libvcell 0.0.1__tar.gz

libvcell-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2025, Jim Schaff
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+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.

libvcell-0.0.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: libvcell
+Version: 0.0.1
+Summary: This is a python package which wraps a subset of VCell Java code as a native python package.
+Author: Jim Schaff
+Author-email: schaff@uchc.edu
+Requires-Python: >=3.9,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Dist: pydantic (>=2.10.6,<3.0.0)
+Project-URL: Documentation, https://virtualcell.github.io/libvcell/
+Project-URL: Repository, https://github.com/virtualcell/libvcell
+Description-Content-Type: text/markdown
+
+# libvcell
+
+[![Release](https://img.shields.io/github/v/release/virtualcell/libvcell)](https://img.shields.io/github/v/release/virtualcell/libvcell)
+[![Build status](https://img.shields.io/github/actions/workflow/status/virtualcell/libvcell/main.yml?branch=main)](https://github.com/virtualcell/libvcell/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/virtualcell/libvcell/branch/main/graph/badge.svg)](https://codecov.io/gh/virtualcell/libvcell)
+[![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.
+
+- **Github repository**: <https://github.com/virtualcell/libvcell/>
+- **Documentation** <https://virtualcell.github.io/libvcell/>
+
+## Getting started with your project
+
+First, create a repository on GitHub with the same name as this project, and then run the following commands:
+
+```bash
+git init -b main
+git add .
+git commit -m "init commit"
+git remote add origin git@github.com:virtualcell/libvcell.git
+git push -u origin main
+```
+
+Finally, install the environment and the pre-commit hooks with
+
+```bash
+make install
+```
+
+You are now ready to start development on your project!
+The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
+
+To finalize the set-up for publishing to PyPI or Artifactory, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/publishing/#set-up-for-pypi).
+For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/mkdocs/#enabling-the-documentation-on-github).
+To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/codecov/).
+
+## Releasing a new version
+
+- Create an API Token on [PyPI](https://pypi.org/).
+- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/virtualcell/libvcell/settings/secrets/actions/new).
+- Create a [new release](https://github.com/virtualcell/libvcell/releases/new) on Github.
+- Create a new tag in the form `*.*.*`.
+- For more details, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/cicd/#how-to-trigger-a-release).
+
+---
+
+Repository initiated with [fpgmaas/cookiecutter-poetry](https://github.com/fpgmaas/cookiecutter-poetry).
+

libvcell-0.0.1/README.md

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+# libvcell
+
+[![Release](https://img.shields.io/github/v/release/virtualcell/libvcell)](https://img.shields.io/github/v/release/virtualcell/libvcell)
+[![Build status](https://img.shields.io/github/actions/workflow/status/virtualcell/libvcell/main.yml?branch=main)](https://github.com/virtualcell/libvcell/actions/workflows/main.yml?query=branch%3Amain)
+[![codecov](https://codecov.io/gh/virtualcell/libvcell/branch/main/graph/badge.svg)](https://codecov.io/gh/virtualcell/libvcell)
+[![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.
+
+- **Github repository**: <https://github.com/virtualcell/libvcell/>
+- **Documentation** <https://virtualcell.github.io/libvcell/>
+
+## Getting started with your project
+
+First, create a repository on GitHub with the same name as this project, and then run the following commands:
+
+```bash
+git init -b main
+git add .
+git commit -m "init commit"
+git remote add origin git@github.com:virtualcell/libvcell.git
+git push -u origin main
+```
+
+Finally, install the environment and the pre-commit hooks with
+
+```bash
+make install
+```
+
+You are now ready to start development on your project!
+The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.
+
+To finalize the set-up for publishing to PyPI or Artifactory, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/publishing/#set-up-for-pypi).
+For activating the automatic documentation with MkDocs, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/mkdocs/#enabling-the-documentation-on-github).
+To enable the code coverage reports, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/codecov/).
+
+## Releasing a new version
+
+- Create an API Token on [PyPI](https://pypi.org/).
+- Add the API Token to your projects secrets with the name `PYPI_TOKEN` by visiting [this page](https://github.com/virtualcell/libvcell/settings/secrets/actions/new).
+- Create a [new release](https://github.com/virtualcell/libvcell/releases/new) on Github.
+- Create a new tag in the form `*.*.*`.
+- For more details, see [here](https://fpgmaas.github.io/cookiecutter-poetry/features/cicd/#how-to-trigger-a-release).
+
+---
+
+Repository initiated with [fpgmaas/cookiecutter-poetry](https://github.com/fpgmaas/cookiecutter-poetry).

libvcell-0.0.1/libvcell/_internal/libs/.gitignore

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+# Ignore everything in this directory
+*
+# Except this file
+!.gitignore

libvcell-0.0.1/libvcell/_internal/native_calls.py

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+import ctypes
+import logging
+from pathlib import Path
+
+from pydantic import BaseModel
+
+from libvcell._internal.native_utils import IsolateManager, VCellNativeLibraryLoader
+
+
+class ReturnValue(BaseModel):
+    success: bool
+    message: str
+
+
+class VCellNativeCalls:
+    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:
+        try:
+            with IsolateManager(self.lib) as isolate_thread:
+                json_ptr: ctypes.c_char_p = self.lib.vcmlToFiniteVolumeInput(
+                    isolate_thread,
+                    ctypes.c_char_p(vcml_content.encode("utf-8")),
+                    ctypes.c_char_p(simulation_name.encode("utf-8")),
+                    ctypes.c_char_p(str(output_dir_path).encode("utf-8")),
+                )
+
+            value: bytes | None = ctypes.cast(json_ptr, ctypes.c_char_p).value
+            if value is None:
+                logging.error("Failed to convert vcml to finite volume input")
+                return ReturnValue(success=False, message="Failed to convert vcml to finite volume input")
+            json_str: str = value.decode("utf-8")
+            # self.lib.freeString(json_ptr)
+            return ReturnValue.model_validate_json(json_data=json_str)
+        except Exception as e:
+            logging.exception("Error in vcml_to_finite_volume_input()", exc_info=e)
+            raise
+
+    def sbml_to_finite_volume_input(self, sbml_content: str, output_dir_path: Path) -> ReturnValue:
+        try:
+            with IsolateManager(self.lib) as isolate_thread:
+                json_ptr: ctypes.c_char_p = 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")),
+                )
+            value: bytes | None = ctypes.cast(json_ptr, ctypes.c_char_p).value
+            if value is None:
+                logging.error("Failed to convert sbml to finite volume input")
+                return ReturnValue(success=False, message="Failed to convert sbml to finite volume input")
+            json_str: str = value.decode("utf-8")
+            # self.lib.freeString(json_ptr)
+            return ReturnValue.model_validate_json(json_data=json_str)
+        except Exception as e:
+            logging.exception("Error in sbml_to_finite_volume_input()", exc_info=e)
+            raise

libvcell-0.0.1/libvcell/_internal/native_utils.py

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+import ctypes
+import platform
+from _ctypes import byref
+from importlib.resources import files
+
+import libvcell
+
+
+class VCellNativeLibraryLoader:
+    lib: ctypes.CDLL
+
+    def __init__(self) -> None:
+        self.lib = self._load_library()
+        self._define_entry_points()
+
+    def _load_library(self) -> ctypes.CDLL:
+        system = platform.system()
+        lib_ext = {"Linux": ".so", "Darwin": ".dylib", "Windows": ".dll"}.get(system)
+
+        if lib_ext is None:
+            raise OSError(f"Unsupported operating system: {system}")
+
+        libs_dir = files(libvcell).joinpath("_internal/libs")
+        if not libs_dir.is_dir():
+            raise OSError(f"Could not find the shared library directory {libs_dir}")
+
+        for file in libs_dir.iterdir():
+            if file.name.endswith(lib_ext):
+                print(f"Found shared library: {file}")
+                return ctypes.CDLL(name=str(file))
+
+        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]
+
+        self.lib.sbmlToFiniteVolumeInput.restype = ctypes.c_char_p
+        self.lib.sbmlToFiniteVolumeInput.argtypes = [ctypes.c_void_p, ctypes.c_char_p, ctypes.c_char_p]
+
+        self.lib.freeString.restype = None
+        self.lib.freeString.argtypes = [ctypes.c_char_p]
+
+
+class IsolateManager:
+    lib: ctypes.CDLL
+    isolate: ctypes.c_void_p
+    isolate_thread: ctypes.c_void_p
+
+    def __init__(self, lib: ctypes.CDLL) -> None:
+        self.lib = lib
+        self.isolate = ctypes.c_void_p()
+        self.isolate_thread = ctypes.c_void_p()
+
+    def __enter__(self) -> ctypes.c_void_p:
+        self.lib.graal_create_isolate(None, byref(self.isolate), byref(self.isolate_thread))
+        return self.isolate_thread
+
+    def __exit__(self, exc_type: type | None, exc_val: Exception, exc_tb: object | None) -> None:
+        self.lib.graal_tear_down_isolate(self.isolate_thread)

libvcell-0.0.1/libvcell/libvcell.py

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+from pathlib import Path
+
+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()
+        return_value: ReturnValue = native.vcml_to_finite_volume_input(vcml_content, simulation_name, output_dir_path)
+        if not return_value.success:
+            raise RuntimeError(f"Error in vcml_to_finite_volume_input: {return_value.message}")
+
+    @staticmethod
+    def sbml_to_finite_volume_input(sbml_content: str, output_dir_path: Path) -> None:
+        native = VCellNativeCalls()
+        return_value: ReturnValue = native.sbml_to_finite_volume_input(sbml_content, output_dir_path)
+        if not return_value.success:
+            raise RuntimeError(f"Error in sbml_to_finite_volume_input: {return_value.message}")

libvcell-0.0.1/pyproject.toml

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+[tool.poetry]
+name = "libvcell"
+version = "0.0.1"
+description = "This is a python package which wraps a subset of VCell Java code as a native python package."
+authors = ["Jim Schaff <schaff@uchc.edu>"]
+repository = "https://github.com/virtualcell/libvcell"
+documentation = "https://virtualcell.github.io/libvcell/"
+readme = "README.md"
+packages = [
+  {include = "libvcell"}
+]
+include = [
+    {path="libvcell/_internal/libs/*", format="wheel"}
+]
+
+[tool.poetry.dependencies]
+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 = "^3.8.0"
+tox = "^4.11.1"
+
+[tool.poetry.group.docs.dependencies]
+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", "tests"]
+exclude = [ "vcell_submodule"]
+strict = true
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.ruff]
+target-version = "py39"
+line-length = 120
+fix = true
+lint.select = [
+    # flake8-2020
+    "YTT",
+    # flake8-bandit
+    "S",
+    # flake8-bugbear
+    "B",
+    # flake8-builtins
+    "A",
+    # flake8-comprehensions
+    "C4",
+    # flake8-debugger
+    "T10",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # mccabe
+    "C90",
+    # pycodestyle
+    "E", "W",
+    # pyflakes
+    "F",
+    # pygrep-hooks
+    "PGH",
+    # pyupgrade
+    "UP",
+    # ruff
+    "RUF",
+    # tryceratops
+    "TRY",
+]
+lint.ignore = [
+    # LineTooLong
+    "E501",
+    # DoNotAssignLambda
+    "E731",
+    # avoid specifiying long messages outside the exception class
+    "TRY003",
+]
+
+[tool.ruff.format]
+preview = true
+
+[tool.coverage.report]
+skip_empty = true
+
+[tool.coverage.run]
+branch = true
+source = ["libvcell"]
+
+
+[tool.ruff.per-file-ignores]
+"tests/*" = ["S101"]