v0.4.0

MomentClosure v0.4.0

Diff since v0.3.1

Breaking changes

• Updated compatibility with Catalyst v15 and ModelingToolkit v9.

Minor changes

• Named initial condition maps can now be passed to the deterministic_IC function, making it functionally similar to Catalyst. This eliminates the need to manually define the initial state vector with the correct order as in speciesmap. In addition, constructing an ODEProblem is now more streamlined: the map of initial molecule numbers can be directly passed to ODEProblem, and deterministic_IC will automatically run under the hood to correctly map the initial values to the respective moments. This behaviour can be controlled with the optional parameter use_deterministic_IC (set to true by default).

Merged pull requests:

• Bump actions/cache from 3 to 4 (#57) (@dependabot[bot])
• Bump codecov/codecov-action from 3 to 4 (#58) (@dependabot[bot])
• Bump codecov/codecov-action from 4 to 5 (#67) (@dependabot[bot])
• Updating to Catalyst v15 (#68) (@kaandocal)
• Support initial state mapping and streamline ODEProblem (#70) (@augustinas1)

v0.3.1

MomentClosure v0.3.1

Diff since v0.3.0

Merged pull requests:

• Bump actions/checkout from 3 to 4 (#54) (@dependabot[bot])
• Allow SciMLBase v2 (#56) (@ChrisRackauckas)

Closed issues:

• Updating to new SymbolicUtils version (#53)

v0.3.0

MomentClosure v0.3.0

Diff since v0.2.0

Merged pull requests:

• Check Catalyst 13 (#48) (@ChrisRackauckas)

v0.2.0

MomentClosure v0.2.0

Diff since v0.1.0

Closed issues:

• Add package to Julia registry (#40)
• Update for rename of DiffEqJump (#47)

Merged pull requests:

• Overhaul bursty reaction implementation (#46) (@augustinas1)

v0.1.0

MomentClosure v0.1.0

Closed issues:

• Support SDESystem Input? (#1)
• Failing example model (#2)
• Can't precompile MomentClosure.jl (#5)
• Error while generating moment equations using catalyst (#10)
• Error while generating moment equations using catalyst (#11)
• Migrate to newer versions of SymbolicUtils (#26)

Merged pull requests:

• Fixed extraction of variables from eqs (#3) (@augustinas1)
• CompatHelper: bump compat for "SymbolicUtils" to "0.9" (#4) (@github-actions[bot])
• CompatHelper: bump compat for "SymbolicUtils" to "0.10" (#6) (@github-actions[bot])
• CompatHelper: bump compat for "Latexify" to "0.15" (#7) (@github-actions[bot])
• CompatHelper: bump compat for "Symbolics" to "1" (#13) (@github-actions[bot])
• CompatHelper: bump compat for "SymbolicUtils" to "0.12" (#14) (@github-actions[bot])
• added missing case(s) in propensity parsing step (#16) (@FHoltorf)
• Support for SDEs (#37) (@FHoltorf)
• Cleaned up symbolic.jl (#41) (@kaandocal)
• CompatHelper: bump compat for DocStringExtensions to 0.9, (keep existing compat) (#42) (@github-actions[bot])