Release notes for sbmlutils 0.15.0

We are pleased to release the next version of sbmlutils including the following changes. The ODE export of sbmlutils 0.14.0 is now the package sbmlode, which sbmlutils depends on and re-exports as sbmlutils.converters.ode, so code written against 0.14.0 keeps working. The code, the templates and the testing of the export, with its julia, R and LaTeX toolchains, moved to sbmlode, which makes the continuous integration of sbmlutils faster.

Breaking changes

• sbmlutils.converters.ode re-exports the public API of sbmlode (OdeSystem, FORMATS, Format, render, write, render_template), and every module of sbmlode is importable under it (sbmlutils.converters.ode.system is sbmlode.system, the same module). These submodules exist at runtime only, a type checker no longer resolves from sbmlutils.converters.ode.system import ...; import from sbmlode instead (from sbmlode.system import ...) (#495)
• a custom template reads the version which wrote it as model.sbmlode instead of model.sbmlutils, and the output names sbmlode and its version as the writer; the templates of the formats are those of sbmlode, sbmlutils/resources/converters/ode is removed (#495)
• the example examples.converters.ode and the script scripts/ode_report.py are removed, the documentation of sbmlode shows the output of every format and the verification against roadrunner (#495)

Packaging and development

• sbmlode>=0.1.0 is a dependency; scipy is no longer part of the examples extra and typst no longer part of the dev extra or a test dependency, only the tests of the ODE export needed them; the python code the export writes runs with the simulate extra of sbmlode (pip install "sbmlode[simulate]", numpy, pandas and scipy) (#495)
• the tests of the ODE export (tests/converters/ode/, with the julia environment and the R docker image), the tox environments and CI jobs julia, R and latex and the variables SBMLUTILS_JULIA, SBMLUTILS_RSCRIPT and SBMLUTILS_REQUIRE_TOOLCHAINS are removed; tests/converters/test_ode_reexport.py tests the re-export and create_model(create_markdown=True) (#495)
• the documentation page ODE export is a short introduction which links to the documentation of sbmlode; the vendored MathJax, the styles of the rendered documents and the files of the ODE export of the repressilator are removed from the documentation, they were used by the ODE export only (#495)
• the round trip harness of the tests no longer carries the outcomes and the worker arguments of the ODE sweep (#495)