Merge branch 'master' into test_skip

pyproject.toml

@@ -5,12 +5,19 @@ description = "This package adjusts and cleans the metadata file provided by a u
 authors = ["Zargham Ahmad <[email protected]>" ]
 license = "MIT"
 readme = "README.md"
+packages = [
+  {include = "src/rcx_tk"},
+  {include = "src/rcx_tk/py.typed"},
+]
 keywords = ["metadata", "alkanes", "metabolomics"]
 
 [tool.poetry.dependencies]
 python = "^3.11"
 pandas = "^2.2.2"
 pyxlsx = "^1.1.3"
+pandas-stubs = "^2.2.2.240603"
+mypy = "^1.10.1"
+click = "^8.1.7"
 
 [tool.poetry.group.dev.dependencies]
 build = "^1.2.1"
@@ -106,7 +113,6 @@ exclude = [
 ]
 lint.per-file-ignores = {}
 
-
 # Allow unused variables when underscore-prefixed.
 lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
@@ -125,4 +131,7 @@ filename = "pyproject.toml"
 filename = "CITATION.cff"
 
 [[tool.bumpversion.files]]
-filename = "docs/conf.py"        
+filename = "docs/conf.py"
+
+[tool.poetry.scripts]
+rcx_tk = "rcx_tk.__main__:main"

src/rcx_tk/__main__.py

@@ -0,0 +1,26 @@
+import click
+
+from rcx_tk.process_metadata_file import process_alkane_ri_file, process_metadata_file
+
+
+@click.command()
+@click.option('--method', type=click.Choice(['metadata', 'alkanes']), required = True, help = 'A file type to be processed, either metadata or alkanes file.')
+@click.argument('file_path')
+@click.argument('out_path')
+def main(method, file_path, out_path):
+    """Process metadata or alkane file.
+
+    Args:
+        file_path (path): A path to the input data.
+        out_path (path): A path where the processed data will be exported to.
+    """
+    if method == "metadata":
+        process_metadata_file(file_path, out_path)
+        click.echo("Metadata done!")
+    elif method == "alkanes":
+        process_alkane_ri_file(file_path, out_path)
+        click.echo("Alkanes done!")
+
+
+if __name__ == "__main__":
+    main()