added functionality to load input files using try except, added user_filesystem for testing output and input directories but probably contains errors

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -1,3 +1,4 @@
+import glob
 import sys
 from argparse import ArgumentParser
 from pathlib import Path
@@ -67,42 +68,49 @@ def main():
     args = set_input_directory(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
+    input_files = glob.glob(str(args.input_directory) + "/*", recursive=True)
 
-    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")
+    for input_file in input_files:
+        filepath = Path(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."
-        )
+        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},
-    )
+        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},
+        )
 
-    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

@@ -0,0 +1,18 @@
+import os
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def user_filesystem(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)
+
+    existing_file = Path(tmp_path).resolve() / "existing_file.py"
+    existing_file.touch()
+
+    yield tmp_path

src/diffpy/labpdfproc/tests/test_tools.py

@@ -1,5 +1,4 @@
 import argparse
-import os
 import re
 from pathlib import Path
 
@@ -16,31 +15,21 @@
 
 
 @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)
+def test_set_output_directory(inputs, expected, user_filesystem):
+    tmp_dir = user_filesystem
+    expected_output_directory = tmp_dir / expected[0]
 
     actual_parser = argparse.ArgumentParser()
     actual_parser.add_argument("--output_directory")
     actual_args = actual_parser.parse_args(["--output_directory", inputs[0]])
     actual_args.output_directory = set_output_directory(actual_args)
-
-    expected_output_directory = Path(tmp_path).resolve() / expected[0]
     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()
-
+def test_set_output_directory_bad(user_filesystem):
+    # tmp_dir = user_filesystem
     actual_parser = argparse.ArgumentParser()
     actual_parser.add_argument("--output_directory")
     actual_args = actual_parser.parse_args(["--output_directory", "existing_file.py"])
@@ -53,25 +42,21 @@ def test_set_output_directory_bad(tmp_path):
 
 params2 = [
     ([None], ["."]),
-    (["data.xy"], ["."]),
-    (["existing_dir/data.xy"], ["existing_dir"]),
+    (["existing_input_file.xy"], ["."]),
+    (["existing_dir/existing_input_file.xy"], ["existing_dir"]),
+    # ([Path.cwd()], [Path.cwd()]),
 ]
 
 
 @pytest.mark.parametrize("inputs, expected", params2)
-def test_set_input_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)
+def test_set_input_directory(inputs, expected, user_filesystem):
+    tmp_dir = user_filesystem
+    expected_input_directory = tmp_dir / expected[0]
 
     actual_parser = argparse.ArgumentParser()
     actual_parser.add_argument("--input_file")
     actual_args = actual_parser.parse_args(["--input_file", inputs[0]])
     actual_args = set_input_directory(actual_args)
-
-    expected_input_directory = Path(tmp_path).resolve() / expected[0]
     assert actual_args.input_directory == expected_input_directory