reset commit to fixture in conftest and grid size in functions

Author: yucongalicechen

src/diffpy/labpdfproc/functions.py

@@ -5,7 +5,7 @@
 from diffpy.utils.scattering_objects.diffraction_objects import Diffraction_object
 
 RADIUS_MM = 1
-N_POINTS_ON_DIAMETER = 249
+N_POINTS_ON_DIAMETER = 300
 TTH_GRID = np.arange(1, 141, 1)
 
 

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import known_sources, set_input_files, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import known_sources, set_output_directory, set_wavelength
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
@@ -64,51 +64,44 @@ def get_args():
 
 def main():
     args = get_args()
-    args = set_input_files(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
 
-    for input_file in args.input_file:
-        filepath = Path(input_file)
-        outfilestem = filepath.stem + "_corrected"
-        corrfilestem = filepath.stem + "_cve"
-        outfile = args.output_directory / (outfilestem + ".chi")
-        corrfile = args.output_directory / (corrfilestem + ".chi")
+    filepath = Path(args.input_file)
+    outfilestem = filepath.stem + "_corrected"
+    corrfilestem = filepath.stem + "_cve"
+    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."
-            )
-        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."
-            )
-
-        input_pattern = Diffraction_object(wavelength=args.wavelength)
-
-        try:
-            xarray, yarray = loadData(args.input_file, unpack=True)
-        except Exception as e:
-            raise ValueError(f"Failed to load data from {filepath}: {e}.")
-
-        input_pattern.insert_scattering_quantity(
-            xarray,
-            yarray,
-            "tth",
-            scat_quantity="x-ray",
-            name=str(args.input_file),
-            metadata={"muD": args.mud, "anode_type": args.anode_type},
+    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."
         )
+    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."
+        )
+
+    input_pattern = Diffraction_object(wavelength=args.wavelength)
+    xarray, yarray = loadData(args.input_file, unpack=True)
+    input_pattern.insert_scattering_quantity(
+        xarray,
+        yarray,
+        "tth",
+        scat_quantity="x-ray",
+        name=str(args.input_file),
+        metadata={"muD": args.mud, "anode_type": args.anode_type},
+    )
 
-        absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)
-        corrected_data = apply_corr(input_pattern, absorption_correction)
-        corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
-        corrected_data.dump(f"{outfile}", xtype="tth")
+    absorption_correction = compute_cve(input_pattern, args.mud, args.wavelength)
+    corrected_data = apply_corr(input_pattern, absorption_correction)
+    corrected_data.name = f"Absorption corrected input_data: {input_pattern.name}"
+    corrected_data.dump(f"{outfile}", xtype="tth")
 
-        if args.output_correction:
-            absorption_correction.dump(f"{corrfile}", xtype="tth")
+    if args.output_correction:
+        absorption_correction.dump(f"{corrfile}", xtype="tth")
 
 
 if __name__ == "__main__":

src/diffpy/labpdfproc/tests/conftest.py

@@ -14,7 +14,6 @@ def user_filesystem(tmp_path):
 
     chi_data = "dataformat = twotheta\n mode = xray\n # chi_Q chi_I\n 1 2\n 3 4\n 5 6\n 7 8\n"
     xy_data = "1 2\n 3 4\n 5 6\n 7 8"
-    txt_data = "dataformat = twotheta\n mode = xray\n # chi_Q chi_I\n 1 2\n 3 4\n 5 6\n 7 8\n"
     unreadable_data = "This is an unreadable file."
     binary_data = b"\x00\x01\x02\x03\x04"
 
@@ -23,7 +22,7 @@ def user_filesystem(tmp_path):
     with open("good_data.xy", "w") as f:
         f.write(xy_data)
     with open("good_data.txt", "w") as f:
-        f.write(txt_data)
+        f.write(chi_data)
     with open("unreadable_file.txt", "w") as f:
         f.write(unreadable_data)
     with open("binary.pkl", "wb") as f:
@@ -34,7 +33,7 @@ def user_filesystem(tmp_path):
     with open(os.path.join(input_dir, "good_data.xy"), "w") as f:
         f.write(xy_data)
     with open(os.path.join(input_dir, "good_data.txt"), "w") as f:
-        f.write(txt_data)
+        f.write(chi_data)
     with open(os.path.join(input_dir, "unreadable_file.txt"), "w") as f:
         f.write(unreadable_data)
     with open(os.path.join(input_dir, "binary.pkl"), "wb") as f:

src/diffpy/labpdfproc/tests/test_tools.py

@@ -1,83 +1,50 @@
 import argparse
+import os
 import re
 from pathlib import Path
 
 import pytest
 
-from diffpy.labpdfproc.tools import known_sources, set_input_files, set_output_directory, set_wavelength
-from diffpy.utils.parsers.loaddata import loadData
+from diffpy.labpdfproc.tools import known_sources, set_output_directory, set_wavelength
 
 params1 = [
     ([None], ["."]),
     (["."], ["."]),
     (["new_dir"], ["new_dir"]),
-    (["input_dir"], ["input_dir"]),
+    (["existing_dir"], ["existing_dir"]),
 ]
 
 
 @pytest.mark.parametrize("inputs, expected", params1)
-def test_set_output_directory(inputs, expected, user_filesystem):
-    tmp_dir = user_filesystem
-    expected_output_directory = tmp_dir / expected[0]
+def test_set_output_directory(inputs, expected, tmp_path):
+    directory = Path(tmp_path)
+    os.chdir(directory)
 
-    actual_parser = argparse.ArgumentParser()
-    actual_parser.add_argument("--output_directory")
-    actual_args = actual_parser.parse_args(["--output_directory", inputs[0]])
+    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(user_filesystem):
-    actual_parser = argparse.ArgumentParser()
-    actual_parser.add_argument("--output_directory")
-    actual_args = actual_parser.parse_args(["--output_directory", "good_data.chi"])
+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],
-        [
-            ".",
-            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl", "input_dir"],
-        ],
-    ),
-    (["good_data.chi"], [".", "good_data.chi"]),
-    (["input_dir/unreadable_file.txt"], ["input_dir", "input_dir/unreadable_file.txt"]),
-    # ([Path.cwd()], [Path.cwd()]),
-]
-
-
-@pytest.mark.parametrize("inputs, expected", params2)
-def test_set_input_files(inputs, expected, user_filesystem):
-    tmp_dir = user_filesystem
-    expected_input_directory = tmp_dir / expected[0]
-    expected_input_files = expected[1]
-
-    actual_parser = argparse.ArgumentParser()
-    actual_parser.add_argument("--input_file")
-    actual_args = actual_parser.parse_args(["--input_file", inputs[0]])
-    actual_args = set_input_files(actual_args)
-    assert actual_args.input_directory == expected_input_directory
-    assert set(actual_args.input_file) == set(expected_input_files)
-
-
-def test_loadData_with_input_files(user_filesystem):
-    xarray_chi, yarray_chi = loadData("good_data.chi", unpack=True)
-    xarray_xy, yarray_xy = loadData("good_data.xy", unpack=True)
-    xarray_txt, yarray_txt = loadData("good_data.txt", unpack=True)
-    with pytest.raises(ValueError):
-        xarray_txt, yarray_txt = loadData("unreadable_file.txt", unpack=True)
-    with pytest.raises(ValueError):
-        xarray_pkl, yarray_pkl = loadData("binary.pkl", unpack=True)
-
-
 params2 = [
     ([None, None], [0.71]),
     ([None, "Ag"], [0.59]),

src/diffpy/labpdfproc/tools.py

@@ -1,5 +1,3 @@
-import glob
-import os
 from pathlib import Path
 
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
@@ -30,30 +28,6 @@ def set_output_directory(args):
     return output_dir
 
 
-def set_input_files(args):
-    """
-    Set input directory and files, default is current working directory and all files in it
-
-    Parameters
-    ----------
-    args argparse.Namespace
-        the arguments from the parser
-
-    Returns
-    -------
-    args argparse.Namespace
-        the arguments from the parser with a new argument input_directory and processed input_files
-
-    """
-    input_dir = Path.cwd() / Path(args.input_file).parent if args.input_file else Path.cwd()
-    setattr(args, "input_directory", input_dir)
-    if not args.input_file:
-        input_files = glob.glob(str(input_dir) + "/*", recursive=True)
-        input_file_names = [os.path.basename(input_file_path) for input_file_path in input_files]
-        args.input_file = input_file_names
-    return args
-
-
 def set_wavelength(args):
     """
     Set the wavelength based on the given input arguments