feat: config workflow for wavelength / anode type

news/wavelength-config.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Functionality to allow users to specify wavelength or anode type in a diffpy config file.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

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 +160,33 @@ def set_input_lists(args):
     return args
 
 
+def _load_wavelength_from_config_file(args):
+    """Load wavelength and anode type from config files.
+    It takes cli inputs first, and local config, and then global config.
+
+    Parameters
+    ----------
+    args : argparse.Namespace
+        The arguments from the parser.
+
+    Returns
+    -------
+    args : argparse.Namespace
+        The updated arguments with the updated wavelength and anode type.
+    """
+    if args.wavelength or args.anode_type:
+        return args
+    global_config = _load_config(Path().home() / "diffpyconfig.json")
+    local_config = _load_config(Path().cwd() / "diffpyconfig.json")
+    if local_config:
+        args.wavelength = local_config.get("wavelength")
+        args.anode_type = local_config.get("anode_type")
+    elif global_config:
+        args.wavelength = global_config.get("wavelength")
+        args.anode_type = global_config.get("anode_type")
+    return args
+
+
 def set_wavelength(args):
     """Set the wavelength based on the given anode_type or wavelength.
 
@@ -185,7 +213,7 @@ 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(

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",

tests/test_tools.py

@@ -1,3 +1,4 @@
+import json
 import os
 import re
 from pathlib import Path
@@ -6,6 +7,7 @@
 
 from diffpy.labpdfproc.labpdfprocapp import get_args
 from diffpy.labpdfproc.tools import (
+    _load_wavelength_from_config_file,
     known_sources,
     load_metadata,
     load_package_info,
@@ -195,6 +197,121 @@ def test_set_output_directory_bad(user_filesystem):
         assert not Path(actual_args.output_directory).is_dir()
 
 
+@pytest.mark.parametrize(
+    "inputs, expected",
+    [
+        # Test when only a home config file exists (no local config file),
+        # expect to return args if wavelength or anode type is specified,
+        # otherwise update args with values from the home config file.
+        # 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 = ["2.5", "data.xy"] + 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 args if wavelength or anode type is specified,
+        # otherwise update args with values from the home config file.
+        # Results should be the same whether if the home config exists.
+        # 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 = ["2.5", "data.xy"] + 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.
+        # 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 = ["2.5", "data.xy"] + 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",
     [