Merge pull request #196 from yucongalicechen/applymud-cli

feat: add ``applymud`` subcommand

Author: sbillinge

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -44,7 +44,7 @@ jobs:
 
       - name: Install diffpy.labpdfproc and requirements
         run: |
-          conda install --file requirements/test.txt
+          conda install --file requirements/tests.txt
           conda install --file requirements/conda.txt
           pip install gooey
           python -m pip install . --no-deps

.github/workflows/tests-on-pr.yml

@@ -34,7 +34,7 @@ jobs:
 
       - name: Install diffpy.labpdfproc and requirements
         run: |
-          conda install --file requirements/test.txt
+          conda install --file requirements/tests.txt
           conda install --file requirements/conda.txt
           pip install gooey
           python -m pip install . --no-deps

news/applymud.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* new subcommand ``applymud`` to run the original absorption correction process through CLI.
+
+**Changed:**
+
+* GitHub workflows for renamed test file.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -73,6 +73,7 @@ def _define_arguments():
                 "If the specified directory doesn't exist it will be created."
             ),
             "default": None,
+            "widget": "DirChooser",
         },
         {
             "name": ["-x", "--xtype"],
@@ -158,7 +159,7 @@ def _define_arguments():
     return args
 
 
-def _add_mud_selection_group(p, is_gui=False):
+def _add_mud_selection_group(p, use_gui=False):
     """Current Options:
     1. Manually enter muD (`--mud`).
     2. Estimate from a z-scan file (`-z` or `--z-scan-file`).
@@ -173,7 +174,7 @@ def _add_mud_selection_group(p, is_gui=False):
         "--mud",
         type=float,
         help="Enter the mu*D value manually.",
-        **({"widget": "DecimalField"} if is_gui else {}),
+        **({"widget": "DecimalField"} if use_gui else {}),
     )
     g.add_argument(
         "-z",
@@ -183,7 +184,7 @@ def _add_mud_selection_group(p, is_gui=False):
             "Specify the path to the file "
             "used to compute the mu*D value."
         ),
-        **({"widget": "FileChooser"} if is_gui else {}),
+        **({"widget": "FileChooser"} if use_gui else {}),
     )
     g.add_argument(
         "-d",
@@ -207,39 +208,50 @@ def _add_mud_selection_group(p, is_gui=False):
     return p
 
 
-def get_args(override_cli_inputs=None):
-    p = ArgumentParser()
-    p = _add_mud_selection_group(p, is_gui=False)
+def _register_applymud_subparser(subp, use_gui=False):
+    applymudp = subp.add_parser(
+        "applymud", help="Apply absorption correction."
+    )
+    _add_mud_selection_group(applymudp, use_gui=use_gui)
     for arg in _define_arguments():
-        kwargs = {
-            key: value
-            for key, value in arg.items()
-            if key != "name" and key != "widget"
-        }
-        p.add_argument(*arg["name"], **kwargs)
-    args = p.parse_args(override_cli_inputs)
-    return args
+        names = arg["name"]
+        options = {k: v for k, v in arg.items() if k != "name"}
+        if not use_gui and "widget" in options:
+            options.pop("widget")
+        applymudp.add_argument(*names, **options)
 
 
-@Gooey(required_cols=1, optional_cols=2, program_name="labpdfproc GUI")
-def gooey_parser():
-    p = GooeyParser()
-    p = _add_mud_selection_group(p, is_gui=True)
-    for arg in _define_arguments():
-        kwargs = {key: value for key, value in arg.items() if key != "name"}
-        p.add_argument(*arg["name"], **kwargs)
+def create_parser(use_gui=False):
+    p = GooeyParser() if use_gui else ArgumentParser()
+    subp = p.add_subparsers(title="subcommand", dest="subcommand")
+    _register_applymud_subparser(subp, use_gui)
+    return p
+
+
+@Gooey(
+    required_cols=1,
+    optional_cols=1,
+    show_sidebar=True,
+    program_name="labpdfproc GUI",
+)
+def _get_args_gui():
+    p = create_parser(use_gui=True)
     args = p.parse_args()
     return args
 
 
-def main():
-    args = (
-        gooey_parser()
-        if len(sys.argv) == 1 or "--gui" in sys.argv
-        else get_args()
-    )
-    args = preprocessing_args(args)
+def _get_args_cli(override_cli_inputs=None):
+    p = create_parser(use_gui=False)
+    args = p.parse_args(override_cli_inputs)
+    return args
+
 
+def get_args(override_cli_inputs=None, use_gui=False):
+    return _get_args_gui() if use_gui else _get_args_cli(override_cli_inputs)
+
+
+def applymud(args):
+    args = preprocessing_args(args)
     for filepath in args.input_paths:
         outfilestem = filepath.stem + "_corrected"
         corrfilestem = filepath.stem + "_cve"
@@ -286,5 +298,18 @@ def main():
             absorption_correction.dump(f"{corrfile}", xtype=args.xtype)
 
 
+def run_subcommand(args):
+    if args.subcommand == "applymud":
+        return applymud(args)
+    else:
+        raise ValueError(f"Unknown subcommand: {args.subcommand}")
+
+
+def main():
+    use_gui = len(sys.argv) == 1 or "--gui" in sys.argv
+    args = get_args(use_gui=use_gui)
+    return run_subcommand(args)
+
+
 if __name__ == "__main__":
     main()

src/diffpy/labpdfproc/tools.py

@@ -45,6 +45,7 @@
     "wavelength",
     "theoretical_from_density",
     "theoretical_from_packing",
+    "subcommand",
 ]
 
 

tests/test_tools.py

@@ -115,7 +115,7 @@ def test_set_input_lists(inputs, expected, user_filesystem):
         base_dir.resolve() / expected_path for expected_path in expected
     ]
 
-    cli_inputs = inputs + ["--mud", "2.5"]
+    cli_inputs = ["applymud"] + inputs + ["--mud", "2.5"]
     actual_args = get_args(cli_inputs)
     actual_args = set_input_lists(actual_args)
     assert sorted(actual_args.input_paths) == sorted(expected_paths)
@@ -161,7 +161,7 @@ def test_set_input_lists(inputs, expected, user_filesystem):
 def test_set_input_files_bad(inputs, expected_error_msg, user_filesystem):
     base_dir = Path(user_filesystem)
     os.chdir(base_dir)
-    cli_inputs = inputs + ["--mud", "2.5"]
+    cli_inputs = ["applymud"] + inputs + ["--mud", "2.5"]
     actual_args = get_args(cli_inputs)
     with pytest.raises(FileNotFoundError, match=re.escape(expected_error_msg)):
         actual_args = set_input_lists(actual_args)
@@ -179,7 +179,7 @@ def test_set_input_files_bad(inputs, expected_error_msg, user_filesystem):
 def test_set_output_directory(inputs, expected, user_filesystem):
     os.chdir(user_filesystem)
     expected_output_directory = Path(user_filesystem) / expected[0]
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = set_output_directory(actual_args)
     assert actual_args.output_directory == expected_output_directory
@@ -190,6 +190,7 @@ def test_set_output_directory(inputs, expected, user_filesystem):
 def test_set_output_directory_bad(user_filesystem):
     os.chdir(user_filesystem)
     cli_inputs = [
+        "applymud",
         "data.xy",
         "--mud",
         "2.5",
@@ -235,7 +236,7 @@ def test_load_wavelength_from_config_file_with_home_conf_file(
     mocker.patch("pathlib.Path.home", lambda _: home_dir)
     os.chdir(cwd)
 
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = load_wavelength_from_config_file(actual_args)
     assert actual_args.wavelength == expected["wavelength"]
@@ -278,7 +279,7 @@ def test_load_wavelength_from_config_file_with_local_conf_file(
     with open(cwd / "diffpyconfig.json", "w") as f:
         json.dump(local_config_data, f)
 
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = load_wavelength_from_config_file(actual_args)
     assert actual_args.wavelength == expected["wavelength"]
@@ -321,7 +322,7 @@ def test_load_wavelength_from_config_file_without_conf_files(
     confile = home_dir / "diffpyconfig.json"
     os.remove(confile)
 
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = load_wavelength_from_config_file(actual_args)
     assert actual_args.wavelength == expected["wavelength"]
@@ -380,7 +381,7 @@ def test_load_wavelength_from_config_file_without_conf_files(
     ],
 )
 def test_set_wavelength(inputs, expected):
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = set_wavelength(actual_args)
     assert actual_args.wavelength == expected["wavelength"]
@@ -419,7 +420,7 @@ def test_set_wavelength(inputs, expected):
     ],
 )
 def test_set_wavelength_bad(inputs, expected_error_msg):
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     with pytest.raises(ValueError, match=re.escape(expected_error_msg)):
         actual_args = set_wavelength(actual_args)
@@ -435,14 +436,14 @@ def test_set_wavelength_bad(inputs, expected_error_msg):
     ],
 )
 def test_set_xtype(inputs, expected_xtype):
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = set_xtype(actual_args)
     assert actual_args.xtype == expected_xtype
 
 
 def test_set_xtype_bad():
-    cli_inputs = ["data.xy", "--mud", "2.5", "--xtype", "invalid"]
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5", "--xtype", "invalid"]
     actual_args = get_args(cli_inputs)
     with pytest.raises(
         ValueError,
@@ -474,7 +475,7 @@ def test_set_xtype_bad():
 def test_set_mud(user_filesystem, inputs, expected_mud):
     cwd = Path(user_filesystem)
     os.chdir(cwd)
-    cli_inputs = ["data.xy"] + inputs
+    cli_inputs = ["applymud", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = set_mud(actual_args)
     assert actual_args.mud == pytest.approx(expected_mud, rel=1e-4, abs=0.1)
@@ -550,7 +551,7 @@ def test_set_mud_bad(user_filesystem, inputs, expected):
     expected_error, expected_error_msg = expected
     cwd = Path(user_filesystem)
     os.chdir(cwd)
-    cli_inputs = ["data.xy"] + inputs
+    cli_inputs = ["applymud", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     with pytest.raises(expected_error, match=re.escape(expected_error_msg)):
         actual_args = set_mud(actual_args)
@@ -577,12 +578,12 @@ def test_set_mud_bad(user_filesystem, inputs, expected):
     ],
 )
 def test_load_user_metadata(inputs, expected):
-    expected_args = get_args(["data.xy", "--mud", "2.5"])
+    expected_args = get_args(["applymud", "data.xy", "--mud", "2.5"])
     for expected_pair in expected:
         setattr(expected_args, expected_pair[0], expected_pair[1])
     delattr(expected_args, "user_metadata")
 
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = load_user_metadata(actual_args)
     assert actual_args == expected_args
@@ -618,7 +619,7 @@ def test_load_user_metadata(inputs, expected):
     ],
 )
 def test_load_user_metadata_bad(inputs, expected_error_msg):
-    cli_inputs = ["data.xy", "--mud", "2.5"] + inputs
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"] + inputs
     actual_args = get_args(cli_inputs)
     with pytest.raises(ValueError, match=re.escape(expected_error_msg)):
         actual_args = load_user_metadata(actual_args)
@@ -681,6 +682,7 @@ def test_load_user_info(monkeypatch, inputs, expected, user_filesystem):
     os.chdir(cwd)
 
     cli_inputs = [
+        "applymud",
         "data.xy",
         "--mud",
         "2.5",
@@ -705,7 +707,7 @@ def test_load_package_info(mocker):
             "3.3.0" if package_name == "diffpy.utils" else "1.2.3"
         ),
     )
-    cli_inputs = ["data.xy", "--mud", "2.5"]
+    cli_inputs = ["applymud", "data.xy", "--mud", "2.5"]
     actual_args = get_args(cli_inputs)
     actual_args = load_package_info(actual_args)
     assert actual_args.package_info == {
@@ -731,6 +733,7 @@ def test_load_metadata(mocker, user_filesystem):
         ),
     )
     cli_inputs = [
+        "applymud",
         ".",
         "--mud",
         "2.5",