fusion.json: Do not crash when species == [] (#251)

* Fix empty species

* add test

* docs

Author: PeterKraus

docs/source/version.7_0.rst

@@ -25,4 +25,5 @@ Bug fixes in ``yadg-next`` include:
 
   - The parameter ``Set I/C`` in :mod:`yadg.extractors.eclab.mpr` files should be ``C / N`` when set to 1, not ``C``.
   - The command line argument ``--ignore-merge-errors`` was not being passed to the individual extractors when using the ``yadg extract`` syntax.
+  - Fixed passing of :mod:`yadg.extractors.fusion.json` files where no species are present.
 

src/yadg/extractors/fusion/json.py

@@ -123,21 +123,22 @@ def chromdata(jsdata: dict, uts: float) -> Dataset:
 
     species = sorted(species)
     data_vars = {}
-    for k, v in units.items():
-        vals, devs = zip(*[raw[k].get(s, (np.nan, np.nan)) for s in species])
-        data_vars[k] = (
-            ["uts", "species"],
-            [vals],
-            {"ancillary_variables": f"{k}_std_err"},
-        )
-        data_vars[f"{k}_std_err"] = (
-            ["uts", "species"],
-            [devs],
-            {"standard_name": f"{k} stdandard_error"},
-        )
-        if v is not None:
-            data_vars[k][2]["units"] = v
-            data_vars[f"{k}_std_err"][2]["units"] = v
+    if len(species) > 0:
+        for k, v in units.items():
+            vals, devs = zip(*[raw[k].get(s, (np.nan, np.nan)) for s in species])
+            data_vars[k] = (
+                ["uts", "species"],
+                [vals],
+                {"ancillary_variables": f"{k}_std_err"},
+            )
+            data_vars[f"{k}_std_err"] = (
+                ["uts", "species"],
+                [devs],
+                {"standard_name": f"{k} stdandard_error"},
+            )
+            if v is not None:
+                data_vars[k][2]["units"] = v
+                data_vars[f"{k}_std_err"][2]["units"] = v
 
     ds = xr.Dataset(
         data_vars=data_vars,

tests/test_x_fusion_json.py

@@ -15,6 +15,7 @@
         "AgPTFE28_100mA_NaS_01 - Aug 13 2021, 18;18.fusion-data",
         "issue_198.fusion-data",
         "issue_213.fusion-data",
+        "issue_249.fusion-data",
     ],
 )
 def test_fusion_json(infile, datadir):

tests/test_x_fusion_json/issue_249.fusion-data

@@ -0,0 +1 @@
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