changeset 7:e0407f36fcea draft default tip

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 7f52c8654581d23a2acffc818e0c197cf8e04504

--- a/common.py	Fri Aug 23 16:44:13 2024 +0000
+++ b/common.py	Tue Sep 03 11:51:27 2024 +0000
@@ -75,22 +75,22 @@
             bkg_parameters = None
 
     keys = (
-        ("e0", "e0", None),
-        ("pre1", "pre1", None),
-        ("pre2", "pre2", None),
-        ("norm1", "nor1", None),
-        ("norm2", "nor2", None),
-        ("nnorm", "nnorm", None),
-        ("make_flat", "flatten", None),
-        ("step", "step", None),
-        ("nvict", "nvict", None),
+        ("e0", ("e0"), None),
+        ("pre1", ("pre1"), None),
+        ("pre2", ("pre2"), None),
+        ("norm1", ("nor1"), None),
+        ("norm2", ("nor2"), None),
+        ("nnorm", ("nnorm"), None),
+        ("make_flat", ("flatten"), None),
+        ("step", ("step"), None),
+        ("nvict", ("nvict"), None),
     )
-    for key, parameters_key, default in keys:
+    for key, parameter_keys, default in keys:
         extract_attribute(
             merged_settings=merged_settings,
             key=key,
             parameters_group=bkg_parameters,
-            parameters_key=parameters_key,
+            parameter_keys=parameter_keys,
             default=default,
         )
 
@@ -125,19 +125,18 @@
         fft_parameters = None
 
     keys = (
-        ("kmin", "kmin", 0),
-        ("kmax", "kmax", 20),
-        ("dk", "dk", 1),
-        ("kweight", "kw", 2),
-        ("kweight", "kweight", 2),
-        ("window", "kwindow", "kaiser"),
+        ("kmin", ("kmin",), 0),
+        ("kmax", ("kmax",), 20),
+        ("dk", ("dk",), 1),
+        ("kweight", ("kw", "kweight"), 2),
+        ("window", ("kwindow",), "kaiser"),
     )
-    for key, parameters_key, default in keys:
+    for key, parameter_keys, default in keys:
         extract_attribute(
             merged_settings=merged_settings,
             key=key,
             parameters_group=fft_parameters,
-            parameters_key=parameters_key,
+            parameter_keys=parameter_keys,
             default=default,
         )
 
@@ -156,15 +155,26 @@
     merged_settings: dict,
     key: str,
     parameters_group: Group,
-    parameters_key: str,
+    parameter_keys: "tuple[str]",
     default: "str|int" = None,
 ):
     if parameters_group is not None:
-        try:
-            merged_settings[key] = getattr(parameters_group, parameters_key)
+        values = []
+        for parameter_key in parameter_keys:
+            try:
+                values.append(getattr(parameters_group, parameter_key))
+            except AttributeError:
+                pass
+
+        if len(values) > 1:
+            print(
+                f"WARNING: values {values} for for keys {parameter_keys}, "
+                "using first entry"
+            )
+
+        if len(values) > 0:
+            merged_settings[key] = values[0]
             return
-        except AttributeError:
-            pass
 
     if default is not None:
         merged_settings[key] = default

--- a/larch_artemis.xml	Fri Aug 23 16:44:13 2024 +0000
+++ b/larch_artemis.xml	Tue Sep 03 11:51:27 2024 +0000
@@ -4,7 +4,7 @@
         <!-- version of underlying tool (PEP 440) -->
         <token name="@TOOL_VERSION@">0.9.80</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">1</token>
+        <token name="@WRAPPER_VERSION@">2</token>
         <!-- citation should be updated with every underlying tool version -->
         <!-- typical fields to update are version, month, year, and doi -->
         <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>

--- a/test-data/fit_report.txt	Fri Aug 23 16:44:13 2024 +0000
+++ b/test-data/fit_report.txt	Tue Sep 03 11:51:27 2024 +0000
@@ -1,6 +1,6 @@
 =================== FEFFIT RESULTS ====================
 \[\[Statistics\]\]
-  n_function_calls     = 4\d\d
+  n_function_calls     = \d{3}
   n_variables          = 6
   n_data_points        = 104
   n_independent        = 12\.2045080
@@ -37,14 +37,14 @@
 
 
 \[\[Dataset\]\]
-  unique_id            = 'dm7xe57x'
+  unique_id            = '\w{8}'
   fit space            = 'r'
   r-range              = 1\.400, 3\.000
   k-range              = 3\.000, 14\.000
   k window, dk         = 'hanning', 1\.000
   paths used in fit    = \['feff/feff0001\.dat', 'feff/feff0002\.dat', 'feff/feff0003\.dat', 'feff/feff0004\.dat'\]
   k-weight             = 2
-  epsilon_k            = Array\(mean=5\.1913e-4, std=4\.5676e-4\)
+  epsilon_k            = Array\(mean=5\.\d{4}e-4, std=4\.5\d{3}e-4\)
   epsilon_r            = [\d\.]{9}
   n_independent        = 12\.205
 

--- a/test-data/fit_report_simultaneous.txt	Fri Aug 23 16:44:13 2024 +0000
+++ b/test-data/fit_report_simultaneous.txt	Tue Sep 03 11:51:27 2024 +0000
@@ -1,6 +1,6 @@
 =================== FEFFIT RESULTS ====================
 \[\[Statistics\]\]
-  n_function_calls     = 4\d\d
+  n_function_calls     = \d{3}
   n_variables          = 6
   n_data_points        = 208
   n_independent        = 24\.4090160
@@ -37,14 +37,14 @@
 
 
 \[\[Dataset 1 of 2\]\]
-  unique_id            = 'dm7xe57x'
+  unique_id            = '\w{8}'
   fit space            = 'r'
   r-range              = 1\.400, 3\.000
   k-range              = 3\.000, 14\.000
   k window, dk         = 'hanning', 1\.000
   paths used in fit    = \['feff/feff0001\.dat', 'feff/feff0002\.dat', 'feff/feff0003\.dat', 'feff/feff0004\.dat'\]
   k-weight             = 2
-  epsilon_k            = Array\(mean=5\.1913e-4, std=4\.5676e-4\)
+  epsilon_k            = Array\(mean=5\.\d{4}e-4, std=4\.5\d{3}e-4\)
   epsilon_r            = [\d\.]{9}
   n_independent        = 12\.205
 
@@ -109,7 +109,7 @@
   k window, dk         = 'hanning', 1\.000
   paths used in fit    = \['feff/feff0001\.dat', 'feff/feff0002\.dat', 'feff/feff0003\.dat', 'feff/feff0004\.dat'\]
   k-weight             = 2
-  epsilon_k            = Array\(mean=5\.1913e-4, std=4\.5676e-4\)
+  epsilon_k            = Array\(mean=5\.\d{4}e-4, std=4\.5\d{3}e-4\)
   epsilon_r            = [\d\.]{9}
   n_independent        = 12\.205