v0.9.2

AlgebraicPetri v0.9.2

Diff since v0.9.1

Merged pull requests:

• Allow Catlab v0.16 in compat (#164) (@epatters)

Closed issues:

• Gatlab Migration (#161)

v0.9.1

AlgebraicPetri v0.9.1

Diff since v0.9.0

Merged pull requests:

• fix: uncomment tests now that Catlab v0.15.1 supports them again (#156) (@mehalter)
• docs: multi-strain disease example for doc pages (#157) (@p-stokes)
• Fix bad assumption in oapply_typed (#158) (@epatters)
• Fix various breaking changes in dependencies (#163) (@mehalter)

Closed issues:

• oapply_typed results in wrong wiring (#155)

v0.9.0

AlgebraicPetri v0.9.0

Diff since v0.8.11

Closed issues:

• Forgotten Exponential? (#33)
• Generated Vectorfield Function (#66)
• Type piracy in visualization functions (#73)
• ReactionNet documentation example (#78)
• naive questions on removing edges and states (#93)
• Should not use Graph for graphing (#100)
• Remove SubACSets from AlgebraicPetri (#118)
• Have mca find the morphisms and return the spans (#132)
• Generalize mca to work for more than two input ACSets (#133)
• Utilize PrecompileTools.jl for Caching (#138)
• Use cascading delete provided by Catlab (#141)
• AlgebraicPetri v0.9 (#148)

Merged pull requests:

• Migrate to Catlab v0.15 (#146) (@mehalter)
• refactor!: move to to_graphviz for visualization (#147) (@mehalter)
• docs: fix LabelledReactionNet docstring (#149) (@mehalter)
• Add OrdinaryDiffEq package extension (#150) (@mehalter)

v0.8.11

AlgebraicPetri v0.8.11

Diff since v0.8.10

Closed issues:

• prim_petri of TypedPetri.jl not labeling types of states correctly (#142)

Merged pull requests:

• refactor(docs): move examples to docs and clean up random environments (#134) (@mehalter)
• perf: use native package extensions in julia 1.9+ (#135) (@mehalter)
• Allow vectorfield_expr work with more types (#136) (@mehalter)
• Slwu89/vfield expr (#139) (@slwu89)
• Changed prim_petri to fix issue when type system has multiple states. (#143) (@p-stokes)

v0.8.10

AlgebraicPetri v0.8.10

Diff since v0.8.9

Closed issues:

• It appears MCA recursion can StackOverflow (#127)
• mca not searching in order of size (#128)
• one_removed_subobs does not remove arcs from Petri net (#129)

Merged pull requests:

• Fix MCA recursion overflowing (#131) (@p-stokes)

v0.8.9

AlgebraicPetri v0.8.9

Diff since v0.8.8

Closed issues:

• mca_help within mca in SubACSets.jl doesn't recurse. (#124)

Merged pull requests:

• Move to organization level github actions (#117) (@mehalter)
• add example of stratification of covid models (#123) (@mehalter)
• Fixes issue with mca_help not recursing. (#125) (@p-stokes)
• Minor spelling fixes (#126) (@JonathanHallstrom)

v0.8.8

AlgebraicPetri v0.8.8

Diff since v0.8.7

Closed issues:

• Adding reflexive transitions to an already stratified model doesn't work because the transition names are tuples (#114)

Merged pull requests:

• Flatten ACSetTransformations (#122) (@mehalter)

v0.8.7

AlgebraicPetri v0.8.7

Diff since v0.8.6

Merged pull requests:

• update version number (#116) (@mehalter)
• Property Petri Nets (#120) (@mehalter)
• Fix ASKEM integration workflow (#121) (@mehalter)

v0.8.6

What's Changed

• Do not canonicalize + and - during ODESystem conversion by @YingboMa in #115
• update version number by @mehalter in #116

Full Changelog: v0.8.5...v0.8.6

v0.8.5

What's Changed

• Simplify implementation of flatten_labels by @epatters in #99
• Petri nets open along transitions by @slwu89 in #92
• update for Catalyst v13.0.0 by @slwu89 in #106
• more efficient vectorfield by @slwu89 in #107
• Create .github/workflows/integration-issues.yml by @mehalter in #108
• allow defaults in LabrelledPetriNet(ODESystem) by @anandijain in #113
• CompatHelper: add new compat entry for GeneralizedGenerated at version 0.3, (keep existing compat) by @github-actions in #110
• implement simple tests for DPO rewriting by @slwu89 in #112

New Contributors

• @slwu89 made their first contribution in #92
• @anandijain made their first contribution in #113

Full Changelog: v0.8.4...v0.8.5