v0.5.21

StructuralIdentifiability v0.5.21

Diff since v0.5.20

Merged pull requests:

• Bump julia-actions/setup-julia from 2 to 3 (#506) (@dependabot[bot])
• Treating missing in MTK bindings (#508) (@pogudingleb)
• Bump version from 0.5.20 to 0.5.21 (#509) (@pogudingleb)

Closed issues:

• assess_identifiability with known_ic hangs on model that completes in 16s without it (#503)

v0.5.20

StructuralIdentifiability v0.5.20

Diff since v0.5.19

Merged pull requests:

• Add citations for benchmark models (#497) (@sumiya11)
• Load benchmarks in tests (#498) (@sumiya11)
• MQS -> OMS (#499) (@sumiya11)
• Fixing observables and bindings (addressing #496) (#500) (@pogudingleb)
• Bump codecov/codecov-action from 5 to 6 (#502) (@dependabot[bot])
• Reducing hidden simplifications in the known IC regime (#504) (@pogudingleb)
• Bump version from 0.5.19 to 0.5.20 (#505) (@pogudingleb)

Closed issues:

• Unable to run mtk_to_si() on a ModelingToolkit system with symbolics vectors (#496)

v0.5.19

StructuralIdentifiability v0.5.19

Diff since v0.5.18

Merged pull requests:

• Bump actions/cache from 4 to 5 (#474) (@dependabot[bot])
• Documentation improvements: Fix typos and grammar (#480) (@ChrisRackauckas-Claude)
• Switch from JuliaFormatter to Runic.jl for code formatting (#482) (@ChrisRackauckas-Claude)
• Bump actions/checkout from 4 to 6 (#483) (@dependabot[bot])
• examples (#484) (@pogudingleb)
• Performance improvements: type stability and reduced allocations (#486) (@ChrisRackauckas-Claude)
• CompatHelper: bump compat for AbstractAlgebra to 0.48, (keep existing compat) (#487) (@github-actions[bot])
• CompatHelper: bump compat for Nemo to 0.54, (keep existing compat) (#488) (@github-actions[bot])
• Bump RationalFunctionFields (#490) (@pogudingleb)
• Remove pre-release Julia from CI_extensions (#493) (@ChrisRackauckas-Claude)
• Bump MTK Base to support MTK 11 (#494) (@sumiya11)
• Bump version (#495) (@sumiya11)

Closed issues:

• Nemo 0.53 upgrade blocked by ParamPunPam compatibility (#481)
• ModelingToolkitSIExt tests hang on Julia pre-release (1.12-DEV) (#492)

v0.5.18

StructuralIdentifiability v0.5.18

Diff since v0.5.17

Merged pull requests:

• CompatHelper: bump compat for Symbolics in [weakdeps] to 7, (keep existing compat) (#464) (@github-actions[bot])
• Bump actions/checkout from 5 to 6 (#465) (@dependabot[bot])
• CompatHelper: bump compat for ModelingToolkit in [extras] to 11, (keep existing compat) (#469) (@github-actions[bot])
• CompatHelper: bump compat for ModelingToolkit in [weakdeps] to 11, (keep existing compat) (#470) (@github-actions[bot])
• CompatHelper: bump compat for TestSetExtensions in [extras] to 3, (keep existing compat) (#471) (@github-actions[bot])
• CompatHelper: bump compat for ModelingToolkit to 11 for package docs, (keep existing compat) (#472) (@github-actions[bot])
• Fixing failing CI (#473) (@pogudingleb)
• getting pivot before passing to RFF (#476) (@pogudingleb)
• Making loglevel work correctly for reparametrization (#477) (@pogudingleb)
• Bump version from 0.5.17 to 0.5.18 (#478) (@pogudingleb)

Closed issues:

• find_identifiable_functions is not working (#462)
• Update for new Package versions (#475)

v0.5.17

StructuralIdentifiability v0.5.17

Diff since v0.5.16

Merged pull requests:

• Constructive membership update (#444) (@pogudingleb)
• adding influenza immune response benchmarks (#445) (@pogudingleb)
• CompatHelper: bump compat for AbstractAlgebra to 0.47, (keep existing compat) (#446) (@github-actions[bot])
• CompatHelper: bump compat for Nemo to 0.52, (keep existing compat) (#447) (@github-actions[bot])
• Removing RFF functionality and using the dedicated package (#449) (@pogudingleb)
• adding EAIHRD as test and benchmarks (#451) (@pogudingleb)
• CompatHelper: bump compat for SymbolicUtils in [weakdeps] to 4, (keep existing compat) (#452) (@github-actions[bot])
• bump RFF (#453) (@pogudingleb)
• Output detection in MTK and UTF issue (#457) (@pogudingleb)
• Bump version from 0.5.17 to 0.5.18 (#459) (@pogudingleb)
• Correcting version (#461) (@pogudingleb)

Closed issues:

• ModelingToolkit parsing error (#455)
• Inconsistensies between local and global identifiability (#456)

v0.5.16

StructuralIdentifiability v0.5.16

Diff since v0.5.15

Merged pull requests:

• Variable renaming (#416) (@pogudingleb)
• Benchmarking modernization (#418) (@pogudingleb)
• CompatHelper: bump compat for AbstractAlgebra to 0.46, (keep existing compat) (#422) (@github-actions[bot])
• CompatHelper: bump compat for Nemo to 0.51, (keep existing compat) (#423) (@github-actions[bot])
• fixing the random point generation in the wronskian computation (#424) (@pogudingleb)
• Saturation factorization (#425) (@pogudingleb)
• New Downgrade CI v2 (#426) (@ChrisRackauckas)
• Remove Julia v1.9 get_extension compatibility code (#427) (@ChrisRackauckas)
• Remove outdated Julia v1.7 version checks (#428) (@ChrisRackauckas)
• Add spell checking configuration (#429) (@ChrisRackauckas)
• Fix spelling errors and enhance spell checking for mathematical parameters (#430) (@ChrisRackauckas)
• Update CI to test on Julia 1, lts, and pre versions (#431) (@ChrisRackauckas)
• moving tests for rational functions to the subfolder (#432) (@pogudingleb)
• retaining original generators for the final casting (#435) (@pogudingleb)
• Simplification regimes & Polynomial generators (#436) (@pogudingleb)
• Yet another bump for DataStructures (#437) (@pogudingleb)
• Bump actions/checkout from 4 to 5 (#438) (@dependabot[bot])
• Minor changes in simplification (#440) (@pogudingleb)
• More explicit and informative error message for non-rational models (#441) (@pogudingleb)
• Adding benchmark reproducing the identifiability analysis from https://hal.science/hal-03739205v1 (#442) (@pogudingleb)
• bump version (#443) (@pogudingleb)

Closed issues:

• ModelingToolkit extension completely freezing Julia (#360)
• StackOverflowError during compilation on Julia 1.12 (#362)
• Better error for exponential parameters in structural identifiability extension (#417)
• Pessimistic Wronskian computation when searching for identifiable function (#421)

v0.5.15

StructuralIdentifiability v0.5.15

Diff since v0.5.14

Merged pull requests:

• Bump actions/checkout from 2 to 4 (#401) (@dependabot[bot])
• Fixing the internal_ordering (#403) (@pogudingleb)
• Fix a typo in reparametrization.md (#405) (@sumiya11)
• Bump crate-ci/typos from 1.29.5 to 1.31.2 (#406) (@dependabot[bot])
• CompatHelper: bump compat for AbstractAlgebra to 0.45, (keep existing compat) (#408) (@github-actions[bot])
• CompatHelper: bump compat for Nemo to 0.50, (keep existing compat) (#410) (@github-actions[bot])
• Bump crate-ci/typos from 1.31.2 to 1.33.1 (#413) (@dependabot[bot])
• Update for MTK v10 (#414) (@ChrisRackauckas)
• Fix typo in README.md (#415) (@matbesancon)

Closed issues:

• Structural Identifiability is broken for systems with array parameters (#398)

v0.5.14

StructuralIdentifiability v0.5.14

Diff since v0.5.13

Merged pull requests:

• Forcing zero-dimensionality for rational function field computation: Part I, field membership (#394) (@pogudingleb)
• Bump Groebner 0.9 and use new functionality (#395) (@pogudingleb)
• Adding CI to benchmark performance (#396) (@pogudingleb)
• Separate QA tests from Core (#397) (@ChrisRackauckas)
• Make the performance workflow optional and manually runnable (#399) (@pogudingleb)
• Scalarizing MTK parameters (#400) (@pogudingleb)

v0.5.13

StructuralIdentifiability v0.5.13

Diff since v0.5.12

Merged pull requests:

• Bump crate-ci/typos from 1.28.4 to 1.29.4 (#378) (@dependabot[bot])
• ci(dependabot): open dependabot PRs only for major versions (#380) (@thazhemadam)
• Adding zero-dim check to quotient_basis (#382) (@pogudingleb)
• Bump crate-ci/typos from 1.29.4 to 1.29.5 (#383) (@dependabot[bot])
• Test the size of the generated systems (#384) (@sumiya11)
• Let each numerator have its own denominator (#385) (@sumiya11)
• Lincomp revision (#390) (@pogudingleb)

Closed issues:

• Assert zerodim in quotient_basis (#381)

v0.5.12

StructuralIdentifiability v0.5.12

Diff since v0.5.11

Merged pull requests:

• Updating the ordering used in MQS computation (#377) (@pogudingleb)
• doc: make font style coherent (#379) (@albinahlback)

Closed issues:

• Identifiability for complex models with algebra equations (#376)