Add proper python packaging and command line entrypoint

* Move code into `mcquant/` subdirectory to define the package name.
* Refactor CommandSingleCellExtraction.py into cli.py.
* Add pyproject.toml to define build tooling, dependencies, metadata, etc.
* Define command-line entrypoint `mcquant`.
* Use setuptools_scm to extract our version number directly from git tags.
* Add --version argument to cli. Fixes #45.
* Edit Dockerfile to build and install our package as a wheel rather than
  explicitly specifying all dependencies directly.

.gitignore

@@ -1,3 +1,4 @@
+mcquant/_version.py
 .DS_Store
 
 # Byte-compiled / optimized / DLL files

Dockerfile

@@ -1,5 +1,8 @@
 FROM python:3.11
 
-RUN pip install --no-cache-dir h5py pandas numpy pathlib 'scikit-image>=0.23.2' imagecodecs 
+COPY . src
 
-COPY . /app/
+RUN pip install --no-cache-dir build \
+    && python -m build -w src \
+    && pip install --no-cache-dir src/dist/mcquant*.whl \
+    && rm -r src

ParseInput.py → mcquant/ParseInput.py

@@ -1,5 +1,6 @@
 #Functions for parsing command line arguments for ome ilastik prep
 import argparse
+from . import __version__
 
 
 def ParseInputDataExtract():
@@ -34,6 +35,7 @@ def ParseInputDataExtract():
       """
    )
    #parser.add_argument('--suffix')
+   parser.add_argument('--version', action='version', version=f'mcquant {__version__}')
    args = parser.parse_args()
    #Create a dictionary object to pass to the next function
    dict = {'masks': args.masks, 'image': args.image,\

mcquant/__init__.py

@@ -0,0 +1,4 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"

mcquant/cli.py

@@ -0,0 +1,14 @@
+#Script for parsing command line arguments and running single-cell
+#data extraction functions
+#Joshua Hess
+from . import ParseInput
+from . import SingleCellDataExtraction
+
+def main():
+    #Parse the command line arguments
+    args = ParseInput.ParseInputDataExtract()
+    #Run the MultiExtractSingleCells function
+    SingleCellDataExtraction.MultiExtractSingleCells(**args)
+
+if __name__ == '__main__':
+    main()

pyproject.toml

@@ -0,0 +1,24 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm[toml]>=8"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mcquant"
+dynamic = ["version"]
+requires-python = ">=3.9"
+dependencies = [
+  "h5py",
+  "pandas",
+  "numpy",
+  "scikit-image>=0.23.2",
+  "imagecodecs",
+]
+
+[project.scripts]
+mcquant = "mcquant.cli:main"
+
+[tool.setuptools]
+packages = ["mcquant"]
+
+[tool.setuptools_scm]
+version_file = "mcquant/_version.py"