ruff

Author: dweindl

petab/v1/models/__init__.py

@@ -16,9 +16,9 @@
 from .model import Model  # noqa F401
 
 __all__ = [
-    "MODEL_TYPE_SBML",
-    "MODEL_TYPE_PYSB",
     "MODEL_TYPE_BNGL",
-    "known_model_types",
+    "MODEL_TYPE_PYSB",
+    "MODEL_TYPE_SBML",
     "Model",
+    "known_model_types",
 ]

petab/v1/models/bngl_model.py

@@ -37,7 +37,7 @@
 from . import MODEL_TYPE_BNGL
 from .model import Model
 
-__all__ = ["BnglModel", "BnglEntities", "parse_bngl"]
+__all__ = ["BnglEntities", "BnglModel", "parse_bngl"]
 
 #: The three keywords that open an observable declaration line.
 _OBS_KEYWORDS = frozenset({"Molecules", "Species", "Counter"})
@@ -379,6 +379,7 @@ def is_valid(self) -> bool:
                 text=True,
                 timeout=120,
                 cwd=str(path.parent),
+                check=False,
             )
         except (OSError, subprocess.SubprocessError):
             # A tooling hiccup must not masquerade as an invalid model.

petab/v2/models/bngl_model.py

@@ -1,3 +1,3 @@
 """Functions for handling BNGL models"""
 
-from ...v1.models.bngl_model import *  # noqa: F401, F403
+from ...v1.models.bngl_model import *

tests/v1/test_bngl_corpus.py

@@ -132,8 +132,8 @@ def _strip_to_model(text):
     out, stack = [], []
     for line in text.splitlines():
         s = line.split("#", 1)[0].strip()
-        begin = re.match(r"begin\s+(.+)", s, re.I)
-        end = re.match(r"end\s+(.+)", s, re.I)
+        begin = re.match(r"begin\s+(.+)", s, re.IGNORECASE)
+        end = re.match(r"end\s+(.+)", s, re.IGNORECASE)
         if begin:
             stack.append(begin.group(1).strip().lower())
             if stack[-1] != "actions":
@@ -157,6 +157,7 @@ def _canonical_bngl(model_text, bng2):
             capture_output=True,
             text=True,
             timeout=120,
+            check=False,
         )
         canon = Path(work) / "canon.bngl"
         if result.returncode != 0 or not canon.is_file():