py3.12 incompatibility with scipy and rdkit update (#1500)

* fix: rdkit-dependency-failure-on-py3.12 * scipy version update to be * --------- Co-authored-by: Dhanshree Arora <[email protected]>
ersilia-os · Jan 14, 2025 · 5dc3e30 · 5dc3e30
1 parent 4f099d5
commit 5dc3e30
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -59,8 +59,7 @@ pytest-benchmark = { version = "<=4.0.0", optional = true }
 fuzzywuzzy = { version = "^0.18.0", optional = true }
 sphinx = { version = ">=6.0.0", optional = true }           # for minimum version and support for Python 3.10
 jinja2 = { version = "^3.1.2", optional = true }
-scipy = { version = "<=1.10.0", optional = true }
-rdkit-pypi = { version = "*", optional = true }
+scipy = { version = "*", optional = true }
 nox = { version = "*", optional = true }
 rich = { version = "*", optional = true }
 ruff = { version = "*", optional = true }
@@ -70,7 +69,7 @@ pre-commit = { version = "*", optional = true }
 # Instead of using poetry dependency groups, we use extras to make it pip installable
 lake = ["isaura"]
 docs = ["sphinx", "jinja2"]
-test = ["pytest", "pytest-asyncio", "pytest-benchmark", "nox", "rich", "fuzzywuzzy", "scipy", "rdkit-pypi", "ruff", "pre-commit"]
+test = ["pytest", "pytest-asyncio", "pytest-benchmark", "nox", "rich", "fuzzywuzzy", "scipy", "ruff", "pre-commit"]
 #all = [lake, docs, test]
 
 [tool.poetry.scripts]

diff --git a/test/cli/test_run.py b/test/cli/test_run.py
@@ -9,6 +9,10 @@
 from ersilia.core.model import ErsiliaModel
 from ersilia.core.session import Session
 from ersilia.serve.standard_api import StandardCSVRunApi
+from ersilia.setup.requirements.compound import (
+    ChemblWebResourceClientRequirement,
+    RdkitRequirement,
+)
 from ersilia.utils.logging import logger
 
 from .utils import create_compound_input_csv
@@ -24,6 +28,10 @@
 MAX_WEIGHT = 60.0
 HEADER = ["key", "input", "value"]
 
+@pytest.fixture
+def setup():
+    RdkitRequirement()
+    ChemblWebResourceClientRequirement()
 
 @pytest.fixture
 def mock_fetcher():
@@ -119,7 +127,7 @@ def mock_post_side_effect(input, output, output_source):
 
 
 @pytest.fixture
-def mock_session(compound_csv):
+def mock_session(setup, compound_csv):
     with (
         patch.object(Session, "current_model_id", return_value=MODEL_ID),
         patch.object(Session, "current_service_class", return_value="pulled_docker"),