fixed some errors, fixed setup.cfg, tox.ini

Author: uri.akavia

setup.cfg

@@ -80,6 +80,7 @@ where = src
 [options.package_data]
 cobra =
     data/*
+    io/*.json
 
 [options.extras_require]
 array =

src/cobra/io/web/cobrapy_repository.py

@@ -9,8 +9,15 @@
 class Cobrapy(AbstractModelRepository):
     """
     Define a concrete implementation of the cobrapy (local package) repository.
+
+     Attributes
+    ----------
+    name : str
+        The name of the Cobrapy repository.
     """
 
+    name: str = "Cobrapy"
+
     def __init__(
         self,
         **kwargs,
@@ -40,12 +47,6 @@ def get_sbml(self, model_id: str) -> bytes:
         -------
         bytes
             A gzip-compressed, UTF-8 encoded SBML document.
-
-        Raises
-        ------
-        httpx.HTTPError
-            In case there are any connection problems.
-
         """
         cobra_data_dir = importlib_resources.files("cobra.data")
         model_file = cobra_data_dir.joinpath(f"{model_id}.xml.gz")

src/cobra/io/web/load.py

@@ -28,15 +28,17 @@
 def load_model(
     model_id: str,
     repositories: Iterable[AbstractModelRepository] = (
+        Cobrapy(),
         BiGGModels(),
         BioModels(),
-        Cobrapy(),
     ),
     cache: bool = True,
 ) -> "Model":
     """
     Download an SBML model from a remote repository.
 
+    It will try the local repository first.
+
     Downloaded SBML documents are by default stored in a cache on disk such that future
     access is much faster. By default, models can be loaded from the following
     repositories:
@@ -155,6 +157,11 @@ def _fetch_model(
         )
         try:
             return repository.get_sbml(model_id=model_id)
+        except FileNotFoundError:
+            logger.debug(
+                f"Model '{model_id} not found in the local "
+                f"repository {repository.name}.'"
+            )
         except httpx.HTTPStatusError as error:
             if error.response.status_code == 404:
                 logger.debug(

tests/test_io/test_json.py

@@ -5,7 +5,7 @@
 from typing import Any, Callable, Dict, Union
 
 import pytest
-from importlib_resources import open_text
+from importlib_resources import files
 
 from cobra import Model
 from cobra import io as cio
@@ -14,7 +14,7 @@
 @pytest.fixture(scope="module")
 def json_schema_v1() -> Dict[str, Union[str, bool, Any]]:
     """Fixture for cobra JSON-schema."""
-    with open_text(cio, "schema_v1.json") as handle:
+    with files(cio).joinpath("schema_v1.json").open('r') as handle:
         schema_v1 = json.load(handle)
     return schema_v1
 

tests/test_io/test_web/test_load.py

@@ -71,3 +71,8 @@ def test_cache(monkeypatch, tmp_path, bigg_models, biomodels):
     biomodels.get_sbml.assert_not_called()
     assert len(cached_model.metabolites) == len(remote_model.metabolites)
     assert len(cached_model.reactions) == len(remote_model.reactions)
+
+
+def test_local_load(model, compare_models):
+    model_local = load_model("textbook")
+    compare_models(model, model_local)

tox.ini

@@ -68,7 +68,7 @@ commands=
 
 [pytest]
 testpaths =
-    src/tests
+    tests
 markers =
     raises
 
@@ -81,15 +81,15 @@ source =
 branch = true
 parallel = true
 omit =
-    */tests/*
+    tests/*
 
 [coverage:report]
 exclude_lines =
 # Have to re-enable the standard pragma
     pragma: no cover
 precision = 2
 omit =
-    */tests/*
+    tests/*
 
 [isort]
 skip = __init__.py