0.0.17

What's new in 0.0.17

• Moving Boundary solver input: vcml_to_moving_boundary_input(vcml_content, simulation_name, output_dir_path) converts a VCML simulation (configured for the Moving Boundary solver) into a MovingBoundarySetup XML file — the input format consumed by the vcell-mbsolver package (MovingBoundarySolver.from_xml).

Also includes the 0.0.16 changes (generateErrorReport structured error reports; libvcell.__version__).

Packaging

First release on the streamlined workflow: a single py3-none-<platform> wheel per platform (the package is pure Python + a ctypes-loaded native library, so wheels are not Python-version-specific). Wheels for macOS (Apple Silicon), Windows, and Linux (x86_64 + aarch64, manylinux 2_28 / 2_34).

0.0.16

What's new in 0.0.16

• Moving Boundary solver input: new vcml_to_moving_boundary_input(vcml_content, simulation_name, output_dir_path) API that converts a VCML simulation (configured for the Moving Boundary solver) into a MovingBoundarySetup XML file — the input format consumed by the vcell-mbsolver package (MovingBoundarySolver.from_xml). (#19)
• Structured error reports: generateErrorReport produces clear, nested-cause error messages instead of opaque stack traces. (#17)
• libvcell.__version__: the installed package version is now exposed programmatically for downstream consumers. (#18)

Wheels are built for CPython 3.10–3.14 across macOS (Intel + Apple Silicon), Windows, and Linux (x86_64 + aarch64, manylinux 2_28 / 2_34).

Restore glibc 2.28 to deployment scripts

We have collaborators whose HPC runs an older version of linux, that only goes up to glibc 2.28. We've recently stopped supporting 2.28, because we can not build a python3.14 version of libvcell, while also using manylinux_2_28 images to do so without creating a custom workflow for it and all future versions of python. Also, glibc 2.28 is many, many versions of linux old (CentOS 8 was still around, for example).

Solution is to build with both, and exclude building later versions of python with manylinux 2.28

What's Changed

• Add back support for glibc 2_28 (manylinux_2_28), excluding newer Python versions that require manylinux_2_34
• Update Maven in the Dockerfiles + the GitHub Action that processes them
• Bump version to 0.0.15.4

Full Changelog: 0.0.15.3...0.0.15.4

Adding python 3.10 to official releases

We build and test for python 3.10, so we're editing the pyproject to reflect that.

What's Changed

• Add Python 3.10 to the official build/test matrix and pyproject.toml

Full Changelog: 0.0.15.2...0.0.15.3

Expanding compatability

Increases backwards and forwards compatibility

What's Changed

• Upgrade cibuildwheel for broader platform compatibility
• CI/CD fixes

Full Changelog: 0.0.15.1...0.0.15.2

Exposed NumExpr expressions for post-processing

For PyVCell to process expressions, we need to provide them in a specific format used by the python library NumExpr. This release includes the features necessary to do that.

What's Changed

• Expose NumExpr-format expression generation for post-processing (vcell_infix_to_num_expr_infix)
• Update vcell submodule to track master
• CI: work toward macOS 13 wheels

Full Changelog: 0.0.14.4...0.0.15.1

Exposed python-infix expression notation

Exposes VCell's new python-infix notation generation for Expressions

What's Changed

• Add Python-infix notation generation for VCell expressions (vcell_infix_to_python_infix)
• Restore cloning variable setting
• Logging corrections and fail-testing
• Build/CD configuration fixes

Full Changelog: 0.0.13...0.0.14.4

0.0.13

What's Changed

• serialization bug in java native by @jcschaff in #10

Full Changelog: 0.0.12...0.0.13

0.0.12

What's Changed

• fix field data fvsolver input file generation with null sim key by @jcschaff in #9

Full Changelog: 0.0.11...0.0.12

0.0.11

What's Changed

• export SBML with compatable units and optional validation by @jcschaff in #8

Full Changelog: 0.0.10...0.0.11