Address PR review comments

Log the phixs output file under its real name, phixsdata_v2.txt, rather
than the phixsdata2.txt that no stage of the run writes.

Drop the ionization_energy_ev = 0.0 initialiser in read_ion_data(): all
four handler branches set it and an unknown handler raises, so the
default could only ever mask a branch that forgot to.

In test_add_handler_if_not_set, check the input list once at the end
instead of repeating the same comparison after each call.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: lukeshingles

artisatomic/iondata.py

@@ -87,7 +87,8 @@ def read_ion_data(
     """
     ion_stage, handler = ion_stage_entry
 
-    ionization_energy_ev = 0.0
+    # no default for ionization_energy_ev: every handler branch below sets it, and an unknown
+    # handler raises, so a branch that forgets should fail rather than write a 0 eV threshold
     transition_count_of_level_name: dict[str, int] = {}
     upsilondict: dict[tuple[int, int], float] = {}
     hillier_photoion_targetconfigs: list[list[tuple[str, float]] | None] | None = None

artisatomic/output.py

@@ -292,7 +292,7 @@ def write_phixs_data(
     ]
     skipped_no_threshold = len(levelids_with_targets) - len(levelids_to_write)
 
-    log_and_print(flog, f"Writing {len(levelids_to_write)} phixs tables to 'phixsdata2.txt'")
+    log_and_print(flog, f"Writing {len(levelids_to_write)} phixs tables to 'phixsdata_v2.txt'")
     flog.write(
         f"Downsampling cross sections assuming T={args.optimaltemperature} Kelvin, "
         f"nphixspoints={args.nphixspoints}, phixsnuincrement={args.phixsnuincrement}\n"

artisatomic/test_artisatomic.py

@@ -529,20 +529,21 @@ def test_add_handler_if_not_set():
     ion_handlers: list[tuple[int, list[tuple[int, str]]]] = [(26, [(1, "cmfgen"), (2, "cmfgen")])]
     unchanged = [(26, [(1, "cmfgen"), (2, "cmfgen")])]
 
-    # adding an ion for a new element must not modify the input list
+    # add an ion for a new element
     result = add_handler_if_not_set(ion_handlers, 58, 1, "dream")
-    assert ion_handlers == unchanged
     assert result == [(26, [(1, "cmfgen"), (2, "cmfgen")]), (58, [(1, "dream")])]
 
     # add an ion to an existing element
     result = add_handler_if_not_set(ion_handlers, 26, 3, "dream")
-    assert ion_handlers == unchanged
     assert result == [(26, [(1, "cmfgen"), (2, "cmfgen"), (3, "dream")])]
 
     # an already-present ion stage keeps the handler it was given, whatever the new one says
     result = add_handler_if_not_set(ion_handlers, 26, 2, "dream")
     assert result == unchanged
 
+    # the calls return a new list each time, so none of them touched the one they were given
+    assert ion_handlers == unchanged
+
     # ion stages can be given as tuples or lists (e.g. straight from json.load())
     ion_handlers_json = t.cast("list[tuple[int, list[tuple[int, str]]]]", [(26, [[1, "cmfgen"]])])
     result = add_handler_if_not_set(ion_handlers_json, 26, 1, "dream")