formatting, and synchronizing some repo config settings with pyvcell

jcschaff · jcschaff · commit 2ffc4caca63b · 2025-03-09T22:31:43.000-04:00
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -29,7 +29,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
       fail-fast: false
     defaults:
       run:
diff --git a/.github/workflows/on-release-main.yml b/.github/workflows/on-release-main.yml
@@ -39,4 +39,3 @@ jobs:
 
       - name: Deploy documentation
         run: poetry run mkdocs gh-deploy --force
-
diff --git a/LICENSE b/LICENSE
@@ -19,4 +19,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
-
diff --git a/Makefile b/Makefile
@@ -14,7 +14,7 @@ check: ## Run code quality tools.
 	@echo "🚀 Static type checking: Running mypy"
 	@poetry run mypy
 	@echo "🚀 Checking for obsolete dependencies: Running deptry"
-	@poetry run deptry .
+	@poetry run deptry --exclude=.venv --exclude=tests .
 
 .PHONY: test
 test: ## Test the code with pytest
diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 [![Commit activity](https://img.shields.io/github/commit-activity/m/virtualcell/libvcell)](https://img.shields.io/github/commit-activity/m/virtualcell/libvcell)
 [![License](https://img.shields.io/github/license/virtualcell/libvcell)](https://img.shields.io/github/license/virtualcell/libvcell)
 
-libvcell is a subset of VCell algorithms intended to support the [pyvcell](https://pypi.org/project/pyvcell/) python package.  libvcell is available as a native executable and a python package.
+libvcell is a subset of VCell algorithms intended to support the [pyvcell](https://pypi.org/project/pyvcell/) python package. libvcell is available as a native executable and a python package.
 
 - **Github repository**: <https://github.com/virtualcell/libvcell/>
 - **Documentation** <https://virtualcell.github.io/libvcell/>
diff --git a/libvcell/_internal/native_calls.py b/libvcell/_internal/native_calls.py
@@ -4,7 +4,7 @@
 
 from pydantic import BaseModel
 
-from libvcell._internal.native_utils import VCellNativeLibraryLoader, IsolateManager
+from libvcell._internal.native_utils import IsolateManager, VCellNativeLibraryLoader
 
 
 class ReturnValue(BaseModel):
@@ -17,7 +17,9 @@ def __init__(self) -> None:
         self.loader = VCellNativeLibraryLoader()
         self.lib = self.loader.lib
 
-    def vcml_to_finite_volume_input(self, vcml_content: str, simulation_name: str, output_dir_path: Path) -> ReturnValue:
+    def vcml_to_finite_volume_input(
+        self, vcml_content: str, simulation_name: str, output_dir_path: Path
+    ) -> ReturnValue:
         try:
             with IsolateManager(self.lib) as isolate_thread:
                 json_ptr: ctypes.c_char_p = self.lib.vcmlToFiniteVolumeInput(
@@ -32,7 +34,7 @@ def vcml_to_finite_volume_input(self, vcml_content: str, simulation_name: str, o
             # self.lib.freeString(json_ptr)
             return ReturnValue.model_validate_json(json_data=json_str)
         except Exception as e:
-            logging.error(f"Error in vcml_to_finite_volume_input: {e}")
+            logging.exception(f"Error in vcml_to_finite_volume_input: {e}")
             raise
 
     def sbml_to_finite_volume_input(self, sbml_content: str, output_dir_path: Path) -> ReturnValue:
@@ -41,13 +43,13 @@ def sbml_to_finite_volume_input(self, sbml_content: str, output_dir_path: Path)
                 json_ptr: bytes | None = self.lib.sbmlToFiniteVolumeInput(
                     isolate_thread,
                     ctypes.c_char_p(sbml_content.encode("utf-8")),
-                    ctypes.c_char_p(str(output_dir_path).encode("utf-8"))
+                    ctypes.c_char_p(str(output_dir_path).encode("utf-8")),
                 )
             if json_ptr is None:
                 raise ValueError("Native function returned null")
             json_str: str = ctypes.cast(json_ptr, ctypes.c_char_p).value.decode("utf-8")
             # self.lib.freeString(json_ptr)
             return ReturnValue.model_validate_json(json_data=json_str)
         except Exception as e:
-            logging.error(f"Error in sbml_to_finite_volume_input: {e}")
-            raise
+            logging.exception(f"Error in sbml_to_finite_volume_input: {e}")
+            raise
diff --git a/libvcell/_internal/native_utils.py b/libvcell/_internal/native_utils.py
@@ -32,7 +32,6 @@ def _load_library(self) -> ctypes.CDLL:
         raise OSError("Could not find the shared library")
 
     def _define_entry_points(self) -> None:
-
         self.lib.vcmlToFiniteVolumeInput.restype = ctypes.c_char_p
         self.lib.vcmlToFiniteVolumeInput.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p, ctypes.c_char_p]
 
@@ -59,4 +58,3 @@ def __enter__(self):
 
     def __exit__(self, exc_type, exc_val, exc_tb):
         self.lib.graal_tear_down_isolate(self.isolate_thread)
-
diff --git a/libvcell/libvcell.py b/libvcell/libvcell.py
@@ -1,10 +1,9 @@
 from pathlib import Path
 
-from libvcell._internal.native_calls import VCellNativeCalls, ReturnValue
+from libvcell._internal.native_calls import ReturnValue, VCellNativeCalls
 
 
 class libvcell:
-
     @staticmethod
     def vcml_to_finite_volume_input(vcml_content: str, simulation_name: str, output_dir_path: Path) -> None:
         native = VCellNativeCalls()
diff --git a/pyproject.toml b/pyproject.toml
@@ -9,37 +9,34 @@ readme = "README.md"
 packages = [
   {include = "libvcell"}
 ]
+include = [
+    {path="libvcell/_internal/libs/*", format="wheel"}
+]
 
 [tool.poetry.dependencies]
-python = ">=3.8,<4.0"
+python = ">=3.9,<4.0"
 pydantic = "^2.10.6"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.0"
 pytest-cov = "^4.0.0"
 deptry = "^0.16.2"
 mypy = "^1.5.1"
-pre-commit = "^3.4.0"
+pre-commit = "^3.8.0"
 tox = "^4.11.1"
 
 [tool.poetry.group.docs.dependencies]
-mkdocs = "^1.4.2"
-mkdocs-material = "^9.2.7"
-mkdocstrings = {extras = ["python"], version = "^0.26.1"}
+mkdocs = "^1.6.1"
+mkdocs-material = "^9.5.50"
+mkdocstrings = {extras = ["python"], version = "^0.27.0"}
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.mypy]
-files = ["libvcell"]
-disallow_untyped_defs = "True"
-disallow_any_unimported = "True"
-no_implicit_optional = "True"
-check_untyped_defs = "True"
-warn_return_any = "True"
-warn_unused_ignores = "True"
-show_error_codes = "True"
+files = ["libvcell", "tests"]
+strict = true
 
 
 
@@ -50,7 +47,7 @@ testpaths = ["tests"]
 target-version = "py39"
 line-length = 120
 fix = true
-select = [
+lint.select = [
     # flake8-2020
     "YTT",
     # flake8-bandit
@@ -82,11 +79,13 @@ select = [
     # tryceratops
     "TRY",
 ]
-ignore = [
+lint.ignore = [
     # LineTooLong
     "E501",
     # DoNotAssignLambda
     "E731",
+    # avoid specifiying long messages outside the exception class
+    "TRY003",
 ]
 
 [tool.ruff.format]
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1 +1 @@
-from tests.fixtures.data_fixtures import vcml_file_path, vcml_sim_name, sbml_file_path, temp_output_dir  # noqa: F401
+from tests.fixtures.data_fixtures import sbml_file_path, temp_output_dir, vcml_file_path, vcml_sim_name  # noqa: F401
diff --git a/tests/fixtures/data_fixtures.py b/tests/fixtures/data_fixtures.py
@@ -1,7 +1,7 @@
 import os
 import shutil
+from collections.abc import Generator
 from pathlib import Path
-from typing import Generator
 
 import pytest
 
@@ -35,4 +35,3 @@ def temp_output_dir() -> Generator[Path, None, None]:
     yield output_dir
 
     shutil.rmtree(output_dir)
-
diff --git a/tests/test_libvcell.py b/tests/test_libvcell.py
@@ -1,17 +1,17 @@
 from pathlib import Path
 
 from libvcell.libvcell import libvcell
-from tests.fixtures.data_fixtures import temp_output_dir
 
 
 def test_vcml_to_finite_volume_input(temp_output_dir: Path, vcml_file_path: Path, vcml_sim_name: str) -> None:
     vcml_content = vcml_file_path.read_text()
-    libvcell.vcml_to_finite_volume_input(vcml_content=vcml_content, simulation_name=vcml_sim_name, output_dir_path=temp_output_dir)
+    libvcell.vcml_to_finite_volume_input(
+        vcml_content=vcml_content, simulation_name=vcml_sim_name, output_dir_path=temp_output_dir
+    )
     assert len(list(temp_output_dir.iterdir())) > 0
 
 
 def test_sbml_to_finite_volume_input(temp_output_dir: Path, sbml_file_path: Path, vcml_sim_name: str) -> None:
     sbml_content = sbml_file_path.read_text()
     libvcell.sbml_to_finite_volume_input(sbml_content=sbml_content, output_dir_path=temp_output_dir)
     assert len(list(temp_output_dir.iterdir())) > 0
-
diff --git a/vcell-native/README.md b/vcell-native/README.md
@@ -1,13 +1,16 @@
 1. Create native executable of module
    1. Create clean instance
    2. Record runtime dependent operations for future replay
-   3. Build the native executable 
+   3. Build the native executable
+
 ```bash
 pushd ../vcell
 mvn clean install -DskipTests
 popd
 ```
+
 export JAVA_HOME=$(jenv javahome)
+
 ```bash
 mvn clean install
 java -agentlib:native-image-agent=config-output-dir=target/recording \
@@ -18,15 +21,17 @@ java -agentlib:native-image-agent=config-output-dir=target/recording \
 mvn package -P shared-dll -DskipTests=true
 ```
 
-Sources: 
+Sources:
+
 - https://www.graalvm.org/jdk21/reference-manual/native-image/dynamic-features/Resources/
 - https://www.graalvm.org/latest/reference-manual/native-image/metadata/AutomaticMetadataCollection/
 
 2. Run native executable
+
 ```bash
 pushd ..
 ./target/sbml_to* -Dheadless=true \
 "./vcell/vcell-rest/src/test/resources/TinySpacialProject_Application0.xml" \
-".vcell/vcell-nativelib/target/sbml-input" 
+".vcell/vcell-nativelib/target/sbml-input"
 popd
-```
+```
diff --git a/vcell-native/pom.xml b/vcell-native/pom.xml
@@ -282,4 +282,4 @@
         </build>
     </profile>
 </profiles>
-</project>
+</project>
diff --git a/vcell-native/src/main/java/org/vcell/libvcell/Entrypoints.java b/vcell-native/src/main/java/org/vcell/libvcell/Entrypoints.java
@@ -178,4 +178,4 @@ public static void main(String[] args) {
             logger.error("Error processing spatial model", e);
         }
     }
-}
+}
diff --git a/vcell-native/src/main/resources/custom.security b/vcell-native/src/main/resources/custom.security
@@ -1 +1 @@
-jdk.jar.disabledAlgorithms=MD2, MD5, RSA, DSA
+jdk.jar.disabledAlgorithms=MD2, MD5, RSA, DSA
diff --git a/vcell-native/src/main/resources/log4j2.xml b/vcell-native/src/main/resources/log4j2.xml
@@ -12,4 +12,4 @@
         </Root>
     </Loggers>
 
-</Configuration>
+</Configuration>
diff --git a/vcell-native/src/test/java/org/vcell/libvcell/EntrypointsTest.java b/vcell-native/src/test/java/org/vcell/libvcell/EntrypointsTest.java
@@ -35,4 +35,4 @@ private static String getFileContentsAsString(String filename) throws IOExceptio
             return textContent;
         }
     }
-}
+}
diff --git a/vcell-native/src/test/resources/TinySpacialProject_Application0.xml b/vcell-native/src/test/resources/TinySpacialProject_Application0.xml
@@ -34,7 +34,7 @@
           </annotation>
                   <spatial:listOfAnalyticVolumes>
             <spatial:analyticVolume spatial:domainType="subdomain0" spatial:functionType="layered" spatial:id="AnalyticVol_subdomain0" spatial:ordinal="0">
-              <math xmlns="http://www.w3.org/1998/Math/MathML">              
+              <math xmlns="http://www.w3.org/1998/Math/MathML">
                 <cn> 1 </cn>
               </math>
                         </spatial:analyticVolume>
@@ -179,7 +179,7 @@
     </listOfParameters>
     <listOfInitialAssignments>
       <initialAssignment symbol="s0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <times/>
             <cn> 100000 </cn>
@@ -188,7 +188,7 @@
         </math>
             </initialAssignment>
       <initialAssignment symbol="s1">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <plus/>
             <cn> 10 </cn>
@@ -214,7 +214,7 @@
           <speciesReference constant="true" id="r0_s1p" species="s1" stoichiometry="1"/>
         </listOfProducts>
         <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <plus/>
               <apply>
@@ -236,4 +236,4 @@
       </reaction>
     </listOfReactions>
   </model>
-</sbml>
+</sbml>

Original file line number	Diff line number	Diff line change
`@@ -39,4 +39,3 @@ jobs:`
`39`	`39`
`40`	`40`	`- name: Deploy documentation`
`41`	`41`	`run: poetry run mkdocs gh-deploy --force`
`42`		`-`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-from tests.fixtures.data_fixtures import vcml_file_path, vcml_sim_name, sbml_file_path, temp_output_dir # noqa: F401`
	`1`	`+from tests.fixtures.data_fixtures import sbml_file_path, temp_output_dir, vcml_file_path, vcml_sim_name # noqa: F401`