merge updated main

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -3,59 +3,60 @@
 from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_wavelength
+from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
 
 def get_args():
     p = ArgumentParser()
     p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
-    p.add_argument("-i", "--input-file", help="The filename of the " "datafile to load")
+    p.add_argument("-i", "--input-file", help="The filename of the " "datafile to load.")
     p.add_argument(
         "-a",
         "--anode-type",
         help=f"The type of the x-ray source. Allowed values are "
-        f"{*[known_sources], }. Either specify a known x-ray source or specify wavelength",
+        f"{*[known_sources], }. Either specify a known x-ray source or specify wavelength.",
         default="Mo",
     )
     p.add_argument(
         "-w",
         "--wavelength",
         help="X-ray source wavelength in angstroms. Not needed if the anode-type "
-        "is specified. This wavelength will override the anode wavelength if both are specified",
+        "is specified. This wavelength will override the anode wavelength if both are specified.",
         default=None,
         type=float,
     )
     p.add_argument(
         "-o",
         "--output-directory",
-        help="the name of the output directory. If it doesn't exist it "
-        "will be created.  Not currently implemented",
+        help="The name of the output directory. If not specified "
+        "then corrected files will be written to the current directory."
+        "If the specified directory doesn't exist it will be created.",
         default=None,
     )
     p.add_argument(
         "-x",
         "--xtype",
-        help=f"the quantity on the independent variable axis. allowed "
+        help=f"The quantity on the independent variable axis. Allowed "
         f"values: {*XQUANTITIES, }. If not specified then two-theta "
         f"is assumed for the independent variable. Only implemented for "
-        f"tth currently",
+        f"tth currently.",
         default="tth",
     )
     p.add_argument(
         "-c",
         "--output-correction",
         action="store_true",
-        help="the absorption correction will be output to a file if this "
-        "flag is set. Default is that it is not output",
+        help="The absorption correction will be output to a file if this "
+        "flag is set. Default is that it is not output.",
         default="tth",
     )
     p.add_argument(
         "-f",
         "--force-overwrite",
         action="store_true",
-        help="outputs will not overwrite existing file unless --force is specified",
+        help="Outputs will not overwrite existing file unless --force is specified.",
     )
     p.add_argument(
         "-u",
@@ -73,23 +74,24 @@ def get_args():
 def main():
     args = get_args()
     args = load_user_metadata(args)
+    args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
 
     filepath = Path(args.input_file)
     outfilestem = filepath.stem + "_corrected"
     corrfilestem = filepath.stem + "_cve"
-    outfile = Path(outfilestem + ".chi")
-    corrfile = Path(corrfilestem + ".chi")
+    outfile = args.output_directory / (outfilestem + ".chi")
+    corrfile = args.output_directory / (corrfilestem + ".chi")
 
     if outfile.exists() and not args.force_overwrite:
         sys.exit(
-            f"output file {str(outfile)} already exists. Please rerun "
-            f"specifying -f if you want to overwrite it"
+            f"Output file {str(outfile)} already exists. Please rerun "
+            f"specifying -f if you want to overwrite it."
         )
     if corrfile.exists() and args.output_correction and not args.force_overwrite:
         sys.exit(
-            f"corrections file {str(corrfile)} was requested and already "
-            f"exists. Please rerun specifying -f if you want to overwrite it"
+            f"Corrections file {str(corrfile)} was requested and already "
+            f"exists. Please rerun specifying -f if you want to overwrite it."
         )
 
     input_pattern = Diffraction_object(wavelength=args.wavelength)

src/diffpy/labpdfproc/tests/test_tools.py

@@ -1,10 +1,50 @@
 import argparse
+import os
 import re
 from argparse import ArgumentParser
+from pathlib import Path
 
 import pytest
 
-from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_wavelength
+from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
+
+params1 = [
+    ([None], ["."]),
+    (["."], ["."]),
+    (["new_dir"], ["new_dir"]),
+    (["existing_dir"], ["existing_dir"]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params1)
+def test_set_output_directory(inputs, expected, tmp_path):
+    directory = Path(tmp_path)
+    os.chdir(directory)
+
+    existing_dir = Path(tmp_path).resolve() / "existing_dir"
+    existing_dir.mkdir(parents=True, exist_ok=True)
+
+    expected_output_directory = Path(tmp_path).resolve() / expected[0]
+    actual_args = argparse.Namespace(output_directory=inputs[0])
+    actual_args.output_directory = set_output_directory(actual_args)
+    assert actual_args.output_directory == expected_output_directory
+    assert Path(actual_args.output_directory).exists()
+    assert Path(actual_args.output_directory).is_dir()
+
+
+def test_set_output_directory_bad(tmp_path):
+    directory = Path(tmp_path)
+    os.chdir(directory)
+
+    existing_file = Path(tmp_path).resolve() / "existing_file.py"
+    existing_file.touch()
+
+    actual_args = argparse.Namespace(output_directory="existing_file.py")
+    with pytest.raises(FileExistsError):
+        actual_args.output_directory = set_output_directory(actual_args)
+        assert Path(actual_args.output_directory).exists()
+        assert not Path(actual_args.output_directory).is_dir()
+
 
 params2 = [
     ([None, None], [0.71]),
@@ -25,10 +65,10 @@ def test_set_wavelength(inputs, expected):
 params3 = [
     (
         [None, "invalid"],
-        [f"Anode type not recognized. please rerun specifying an anode_type from {*known_sources, }"],
+        [f"Anode type not recognized. Please rerun specifying an anode_type from {*known_sources, }."],
     ),
-    ([0, None], ["No valid wavelength. Please rerun specifying a known anode_type or a positive wavelength"]),
-    ([-1, "Mo"], ["No valid wavelength. Please rerun specifying a known anode_type or a positive wavelength"]),
+    ([0, None], ["No valid wavelength. Please rerun specifying a known anode_type or a positive wavelength."]),
+    ([-1, "Mo"], ["No valid wavelength. Please rerun specifying a known anode_type or a positive wavelength."]),
 ]
 
 

src/diffpy/labpdfproc/tools.py

@@ -1,7 +1,33 @@
+from pathlib import Path
+
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
 known_sources = [key for key in WAVELENGTHS.keys()]
 
 
+def set_output_directory(args):
+    """
+    set the output directory based on the given input arguments
+
+    Parameters
+    ----------
+    args argparse.Namespace
+        the arguments from the parser
+
+    Returns
+    -------
+    pathlib.PosixPath that contains the full path of the output directory
+
+    it is determined as follows:
+    If user provides an output directory, use it.
+    Otherwise, we set it to the current directory if nothing is provided.
+    We then create the directory if it does not exist.
+
+    """
+    output_dir = Path(args.output_directory).resolve() if args.output_directory else Path.cwd().resolve()
+    output_dir.mkdir(parents=True, exist_ok=True)
+    return output_dir
+
+
 def set_wavelength(args):
     """
     Set the wavelength based on the given input arguments
@@ -21,11 +47,11 @@ def set_wavelength(args):
     """
     if args.wavelength is not None and args.wavelength <= 0:
         raise ValueError(
-            "No valid wavelength. Please rerun specifying a known anode_type or a positive wavelength"
+            "No valid wavelength. Please rerun specifying a known anode_type or a positive wavelength."
         )
     if not args.wavelength and args.anode_type and args.anode_type not in WAVELENGTHS:
         raise ValueError(
-            f"Anode type not recognized. please rerun specifying an anode_type from {*known_sources, }"
+            f"Anode type not recognized. Please rerun specifying an anode_type from {*known_sources, }."
         )
 
     if args.wavelength: