changed set_input_dir to set_input_files

Author: yucongalicechen

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -1,10 +1,9 @@
-import glob
 import sys
 from argparse import ArgumentParser
 from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import known_sources, set_input_directory, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import known_sources, set_input_files, set_output_directory, set_wavelength
 from diffpy.utils.parsers.loaddata import loadData
 from diffpy.utils.scattering_objects.diffraction_objects import XQUANTITIES, Diffraction_object
 
@@ -65,12 +64,11 @@ def get_args():
 
 def main():
     args = get_args()
-    args = set_input_directory(args)
+    args = set_input_files(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
-    input_files = glob.glob(str(args.input_directory) + "/*", recursive=True)
 
-    for input_file in input_files:
+    for input_file in args.input_file:
         filepath = Path(input_file)
         outfilestem = filepath.stem + "_corrected"
         corrfilestem = filepath.stem + "_cve"

src/diffpy/labpdfproc/tests/conftest.py

@@ -9,22 +9,35 @@ 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()
-
-    input_directory = Path(tmp_path).resolve() / "input_directory"
-    input_directory.mkdir(parents=True, exist_ok=True)
-
-    with open(os.path.join(input_directory, "good_data.chi"), "w") as f:
-        f.write("1 2 \n 3 4 \n 5 6 \n 7 8")
-    with open(os.path.join(input_directory, "good_data.xy"), "w") as f:
-        f.write("1 2 \n 3 4 \n 5 6 \n 7 8")
-    with open(os.path.join(input_directory, "unreadable_file.txt"), "w") as f:
-        f.write("This is an unreadable file.")
-    with open(os.path.join(input_directory, "binary.pkl"), "wb") as f:
-        f.write(b"\x00\x01\x02\x03\x04")
+    input_dir = Path(tmp_path).resolve() / "input_dir"
+    input_dir.mkdir(parents=True, exist_ok=True)
+
+    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"
+
+    with open("good_data.chi", "w") as f:
+        f.write(chi_data)
+    with open("good_data.xy", "w") as f:
+        f.write(xy_data)
+    with open("good_data.txt", "w") as f:
+        f.write(txt_data)
+    with open("unreadable_file.txt", "w") as f:
+        f.write(unreadable_data)
+    with open("binary.pkl", "wb") as f:
+        f.write(binary_data)
+
+    with open(os.path.join(input_dir, "good_data.chi"), "w") as f:
+        f.write(chi_data)
+    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)
+    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:
+        f.write(binary_data)
 
     yield tmp_path

src/diffpy/labpdfproc/tests/test_tools.py

@@ -1,18 +1,17 @@
 import argparse
-import os
 import re
 from pathlib import Path
 
 import pytest
 
-from diffpy.labpdfproc.tools import known_sources, set_input_directory, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import known_sources, set_input_files, set_output_directory, set_wavelength
 from diffpy.utils.parsers.loaddata import loadData
 
 params1 = [
     ([None], ["."]),
     (["."], ["."]),
     (["new_dir"], ["new_dir"]),
-    (["existing_dir"], ["existing_dir"]),
+    (["input_dir"], ["input_dir"]),
 ]
 
 
@@ -33,7 +32,7 @@ def test_set_output_directory(inputs, expected, user_filesystem):
 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", "existing_file.py"])
+    actual_args = actual_parser.parse_args(["--output_directory", "good_data.chi"])
 
     with pytest.raises(FileExistsError):
         actual_args.output_directory = set_output_directory(actual_args)
@@ -42,29 +41,37 @@ def test_set_output_directory_bad(user_filesystem):
 
 
 params2 = [
-    ([None], ["."]),
-    (["existing_input_file.xy"], ["."]),
-    (["existing_dir/existing_input_file.xy"], ["existing_dir"]),
+    (
+        [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_directory(inputs, expected, user_filesystem):
+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_directory(actual_args)
+    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_input_files(user_filesystem):
-    os.chdir("input_directory")
+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):

src/diffpy/labpdfproc/tools.py

@@ -1,3 +1,5 @@
+import glob
+import os
 from pathlib import Path
 
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
@@ -28,9 +30,9 @@ def set_output_directory(args):
     return output_dir
 
 
-def set_input_directory(args):
+def set_input_files(args):
     """
-    Set the input directory based on input file, default is current working directory if nothing is given
+    Set input directory and files, default is current working directory and all files in it
 
     Parameters
     ----------
@@ -40,11 +42,15 @@ def set_input_directory(args):
     Returns
     -------
     args argparse.Namespace
-        the arguments from the parser with a new argument input_directory
+        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