From 74f99594a48a28af05cb760be595f1f992ae3b4e Mon Sep 17 00:00:00 2001 From: axiomcura Date: Tue, 14 Mar 2023 13:44:08 -0600 Subject: [PATCH 1/5] fixed minor pathing bugs --- cytosnake/cli/args.py | 2 +- cytosnake/helpers/helper_funcs.py | 2 +- workflows/scripts/consensus.py | 1 - workflows/workflow/cp_process.smk | 3 ++- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/cytosnake/cli/args.py b/cytosnake/cli/args.py index ec97343f..f7b1315d 100644 --- a/cytosnake/cli/args.py +++ b/cytosnake/cli/args.py @@ -60,7 +60,7 @@ def __call__(self, parser, args, values, option_string=None): f"Unable to find '{values}'. Please specify a supported workflow: {supported_wf}" ) # grabbing and setting the new value with the extracted path - values = load_workflow_path(values) + values = str(load_workflow_path(values)) # return new attributes of the `workflow` parameter setattr(args, self.dest, values) diff --git a/cytosnake/helpers/helper_funcs.py b/cytosnake/helpers/helper_funcs.py index e18f4d46..8033dea8 100644 --- a/cytosnake/helpers/helper_funcs.py +++ b/cytosnake/helpers/helper_funcs.py @@ -68,7 +68,7 @@ def get_barcodes() -> str: """ # Barcodes are optional. If not added, set to "None" try: - barcode_path = PATHS["project_dir"]["data_dir_conts"]["barcode"] + barcode_path = PATHS["project_dir"]["data_directory_contents"]["barcode"] except KeyError: barcode_path = None diff --git a/workflows/scripts/consensus.py b/workflows/scripts/consensus.py index a554418c..29619446 100644 --- a/workflows/scripts/consensus.py +++ b/workflows/scripts/consensus.py @@ -2,7 +2,6 @@ from pathlib import Path import pandas as pd -import snakemake import yaml from pycytominer import consensus from pycytominer.operations import get_na_columns diff --git a/workflows/workflow/cp_process.smk b/workflows/workflow/cp_process.smk index 6e8ae4a8..86413891 100644 --- a/workflows/workflow/cp_process.smk +++ b/workflows/workflow/cp_process.smk @@ -2,7 +2,7 @@ import glob from cytosnake.helpers import helper_funcs as hf -# importing Modules +# importing rule modules include: "../rules/common.smk" include: "../rules/preprocessing.smk" include: "../rules/feature_select.smk" @@ -16,3 +16,4 @@ rule all: ANNOTATED_DATA_EXPAND, NORMALIZED_DATA_EXPAND, SELECTED_FEATURE_DATA_EXPAND, + CONSENSUS_DATA, From a693a80bdafce75a5f3283d3be0a331878896de0 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Tue, 16 May 2023 10:53:19 -0600 Subject: [PATCH 2/5] applied pre-commit changes --- cytosnake/helpers/datapaths.py | 5 ++--- workflows/scripts/aggregate_cells.py | 1 - 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/cytosnake/helpers/datapaths.py b/cytosnake/helpers/datapaths.py index 0d5c857f..fafc4b3e 100644 --- a/cytosnake/helpers/datapaths.py +++ b/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() diff --git a/workflows/scripts/aggregate_cells.py b/workflows/scripts/aggregate_cells.py index b970b3be..89b6de8a 100644 --- a/workflows/scripts/aggregate_cells.py +++ b/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(): From b259a8a1576927ed80ea0c4b674c24839c100697 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Tue, 16 May 2023 10:55:56 -0600 Subject: [PATCH 3/5] update cytotable env file --- workflows/envs/cytotable.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/envs/cytotable.yaml b/workflows/envs/cytotable.yaml index 5d52d2d2..90e7b8a7 100644 --- a/workflows/envs/cytotable.yaml +++ b/workflows/envs/cytotable.yaml @@ -7,4 +7,4 @@ dependencies: - python==3.8 - pip - pip: - - git+https://github.com/cytomining/CytoTable.git@f336d26baf96b8b3d9ed6ca07f617895030bf038 + - cytotable From 694473cdb8a16ef30d186596060a0fa6c780a5e1 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Tue, 16 May 2023 13:34:37 -0600 Subject: [PATCH 4/5] removed prefix parameter --- cytosnake/cli/exec/workflow_exec.py | 1 - 1 file changed, 1 deletion(-) diff --git a/cytosnake/cli/exec/workflow_exec.py b/cytosnake/cli/exec/workflow_exec.py index f51a9df2..a9dc3738 100644 --- a/cytosnake/cli/exec/workflow_exec.py +++ b/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, ) From 959c22f4ff5685e50859fd9bfd5a60c0e61d5f05 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Tue, 16 May 2023 19:58:48 -0600 Subject: [PATCH 5/5] update python version --- workflows/envs/cytotable.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/envs/cytotable.yaml b/workflows/envs/cytotable.yaml index 90e7b8a7..9fd1c237 100644 --- a/workflows/envs/cytotable.yaml +++ b/workflows/envs/cytotable.yaml @@ -4,7 +4,7 @@ channels: - anaconda - defaults dependencies: - - python==3.8 + - python==3.10 - pip - pip: - cytotable