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Causal Loop with Polarities #128

Merged
merged 77 commits into from
Aug 19, 2024
Merged

Causal Loop with Polarities #128

merged 77 commits into from
Aug 19, 2024

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neonWhiteout
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I'm far from satisfied with it, but it's taken long enough, need to get the ball rolling.

@neonWhiteout
Added composition for causal loop. Temporarily swapped polarities to …
2922dca 
…symbols.
@neonWhiteout
Restored Polarities to be an enum instead of Symbol. Updated causal l…
ee19112 
…oop syntax to use -> +, -> -, -> ±, -> ~, -> !.
@neonWhiteout
Added a one-line Causal Loop DSL, similar to feet. Invoked via @cl
eb77d69
@neonWhiteout
Edits to Composition DSL to also work with CausalLoopF
cac81b2
@neonWhiteout
Fixed enames to provide the symbols for the nodes instead of the indi…
366d0fb 
…ces, allows causal loop composition to work.
@neonWhiteout
Added two simple tests for causal loop composition
dbe737c
@neonWhiteout
export create_foot and cl_macro from Syntax
63d72d7
@neonWhiteout
Updated causal loop tests to reflect new syntax
7292b32
@neonWhiteout
Updated another test's syntax to reflect new causal loop syntax
c194530
@neonWhiteout
Removed some commented out code
66b88ee
@neonWhiteout
Change Graph to GraphSF to not interfere with Catlab Graph.
52ab674
@neonWhiteout
Replace Graph with GraphSF in visualization tests
cb1d355
@neonWhiteout
Eliminate third nested for loop in extract loops with calls to incident
6fa1ee6
@neonWhiteout
Split cycle detection into its own function
432218b
@neonWhiteout
Define operations on polarities and rewrite extract_loops to use a foldl
f4d7d94
@neonWhiteout
Polarity operations. is_walk and is_circuit functions.
bde5b0d
@neonWhiteout
Began work to migrate over to newly defined causal loop schema
0e19b0c
@neonWhiteout
Merge branch 'GraphFix' into SemanticDomainsRough
8148ac2
@neonWhiteout
Merge branch 'CausalLoopCompose' into SemanticDomainsRough; Introduce…
7ab54c5 
… conversion between new causal loop schema and old; both can be useful.
@neonWhiteout
Add function to extract all paths with nonduplicated nodes
d6a6cc0
@neonWhiteout
Began testing on causal loop functions
455751b
@neonWhiteout
Begin work on composition for new causal loop schemas. Update project…
ba211fc 
….toml.
@neonWhiteout
Added stockflow migration to cl
f642d07
@neonWhiteout
Composition for CausalLoopPM
484c9b7
@neonWhiteout
Fix visualization with CL; replace balancing and reinforcing with pos…
68f1d29 
…itive and negative
@neonWhiteout
Removed dangling CausalLoopF()
abd1055
@neonWhiteout
Export betweenness
7332a55
@neonWhiteout
Added some tests for CausalLoop.jl
69017cd
@neonWhiteout
Update tests
cdb52ad
@neonWhiteout
Further cl tests
74bb6d3
@neonWhiteout
Allow creating cl without polarities using @cl macro. Add functions t…
c83b21c 
…o find shortest paths. Correctly calculate betweenness centrality.
@neonWhiteout
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Dang, I didn't think the changes would break existing tests...

@neonWhiteout
Began adding shortest path checks. Actually check the list of nodes b…
468b6f5 
…efore recursing, to prevent infinite loop.
@neonWhiteout
Add tests for all_shortest_paths
03ab046
@neonWhiteout
Add a few betweenness tests; remove export of shortest_path
91163a5
@neonWhiteout
Additional betweeness tests.
2760aa3
@neonWhiteout
Betweenness returns a vector of rationals, rather than a float, to pr…
f1bfc47 
…eserve precision.
@neonWhiteout
Fix error in converting CausalLoopPM to CausalLoop. Rewrite all_short…
397d084 
…est_paths.
@neonWhiteout
Remove show all_paths
a9438ee
@neonWhiteout
Fix typo in all_shortest_paths causing miscalculation of len(A -> B -…
379c5c9 
…> C) (Was adding node -> target + node -> tdest, rather than node -> target + target -> tdest)
@neonWhiteout
Redid all_shortest_paths, more brief
0824cd5
@neonWhiteout
Redo all_shortest_paths again, using adjacency matrix.
5498a07
@neonWhiteout
Added jupyter file and corresponding .jl for causal loop operations.
849035a
@neonWhiteout
Causal -> Casual in make.jl, to keep folder names consistent.
0d851c1
@neonWhiteout
Further shortest path tests
77de7c7
@neonWhiteout
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Yeah @Saityi @Xiaoyan-Li please have a look and confirm it looks good.

neonWhiteout and others added 4 commits August 13, 2024 12:07
@neonWhiteout
Update runtests.jl
1582ce7 
Remove the dang testing code at the top of the file.
@neonWhiteout
Update DSL.md. Remove homomorphism (hasn't merged), add causal_loop a…
cfe4749 
…nd cl, fix a few underscore errors.
@neonWhiteout
Merge branch 'SemanticDomainsNoZero' of github.com:neonWhiteout/Stock…
4dcde84 
…Flow.jl into SemanticDomainsNoZero
@neonWhiteout
"Add documentation for causal loop composition, modify composition to…
d679f4b 
… work with causal loop without polarities."
Saityi
Saityi approved these changes Aug 13, 2024
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@Saityi Saityi left a comment •
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Looks great! Nice work

I think we should consider a naming & cleaning pass through the entire library, giving consideration to what the initial version of the public consumption API could look like.

(Edit to add: In the future, not this pull request. 😅)

@neonWhiteout
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I think we should consider a naming & cleaning pass through the entire library, giving consideration to what the initial version of the public consumption API could look like.

I agree. Also need a passover to ensure it adheres to Catlab formatting standards.

@neonWhiteout
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Ah damn commit didn't seem to merge correctly.

@neonWhiteout neonWhiteout merged commit b4043b8 into AlgebraicJulia:main Aug 19, 2024
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@Saityi Saityi mentioned this pull request Aug 22, 2024
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@Xiaoyan-Li Xiaoyan-Li Xiaoyan-Li approved these changes

@Saityi Saityi Saityi approved these changes

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3 participants
@neonWhiteout @Saityi @Xiaoyan-Li