Renaming CytoPipe to CytoSnake

cytopipe/cli/args.py → cytosnake/cli/args.py

@@ -4,7 +4,7 @@
 args.py Module
 
 Responsible for centralizing and handling all user inputted
-parameters for cytopipe.
+parameters for cytosnake.
 
 Contains different modes with their respected parameters
 """
@@ -51,7 +51,7 @@ class CliControlPanel
     data_type: tuple[str] = ("cell_profiler", "deep_profiler")
     modes: tuple[str] = ("init", "run", "test", "help")
     workflows: tuple[str] = ("cp_process", "dp_process", "help")
-    __exec_name: str = "cytopipe"
+    __exec_name: str = "cytosnake"
 
     # ----------------------------------------
     # Metaclass class methods
@@ -111,7 +111,7 @@ def parse_init_args(self) -> argparse.Namespace:
         parser.add_argument(
             "mode",
             choices=["init"],
-            help="Init mode sets up the all files for cytopipe processing",
+            help="Init mode sets up the all files for cytosnake processing",
         )
         parser.add_argument(
             "-d", "--data", nargs="+", required=True, help="list of plate data files"

cytopipe/cli/cli_checker.py → cytosnake/cli/cli_checker.py

@@ -5,7 +5,7 @@
 cli_checker.py Module
 
 Argument checking module that checks and validates user input
-arguments from cytopipe's cli interface,
+arguments from CytoSnake's cli interface,
 """
 import sys
 from typing import Union
@@ -19,14 +19,14 @@
 @dataclass
 class CliProperties:
     """Struct object that contains information of all arguments in
-    cytopipe's cli interface
+    CytoSnake's cli interface
 
     Attributes
     -----------
     modes : tuple[str]
-        Supported modes in CytoPipe's CLI
+        Supported modes in CytoSnake's CLI
     workflows : tuple[str]
-        Available cytopipe workflows
+        Available CytoSnake workflows
     """
 
     modes: tuple[str] = ("init", "run", "test", "help")
@@ -39,7 +39,7 @@ def cli_check(args_list: list[Union[str, int, bool]]) -> bool:
     Parameters
     ----------
     mode : str
-        cytopipe mode
+        CytoSnake mode
     args_list : list[Union[str, int, bool]]
         list of user inputted arguments
 
@@ -54,7 +54,7 @@ def cli_check(args_list: list[Union[str, int, bool]]) -> bool:
     NoArgumentsException
         Raised if the user provides no arguments
     InvalidModeException
-        Raised if user inputs an invalid cytopipe mode
+        Raised if user inputs an invalid CytoSnake mode
     InvalidWorkflowException
         Raised if user inputs an invalid workflow name
     MultipleModesException

cytopipe/cli/cli_docs.py → cytosnake/cli/cli_docs.py

@@ -2,11 +2,11 @@
 Command line::
 Run Documentation
 
-Cytopipe's run mode allows users to execute Cytopipes available workflows
+CytoSnake's run mode allows users to execute CytoSnake's available workflows
 
 Usage:
-    cytopipe run workflow [-c]
-    cytopipe run help
+    cytosnake run workflow [-c]
+    cytosnake run help
 
 Required Arguments:
     workflow            Name of the workflow to execute
@@ -26,22 +26,22 @@
 
 cp_process              Workflow for analyzing cell morphology reads
                         obtained from CellProfiler
-dp_process              Workflow for analyzing cell morphology reads 
+dp_process              Workflow for analyzing cell morphology reads
                         obtained from DeepProfiler
 
 
 Help Arguments:
-    help                Displays cytopipe's Run mode documentation
+    help                Displays CytoSnake's Run mode documentation
 """
 
 init_doc = """
 Command line::
 Init mode Documentation
 
-Cytopipe's init mode allows user to setup up the require files for processing.
+CytoSnake's init mode allows user to setup up the require files for processing.
 
 Usage:
-    cytopipe init [-d] [-m] [-b] [-p]
+    cytosnake init [-d] [-m] [-b] [-p]
 
 Required Arguments:
     -d, --data          List of plate data files
@@ -51,31 +51,31 @@
     -b, --barcode       Path to file containing barcode labeling. This is used
                         for cell morphology reads obtained by CellProfiler.
                         [Default=None]
-    --datatype          Datatype flag helps cytopipe in how to setup the input
+    --datatype          Datatype flag helps CytoSnake in how to setup the input
                         files for processing.
                         [Choices = "cell_profiler", "deep_profiler"]
                         [Default="cell_profiler"]
 
 Help Arguments:
-    help                Displays cytopipe's init mode documentation
+    help                Displays CytoSnake's init mode documentation
 """
 
 cli_docs = f"""
-Cytopipe Documentation
+CytoSnake Documentation
 
-Cytpipe's command line interface
+CytoSnake's command line interface
 
 Usage:
-    cytopipe [mode] [ mode options]
-    cytopipe help
+    cytosnake [mode] [ mode options]
+    cyotsnake help
 
 Required Arguments:
-    mode                Cytopipe cli instruction on what to execute. There are
+    mode                CytoSnake cli instruction on what to execute. There are
                         3 modes [init, run, help]. Init setups ups the required
-                        files for processing. Run executes cytopipe's workflows.
+                        files for processing. Run executes CytoSnake's workflows.
                         Help displays the help message documentation.
 Help Argument:
-    help                Displays cytopipe's CLI help and mode documentation
+    help                Displays CytoSnake's CLI help and mode documentation
 
 Mode Documentations:
 {init_doc.replace("Command line::", "")}

cytopipe/cli/cmd.py → cytosnake/cli/cmd.py

@@ -3,7 +3,7 @@
 
 cmd.py Module
 
-Generates CLI interface in order to interact with cytopipe.
+Generates CLI interface in order to interact with CytoSnake.
 """
 import sys
 
@@ -20,8 +20,7 @@ def run_cmd() -> None:
     Parameters
     ----------
     params : list
-        list of user provided parameters
-
+        list of user provided parametersCytoSnake
     Returns
     -------
     None
@@ -45,7 +44,7 @@ def run_cmd() -> None:
                 print(init_doc)
                 sys.exit(0)
 
-            # setting up input files for cytopipe
+            # setting up input files for cytosnake
             print("INFO: Formatting input files")
             init_args = args_handler.parse_init_args()
 
@@ -75,7 +74,6 @@ def run_cmd() -> None:
             # parsing workflow parameters
             print(f"INFO: Executing {args_handler.workflow} workflow")
             wf_params = args_handler.parse_workflow_args()
-
             wf_executor = workflow_executor(
                 workflow=wf_params.workflow,
                 n_cores=wf_params.max_cores,

cytopipe/cli/exec/workflow_exec.py → cytosnake/cli/exec/workflow_exec.py

@@ -7,7 +7,7 @@
 from typing import Optional
 import snakemake
 
-from cytopipe.utils.config_utils import load_workflow_path
+from cytosnake.utils.config_utils import load_workflow_path
 
 
 def __base_exec(

rules/merge_logs.smk

@@ -1,20 +1,19 @@
-# ----------------------------------------------------------------
-# Documentation:
-# Rule collects all generated logs from all porcessess and merges
-# them into a single log file.
-#
-# individual log files are stored into an archive file along with
-# the generated merged log.
-#
-# The archive file is taged with (Month-day-year)-(hour-min-sec)
-# Example: 072922-083033_archived_logs
-# ----------------------------------------------------------------
+"""
+Documentation:
+Rule collects all generated logs from all porcessess and merges
+them into a single log file.
 
+individual log files are stored into an archive file along with
+the generated merged log.
+
+The archive file is taged with (Month-day-year)-(hour-min-sec)
+Example: 072922-083033_archived_logs
+"""
 
 rule merge_logs:
     input:
         expand("logs/{logname}.log", logname=LOG_NAMES),
     output:
-        "logs/CytoPipe_preprocess.log",
+        "logs/CytoSnake_preprocess.log",
     script:
         "../scripts/merge_logs.py"

rules/preprocessing.smk

@@ -1,26 +1,27 @@
-# Documentation:
-# Workflow that involves preprocessing raw single-cell plate data and
-# transforming it into normalized aggregate profiles.
-#
-# Parameters
-# ----------
-# sql_files : List[str]
-#   List of SQL files containing plate data
-# barcodes : str
-#   path pointing to the barcode file storing platemap IDs
-# metadata : str
-#   path pointing to plate metadata
-#
-# Generates
-# ---------
-# cell_counts: .csv file
-#   csv file containing n_cells per well
-# augmented: csv.gz file
-#   Annotated aggregated profiles
-# normalized: csv.gz file
-#   Normalized annotated aggregate profiles
-# --------------------
+"""
+Documentation:
+Workflow that involves preprocessing raw single-cell plate data and
+transforming it into normalized aggregate profiles.
+
+Parameters
+----------
+sql_files : List[str]
+  List of SQL files containing plate data
+barcodes : str
+  path pointing to the barcode file storing platemap IDs
+metadata : str
+  path pointing to plate metadata
 
+Generates
+---------
+cell_counts: .csv file
+  csv file containing n_cells per well
+augmented: csv.gz file
+  Annotated aggregated profiles
+normalized: csv.gz file
+  Normalized annotated aggregate profiles
+# --------------------
+"""
 
 # collecting all unique IDs from plate
 configfile: "configs/configuration.yaml"

setup.py

@@ -1,15 +1,15 @@
 from setuptools import setup, find_packages
 
 setup(
-    name="cytopipe",
+    name="CytoSnake",
     version="0.0.1",
     url="https://github.com/WayScience/CytoPipe",
     author="Way Lab",
     packages=find_packages(),
     python_requires=">=3.10",
     entry_points={
         "console_scripts": [
-            "cytopipe=cytopipe.cli.cmd:run_cmd",
+            "cytosnake=cytosnake.cli.cmd:run_cmd",
         ]
     },
 )