Merge pull request #162 from yucongalicechen/wavelength-workflow

feat: new wavelength workflow

Author: sbillinge

news/wavelength-workflow.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Workflow for loading wavelength - raise an error when both wavelength and anode type are specified.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/labpdfproc/labpdfprocapp.py

@@ -30,8 +30,7 @@ def define_arguments():
                 "in a file with name file_list.txt. "
                 "If one or more directory is provided, all valid "
                 "data-files in that directory will be processed. "
-                "Examples of valid "
-                "inputs are 'file.xy', 'data/file.xy', "
+                "Examples of valid inputs are 'file.xy', 'data/file.xy', "
                 "'file.xy, data/file.xy', "
                 "'.' (load everything in the current directory), "
                 "'data' (load everything in the folder ./data), "
@@ -48,18 +47,16 @@ def define_arguments():
             "name": ["-a", "--anode-type"],
             "help": (
                 f"The type of the x-ray source. "
-                f"Allowed values are {*[known_sources], }. "
+                f"Allowed values are {*known_sources, }. "
                 f"Either specify a known x-ray source or specify wavelength."
             ),
-            "default": "Mo",
+            "default": None,
         },
         {
             "name": ["-w", "--wavelength"],
             "help": (
                 "X-ray source wavelength in angstroms. "
-                "Not needed if the anode-type is specified. "
-                "This wavelength will override the anode wavelength "
-                "if both are specified."
+                "Not needed if the anode-type is specified."
             ),
             "type": float,
         },
@@ -104,7 +101,7 @@ def define_arguments():
                 f"The method for computing absorption correction. "
                 f"Allowed methods: {*CVE_METHODS, }. "
                 f"Default method is polynomial interpolation "
-                f"if not specified. "
+                f"if not specified."
             ),
             "default": "polynomial_interpolation",
         },
@@ -121,7 +118,7 @@ def define_arguments():
                 "For example, facility='NSLS II', "
                 "'facility=NSLS II', beamline=28ID-2, "
                 "'beamline'='28ID-2', 'favorite color'=blue, "
-                "are all valid key=value items. "
+                "are all valid key=value items."
             ),
             "nargs": "+",
             "metavar": "KEY=VALUE",
@@ -131,7 +128,7 @@ def define_arguments():
             "help": (
                 "Username will be loaded from config files. "
                 "Specify here only if you want to "
-                "override that behavior at runtime. "
+                "override that behavior at runtime."
             ),
             "default": None,
         },
@@ -140,7 +137,7 @@ def define_arguments():
             "help": (
                 "Email will be loaded from config files. "
                 "Specify here only if you want to "
-                "override that behavior at runtime. "
+                "override that behavior at runtime."
             ),
             "default": None,
         },
@@ -149,7 +146,7 @@ def define_arguments():
             "help": (
                 "ORCID will be loaded from config files. "
                 "Specify here only if you want to "
-                "override that behavior at runtime. "
+                "override that behavior at runtime."
             ),
             "default": None,
         },

src/diffpy/labpdfproc/tools.py

@@ -160,9 +160,10 @@ def set_input_lists(args):
 
 
 def set_wavelength(args):
-    """Set the wavelength based on the given anode_type.
-    If a wavelength is provided,
-    it will be used, and the anode_type argument will be removed.
+    """Set the wavelength based on the given anode_type or wavelength.
+
+    First checks from args. If neither is provided,
+    it attempts to load from local and then global config file.
 
     Parameters
     ----------
@@ -172,15 +173,32 @@ def set_wavelength(args):
     Raises
     ------
     ValueError
-        Raised when input wavelength is non-positive
-        or if input anode_type is not one of the known sources.
+        Raised if:
+        (1) neither wavelength or anode type is provided,
+            and xtype is not the two-theta grid,
+        (2) both are provided,
+        (3) anode_type is not one of the known sources,
+        (4) wavelength is non-positive.
 
     Returns
     -------
     args : argparse.Namespace
         The updated arguments with the wavelength.
     """
-    if args.wavelength is None:
+    # first load values from config file
+    if args.wavelength is None and args.anode_type is None:
+        if args.xtype not in ANGLEQUANTITIES:
+            raise ValueError(
+                f"Please provide a wavelength or anode type "
+                f"because the independent variable axis is not on two-theta. "
+                f"Allowed anode types are {*known_sources, }."
+            )
+    elif args.wavelength is not None and args.anode_type is not None:
+        raise ValueError(
+            f"Please provide either a wavelength or an anode type, not both. "
+            f"Allowed anode types are {*known_sources, }."
+        )
+    elif args.anode_type is not None:
         matched_anode_type = next(
             (
                 key
@@ -197,15 +215,12 @@ def set_wavelength(args):
             )
         args.anode_type = matched_anode_type
         args.wavelength = WAVELENGTHS[args.anode_type]
-    else:
-        if args.wavelength <= 0:
-            raise ValueError(
-                "No valid wavelength. "
-                "Please rerun specifying a known anode_type "
-                "or a positive wavelength."
-            )
-        else:
-            delattr(args, "anode_type")
+    elif args.wavelength is not None and args.wavelength <= 0:
+        raise ValueError(
+            "No valid wavelength. "
+            "Please rerun specifying a known anode_type "
+            "or a positive wavelength."
+        )
     return args
 
 
@@ -362,7 +377,8 @@ def load_package_info(args):
 def preprocessing_args(args):
     """Perform preprocessing on the provided args.
     The process includes loading package and user information,
-    setting input, output, wavelength, xtype, mu*D, and loading user metadata.
+    setting input, output, wavelength, anode type, xtype, mu*D,
+    and loading user metadata.
 
     Parameters
     ----------

tests/test_tools.py

@@ -198,9 +198,7 @@ def test_set_output_directory_bad(user_filesystem):
 @pytest.mark.parametrize(
     "inputs, expected",
     [
-        # C1: nothing passed in, expect default is Mo
-        ([], {"wavelength": 0.71073, "anode_type": "Mo"}),
-        # C2: only a valid anode type was entered (case independent),
+        # C1: only a valid anode type was entered (case independent),
         # expect to match the corresponding wavelength
         # and preserve the correct case anode type
         (["--anode-type", "Mo"], {"wavelength": 0.71073, "anode_type": "Mo"}),
@@ -239,45 +237,52 @@ def test_set_output_directory_bad(user_filesystem):
             ["--anode-type", "cuka1"],
             {"wavelength": 1.54056, "anode_type": "CuKa1"},
         ),
-        # C3: only a valid wavelength was entered,
+        # C2: a valid wavelength was entered,
         # expect to include the wavelength only and anode type is None
         (["--wavelength", "0.25"], {"wavelength": 0.25, "anode_type": None}),
-        # C4: both valid anode type and wavelength were entered,
-        # expect to remove the anode type and preserve wavelength only
-        (
-            ["--wavelength", "0.25", "--anode-type", "Ag"],
-            {"wavelength": 0.25, "anode_type": None},
-        ),
+        # C3: nothing passed in, but mu*D was provided and xtype is on tth
+        # expect wavelength and anode type to be None
+        # and program proceeds without error
+        ([], {"wavelength": None, "anode_type": None}),
     ],
 )
 def test_set_wavelength(inputs, expected):
     cli_inputs = ["2.5", "data.xy"] + inputs
     actual_args = get_args(cli_inputs)
     actual_args = set_wavelength(actual_args)
     assert actual_args.wavelength == expected["wavelength"]
-    assert getattr(actual_args, "anode_type", None) == expected["anode_type"]
+    assert actual_args.anode_type == expected["anode_type"]
 
 
 @pytest.mark.parametrize(
     "inputs, expected_error_msg",
     [
-        (
+        (  # C1: nothing passed in, xtype is not on tth
+            # expect error asking for either wavelength or anode type
+            ["--xtype", "q"],
+            f"Please provide a wavelength or anode type "
+            f"because the independent variable axis is not on two-theta. "
+            f"Allowed anode types are {*known_sources, }.",
+        ),
+        (  # C2: both wavelength and anode type were specified
+            # expect error asking not to specify both
+            ["--wavelength", "0.7", "--anode-type", "Mo"],
+            f"Please provide either a wavelength or an anode type, not both. "
+            f"Allowed anode types are {*known_sources, }.",
+        ),
+        (  # C3: invalid anode type
+            # expect error asking to specify a valid anode type
             ["--anode-type", "invalid"],
             f"Anode type not recognized. "
             f"Please rerun specifying an anode_type from {*known_sources, }.",
         ),
-        (
+        (  # C4: invalid wavelength
+            # expect error asking to specify a valid wavelength or anode type
             ["--wavelength", "0"],
             "No valid wavelength. "
             "Please rerun specifying a known anode_type "
             "or a positive wavelength.",
         ),
-        (
-            ["--wavelength", "-1", "--anode-type", "Mo"],
-            "No valid wavelength. "
-            "Please rerun specifying a known anode_type "
-            "or a positive wavelength.",
-        ),
     ],
 )
 def test_set_wavelength_bad(inputs, expected_error_msg):
@@ -502,6 +507,11 @@ def test_load_package_info(mocker):
 
 
 def test_load_metadata(mocker, user_filesystem):
+    # Test if the function loads args
+    # (which will be loaded into the header file).
+    # Expect to include mu*D, anode type, xtype, cve method,
+    # user-specified metadata, user info, package info, z-scan file,
+    # and full paths for current input and output directories.
     cwd = Path(user_filesystem)
     home_dir = cwd / "home_dir"
     mocker.patch("pathlib.Path.home", lambda _: home_dir)
@@ -515,6 +525,8 @@ def test_load_metadata(mocker, user_filesystem):
     cli_inputs = [
         "2.5",
         ".",
+        "--anode-type",
+        "Mo",
         "--user-metadata",
         "key=value",
         "--username",