Merge pull request #3 from virtualcell/api-cleanup

cleanup API error handling

Author: jcschaff

.github/workflows/on-release-main.yml

@@ -59,11 +59,16 @@ jobs:
           mkdir -p dist
           cp wheelhouse/*.whl dist/
 
-      - name: Publish to PyPI
+      - name: Publish to PyPI (dry run)
         run: |
           poetry config pypi-token.pypi "${{ secrets.PYPI_TOKEN }}"
           poetry publish --dry-run
+
+      - name: Publish to PyPI (release-only - push to PyPI)
+        run: |
+          poetry config pypi-token.pypi "${{ secrets.PYPI_TOKEN }}"
           poetry publish --skip-existing
+        if: github.event_name == 'release'
 
       - name: Setup tmate
         if: failure()

build.py

@@ -30,7 +30,9 @@ def main() -> None:
     run_command(
         "java -agentlib:native-image-agent=config-output-dir=target/recording "
         "-jar target/vcell-native-1.0-SNAPSHOT.jar "
-        "src/test/resources/TinySpacialProject_Application0.xml "
+        "src/test/resources/TinySpatialProject_Application0.xml "
+        "src/test/resources/TinySpatialProject_Application0.vcml "
+        "Simulation0 "
         "target/sbml-input",
         cwd=vcell_native_dir,
     )

docs/modules.md

@@ -1,5 +1,21 @@
 # Modules
 
-## libvcell.libvcell
+## libvcell
 
-::: libvcell.libvcell
+::: libvcell
+
+# Modules
+
+## libvcell
+
+::: libvcell
+
+### Functions
+
+#### sbml_to_finite_volume_input
+
+::: libvcell.solver_utils.sbml_to_finite_volume_input
+
+#### vcml_to_finite_volume_input
+
+::: libvcell.solver_utils.vcml_to_finite_volume_input

libvcell/__init__.py

@@ -0,0 +1,3 @@
+from libvcell.solver_utils import sbml_to_finite_volume_input, vcml_to_finite_volume_input
+
+__all__ = ["vcml_to_finite_volume_input", "sbml_to_finite_volume_input"]

libvcell/libvcell.py

@@ -0,0 +1,36 @@
+from pathlib import Path
+
+from libvcell._internal.native_calls import ReturnValue, VCellNativeCalls
+
+
+def vcml_to_finite_volume_input(vcml_content: str, simulation_name: str, output_dir_path: Path) -> tuple[bool, str]:
+    """
+    Convert VCML content to finite volume input files
+
+    Args:
+        vcml_content (str): VCML content
+        simulation_name (str): simulation name
+        output_dir_path (Path): output directory path
+
+    Returns:
+        tuple[bool, str]: A tuple containing the success status and a message
+    """
+    native = VCellNativeCalls()
+    return_value: ReturnValue = native.vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)
+    return return_value.success, return_value.message
+
+
+def sbml_to_finite_volume_input(sbml_content: str, output_dir_path: Path) -> tuple[bool, str]:
+    """
+    Convert SBML content to finite volume input files
+
+    Args:
+        sbml_content (str): SBML content
+        output_dir_path (Path): output directory path
+
+    Returns:
+        tuple[bool, str]: A tuple containing the success status and a message
+    """
+    native = VCellNativeCalls()
+    return_value: ReturnValue = native.sbml_to_finite_volume_input(sbml_content, output_dir_path)
+    return return_value.success, return_value.message

libvcell/solver_utils.py

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "libvcell"
-version = "0.0.4"
+version = "0.0.5"
 description = "This is a python package which wraps a subset of VCell Java code as a native python package."
 authors = ["Jim Schaff <[email protected]>", "Ezequiel Valencia <[email protected]>"]
 repository = "https://github.com/virtualcell/libvcell"

pyproject.toml

@@ -33,7 +33,9 @@ mvn clean install
 # run with native-image-agent to record configuration for native-image
 java -agentlib:native-image-agent=config-output-dir=target/recording \
      -jar target/vcell-native-1.0-SNAPSHOT.jar \
-     "$ROOT_DIR/vcell-native/src/test/resources/TinySpacialProject_Application0.xml" \
+     "$ROOT_DIR/vcell-native/src/test/resources/TinySpatialProject_Application0.xml" \
+     "$ROOT_DIR/vcell-native/src/test/resources/TinySpatialProject_Application0.vcml" \
+     "Simulation0" \
      "$ROOT_DIR/vcell-native/target/sbml-input"
 
 # build vcell-native as native shared object library

scripts/build_native.sh renamed to scripts/local_build_native.sh

@@ -1,17 +1,21 @@
 from pathlib import Path
 
-from libvcell.libvcell import libvcell
+from libvcell import sbml_to_finite_volume_input, vcml_to_finite_volume_input
 
 
 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(
+    success, msg = 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
+    assert success is True
+    assert msg == "Success"
 
 
 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)
+    success, msg = sbml_to_finite_volume_input(sbml_content=sbml_content, output_dir_path=temp_output_dir)
     assert len(list(temp_output_dir.iterdir())) > 0
+    assert success is True
+    assert msg == "Success"

tests/test_libvcell.py

@@ -23,7 +23,7 @@
     <maven.compiler.source>${java.specification.version}</maven.compiler.source>
     <maven.compiler.target>${java.specification.version}</maven.compiler.target>
     <imageName>libvcell</imageName>
-    <mainClass>org.vcell.libvcell.Entrypoints</mainClass>
+    <mainClass>org.vcell.libvcell.MainRecorder</mainClass>
 </properties>
 
 <dependencies>