CI: Fix/skip biomodels download failures

.github/workflows/test_conda_install.yml

@@ -31,19 +31,14 @@ jobs:
       - name: Install AMICI
         shell: bash -l {0}
         run: |
-          pip3 install -v ./python/sdist
+          pip3 install -v ./python/sdist[test]
       - name: Show environment
         shell: bash -l {0}
         run: |
           python -c "import os; import pprint; pprint.pprint(dict(os.environ))"
           which cmake
           which ninja
           ls -l /Users/runner/miniconda3/envs/amici/bin || true
-      - name: Install test dependencies
-        shell: bash -l {0}
-        run: |
-          # Install test extras (pytest, scipy, etc.)
-          pip3 install pytest pytest-cov scipy h5py antimony
       - name: Test import
         shell: bash -l {0}
         run: |

pytest.ini

@@ -5,6 +5,9 @@ addopts = -vv --strict-markers --doctest-modules
 filterwarnings =
     # warnings are errors
     error
+    # Unrelated to our code, unclosed SSL socket when downloading test assets
+    #  (probably improper cleanup upstream in case of exceptions)
+    ignore:Exception ignored while finalizing socket:pytest.PytestUnraisableExceptionWarning
     # Known issue with numpy under valgrind - don't error on this
     once:Signature .* for <class 'numpy.longdouble'> does not match any known type. falling back to type probe function:UserWarning
     # petab

python/tests/test_sbml_import.py

@@ -41,6 +41,7 @@
 from amici.testing import skip_on_valgrind
 from conftest import MODEL_STEADYSTATE_SCALED_XML
 from numpy.testing import assert_allclose, assert_array_equal
+from requests import HTTPError
 
 
 def simple_sbml_model():
@@ -649,16 +650,31 @@ def test_units(model_units_module):
 )
 def test_sympy_exp_monkeypatch(tempdir):
     """
-    This model contains a removeable discontinuity at t=0 that requires
+    This model contains a removable discontinuity at t=0 that requires
     monkeypatching sympy.Pow._eval_derivative in order to be able to compute
     non-nan sensitivities
     """
     import pooch
 
-    model_file = pooch.retrieve(
-        url="https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000529.2?filename=BIOMD0000000529_url.xml",
-        known_hash="md5:c6e0b298397485b93d7acfab80b21fd4",
-    )
+    downloader = pooch.HTTPDownloader(headers={"User-Agent": "Mozilla/5.0"})
+
+    try:
+        model_file = pooch.retrieve(
+            url="https://www.biomodels.org/model/download/BIOMD0000000529.2?filename=BIOMD0000000529_url.xml",
+            known_hash="md5:c6e0b298397485b93d7acfab80b21fd4",
+            downloader=downloader,
+        )
+    except HTTPError as e:
+        # When running on GHA, we might be subject to some rate limiting
+        #  or similar. In that case, skip instead of failing.
+        if (
+            "GITHUB_ACTIONS" in os.environ
+            and e.response is not None
+            and e.response.status_code in {403, 429, 503}
+        ):
+            pytest.skip(f"BioModels temporarily unavailable/rate-limited: {e}")
+        raise
+
     importer = amici.SbmlImporter(model_file)
     module_name = "BIOMD0000000529"