Merge pull request #169 from yucongalicechen/wavelength-config

feat: config workflow for wavelength / anode type

Author: sbillinge

Diff for: news/wavelength-config.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Functionality to read wavelength and anode type directly from a diffpy configuration file.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

Diff for: src/diffpy/labpdfproc/tools.py

@@ -7,6 +7,7 @@
     XQUANTITIES,
 )
 from diffpy.utils.tools import (
+    _load_config,
     check_and_build_global_config,
     compute_mud,
     get_package_info,
@@ -159,6 +160,52 @@ def set_input_lists(args):
     return args
 
 
+def load_wavelength_from_config_file(args):
+    """Load wavelength and anode type from config files.
+
+    It prioritizes values in the following order:
+    1. cli inputs, 2. local config file, 3. global config file.
+
+    Parameters
+    ----------
+    args : argparse.Namespace
+        The arguments from the parser.
+
+    Returns
+    -------
+    args : argparse.Namespace
+        The updated arguments with the updated wavelength and anode type.
+    """
+    global_config = _load_config(Path().home() / "diffpyconfig.json")
+    local_config = _load_config(Path().cwd() / "diffpyconfig.json")
+    local_has_data = local_config and (
+        "wavelength" in local_config or "anode_type" in local_config
+    )
+    global_has_data = global_config and (
+        "wavelength" in global_config or "anode_type" in global_config
+    )
+    if not local_has_data and not global_has_data:
+        print(
+            "No configuration file was found containing information "
+            "about the wavelength or anode type. \n"
+            "You can add the wavelength or anode type "
+            "to a configuration file on the current computer "
+            "and it will be automatically associated with "
+            "subsequent diffpy data by default. \n"
+            "You will only have to do that once. \n"
+            "For more information, please refer to www.diffpy.org/"
+            "diffpy.labpdfproc/examples/toolsexample.html"
+        )
+
+    if args.wavelength or args.anode_type:
+        return args
+    config = local_config if local_has_data else global_config
+    if config:
+        args.wavelength = args.wavelength or config.get("wavelength")
+        args.anode_type = args.anode_type or config.get("anode_type")
+    return args
+
+
 def set_wavelength(args):
     """Set the wavelength based on the given anode_type or wavelength.
 
@@ -174,7 +221,7 @@ def set_wavelength(args):
     ------
     ValueError
         Raised if:
-        (1) neither wavelength or anode type is provided,
+        (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,
@@ -185,7 +232,7 @@ def set_wavelength(args):
     args : argparse.Namespace
         The updated arguments with the wavelength.
     """
-    # first load values from config file
+    args = load_wavelength_from_config_file(args)
     if args.wavelength is None and args.anode_type is None:
         if args.xtype not in ANGLEQUANTITIES:
             raise ValueError(
@@ -209,15 +256,15 @@ def set_wavelength(args):
         )
         if matched_anode_type is None:
             raise ValueError(
-                f"Anode type not recognized. "
+                f"Anode type '{args.anode_type}' not recognized. "
                 f"Please rerun specifying an anode_type "
                 f"from {*known_sources, }."
             )
         args.anode_type = matched_anode_type
         args.wavelength = WAVELENGTHS[args.anode_type]
     elif args.wavelength is not None and args.wavelength <= 0:
         raise ValueError(
-            "No valid wavelength. "
+            f"Wavelength = {args.wavelength} is not valid. "
             "Please rerun specifying a known anode_type "
             "or a positive wavelength."
         )

Diff for: tests/conftest.py

@@ -60,6 +60,7 @@ def user_filesystem(tmp_path):
         f.write(f"{str(input_dir.resolve() / 'good_data.txt')}\n")
 
     home_config_data = {
+        "wavelength": 0.3,
         "owner_name": "home_username",
         "owner_email": "[email protected]",
         "owner_orcid": "home_orcid",

Diff for: tests/test_tools.py

@@ -1,3 +1,4 @@
+import json
 import os
 import re
 from pathlib import Path
@@ -11,6 +12,7 @@
     load_package_info,
     load_user_info,
     load_user_metadata,
+    load_wavelength_from_config_file,
     preprocessing_args,
     set_input_lists,
     set_mud,
@@ -201,6 +203,131 @@ def test_set_output_directory_bad(user_filesystem):
         assert not Path(actual_args.output_directory).is_dir()
 
 
+@pytest.mark.parametrize(
+    "inputs, expected",
+    [
+        # Test with only a home config file (no local config),
+        # expect to return values directly from args
+        # if either wavelength or anode type is specified,
+        # otherwise update args with values from the home config file
+        # (wavelength=0.3, no anode type).
+        # This test only checks loading behavior,
+        # not value validation (which is handled by `set_wavelength`).
+        # C1: no args, expect to update arg values from home config
+        ([], {"wavelength": 0.3, "anode_type": None}),
+        # C2: wavelength provided, expect to return args unchanged
+        (["--wavelength", "0.25"], {"wavelength": 0.25, "anode_type": None}),
+        # C3: anode type provided, expect to return args unchanged
+        (["--anode-type", "Mo"], {"wavelength": None, "anode_type": "Mo"}),
+        # C4: both wavelength and anode type provided,
+        # expect to return args unchanged
+        (
+            ["--wavelength", "0.7", "--anode-type", "Mo"],
+            {"wavelength": 0.7, "anode_type": "Mo"},
+        ),
+    ],
+)
+def test_load_wavelength_from_config_file_with_home_conf_file(
+    mocker, user_filesystem, inputs, expected
+):
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    mocker.patch("pathlib.Path.home", lambda _: home_dir)
+    os.chdir(cwd)
+
+    cli_inputs = ["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"]
+    assert actual_args.anode_type == expected["anode_type"]
+
+
+@pytest.mark.parametrize(
+    "inputs, expected",
+    [
+        # Test when a local config file exists,
+        # expect to return values directly from args
+        # if either wavelength or anode type is specified,
+        # otherwise update args with values from the local config file
+        # (wavelength=0.6, no anode type).
+        # Results should be the same whether if the home config exists.
+        # This test only checks loading behavior,
+        # not value validation (which is handled by `set_wavelength`).
+        # C1: no args, expect to update arg values from local config
+        ([], {"wavelength": 0.6, "anode_type": None}),
+        # C2: wavelength provided, expect to return args unchanged
+        (["--wavelength", "0.25"], {"wavelength": 0.25, "anode_type": None}),
+        # C3: anode type provided, expect to return args unchanged
+        (["--anode-type", "Mo"], {"wavelength": None, "anode_type": "Mo"}),
+        # C4: both wavelength and anode type provided,
+        # expect to return args unchanged
+        (
+            ["--wavelength", "0.7", "--anode-type", "Mo"],
+            {"wavelength": 0.7, "anode_type": "Mo"},
+        ),
+    ],
+)
+def test_load_wavelength_from_config_file_with_local_conf_file(
+    mocker, user_filesystem, inputs, expected
+):
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    mocker.patch("pathlib.Path.home", lambda _: home_dir)
+    os.chdir(cwd)
+    local_config_data = {"wavelength": 0.6}
+    with open(cwd / "diffpyconfig.json", "w") as f:
+        json.dump(local_config_data, f)
+
+    cli_inputs = ["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"]
+    assert actual_args.anode_type == expected["anode_type"]
+
+    # remove home config file, expect the same results
+    confile = home_dir / "diffpyconfig.json"
+    os.remove(confile)
+    assert actual_args.wavelength == expected["wavelength"]
+    assert actual_args.anode_type == expected["anode_type"]
+
+
+@pytest.mark.parametrize(
+    "inputs, expected",
+    [
+        # Test when no config files exist,
+        # expect to return args without modification.
+        # This test only checks loading behavior,
+        # not value validation (which is handled by `set_wavelength`).
+        # C1: no args
+        ([], {"wavelength": None, "anode_type": None}),
+        # C1: wavelength provided
+        (["--wavelength", "0.25"], {"wavelength": 0.25, "anode_type": None}),
+        # C2: anode type provided
+        (["--anode-type", "Mo"], {"wavelength": None, "anode_type": "Mo"}),
+        # C4: both wavelength and anode type provided
+        (
+            ["--wavelength", "0.7", "--anode-type", "Mo"],
+            {"wavelength": 0.7, "anode_type": "Mo"},
+        ),
+    ],
+)
+def test_load_wavelength_from_config_file_without_conf_files(
+    mocker, user_filesystem, inputs, expected
+):
+    cwd = Path(user_filesystem)
+    home_dir = cwd / "home_dir"
+    mocker.patch("pathlib.Path.home", lambda _: home_dir)
+    os.chdir(cwd)
+    confile = home_dir / "diffpyconfig.json"
+    os.remove(confile)
+
+    cli_inputs = ["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"]
+    assert actual_args.anode_type == expected["anode_type"]
+
+
 @pytest.mark.parametrize(
     "inputs, expected",
     [
@@ -279,13 +406,13 @@ def test_set_wavelength(inputs, expected):
         (  # C3: invalid anode type
             # expect error asking to specify a valid anode type
             ["--anode-type", "invalid"],
-            f"Anode type not recognized. "
+            f"Anode type 'invalid' 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. "
+            ["--wavelength", "-0.2"],
+            "Wavelength = -0.2 is not valid. "
             "Please rerun specifying a known anode_type "
             "or a positive wavelength.",
         ),