conditions: switch from PyYAML to ruamel.yaml

PyYAML is not a project dependency; raven-python uses ruamel.yaml
(already pulled in via cobra) everywhere else. The conditions
module and its tests still imported PyYAML, which broke pytest
collection on clean CI runners with 'No module named yaml'.

Both apply.py and the test now use a YAML(typ='safe') instance
from ruamel.yaml — same plain-dict semantics as PyYAML's
safe_load / safe_dump, no new dependency.

Author: edkerk

src/raven_python/conditions/apply.py

@@ -49,7 +49,13 @@
 from typing import Any
 
 import cobra
-import yaml
+from ruamel.yaml import YAML
+
+# A safe loader keeps the parsed document as plain dict / list / scalars,
+# which matches what callers expect from ``load_condition``. ruamel.yaml
+# is already a transitive dependency via cobra, so we don't take on
+# PyYAML on top.
+_SAFE_YAML = YAML(typ="safe")
 
 #: ``prelude.reset_exchanges`` puts every exchange reaction at this
 #: upper bound (and lower bound = 0).
@@ -62,7 +68,7 @@ def load_condition(path: str | Path) -> dict[str, Any]:
     if not path.exists():
         raise FileNotFoundError(f"Condition file not found: {path}")
     with open(path) as f:
-        return yaml.safe_load(f)
+        return _SAFE_YAML.load(f)
 
 
 def apply_condition(

tests/test_conditions.py

@@ -1,16 +1,28 @@
 """Tests for raven_python.conditions.apply (generic condition mechanism)."""
 from __future__ import annotations
 
+import io
+
 import cobra
 import pytest
-import yaml
+from ruamel.yaml import YAML
 
 from raven_python.conditions import (
     apply_condition,
     load_condition,
     set_reaction_bounds,
 )
 
+_SAFE_YAML = YAML(typ="safe")
+
+
+def _yaml_dump(cfg: dict) -> str:
+    """Helper: dump a dict to YAML via ruamel.yaml (PyYAML.safe_dump
+    equivalent). Used here because PyYAML isn't a project dependency."""
+    buf = io.StringIO()
+    _SAFE_YAML.dump(cfg, buf)
+    return buf.getvalue()
+
 
 def _toy_model() -> cobra.Model:
     m = cobra.Model("toy")
@@ -164,7 +176,7 @@ def test_expected_uptake_count_match_silent(recwarn):
 def test_apply_condition_accepts_yaml_path(tmp_path):
     cfg = {"bounds": [{"rxn": "EX_glc", "lb": -42}]}
     path = tmp_path / "cond.yml"
-    path.write_text(yaml.safe_dump(cfg))
+    path.write_text(_yaml_dump(cfg))
     m = _toy_model()
     apply_condition(m, path)
     assert m.reactions.get_by_id("EX_glc").lower_bound == -42
@@ -173,7 +185,7 @@ def test_apply_condition_accepts_yaml_path(tmp_path):
 def test_load_condition_round_trip(tmp_path):
     cfg = {"name": "x", "bounds": [{"rxn": "r1", "lb": 0}]}
     path = tmp_path / "cond.yml"
-    path.write_text(yaml.safe_dump(cfg))
+    path.write_text(_yaml_dump(cfg))
     assert load_condition(path) == cfg