Release notes for sbmlsim 0.10.0

A release of the reports of the fits: every fit writes, without an extra command, a report of its parameter optimization that can go into the supplement of a manuscript, with the methods specific to its settings, the tables of the parameters, the data, the metrics and the provenance, the figures and the references. The simulations and the fits are unchanged.

Features

• Fit reports write the methods, the provenance and the references as HTML, Typst/PDF and LaTeX (#336, #342). FitReport.create writes, in addition to everything it wrote before:
  • index.html with two tabs, Report (the methods and results document, then the overview, results and identifiability sections) and Fit mappings (the cost, the weight and the residual figures of every mapping, the metrics of the fit mappings, the cards); self-contained, the math as MathML, no network;
  • report.typ and report.pdf (compiled with the python package typst, no installation of LaTeX needed; a failed compilation keeps the fit and every other output and is stated in the HTML), report.tex (a fragment) and report_standalone.tex, references.bib (the cited entries, the software with its version) and references.csl, PNG copies of the overview figures for LaTeX.
• The building blocks of the reports are public: sbmlsim.report.document and its renderers (sections, paragraphs with inline math, code, citations, equations, tables which break across pages, figures; HTML, Typst and LaTeX), sbmlsim.report.references (the bundled references.bib and the IEEE style references.csl of the CSL project, CC BY-SA 3.0, adapted to print the version note: the license of the package is MIT AND CC-BY-SA-3.0), sbmlsim.fit.methods (the methods text written from the settings, the optimizer, the analyses and the provenance; only what the fit used appears, an unknown setting raises UnsupportedSetting) and sbmlsim.fit.report_document (the tables of the results and the figures).
• Callers describe their fits: FitParameter.description, FitDefinition.description and ReportContext (title, description, descriptions of the parameters, notes), which report_cli(context=...) takes, and report_from_records, the report of stored fit records; FisherInformation.from_dict.

Fixes

• The provenance of a fit hashes the data files without the python files and the caches, with checksum keys which do not depend on the platform (the provenance commit of the branch of #337 which #337 did not contain).