initial commit

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -4,6 +4,7 @@
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
 from diffpy.labpdfproc.tools import (
     known_sources,
+    load_metadata,
     load_package_info,
     load_user_info,
     load_user_metadata,
@@ -144,7 +145,7 @@ def main():
             "tth",
             scat_quantity="x-ray",
             name=filepath.stem,
-            metadata={"muD": args.mud, "anode_type": args.anode_type},
+            metadata=load_metadata(args, filepath),
         )
 
         absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)

src/diffpy/labpdfproc/tests/test_tools.py

@@ -7,6 +7,7 @@
 from diffpy.labpdfproc.labpdfprocapp import get_args
 from diffpy.labpdfproc.tools import (
     known_sources,
+    load_metadata,
     load_package_info,
     load_user_info,
     load_user_metadata,
@@ -277,3 +278,57 @@ def test_load_package_info(mocker):
     actual_args = get_args(cli_inputs)
     actual_args = load_package_info(actual_args)
     assert actual_args.package_info == {"diffpy.labpdfproc": "1.2.3", "diffpy.utils": "3.3.0"}
+
+
+def _setup(mocker, user_filesystem):
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    mocker.patch("pathlib.Path.home", lambda _: home_dir)
+    os.chdir(cwd)
+    mocker.patch(
+        "importlib.metadata.version",
+        side_effect=lambda package_name: "3.3.0" if package_name == "diffpy.utils" else "1.2.3",
+    )
+
+
+def _preprocess_args(args):
+    args = load_package_info(args)
+    args = load_user_info(args)
+    args = set_input_lists(args)
+    args.output_directory = set_output_directory(args)
+    args.wavelength = set_wavelength(args)
+    args = load_user_metadata(args)
+    return args
+
+
+def test_load_metadata(mocker, user_filesystem):
+    _setup(mocker, user_filesystem)
+    cli_inputs = [
+        "2.5",
+        ".",
+        "--wavelength",
+        "1.54",
+        "--user-metadata",
+        "key=value",
+        "--username",
+        "cli_username",
+        "--email",
+        "[email protected]",
+    ]
+    actual_args = get_args(cli_inputs)
+    actual_args = _preprocess_args(actual_args)
+    for filepath in actual_args.input_paths:
+        actual_metadata = load_metadata(actual_args, filepath)
+        expected_metadata = {
+            "mud": 2.5,
+            "input_directory": str(filepath),
+            "anode_type": "Cu",
+            "wavelength": 1.54,
+            "output_directory": str(Path.cwd().resolve()),
+            "xtype": "tth",
+            "key": "value",
+            "username": "cli_username",
+            "email": "[email protected]",
+            "package_info": {"diffpy.labpdfproc": "1.2.3", "diffpy.utils": "3.3.0"},
+        }
+        assert actual_metadata == expected_metadata

src/diffpy/labpdfproc/tools.py

@@ -213,3 +213,36 @@ def load_package_info(args):
     metadata = get_package_info("diffpy.labpdfproc")
     setattr(args, "package_info", metadata["package_info"])
     return args
+
+
+def _set_anode_type(args):
+    if args.wavelength in WAVELENGTHS.values():
+        args.anode_type = next(key for key, value in WAVELENGTHS.items() if value == args.wavelength)
+    else:
+        delattr(args, "anode_type")
+    return args
+
+
+def load_metadata(args, filepath):
+    """
+    Load metadata from args,
+    except for anode type if wavelength does not match, and do not load output_correction or force_overwrite
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
+
+    Returns
+    -------
+    A dictionary with all arguments from the parser
+    """
+
+    args = _set_anode_type(args)
+    metadata = vars(args)
+    exclude_keys = ["output_correction", "force_overwrite", "input", "input_paths"]
+    for key in exclude_keys:
+        metadata.pop(key, None)
+    metadata["input_directory"] = str(filepath)
+    metadata["output_directory"] = str(metadata["output_directory"])
+    return metadata