From b61906b41ccc06e5493f008164c1f65dd658c7d3 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Tue, 7 May 2024 09:49:28 -0400
Subject: [PATCH 1/9] current progress on loading specified input file and glob
 all files if no input file provided

---
 src/diffpy/labpdfproc/labpdfprocapp.py    | 79 +++++++++++++----------
 src/diffpy/labpdfproc/tests/test_tools.py | 45 ++++++++++++-
 src/diffpy/labpdfproc/tools.py            | 25 +++++++
 3 files changed, 115 insertions(+), 34 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 72ca6b7..d367ce6 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -3,7 +3,13 @@
 from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
-from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import (
+    known_sources,
+    load_user_metadata,
+    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
 
@@ -76,45 +82,52 @@ def get_args(override_cli_inputs=None):
 
 def main():
     args = get_args()
-    args = load_user_metadata(args)
+    args = set_input_files(args)
     args.output_directory = set_output_directory(args)
     args.wavelength = set_wavelength(args)
+    args = load_user_metadata(args)
 
-    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 args.input_file:
+        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."
-        )
+        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__":
diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 5121e9f..6fa7aea 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -6,7 +6,50 @@
 import pytest
 
 from diffpy.labpdfproc.labpdfprocapp import get_args
-from diffpy.labpdfproc.tools import known_sources, load_user_metadata, set_output_directory, set_wavelength
+from diffpy.labpdfproc.tools import (
+    known_sources,
+    load_user_metadata,
+    set_input_files,
+    set_output_directory,
+    set_wavelength,
+)
+from diffpy.utils.parsers.loaddata import loadData
+
+params1 = [
+    (
+        [],
+        [
+            ".",
+            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl", "input_dir"],
+        ],
+    ),
+    (["--input-file", "good_data.chi"], [".", "good_data.chi"]),
+    (["--input-file", "input_dir/unreadable_file.txt"], ["input_dir", "input_dir/unreadable_file.txt"]),
+    # ([Path.cwd()], [Path.cwd()]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params1)
+def test_set_input_files(inputs, expected, user_filesystem):
+    expected_input_directory = Path(user_filesystem) / expected[0]
+    expected_input_files = expected[1]
+
+    cli_inputs = ["2.5"] + inputs
+    actual_args = get_args(cli_inputs)
+    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)
+
 
 params1 = [
     ([None], ["."]),
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index caa012d..f05819a 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -1,9 +1,34 @@
+import glob
+import os
 from pathlib import Path
 
 WAVELENGTHS = {"Mo": 0.71, "Ag": 0.59, "Cu": 1.54}
 known_sources = [key for key in WAVELENGTHS.keys()]
 
 
+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
+
+    """
+    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_output_directory(args):
     """
     set the output directory based on the given input arguments

From d164dbaf57d099a48cda1eccc8c43dddf6c98495 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Tue, 7 May 2024 10:48:29 -0400
Subject: [PATCH 2/9] modified input file function to accept either one file or
 one directory

---
 src/diffpy/labpdfproc/tests/test_tools.py |  6 +++---
 src/diffpy/labpdfproc/tools.py            | 17 ++++++++++++-----
 2 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 64c4144..9a17981 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -15,14 +15,14 @@
 
 params1 = [
     (
-        [],
+        ["--input-file", "."],
         [
             ".",
-            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl", "input_dir"],
+            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
     (["--input-file", "good_data.chi"], [".", "good_data.chi"]),
-    (["--input-file", "input_dir/unreadable_file.txt"], ["input_dir", "input_dir/unreadable_file.txt"]),
+    (["--input-file", "input_dir/unreadable_file.txt"], ["input_dir", "unreadable_file.txt"]),
     # ([Path.cwd()], [Path.cwd()]),
 ]
 
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index f05819a..a93bbf3 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -8,7 +8,7 @@
 
 def set_input_files(args):
     """
-    Set input directory and files, default is current working directory and all files in it
+    Set input directory and files
 
     Parameters
     ----------
@@ -20,12 +20,19 @@ def set_input_files(args):
     args argparse.Namespace
 
     """
-    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)
+    if not args.input_file or not Path(args.input_file).exists():
+        raise ValueError("Please specify valid input file or directory.")
+
+    if not Path(args.input_file).is_dir():
+        input_dir = Path.cwd() / Path(args.input_file).parent
+        input_file_name = Path(args.input_file).name
+        args.input_file = input_file_name
+    else:
+        input_dir = Path(args.input_file).resolve()
+        input_files = [file for file in glob.glob(str(input_dir) + "/*", recursive=True) if os.path.isfile(file)]
         input_file_names = [os.path.basename(input_file_path) for input_file_path in input_files]
         args.input_file = input_file_names
+    setattr(args, "input_directory", input_dir)
     return args
 
 

From 3c49a18316abebba908977aa5001d76c917f2fec Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Tue, 7 May 2024 12:21:00 -0400
Subject: [PATCH 3/9] added test cases for UC1-4 and made input a required
 argument

---
 src/diffpy/labpdfproc/labpdfprocapp.py    |  2 +-
 src/diffpy/labpdfproc/tests/test_tools.py | 56 +++++++++++++++++------
 src/diffpy/labpdfproc/tools.py            | 15 +++---
 3 files changed, 51 insertions(+), 22 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index d367ce6..bc09b9d 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -17,7 +17,7 @@
 def get_args(override_cli_inputs=None):
     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("input", help="The filename or directory of the " "datafile to load.")
     p.add_argument(
         "-a",
         "--anode-type",
diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 9a17981..f1f3f52 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -13,21 +13,36 @@
 )
 from diffpy.utils.parsers.loaddata import loadData
 
-params1 = [
+# Use cases can be found here: https://github.com/diffpy/diffpy.labpdfproc/issues/48
+params_input = [
+    (["good_data.chi"], [".", "good_data.chi"]),
+    (["input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),
+    (["./input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),
     (
-        ["--input-file", "."],
+        ["."],
         [
             ".",
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
-    (["--input-file", "good_data.chi"], [".", "good_data.chi"]),
-    (["--input-file", "input_dir/unreadable_file.txt"], ["input_dir", "unreadable_file.txt"]),
-    # ([Path.cwd()], [Path.cwd()]),
+    (
+        ["./input_dir"],
+        [
+            "input_dir",
+            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
+        ],
+    ),
+    (
+        ["input_dir"],
+        [
+            "input_dir",
+            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
+        ],
+    ),
 ]
 
 
-@pytest.mark.parametrize("inputs, expected", params1)
+@pytest.mark.parametrize("inputs, expected", params_input)
 def test_set_input_files(inputs, expected, user_filesystem):
     expected_input_directory = Path(user_filesystem) / expected[0]
     expected_input_files = expected[1]
@@ -39,6 +54,21 @@ def test_set_input_files(inputs, expected, user_filesystem):
     assert set(actual_args.input_file) == set(expected_input_files)
 
 
+params_input_bad = [
+    (["new_file.xy"]),
+    (["./input_dir/new_file.xy"]),
+    (["./new_dir"]),
+]
+
+
+@pytest.mark.parametrize("inputs", params_input_bad)
+def test_set_input_files_bad(inputs, user_filesystem):
+    cli_inputs = ["2.5"] + inputs
+    actual_args = get_args(cli_inputs)
+    with pytest.raises(ValueError):
+        actual_args = set_input_files(actual_args)
+
+
 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)
@@ -60,7 +90,7 @@ def test_loadData_with_input_files(user_filesystem):
 @pytest.mark.parametrize("inputs, expected", params1)
 def test_set_output_directory(inputs, expected, user_filesystem):
     expected_output_directory = Path(user_filesystem) / expected[0]
-    cli_inputs = ["2.5"] + inputs
+    cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args.output_directory = set_output_directory(actual_args)
     assert actual_args.output_directory == expected_output_directory
@@ -69,7 +99,7 @@ def test_set_output_directory(inputs, expected, user_filesystem):
 
 
 def test_set_output_directory_bad(user_filesystem):
-    cli_inputs = ["2.5", "--output-directory", "good_data.chi"]
+    cli_inputs = ["2.5", "data.xy", "--output-directory", "good_data.chi"]
     actual_args = get_args(cli_inputs)
     with pytest.raises(FileExistsError):
         actual_args.output_directory = set_output_directory(actual_args)
@@ -88,7 +118,7 @@ def test_set_output_directory_bad(user_filesystem):
 @pytest.mark.parametrize("inputs, expected", params2)
 def test_set_wavelength(inputs, expected):
     expected_wavelength = expected[0]
-    cli_inputs = ["2.5"] + inputs
+    cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args.wavelength = set_wavelength(actual_args)
     assert actual_args.wavelength == expected_wavelength
@@ -112,7 +142,7 @@ def test_set_wavelength(inputs, expected):
 
 @pytest.mark.parametrize("inputs, msg", params3)
 def test_set_wavelength_bad(inputs, msg):
-    cli_inputs = ["2.5"] + inputs
+    cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     with pytest.raises(ValueError, match=re.escape(msg[0])):
         actual_args.wavelength = set_wavelength(actual_args)
@@ -130,12 +160,12 @@ def test_set_wavelength_bad(inputs, msg):
 
 @pytest.mark.parametrize("inputs, expected", params5)
 def test_load_user_metadata(inputs, expected):
-    expected_args = get_args(["2.5"])
+    expected_args = get_args(["2.5", "data.xy"])
     for expected_pair in expected:
         setattr(expected_args, expected_pair[0], expected_pair[1])
     delattr(expected_args, "user_metadata")
 
-    cli_inputs = ["2.5"] + inputs
+    cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = load_user_metadata(actual_args)
     assert actual_args == expected_args
@@ -172,7 +202,7 @@ def test_load_user_metadata(inputs, expected):
 
 @pytest.mark.parametrize("inputs, msg", params6)
 def test_load_user_metadata_bad(inputs, msg):
-    cli_inputs = ["2.5"] + inputs
+    cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     with pytest.raises(ValueError, match=msg[0]):
         actual_args = load_user_metadata(actual_args)
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index a93bbf3..70bf72a 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -20,19 +20,18 @@ def set_input_files(args):
     args argparse.Namespace
 
     """
-    if not args.input_file or not Path(args.input_file).exists():
+    if not Path(args.input).exists():
         raise ValueError("Please specify valid input file or directory.")
 
-    if not Path(args.input_file).is_dir():
-        input_dir = Path.cwd() / Path(args.input_file).parent
-        input_file_name = Path(args.input_file).name
-        args.input_file = input_file_name
+    if not Path(args.input).is_dir():
+        input_dir = Path.cwd() / Path(args.input).parent
+        input_file_name = Path(args.input).name
     else:
-        input_dir = Path(args.input_file).resolve()
+        input_dir = Path(args.input).resolve()
         input_files = [file for file in glob.glob(str(input_dir) + "/*", recursive=True) if os.path.isfile(file)]
-        input_file_names = [os.path.basename(input_file_path) for input_file_path in input_files]
-        args.input_file = input_file_names
+        input_file_name = [os.path.basename(input_file_path) for input_file_path in input_files]
     setattr(args, "input_directory", input_dir)
+    setattr(args, "input_file", input_file_name)
     return args
 
 

From f8b7203bcec4be870e06c05b8b525223da81e1ca Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Tue, 7 May 2024 17:11:12 -0400
Subject: [PATCH 4/9] added more test cases

---
 src/diffpy/labpdfproc/tests/test_tools.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index f1f3f52..927c5cb 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -39,6 +39,11 @@
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
+    # ([".chi"], [".", ["file1.chi", "file2.chi", "file10.chi"]]),
+    # (["input_dir/.chi"], ["input_dir", ["file1.chi", "file2.chi", "file10.chi"]]),
+    # (["file1.chi", "file10.chi"], [".", ["file1.chi", "file10.chi"]]),
+    # (["file1.chi", "file10.chi"], [".", ["file1.chi", "file10.chi"]]),
+    # (["input_file_list.txt"], [".", ["file1.chi", "file10.chi"]]),
 ]
 
 

From 3d5c5ee1d6d0ff94093e54dc8085432d01402324 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Wed, 8 May 2024 12:39:57 -0400
Subject: [PATCH 5/9] included comments for tests

---
 src/diffpy/labpdfproc/labpdfprocapp.py    |  2 +-
 src/diffpy/labpdfproc/tests/test_tools.py | 22 +++++++++++-----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index bc09b9d..6666ccf 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -17,7 +17,7 @@
 def get_args(override_cli_inputs=None):
     p = ArgumentParser()
     p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
-    p.add_argument("input", help="The filename or directory of the " "datafile to load.")
+    p.add_argument("input", help="The filename or directory of the datafile to load. Required.")
     p.add_argument(
         "-a",
         "--anode-type",
diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 927c5cb..cf6dc38 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -14,6 +14,9 @@
 from diffpy.utils.parsers.loaddata import loadData
 
 # Use cases can be found here: https://github.com/diffpy/diffpy.labpdfproc/issues/48
+
+# This test covers existing single input file or directory
+# We store absolute path into input_directory and file names into input_file
 params_input = [
     (["good_data.chi"], [".", "good_data.chi"]),
     (["input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),
@@ -39,11 +42,6 @@
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
-    # ([".chi"], [".", ["file1.chi", "file2.chi", "file10.chi"]]),
-    # (["input_dir/.chi"], ["input_dir", ["file1.chi", "file2.chi", "file10.chi"]]),
-    # (["file1.chi", "file10.chi"], [".", ["file1.chi", "file10.chi"]]),
-    # (["file1.chi", "file10.chi"], [".", ["file1.chi", "file10.chi"]]),
-    # (["input_file_list.txt"], [".", ["file1.chi", "file10.chi"]]),
 ]
 
 
@@ -59,21 +57,23 @@ def test_set_input_files(inputs, expected, user_filesystem):
     assert set(actual_args.input_file) == set(expected_input_files)
 
 
+# This test covers non-existing single input file or directory, in this case we raise an error with message
 params_input_bad = [
-    (["new_file.xy"]),
-    (["./input_dir/new_file.xy"]),
-    (["./new_dir"]),
+    (["non_existing_file.xy"], "Please specify valid input file or directory."),
+    (["./input_dir/non_existing_file.xy"], "Please specify valid input file or directory."),
+    (["./non_existing_dir"], "Please specify valid input file or directory."),
 ]
 
 
-@pytest.mark.parametrize("inputs", params_input_bad)
-def test_set_input_files_bad(inputs, user_filesystem):
+@pytest.mark.parametrize("inputs, msg", params_input_bad)
+def test_set_input_files_bad(inputs, msg, user_filesystem):
     cli_inputs = ["2.5"] + inputs
     actual_args = get_args(cli_inputs)
-    with pytest.raises(ValueError):
+    with pytest.raises(ValueError, match=msg[0]):
         actual_args = set_input_files(actual_args)
 
 
+# Pass files to loadData and use it to check if file is valid or not
 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)

From 06ae14b64ac2c3add660852cc7361ccc57ed8166 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Wed, 8 May 2024 23:27:17 -0400
Subject: [PATCH 6/9] added tests for a file list and edited help message
 addressing the rules for inputing a file list

---
 src/diffpy/labpdfproc/labpdfprocapp.py    |  8 ++++++-
 src/diffpy/labpdfproc/tests/conftest.py   |  9 ++++++++
 src/diffpy/labpdfproc/tests/test_tools.py | 26 ++++++++++++++++++++++-
 src/diffpy/labpdfproc/tools.py            | 23 +++++++++++++++++++-
 4 files changed, 63 insertions(+), 3 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 6666ccf..adaf0aa 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -17,7 +17,13 @@
 def get_args(override_cli_inputs=None):
     p = ArgumentParser()
     p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
-    p.add_argument("input", help="The filename or directory of the datafile to load. Required.")
+    p.add_argument(
+        "input",
+        help="The filename or directory of the datafile to load. Required. "
+        "Supports either a single input file or directory, or a file containing a list of files. "
+        "If providing a file list, please ensure all files are in the same directory as the file list, "
+        "and each filename is written line by line in the file list. ",
+    )
     p.add_argument(
         "-a",
         "--anode-type",
diff --git a/src/diffpy/labpdfproc/tests/conftest.py b/src/diffpy/labpdfproc/tests/conftest.py
index 1e4ab40..9296425 100644
--- a/src/diffpy/labpdfproc/tests/conftest.py
+++ b/src/diffpy/labpdfproc/tests/conftest.py
@@ -39,4 +39,13 @@ def user_filesystem(tmp_path):
     with open(os.path.join(input_dir, "binary.pkl"), "wb") as f:
         f.write(binary_data)
 
+    file_list_dir = Path(tmp_path).resolve() / "file_list_dir"
+    file_list_dir.mkdir(parents=True, exist_ok=True)
+    with open(os.path.join(file_list_dir, "file_list.txt"), "w") as f:
+        f.write("good_data.chi \n good_data.xy \n good_data.txt")
+    with open(os.path.join(file_list_dir, "invalid_file_list.txt"), "w") as f:
+        f.write("good_data.chi \n non_existing_file.xy \n non_existing_file.txt")
+    with open(os.path.join(file_list_dir, "invalid_format_file_list.txt"), "w") as f:
+        f.write("good_data.chi good_data.xy \n non_existing_file.txt")
+
     yield tmp_path
diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index cf6dc38..7d475d7 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -1,3 +1,4 @@
+import os
 import re
 from pathlib import Path
 
@@ -15,7 +16,7 @@
 
 # Use cases can be found here: https://github.com/diffpy/diffpy.labpdfproc/issues/48
 
-# This test covers existing single input file or directory
+# This test covers existing single input file, directory, or a file list
 # We store absolute path into input_directory and file names into input_file
 params_input = [
     (["good_data.chi"], [".", "good_data.chi"]),
@@ -42,6 +43,7 @@
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
+    (["file_list_dir/file_list.txt"], ["file_list_dir", ["good_data.chi", "good_data.xy", "good_data.txt"]]),
 ]
 
 
@@ -57,6 +59,28 @@ def test_set_input_files(inputs, expected, user_filesystem):
     assert set(actual_args.input_file) == set(expected_input_files)
 
 
+# This test is for existing single input file or directory absolute path not in cwd
+# Here we are in user_filesystem/input_dir, testing for a file or directory in user_filesystem
+params_input_not_cwd = [
+    (["good_data.chi"], [".", "good_data.chi"]),
+    (["."], [".", ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"]]),
+]
+
+
+@pytest.mark.parametrize("inputs, expected", params_input_not_cwd)
+def test_set_input_files_not_cwd(inputs, expected, user_filesystem):
+    expected_input_directory = Path(user_filesystem) / expected[0]
+    expected_input_files = expected[1]
+    actual_input = [str(Path(user_filesystem) / inputs[0])]
+    os.chdir("input_dir")
+
+    cli_inputs = ["2.5"] + actual_input
+    actual_args = get_args(cli_inputs)
+    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)
+
+
 # This test covers non-existing single input file or directory, in this case we raise an error with message
 params_input_bad = [
     (["non_existing_file.xy"], "Please specify valid input file or directory."),
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index 70bf72a..f13543c 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -15,21 +15,42 @@ def set_input_files(args):
     args argparse.Namespace
         the arguments from the parser
 
+    It is implemented as this:
+    If input is a file, we first try to read it as a file list and store all listed file names.
+    If any filename is invalid, then proceed to treat it as a data file.
+    Otherwise if we have a directory, glob all files within it.
+
     Returns
     -------
     args argparse.Namespace
 
     """
+
     if not Path(args.input).exists():
         raise ValueError("Please specify valid input file or directory.")
 
     if not Path(args.input).is_dir():
         input_dir = Path.cwd() / Path(args.input).parent
-        input_file_name = Path(args.input).name
+        file_names = []
+        with open(args.input, "r") as f:
+            for line in f:
+                if not os.path.isfile(line.strip()):
+                    file_names = []
+                    break
+                else:
+                    file_name = line.strip()
+                    file_names.append(file_name)
+
+        if len(file_names) > 0:
+            input_file_name = file_names
+        else:
+            input_file_name = Path(args.input).name
+
     else:
         input_dir = Path(args.input).resolve()
         input_files = [file for file in glob.glob(str(input_dir) + "/*", recursive=True) if os.path.isfile(file)]
         input_file_name = [os.path.basename(input_file_path) for input_file_path in input_files]
+
     setattr(args, "input_directory", input_dir)
     setattr(args, "input_file", input_file_name)
     return args

From a02b573996117daf4166c84439f9a7b811c8a7a3 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 9 May 2024 18:38:51 -0400
Subject: [PATCH 7/9] added tests for file list and multiple files

---
 src/diffpy/labpdfproc/labpdfprocapp.py    |  5 +-
 src/diffpy/labpdfproc/tests/conftest.py   | 10 ++--
 src/diffpy/labpdfproc/tests/test_tools.py | 37 ++++++++++-----
 src/diffpy/labpdfproc/tools.py            | 56 +++++++++++++++--------
 4 files changed, 68 insertions(+), 40 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index adaf0aa..1d08cb9 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -19,10 +19,9 @@ def get_args(override_cli_inputs=None):
     p.add_argument("mud", help="Value of mu*D for your " "sample. Required.", type=float)
     p.add_argument(
         "input",
+        nargs="+",
         help="The filename or directory of the datafile to load. Required. "
-        "Supports either a single input file or directory, or a file containing a list of files. "
-        "If providing a file list, please ensure all files are in the same directory as the file list, "
-        "and each filename is written line by line in the file list. ",
+        "Supports either a single input file, a directory, a file containing a list of files, or multiple files. ",
     )
     p.add_argument(
         "-a",
diff --git a/src/diffpy/labpdfproc/tests/conftest.py b/src/diffpy/labpdfproc/tests/conftest.py
index 9296425..075428c 100644
--- a/src/diffpy/labpdfproc/tests/conftest.py
+++ b/src/diffpy/labpdfproc/tests/conftest.py
@@ -42,10 +42,10 @@ def user_filesystem(tmp_path):
     file_list_dir = Path(tmp_path).resolve() / "file_list_dir"
     file_list_dir.mkdir(parents=True, exist_ok=True)
     with open(os.path.join(file_list_dir, "file_list.txt"), "w") as f:
-        f.write("good_data.chi \n good_data.xy \n good_data.txt")
-    with open(os.path.join(file_list_dir, "invalid_file_list.txt"), "w") as f:
-        f.write("good_data.chi \n non_existing_file.xy \n non_existing_file.txt")
-    with open(os.path.join(file_list_dir, "invalid_format_file_list.txt"), "w") as f:
-        f.write("good_data.chi good_data.xy \n non_existing_file.txt")
+        f.write("good_data.chi \n good_data.xy \n good_data.txt \n missing_file.txt")
+    with open(os.path.join(file_list_dir, "file_list_example2.txt"), "w") as f:
+        f.write("input_dir/good_data.chi \n")
+        f.write("good_data.xy \n")
+        f.write(str(os.path.abspath(os.path.join(input_dir, "good_data.txt"))) + "\n")
 
     yield tmp_path
diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 7d475d7..0cbc41e 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -16,34 +16,47 @@
 
 # Use cases can be found here: https://github.com/diffpy/diffpy.labpdfproc/issues/48
 
-# This test covers existing single input file, directory, or a file list
-# We store absolute path into input_directory and file names into input_file
+# This test covers existing single input file, directory, a file list, and multiple files
+# We store absolute paths into input_directory and file names into input_file
 params_input = [
-    (["good_data.chi"], [".", "good_data.chi"]),
-    (["input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),
-    (["./input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),
-    (
+    (["good_data.chi"], [".", "good_data.chi"]),  # single good file, same directory
+    (["input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),  # single good file, input directory
+    (  # glob current directory
         ["."],
         [
             ".",
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
-    (
+    (  # glob input directory
         ["./input_dir"],
         [
             "input_dir",
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
-    (
-        ["input_dir"],
+    (  # list of files provided (we skip if encountering an invalid files)
+        ["good_data.chi", "good_data.xy", "unreadable_file.txt", "missing_file.txt"],
         [
-            "input_dir",
-            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
+            ".",
+            ["good_data.chi", "good_data.xy", "unreadable_file.txt"],
         ],
     ),
-    (["file_list_dir/file_list.txt"], ["file_list_dir", ["good_data.chi", "good_data.xy", "good_data.txt"]]),
+    (  # list of files provided (with invalid files and files in different directory)
+        ["input_dir/good_data.chi", "good_data.xy", "missing_file.txt"],
+        [
+            ".",
+            ["input_dir/good_data.chi", "good_data.xy"],
+        ],
+    ),
+    (  # file_list.txt list of files provided
+        ["file_list_dir/file_list.txt"],
+        [".", ["good_data.chi", "good_data.xy", "good_data.txt"]],
+    ),
+    (  # file_list_example2.txt list of files provided with different paths
+        ["file_list_dir/file_list_example2.txt"],
+        [".", ["input_dir/good_data.chi", "good_data.xy", "input_dir/good_data.txt"]],
+    ),
 ]
 
 
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index f13543c..0c5b753 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -15,10 +15,12 @@ def set_input_files(args):
     args argparse.Namespace
         the arguments from the parser
 
-    It is implemented as this:
+    It is implemented as the following:
+    If user input multiple files, we store their common directory as input directory and all of their names.
     If input is a file, we first try to read it as a file list and store all listed file names.
-    If any filename is invalid, then proceed to treat it as a data file.
+    If the first filename is invalid, then we proceed to treat it as a data file.
     Otherwise if we have a directory, glob all files within it.
+    If there are any invalid filenames (for the cases of multiple files, file list, or directory), we skip them.
 
     Returns
     -------
@@ -26,28 +28,42 @@ def set_input_files(args):
 
     """
 
-    if not Path(args.input).exists():
+    if len(args.input) > 1:
+        input_paths = []
+        input_paths_parent = []
+        for input in args.input:
+            if Path(input).is_file():
+                input_paths.append(Path(input).resolve())
+                input_paths_parent.append(Path(input).resolve().parent)
+        input_dir = Path(os.path.commonprefix([str(path) for path in input_paths_parent]))
+        input_file_name = [str(path.relative_to(input_dir)) for path in input_paths]
+        setattr(args, "input_directory", input_dir)
+        setattr(args, "input_file", input_file_name)
+        return args
+
+    if not Path(args.input[0]).exists():
         raise ValueError("Please specify valid input file or directory.")
 
-    if not Path(args.input).is_dir():
-        input_dir = Path.cwd() / Path(args.input).parent
-        file_names = []
-        with open(args.input, "r") as f:
-            for line in f:
-                if not os.path.isfile(line.strip()):
-                    file_names = []
-                    break
-                else:
-                    file_name = line.strip()
-                    file_names.append(file_name)
-
-        if len(file_names) > 0:
-            input_file_name = file_names
-        else:
-            input_file_name = Path(args.input).name
+    if not Path(args.input[0]).is_dir():
+        input_paths = []
+        input_paths_parent = []
+        with open(args.input[0], "r") as f:
+            lines = [line.strip() for line in f]
+            if not os.path.isfile(lines[0]):
+                input_dir = Path.cwd() / Path(args.input[0]).parent
+                input_file_name = Path(args.input[0]).name
+            else:
+                for line in lines:
+                    if not os.path.isfile(line):
+                        continue
+                    else:
+                        input_paths.append(Path(line).resolve())
+                        input_paths_parent.append(Path(line).resolve().parent)
+                input_dir = Path(os.path.commonprefix([str(path) for path in input_paths_parent]))
+                input_file_name = [str(path.relative_to(input_dir)) for path in input_paths]
 
     else:
-        input_dir = Path(args.input).resolve()
+        input_dir = Path(args.input[0]).resolve()
         input_files = [file for file in glob.glob(str(input_dir) + "/*", recursive=True) if os.path.isfile(file)]
         input_file_name = [os.path.basename(input_file_path) for input_file_path in input_files]
 

From 7d39a74f08a1443a9c7cd14c0780348c468cda3f Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Thu, 9 May 2024 18:55:46 -0400
Subject: [PATCH 8/9] fix grammar

---
 src/diffpy/labpdfproc/tests/test_tools.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index 0cbc41e..ed02838 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -17,7 +17,7 @@
 # Use cases can be found here: https://github.com/diffpy/diffpy.labpdfproc/issues/48
 
 # This test covers existing single input file, directory, a file list, and multiple files
-# We store absolute paths into input_directory and file names into input_file
+# We store absolute path into input_directory and file names into input_file
 params_input = [
     (["good_data.chi"], [".", "good_data.chi"]),  # single good file, same directory
     (["input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),  # single good file, input directory
@@ -35,14 +35,14 @@
             ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
         ],
     ),
-    (  # list of files provided (we skip if encountering an invalid files)
+    (  # list of files provided (we skip if encountering invalid files)
         ["good_data.chi", "good_data.xy", "unreadable_file.txt", "missing_file.txt"],
         [
             ".",
             ["good_data.chi", "good_data.xy", "unreadable_file.txt"],
         ],
     ),
-    (  # list of files provided (with invalid files and files in different directory)
+    (  # list of files provided (with invalid files and files in different directories)
         ["input_dir/good_data.chi", "good_data.xy", "missing_file.txt"],
         [
             ".",
@@ -53,7 +53,7 @@
         ["file_list_dir/file_list.txt"],
         [".", ["good_data.chi", "good_data.xy", "good_data.txt"]],
     ),
-    (  # file_list_example2.txt list of files provided with different paths
+    (  # file_list_example2.txt list of files provided in different directories
         ["file_list_dir/file_list_example2.txt"],
         [".", ["input_dir/good_data.chi", "good_data.xy", "input_dir/good_data.txt"]],
     ),

From ead58300b3853001117a6f44b0707fa3f7d79221 Mon Sep 17 00:00:00 2001
From: yucongalicechen <yucong0821@g.ucla.edu>
Date: Fri, 10 May 2024 00:29:44 -0400
Subject: [PATCH 9/9] intermediate process (more tests need to be added): using
 input_directory only for simplication

---
 src/diffpy/labpdfproc/labpdfprocapp.py    | 11 ++--
 src/diffpy/labpdfproc/tests/test_tools.py | 58 ++++++++---------
 src/diffpy/labpdfproc/tools.py            | 79 +++++++++++------------
 3 files changed, 68 insertions(+), 80 deletions(-)

diff --git a/src/diffpy/labpdfproc/labpdfprocapp.py b/src/diffpy/labpdfproc/labpdfprocapp.py
index 1d08cb9..ef3f253 100644
--- a/src/diffpy/labpdfproc/labpdfprocapp.py
+++ b/src/diffpy/labpdfproc/labpdfprocapp.py
@@ -1,6 +1,5 @@
 import sys
 from argparse import ArgumentParser
-from pathlib import Path
 
 from diffpy.labpdfproc.functions import apply_corr, compute_cve
 from diffpy.labpdfproc.tools import (
@@ -20,8 +19,11 @@ def get_args(override_cli_inputs=None):
     p.add_argument(
         "input",
         nargs="+",
-        help="The filename or directory of the datafile to load. Required. "
-        "Supports either a single input file, a directory, a file containing a list of files, or multiple files. ",
+        help="The filename(s) or folder(s) of the datafile(s) to load.  Required. "
+        "Supports multiple arguments of input file or directory. "
+        "The file can be either a data file or a file containing a list of files. "
+        "If a directory is provided, we will load all data files in it. "
+        "For example, file.xy, data/file.xy, file_list.txt, ./data/file.xy, ./data are all valid inputs. ",
     )
     p.add_argument(
         "-a",
@@ -92,8 +94,7 @@ def main():
     args.wavelength = set_wavelength(args)
     args = load_user_metadata(args)
 
-    for input_file in args.input_file:
-        filepath = Path(args.input_file)
+    for filepath in args.input_directory:
         outfilestem = filepath.stem + "_corrected"
         corrfilestem = filepath.stem + "_cve"
         outfile = args.output_directory / (outfilestem + ".chi")
diff --git a/src/diffpy/labpdfproc/tests/test_tools.py b/src/diffpy/labpdfproc/tests/test_tools.py
index ed02838..717e5eb 100644
--- a/src/diffpy/labpdfproc/tests/test_tools.py
+++ b/src/diffpy/labpdfproc/tests/test_tools.py
@@ -19,86 +19,80 @@
 # This test covers existing single input file, directory, a file list, and multiple files
 # We store absolute path into input_directory and file names into input_file
 params_input = [
-    (["good_data.chi"], [".", "good_data.chi"]),  # single good file, same directory
-    (["input_dir/good_data.chi"], ["input_dir", "good_data.chi"]),  # single good file, input directory
+    (["good_data.chi"], ["good_data.chi"]),  # single good file, same directory
+    (["input_dir/good_data.chi"], ["input_dir/good_data.chi"]),  # single good file, input directory
     (  # glob current directory
         ["."],
-        [
-            ".",
-            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
-        ],
+        ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
     ),
     (  # glob input directory
         ["./input_dir"],
         [
-            "input_dir",
-            ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"],
+            "input_dir/good_data.chi",
+            "input_dir/good_data.xy",
+            "input_dir/good_data.txt",
+            "input_dir/unreadable_file.txt",
+            "input_dir/binary.pkl",
         ],
     ),
     (  # list of files provided (we skip if encountering invalid files)
         ["good_data.chi", "good_data.xy", "unreadable_file.txt", "missing_file.txt"],
-        [
-            ".",
-            ["good_data.chi", "good_data.xy", "unreadable_file.txt"],
-        ],
+        ["good_data.chi", "good_data.xy", "unreadable_file.txt"],
     ),
     (  # list of files provided (with invalid files and files in different directories)
-        ["input_dir/good_data.chi", "good_data.xy", "missing_file.txt"],
-        [
-            ".",
-            ["input_dir/good_data.chi", "good_data.xy"],
-        ],
+        ["input_dir/good_data.chi", "good_data.chi", "missing_file.txt"],
+        ["input_dir/good_data.chi", "good_data.chi"],
     ),
     (  # file_list.txt list of files provided
         ["file_list_dir/file_list.txt"],
-        [".", ["good_data.chi", "good_data.xy", "good_data.txt"]],
+        ["good_data.chi", "good_data.xy", "good_data.txt"],
     ),
     (  # file_list_example2.txt list of files provided in different directories
         ["file_list_dir/file_list_example2.txt"],
-        [".", ["input_dir/good_data.chi", "good_data.xy", "input_dir/good_data.txt"]],
+        ["input_dir/good_data.chi", "good_data.xy", "input_dir/good_data.txt"],
     ),
 ]
 
 
 @pytest.mark.parametrize("inputs, expected", params_input)
 def test_set_input_files(inputs, expected, user_filesystem):
-    expected_input_directory = Path(user_filesystem) / expected[0]
-    expected_input_files = expected[1]
+    expected_input_directory = []
+    for expected_path in expected:
+        expected_input_directory.append(Path(user_filesystem) / expected_path)
 
     cli_inputs = ["2.5"] + inputs
     actual_args = get_args(cli_inputs)
     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)
+    assert set(actual_args.input_directory) == set(expected_input_directory)
 
 
 # This test is for existing single input file or directory absolute path not in cwd
 # Here we are in user_filesystem/input_dir, testing for a file or directory in user_filesystem
 params_input_not_cwd = [
-    (["good_data.chi"], [".", "good_data.chi"]),
-    (["."], [".", ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"]]),
+    (["good_data.chi"], ["good_data.chi"]),
+    (["."], ["good_data.chi", "good_data.xy", "good_data.txt", "unreadable_file.txt", "binary.pkl"]),
 ]
 
 
 @pytest.mark.parametrize("inputs, expected", params_input_not_cwd)
 def test_set_input_files_not_cwd(inputs, expected, user_filesystem):
-    expected_input_directory = Path(user_filesystem) / expected[0]
-    expected_input_files = expected[1]
+    expected_input_directory = []
+    for expected_path in expected:
+        expected_input_directory.append(Path(user_filesystem) / expected_path)
     actual_input = [str(Path(user_filesystem) / inputs[0])]
     os.chdir("input_dir")
 
     cli_inputs = ["2.5"] + actual_input
     actual_args = get_args(cli_inputs)
     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)
+    assert set(actual_args.input_directory) == set(expected_input_directory)
 
 
 # This test covers non-existing single input file or directory, in this case we raise an error with message
 params_input_bad = [
-    (["non_existing_file.xy"], "Please specify valid input file or directory."),
-    (["./input_dir/non_existing_file.xy"], "Please specify valid input file or directory."),
-    (["./non_existing_dir"], "Please specify valid input file or directory."),
+    (["non_existing_file.xy"], "Please specify at least one valid input file or directory."),
+    (["./input_dir/non_existing_file.xy"], "Please specify at least one valid input file or directory."),
+    (["./non_existing_dir"], "Please specify at least one valid input file or directory."),
 ]
 
 
diff --git a/src/diffpy/labpdfproc/tools.py b/src/diffpy/labpdfproc/tools.py
index 0c5b753..df3139d 100644
--- a/src/diffpy/labpdfproc/tools.py
+++ b/src/diffpy/labpdfproc/tools.py
@@ -16,11 +16,12 @@ def set_input_files(args):
         the arguments from the parser
 
     It is implemented as the following:
-    If user input multiple files, we store their common directory as input directory and all of their names.
+    For each input, we try to read it as a file or a directory.
     If input is a file, we first try to read it as a file list and store all listed file names.
     If the first filename is invalid, then we proceed to treat it as a data file.
     Otherwise if we have a directory, glob all files within it.
-    If there are any invalid filenames (for the cases of multiple files, file list, or directory), we skip them.
+    If any file does not exist, we raise a ValueError telling which file(s) does not exist.
+    If all files are invalid, we raise an Error telling user to specify at least one valid file or directory.
 
     Returns
     -------
@@ -28,47 +29,39 @@ def set_input_files(args):
 
     """
 
-    if len(args.input) > 1:
-        input_paths = []
-        input_paths_parent = []
-        for input in args.input:
-            if Path(input).is_file():
-                input_paths.append(Path(input).resolve())
-                input_paths_parent.append(Path(input).resolve().parent)
-        input_dir = Path(os.path.commonprefix([str(path) for path in input_paths_parent]))
-        input_file_name = [str(path.relative_to(input_dir)) for path in input_paths]
-        setattr(args, "input_directory", input_dir)
-        setattr(args, "input_file", input_file_name)
-        return args
-
-    if not Path(args.input[0]).exists():
-        raise ValueError("Please specify valid input file or directory.")
-
-    if not Path(args.input[0]).is_dir():
-        input_paths = []
-        input_paths_parent = []
-        with open(args.input[0], "r") as f:
-            lines = [line.strip() for line in f]
-            if not os.path.isfile(lines[0]):
-                input_dir = Path.cwd() / Path(args.input[0]).parent
-                input_file_name = Path(args.input[0]).name
-            else:
-                for line in lines:
-                    if not os.path.isfile(line):
-                        continue
-                    else:
-                        input_paths.append(Path(line).resolve())
-                        input_paths_parent.append(Path(line).resolve().parent)
-                input_dir = Path(os.path.commonprefix([str(path) for path in input_paths_parent]))
-                input_file_name = [str(path.relative_to(input_dir)) for path in input_paths]
-
-    else:
-        input_dir = Path(args.input[0]).resolve()
-        input_files = [file for file in glob.glob(str(input_dir) + "/*", recursive=True) if os.path.isfile(file)]
-        input_file_name = [os.path.basename(input_file_path) for input_file_path in input_files]
-
-    setattr(args, "input_directory", input_dir)
-    setattr(args, "input_file", input_file_name)
+    input_paths = []
+    for input in args.input:
+        try:
+            if Path(input).exists():
+                if not Path(input).is_dir():
+                    with open(args.input[0], "r") as f:
+                        lines = [line.strip() for line in f]
+                        if not os.path.isfile(lines[0]):
+                            input_paths.append(Path(input).resolve())
+                        else:
+                            for line in lines:
+                                try:
+                                    if os.path.isfile(line):
+                                        input_paths.append(Path(line).resolve())
+                                except Exception as e:
+                                    raise ValueError(f"{line} does not exist. {e}.")
+
+                else:
+                    input_dir = Path(input).resolve()
+                    input_files = [
+                        Path(file).resolve()
+                        for file in glob.glob(str(input_dir) + "/*", recursive=True)
+                        if os.path.isfile(file)
+                    ]
+                    input_paths.extend(input_files)
+
+        except Exception as e:
+            raise ValueError(f"{input} does not exist. {e}.")
+
+    if len(input_paths) == 0:
+        raise ValueError("Please specify at least one valid input file or directory.")
+
+    setattr(args, "input_directory", input_paths)
     return args