Update to version 0.0.3 and modify parts of the Spot2Cell object

Author: migueLib

.gitignore

@@ -159,4 +159,8 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+.envrc

README.md

@@ -5,21 +5,49 @@
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/spot2cell)](https://pypistats.org/packages/spot2cell)
 [![main](https://github.com/saezlab/liana-py/actions/workflows/main.yml/badge.svg)](https://github.com/schapirolabor/spot2cell/actions)
 
-This tool assigns single-molecule detected spots to their respective cells in a tissue. It is designed to work with single-molecule FISH data technologies, but can be used with other types of data as well.
+Spot2cell is a tool that assigns spots to labeled masks with minimum instalation requirements.  
+It aims to provide a simple, easy-to-use way for assigning spots to cell masks.
 
 ## Installation
+spot2cell is available on PyPI and Conda-Forge and can be installed using `pip` or `conda`.
 
+Install using `pip`:
 ```bash
 pip install spot2cell
 ```
 
+Install using `conda`:
+```bash
+conda install -c conda-forge spot2cell
+```
+
 ## Docker
+
 Build Docker image from Dockerfile
 ```bash
 docker build -t spot2cell .
 ```
+
 ## CLI
 
 ```bash
 spot2cell --help
+
+usage: spots2cells.py [-h] [-s SPOTS] [-m MASK] [-x X_COL] [-y Y_COL] [-o OUTPUT] [--verbose] [--version]
+
+This scripts assigns a list of spots to the objects in an instance mask.
+
+options:
+  -h, --help           show this help message and exit
+  -s, --spots SPOTS    Path to the spot table file.
+  -m, --mask MASK      Path to the isntance mask file.
+  -x, --x-col X_COL    Column index of the x coordinate in the spots table [default: 0].
+  -y, --y-col Y_COL    Column index of the y coordinate in the spots table [default: 1].
+  -o, --output OUTPUT  Path to the output csv file.
+  --verbose            Verbose logging.
+  --version            show programs version number and exit
 ```
+## Expected Inputs
+Spot2cell expects two inputs:
+- `spots`: A comma-separated `.csv` table of spots with x and y coordinates. 
+- `mask`: An instance mask `.tif` file. In which each object is labeled with a unique positive number and each pixel belongs to exactly one object.

pyproject.toml

@@ -2,12 +2,9 @@
 requires = ["setuptools>=61.0"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools]
-packages = ["spot2cell"]
-
 [project]
 name = "spot2cell"
-version = "0.0.2"
+dynamic = ["version"]
 authors = [{ name="Miguel A. Ibarra-Arellano", email="c180l058j@mozmail.com"},]
 license = {text = "AGPL-3.0-or-later"}
 description = "From a X,Y list of detected spots, assigns each spot to a cell based on a segmentation mask"
@@ -17,6 +14,11 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Python :: 3.15",
+    "Programming Language :: Python :: 3.16",
     "Operating System :: OS Independent",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: GNU Affero General Public License v3"
@@ -33,12 +35,16 @@ keywords = [
     "Xenium"
 ]
 
+[tool.setuptools]
+packages = ["spot2cell"]
+
+[tool.setuptools.dynamic]
+version = { attr = "spot2cell.__version__" }
+
 [project.scripts]
 spots2cells = "spot2cell.scripts.spots2cells:main"
 
 [project.urls]
 Repository = "https://github.com/SchapiroLabor/spot2cell"
 Homepage = "https://github.com/SchapiroLabor/spot2cell"
 Issues = "https://github.com/SchapiroLabor/spot2cell/issues"
-
-

spot2cell/__init__.py

@@ -1,2 +1,4 @@
+from . import logger
 from .spot2cell import Spot2Cell
-from .version import __version__
+
+__version__ = "0.0.3"

spot2cell/logger.py

@@ -2,10 +2,12 @@
 import sys
 
 
-def set_logger(logger=None,
-               log_level='info',
-               log_format='%(asctime)s - %(levelname)s - %(message)s'):
-    """ Function to set up the handle error logging.
+def set_logger(
+    logger=None,
+    log_level="info",
+    log_format="%(asctime)s - %(levelname)s - %(message)s",
+):
+    """Function to set up the handle error logging.
 
     logger (obj) = a logger object (optional, creates a default logger if not provided)
     log_level (str) = level of information to print out, options are {info, debug} [Default: info]
@@ -17,9 +19,9 @@ def set_logger(logger=None,
         logger = logging.getLogger(__name__)
 
     # Determine log level
-    if log_level == 'info':
+    if log_level == "info":
         _level = logging.INFO
-    elif log_level == 'debug':
+    elif log_level == "debug":
         _level = logging.DEBUG
     else:
         raise ValueError(f"Log level {log_level} not recognized.")

spot2cell/scripts/spots2cells.py

@@ -1,41 +1,96 @@
-import os
 import argparse
-from spot2cell import __version__
-from spot2cell import Spot2Cell
+import os
 import pathlib
+from math import log
 from pathlib import Path
-if os.name == 'nt':
+from re import L
+from typing import Dict, List, Optional, Sequence, Tuple
+
+from spot2cell import Spot2Cell, __version__, logger
+
+if os.name == "nt":
     pathlib.PosixPath = pathlib.WindowsPath
 
 
-def get_args():
+def CLI() -> argparse.ArgumentParser:
     # Create an argument parser
-    parser = argparse.ArgumentParser(description='Assign spots to cells.')
-    parser.add_argument('-s', '--spots', type=str, help='Path to the spot table csv file.')
-    parser.add_argument('-m', '--mask', type=str, help='Path to the cell mask tif file.')
-    parser.add_argument('-o', '--output', type=str, help='Path to the output csv file.')
-    parser.add_argument('--version', action='version', version=f'{__version__}')
-    args = parser.parse_args()
+    parser = argparse.ArgumentParser(
+        description="This scripts assigns a list of spots to the objects in an instance mask."
+    )
+    parser.add_argument(
+        "-s",
+        "--spots",
+        type=Path,
+        help="Path to the spot table file.",
+    )
+    parser.add_argument(
+        "-m",
+        "--mask",
+        type=Path,
+        help="Path to the isntance mask file.",
+    )
+    parser.add_argument(
+        "-x",
+        "--x-col",
+        type=int,
+        default=0,
+        help="Column index of the x coordinate in the spots table [default: 0].",
+    )
+    parser.add_argument(
+        "-y",
+        "--y-col",
+        type=int,
+        default=1,
+        help="Column index of the y coordinate in the spots table [default: 1].",
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=Path,
+        help="Path to the output csv file.",
+    )
+    parser.add_argument("--verbose", action="store_true", help="Verbose logging.")
+    parser.add_argument("--version", action="version", version=f"{__version__}")
+    return parser
+
+
+def main(argv: Optional[Sequence[str]] = None) -> int:
+    # Get CLI arguments
+    parser = CLI()
+    args = parser.parse_args(argv)
 
-    # Standardize paths
-    # Convert WindowsPath to PosixPath
-    args.spots = Path(args.spots).resolve()
-    args.mask = Path(args.mask).resolve()
-    args.output = Path(args.output).resolve()
+    # Resolves the paths to absolute paths
+    args.spots = args.spots.resolve()
+    args.mask = args.mask.resolve()
+    args.output = args.output.resolve()
 
-    return args
+    # Set logger
+    LOGGER = logger.set_logger(log_level="debug" if args.verbose else "info")
+    LOGGER.info(f"spot2cell version: {__version__}")
+    LOGGER.info(f"Reading mask from: {args.mask}")
+    LOGGER.info(f"Reading spots from: {args.spots}")
 
+    try:
+        # Create an instance of the Spot2Cell class.
+        LOGGER.info(f"Creating Spot2Cell instance")
+        Spots = Spot2Cell(
+            args.spots,
+            args.mask,
+            x_col=args.x_col,
+            y_col=args.y_col,
+            logger=LOGGER,
+        )
 
-def main():
-    # Get the arguments
-    args = get_args()
+        # Save the assigned spots to a csv file.
+        LOGGER.info(f"Writing assigned spots to: {args.output}")
+        Spots.save(args.output)
 
-    # Create an instance of the Spot2Cell class.
-    spots = Spot2Cell(args.spots, args.mask)
+        return 0
 
-    # Save the assigned spots to a csv file.
-    spots.save(args.output)
+    except Exception as e:
+        print(f"spot2cells exit with an error: {e}")
+        return 1
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()