,6 @@ def __base_exec(
         unlock=unlock,
         forceall=force,
         use_conda=True,
-        conda_prefix=env_manager,
         conda_frontend=env_manager,
     )
 

cytosnake/helpers/datapaths.py

@@ -11,14 +11,13 @@
 """
 
 import pathlib
-from typing import Optional
 from collections import defaultdict
+from typing import Optional
 
-from cytosnake.utils import cyto_paths
 from cytosnake.guards.path_guards import is_valid_path
+from cytosnake.utils import cyto_paths
 from cytosnake.utils.config_utils import load_general_configs, load_meta_path_configs
 
-
 # loading in config files
 META_PATH_CONFIGS = load_meta_path_configs()
 GENERAL_CONFIGS = load_general_configs()

workflows/envs/cytotable.yaml

@@ -4,7 +4,7 @@ channels:
   - anaconda
   - defaults
 dependencies:
-  - python==3.8
+  - python==3.10
   - pip
   - pip:
-    - git+https://github.com/cytomining/CytoTable.git@f336d26baf96b8b3d9ed6ca07f617895030bf038
+    - cytotable

workflows/scripts/aggregate_cells.py

@@ -72,7 +72,6 @@ def aggregate(
 
     # Loading appropriate platemaps with given plate data
     logging.info(f"Loading plate data from: {str(sqlite_file_path)}")
-    plate_file_check = pathlib.Path(sql_file).is_file()
 
     # checking if the the sqli_file is found or it's a file type
     if not pathlib.Path(sql_file).is_file():