write_yaml_model omits the enzymes key of an ec reaction without enzymes

CHANGELOG.md

@@ -6,6 +6,7 @@ Milestones in the raven-toolbox port. For function-level status see
 
 ## Unreleased
 
+* `write_yaml_model` writes an ec reaction without enzymes with no `enzymes` entry (was: `enzymes: !!omap []`). `read_yaml_model` reads a missing `enzymes` entry, a content-less `enzymes: !!omap` and `enzymes: !!omap []` as an empty enzyme map, so files written by earlier versions of GECKO, RAVEN and raven-toolbox still load.
 * `init.fill_tasks` with `resolve_ties=True` on Gurobi restores `MIPGap` and `MIPGapAbs` of `reference_model` after each gap-fill (was: 0.0 and 0.4 stayed set).
 * `tasks.find_task_essential_reactions` writes its `cache_path` as JSON (was: pickle) and ignores, with a warning, an existing file that is not a JSON cache of the current version, such as a pickle. `checkpoint_every` below 1 raises `ValueError` (was: a write after every task).
 * `init.hpa_gene_scores` uses the default level scores also for an empty `level_scores` mapping, and `init.rna_gene_scores` compares `tissue` case-insensitively and takes the highest TPM over tissue names that differ in case, as RAVEN's `scoreModel` does.

src/raven_toolbox/io/ec_data.py

@@ -29,7 +29,8 @@
         source: brenda      # optional, omitted if empty
         notes: free-text    # optional, omitted if empty
         eccodes: "1.1.1.1"  # optional; scalar OR a list when multiple
-        enzymes:            # column -> stoichiometric subunit count
+        enzymes:            # optional, omitted if the reaction has no enzymes;
+                            #   column -> stoichiometric subunit count
           P12345: 1.0
           P67890: 2.0       # heteromeric complex with 2 copies of P67890
     ec-enzymes:
@@ -306,7 +307,8 @@ def _build_ec_rxns_list(ec: EcData) -> list[dict[str, Any]]:
     """Translate the per-reaction ec fields and the ``rxn_enz_mat`` rows to the
     list-of-mappings YAML form.
 
-    Empty ``source`` / ``notes`` / ``eccodes`` strings are omitted.
+    Empty ``source`` / ``notes`` / ``eccodes`` strings are omitted, and so is
+    ``enzymes`` for a reaction whose ``rxn_enz_mat`` row has no entry.
     ``kcat`` is always written: a real turnover number when set,
     otherwise ``0`` (0 marks "no kcat assigned").
     """
@@ -330,7 +332,8 @@ def _build_ec_rxns_list(ec: EcData) -> list[dict[str, Any]]:
             entry["notes"] = ec.notes[i]
         if ec.eccodes[i]:
             entry["eccodes"] = _eccodes_to_yaml(ec.eccodes[i])
-        entry["enzymes"] = per_row_enzymes[i]
+        if per_row_enzymes[i]:
+            entry["enzymes"] = per_row_enzymes[i]
         out.append(entry)
     return out
 

src/raven_toolbox/io/yaml.py

@@ -90,8 +90,9 @@
 class _OmapConstructor(RoundTripConstructor):
     """Round-trip constructor that reads a content-less ``!!omap`` as an empty map.
 
-    GECKO and RAVEN write an ec reaction without enzymes as ``- enzymes: !!omap``
-    with nothing under the tag. YAML parses that as a null scalar carrying the omap
+    Files written by earlier GECKO and RAVEN versions have an ec reaction without
+    enzymes as ``- enzymes: !!omap`` with nothing under the tag (current writers
+    omit the ``enzymes`` entry). YAML parses that as a null scalar carrying the omap
     tag, which ruamel's own constructor rejects; RAVEN's ``readYAMLmodel.m`` reads
     it as an empty enzyme list.
     """

tests/test_io_yaml_ec_data.py

@@ -12,6 +12,7 @@
 """
 from __future__ import annotations
 
+import re
 from pathlib import Path
 
 import cobra
@@ -204,6 +205,50 @@ def test_save_round_trip_preserves_all_ec_fields(tmp_path):
     assert reloaded.ec.rxn_enz_mat[0, 0] == 1.0
 
 
+def _make_ec_model_with_enzymeless_rxn() -> cobra.Model:
+    """`_make_ec_model` plus a second ec reaction whose rxn_enz_mat row is empty."""
+    model = _make_ec_model()
+    ec = model.ec
+    mat = sparse.lil_matrix((2, 1), dtype=float)
+    mat[0, 0] = 1.0
+    model.ec = EcData(
+        gecko_light=False,
+        rxns=["R1", "R2"],
+        kcat=np.array([42.0, 7.0]),
+        source=["manual", "standard"],
+        notes=["", ""],
+        eccodes=["1.1.1.1", ""],
+        genes=ec.genes,
+        enzymes=ec.enzymes,
+        mw=ec.mw,
+        sequence=ec.sequence,
+        concs=ec.concs,
+        rxn_enz_mat=mat.tocsr(),
+    )
+    return model
+
+
+def test_save_omits_enzymes_of_rxn_without_enzymes(tmp_path):
+    out = tmp_path / "out.yml"
+    write_yaml_model(_make_ec_model_with_enzymeless_rxn(), out)
+    text = out.read_text()
+    assert text.count("- enzymes:") == 2  # R1 (ec-rxns) and P1 (ec-enzymes)
+    assert "!!omap []" not in text.split("ec-rxns:")[1]
+    block = re.split(r'- id: "?R2"?\n', text)[-1].split("ec-enzymes:")[0]
+    assert "enzymes" not in block
+    assert "standard" in block
+
+
+def test_save_round_trip_rxn_without_enzymes(tmp_path):
+    out = tmp_path / "out.yml"
+    write_yaml_model(_make_ec_model_with_enzymeless_rxn(), out)
+    reloaded = read_yaml_model(out)
+    assert reloaded.ec.rxns == ["R1", "R2"]
+    assert reloaded.ec.kcat.tolist() == [42.0, 7.0]
+    assert reloaded.ec.source == ["manual", "standard"]
+    assert reloaded.ec.rxn_enz_mat.toarray().tolist() == [[1.0], [0.0]]
+
+
 def test_save_skips_nan_and_empty_optional_fields(tmp_path):
     """NaN mw/concs and empty source/notes/eccodes/sequence get omitted
     from the YAML to keep files compact."""
@@ -462,8 +507,7 @@ def test_empty_gecko_light_flag_propagates():
     - id: "std"
     - kcat: 10
     - source: "custom"
-    - notes: {note}
-    - enzymes: !!omap{empty}
+    - notes: {note}{enzymes_line}
   - !!omap
     - id: "enz"
     - kcat: 5
@@ -478,12 +522,17 @@ def test_empty_gecko_light_flag_propagates():
 """
 
 
-@pytest.mark.parametrize("empty", ["", " []"])
-def test_load_reaction_with_empty_enzymes_omap(tmp_path, empty):
-    # GECKO and RAVEN write `- enzymes: !!omap` with nothing under it for an ec
-    # reaction without enzymes; raven-toolbox writes `!!omap []`. Both read as no enzymes.
+@pytest.mark.parametrize(
+    "enzymes_line",
+    ["", "\n    - enzymes: !!omap", "\n    - enzymes: !!omap []"],
+    ids=["missing", "omap", "omap-empty-flow"],
+)
+def test_load_reaction_with_empty_enzymes_omap(tmp_path, enzymes_line):
+    # An ec reaction without enzymes has no `enzymes` entry. Files written by earlier
+    # GECKO and RAVEN versions carry `- enzymes: !!omap` with nothing under it, and
+    # earlier raven-toolbox versions wrote `!!omap []`. All three read as no enzymes.
     path = tmp_path / "m.yml"
-    path.write_text(_GECKO_FILE.format(note='"ok"', empty=empty), encoding="utf-8")
+    path.write_text(_GECKO_FILE.format(note='"ok"', enzymes_line=enzymes_line), encoding="utf-8")
     model = read_yaml_model(path)
     assert model.ec.rxns == ["std", "enz"]
     assert model.ec.enzymes == ["P1"]
@@ -494,7 +543,7 @@ def test_load_notes_in_doubled_quotes_keep_one_pair(tmp_path):
     # An older writer put quotes around a note that carried its own, giving `""text""`,
     # which is not valid YAML. readYAMLmodel.m strips one pair and keeps the other.
     path = tmp_path / "m.yml"
-    path.write_text(_GECKO_FILE.format(note='""Putative: lowest kcat.""', empty=""), encoding="utf-8")
+    path.write_text(_GECKO_FILE.format(note='""Putative: lowest kcat.""', enzymes_line=""), encoding="utf-8")
     model = read_yaml_model(path)
     assert model.ec.notes[0] == '"Putative: lowest kcat."'
     assert model.ec.rxns == ["std", "enz"]
@@ -503,7 +552,7 @@ def test_load_notes_in_doubled_quotes_keep_one_pair(tmp_path):
 def test_doubled_quotes_unescape_like_matlab_and_keep_apostrophes(tmp_path):
     path = tmp_path / "m.yml"
     note = '""it\'s a \\\\ and \\"inner\\" one""'
-    path.write_text(_GECKO_FILE.format(note=note, empty=""), encoding="utf-8")
+    path.write_text(_GECKO_FILE.format(note=note, enzymes_line=""), encoding="utf-8")
     model = read_yaml_model(path)
     assert model.ec.notes[0] == '"it\'s a \\ and "inner" one"'
 
@@ -521,7 +570,7 @@ def test_doubled_quotes_unescape_like_matlab_and_keep_apostrophes(tmp_path):
 def test_interior_unescaped_quote_is_kept_like_matlab(tmp_path, note, expected):
     # readYAMLmodel.m strips the outer pair of quotes and keeps every quote inside.
     path = tmp_path / "m.yml"
-    path.write_text(_GECKO_FILE.format(note=note, empty=""), encoding="utf-8")
+    path.write_text(_GECKO_FILE.format(note=note, enzymes_line=""), encoding="utf-8")
     model = read_yaml_model(path)
     assert model.ec.notes[0] == expected
     assert model.ec.rxns == ["std", "enz"]
@@ -539,7 +588,7 @@ def test_interior_unescaped_quote_is_kept_like_matlab(tmp_path, note, expected):
 def test_interior_apostrophe_in_single_quoted_value_is_kept_like_matlab(tmp_path, value, expected):
     # readYAMLmodel.m strips the outer pair of quotes and turns each '' into ', keeping a lone '.
     path = tmp_path / "m.yml"
-    text = _GECKO_FILE.format(note='"ok"', empty="").replace('- name: "A"', f"- name: {value}")
+    text = _GECKO_FILE.format(note='"ok"', enzymes_line="").replace('- name: "A"', f"- name: {value}")
     path.write_text(text, encoding="utf-8")
     model = read_yaml_model(path)
     assert model.metabolites.get_by_id("a").name == expected
@@ -548,7 +597,7 @@ def test_interior_apostrophe_in_single_quoted_value_is_kept_like_matlab(tmp_path
 
 def test_valid_single_quoted_values_are_read_unchanged(tmp_path):
     path = tmp_path / "m.yml"
-    text = _GECKO_FILE.format(note="'a ''b'' c'", empty="").replace('- name: "A"', "- name: 'it''s'")
+    text = _GECKO_FILE.format(note="'a ''b'' c'", enzymes_line="").replace('- name: "A"', "- name: 'it''s'")
     path.write_text(text, encoding="utf-8")
     model = read_yaml_model(path)
     assert model.metabolites.get_by_id("a").name == "it's"
@@ -557,7 +606,7 @@ def test_valid_single_quoted_values_are_read_unchanged(tmp_path):
 
 def test_valid_quoted_scalars_are_read_unchanged_next_to_a_repaired_one(tmp_path):
     path = tmp_path / "m.yml"
-    text = _GECKO_FILE.format(note='"a "b" c"', empty="").replace(
+    text = _GECKO_FILE.format(note='"a "b" c"', enzymes_line="").replace(
         '- source: "custom"', '- source: "cu\\\\st\\"om"'
     ).replace("- id: \"enz\"", "- id: \"enz\"\n    - notes: \"fine\\n\"")
     path.write_text(text, encoding="utf-8")
@@ -568,6 +617,6 @@ def test_valid_quoted_scalars_are_read_unchanged_next_to_a_repaired_one(tmp_path
 
 def test_invalid_yaml_other_than_doubled_quotes_still_raises(tmp_path):
     path = tmp_path / "m.yml"
-    path.write_text(_GECKO_FILE.format(note='"ok"', empty="").replace("kcat: 10", "kcat: [10"), encoding="utf-8")
+    path.write_text(_GECKO_FILE.format(note='"ok"', enzymes_line="").replace("kcat: 10", "kcat: [10"), encoding="utf-8")
     with pytest.raises(YAMLError):
         read_yaml_model(path)