AlgebraicPetri - v0.10.0

AlgebraicPetri v0.10.0

Diff since v0.9.2

Release notes:

Breaking changes

• Changes related to Catlab upgrade to 0.17. See Catlab migration notes.

Merged pull requests: - DOC: add package extension documentation (#165) (@mehalter) - Improvements to documentation (#169) (@slwu89) - Documentation refactor (#171) (@slwu89) - CompatHelper: bump compat for ModelingToolkit in [weakdeps] to 9, (keep existing compat) (#172) (@algebraicjuliabot) - Updates for Catlab 0.17 (#181) (@kris-brown)

Closed issues: - suggestions for documentation improvement (#168) - Use color to distinguish morphisms of Petri nets (#170) - Is there a function already to generate Petri.Model from LabelledPetriNet? (#177)

- Julia
Published by algebraicjuliabot 10 months ago

AlgebraicPetri - 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)

- Julia
Published by algebraicjuliabot over 2 years ago

AlgebraicPetri - 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)

- Julia
Published by algebraicjuliabot over 2 years ago

AlgebraicPetri - 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)

- Julia
Published by algebraicjuliabot about 3 years ago

AlgebraicPetri - 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)

- Julia
Published by github-actions[bot] about 3 years ago

AlgebraicPetri - 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)

- Julia
Published by github-actions[bot] about 3 years ago

AlgebraicPetri - 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)

- Julia
Published by github-actions[bot] about 3 years ago

AlgebraicPetri - 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)

- Julia
Published by github-actions[bot] about 3 years ago

AlgebraicPetri - 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)

- Julia
Published by github-actions[bot] about 3 years ago

AlgebraicPetri - v0.8.6

What's Changed

• Do not canonicalize + and - during ODESystem conversion by @YingboMa in https://github.com/AlgebraicJulia/AlgebraicPetri.jl/pull/115
• update version number by @mehalter in https://github.com/AlgebraicJulia/AlgebraicPetri.jl/pull/116

Full Changelog: https://github.com/AlgebraicJulia/AlgebraicPetri.jl/compare/v0.8.5...v0.8.6

- Julia
Published by mehalter over 3 years ago

AlgebraicPetri - v0.8.5

What's Changed

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

New Contributors

• @slwu89 made their first contribution in https://github.com/AlgebraicJulia/AlgebraicPetri.jl/pull/92
• @anandijain made their first contribution in https://github.com/AlgebraicJulia/AlgebraicPetri.jl/pull/113

Full Changelog: https://github.com/AlgebraicJulia/AlgebraicPetri.jl/compare/v0.8.4...v0.8.5

- Julia
Published by mehalter over 3 years ago

AlgebraicPetri - v0.8.4

AlgebraicPetri v0.8.4

Diff since v0.8.3

Merged pull requests: - Add utility to flatten labelled petri nets with tuples of symbols (#94) (@mehalter) - Stratification now works with LabelledReactionNets (#95) (@olynch) - Create Petri net with all pairwise 'identity' transformations (#96) (@epatters) - Construct ODEProblem from a ReactionNet (#97) (@olynch) - Pairwise identity transitions with rate parameters (#98) (@epatters)

- Julia
Published by github-actions[bot] over 3 years ago

AlgebraicPetri - v0.8.3

AlgebraicPetri v0.8.3

Diff since v0.8.2

Merged pull requests: - Typed Petri net support (#88) (@olynch) - Update version to v0.8.2 (#89) (@mehalter) - Add SubACSets.jl for mca (#91) (@ChrisRackauckas)

- Julia
Published by github-actions[bot] over 3 years ago

AlgebraicPetri - v0.8.2

What's Changed

• Finalize ModelingToolkit Interoperability by @mehalter in https://github.com/AlgebraicJulia/AlgebraicPetri.jl/pull/87
• Update version to v0.8.2 by @mehalter in https://github.com/AlgebraicJulia/AlgebraicPetri.jl/pull/89

Full Changelog: https://github.com/AlgebraicJulia/AlgebraicPetri.jl/compare/v0.8.1...v0.8.2

- Julia
Published by mehalter over 3 years ago

AlgebraicPetri - v0.8.1

AlgebraicPetri v0.8.1

Diff since v0.8.0

Merged pull requests: - Constructors of Petri net types are too loose (#85) (@epatters)

- Julia
Published by github-actions[bot] over 3 years ago

AlgebraicPetri - v0.8.0

AlgebraicPetri v0.8.0

Diff since v0.7.3

Merged pull requests: - Rename acset schemas with prefix Sch (#82) (@epatters) - Run GitHub CI on Julia v1.8 (#84) (@epatters)

- Julia
Published by epatters over 3 years ago

AlgebraicPetri - v0.7.3

AlgebraicPetri v0.7.3

Diff since v0.7.2

Merged pull requests: - Bug fix: vectorfield errors when there are no transitions in the Petri net (#83) (@olynch)

- Julia
Published by epatters over 3 years ago

AlgebraicPetri - v0.7.2

AlgebraicPetri v0.7.2

Diff since v0.7.1

Merged pull requests: - Update coexist.jl (#75) (@pitmonticone) - Support for Julia v1.7 and Catlab v0.14 (#76) (@mehalter)

- Julia
Published by epatters almost 4 years ago

AlgebraicPetri - Release v0.7.1

• Added support for Catlab v0.13 (structacsets update)
• Refactored Petri visualization for greater flexibility
• Added integration with Catlab's Subobject tooling for model comparison
• Dropped support for Julia 1.0

- Julia
Published by bosonbaas over 4 years ago

AlgebraicPetri - Release v0.7.0

• Added Requires.jl to reduce unnecessary dependencies
• Added Docstrings to core functionality
• Added BilayerNetwork tooling and conversion to and from Petri nets
• Added interop tooling with Catalyst.jl

- Julia
Published by mehalter about 5 years ago

AlgebraicPetri - Release v0.6.5

Removed dependency of Petri.jl using Requires.jl

- Julia
Published by mehalter about 5 years ago

AlgebraicPetri - Release v0.6.4

Add support for Julia v1.6 with the update to Catlab v0.12.0

- Julia
Published by mehalter about 5 years ago

AlgebraicPetri - Release v0.6.3

Updated compatibility and added CompatHelper for future dependency updates.

- Julia
Published by mehalter over 5 years ago

AlgebraicPetri - Release v0.6.2

Add Catlab v0.10 support

- Julia
Published by mehalter over 5 years ago

AlgebraicPetri - Release v0.6.1

Resolved bug with latest Catlab version because of ambiguous ACset constructors (#31)

- Julia
Published by mehalter over 5 years ago

AlgebraicPetri - Release v0.6.0

Add support for UWD and an operadic interface along with the directed wiring diagram layout.

- Julia
Published by mehalter over 5 years ago

AlgebraicPetri - Release v0.5.1

Added native visualization code operating on ACset/Cset data structures

- Julia
Published by mehalter over 5 years ago

AlgebraicPetri - Release v0.5.0

Moved to the new C-Set and generic structured cospan implementations in Catlab

- Julia
Published by mehalter over 5 years ago

AlgebraicPetri - Release v0.4.1

Removed forgotten print statement that was used when testing.

- Julia
Published by mehalter almost 6 years ago

AlgebraicPetri - Release v0.4.0

Implemented Petri nets as attributed C-Sets that allow a user to encode initial variables and parameters into the model along with the structure.

- Julia
Published by mehalter almost 6 years ago

AlgebraicPetri - Release v0.3.2

Update Catlab interface

- Julia
Published by mehalter almost 6 years ago

AlgebraicPetri - Release v0.3.1

Fixed bug in compat definitions

- Julia
Published by mehalter almost 6 years ago

AlgebraicPetri - Release v0.3.0

Updated to Petri v1.0, this will cause breaking changes because of major updates to the Petri.jl API.

- Julia
Published by mehalter almost 6 years ago

AlgebraicPetri - Release v0.2.0

Documentation and improved interface

- Julia
Published by mehalter almost 6 years ago

AlgebraicPetri - Release v0.1.0

Initial release of AlgebraicPetri.jl with basic functionality implemented and epidemiology example included.

- Julia
Published by mehalter almost 6 years ago