Merge pull request #847 from AlgebraicJulia/the-glorious-future

GATlab integration
AlgebraicJulia · Oct 17, 2023 · f02b1ee · f02b1ee
2 parents 1874704 + 3b9e304
commit f02b1ee
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diff --git a/.github/workflows/experiments.yml b/.github/workflows/experiments.yml
@@ -9,7 +9,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        experiment: [CompAlgebra, Markov, TensorNetworks]
+        experiment: [Markov, TensorNetworks]
 
     steps:
       - uses: actions/checkout@v3

diff --git a/Project.toml b/Project.toml
@@ -6,10 +6,12 @@ version = "0.15.5"
 
 [deps]
 ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8"
+AlgebraicInterfaces = "23cfdc9f-0504-424a-be1f-4892b28e2f0c"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 CompTime = "0fb5dd42-039a-4ca4-a1d7-89a96eae6d39"
 Compose = "a81c6b42-2e10-5240-aca2-a61377ecd94b"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+GATlab = "f0ffcf3b-d13a-433e-917c-cc44ccf5ead2"
 GeneralizedGenerated = "6b9d7cbe-bcb9-11e9-073f-15a7a543e2eb"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179"

diff --git a/benchmark/Graphs.jl b/benchmark/Graphs.jl
@@ -7,7 +7,7 @@ import Graphs as SimpleGraphs
 import MetaGraphs
 const LG, MG = SimpleGraphs, MetaGraphs
 
-using Catlab.GATs, Catlab.CategoricalAlgebra, Catlab.Graphs
+using GATlab, Catlab.CategoricalAlgebra, Catlab.Graphs
 using Catlab.WiringDiagrams: query
 using Catlab.Programs: @relation
 

diff --git a/benchmark/Project.toml b/benchmark/Project.toml
@@ -2,6 +2,7 @@
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+GATlab = "f0ffcf3b-d13a-433e-917c-cc44ccf5ead2"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -5,7 +5,9 @@ Compose = "a81c6b42-2e10-5240-aca2-a61377ecd94b"
 Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+GATlab = "f0ffcf3b-d13a-433e-917c-cc44ccf5ead2"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+JSONSchema = "7d188eb4-7ad8-530c-ae41-71a32a6d4692"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"

diff --git a/docs/literate/graphs/graphs.jl b/docs/literate/graphs/graphs.jl
@@ -1,4 +1,4 @@
-using Catlab.GATs, Catlab.Theories
+using GATlab, Catlab.Theories
 using Catlab.CategoricalAlgebra
 using Catlab.Graphs
 using Catlab.Graphics

diff --git a/docs/literate/graphs/graphs_label.jl b/docs/literate/graphs/graphs_label.jl
@@ -1,7 +1,7 @@
 # # Labeled Graphs
 # This example demonstrates how to define new C-Sets from existing C-Sets via the example of adding labels to a graph. We treat labels as members of an arbitrary FinSet of labels rather than a data attribute for pedagogical reasons. When you think of graphs where the labels are numbers, colors, or values of some kind, you would want to make them attributes. The motivation for this example is to be the simplest extension to the theory of graphs that you could possibly make. 
 
-using Catlab.GATs, Catlab.Theories
+using GATlab, Catlab.Theories
 using Catlab.CategoricalAlgebra
 using Catlab.Graphs
 using Catlab.Graphics

diff --git a/docs/literate/sketches/cat_elements.jl b/docs/literate/sketches/cat_elements.jl
@@ -1,6 +1,6 @@
 # # The Category of Elements
 # A very useful construction in applied category theory is the Category of Elements, which is also called the Grothendieck construction. This is a very general technique in category theory, but we will look at how you can use it to explain why graphs are so useful in computer science. We have already seen that C-Sets are a model of relational databases that can be used to store data as a collection of interlocking tables. Relational databases are the bread and butter of the computing industry. Every company on earth uses software that is backed by a relational database. Most data that is not stored in a relational DB is often stored in some kind of graph data structure. This sketch will show how these approaches are interchangeable via the category of elements, which associates to every database instance a graph and a graph homomorphism into the schema of the graph.
-using Catlab.GATs, Catlab.CategoricalAlgebra, Catlab.Graphs, Catlab.Graphics
+using GATlab, Catlab.CategoricalAlgebra, Catlab.Graphs, Catlab.Graphics
 using Colors
 
 # Let's tell Catlab how to draw categories of elements.

diff --git a/docs/literate/sketches/meets.jl b/docs/literate/sketches/meets.jl
@@ -9,7 +9,7 @@
 using Core: GeneratedFunctionStub
 using Test
 
-using Catlab.GATs, Catlab.Theories, Catlab.CategoricalAlgebra
+using GATlab, Catlab.Theories, Catlab.CategoricalAlgebra
 using Catlab.Graphics
 
 import Catlab.Theories: compose

diff --git a/docs/literate/sketches/partitions.jl b/docs/literate/sketches/partitions.jl
@@ -10,7 +10,7 @@
 using Core: GeneratedFunctionStub
 using Test
 
-using Catlab.GATs, Catlab.Theories, Catlab.CategoricalAlgebra
+using GATlab, Catlab.Theories, Catlab.CategoricalAlgebra
 import Catlab.Theories: compose
 using DataStructures
 using PrettyTables

diff --git a/docs/literate/sketches/preorders.jl b/docs/literate/sketches/preorders.jl
@@ -12,7 +12,7 @@
 using Core: GeneratedFunctionStub
 using Test
 
-using Catlab.GATs, Catlab.Theories, Catlab.CategoricalAlgebra
+using GATlab, Catlab.Theories, Catlab.CategoricalAlgebra
 import Catlab.Theories: compose
 
 #=
@@ -114,7 +114,7 @@ end
 # expressions are represented at expression trees
 ex = compose(P, [:f, :g])
 # the head of an expression is the root of the expression tree
-GATs.head(ex)
+head(ex)
 # the julia type of the expression
 typeof(ex)
 # the GAT type of the expression

diff --git a/docs/literate/sketches/smc.jl b/docs/literate/sketches/smc.jl
@@ -3,7 +3,7 @@
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/generated/sketches/smc.ipynb)
 #
 # This vignette supports section 4.4.3 of Seven Sketches in Compositionality, which introduces the definition of symmetric monoidal categories (SMCs). SMCs are a core concept in applied category theory and are a workhorse of Catlab's utility in computing applications. We will discuss the definition as a GAT, see examples of working with formulas, and conversions to wiring diagrams (sometimes called string diagrams). SMCs are useful for modeling mathematical structures like programs or processes where the objects represent data or things and the morphisms represent processes that happen to those things. 
-using Catlab.GATs, Catlab.Theories
+using GATlab, Catlab.Theories
 using Catlab.CategoricalAlgebra
 using Catlab.WiringDiagrams
 using Catlab.Programs

diff --git a/docs/literate/wiring_diagrams/wd_cset.jl b/docs/literate/wiring_diagrams/wd_cset.jl
@@ -1,6 +1,6 @@
 # # Wiring Diagrams as Attributed C-Sets
 # Catlab supports many different flavors of diagrammatic syntax. These support the different combinatorial data structures that we use for representing categorical constructions. We will discuss DirectedWiringDiagrams, UndirectedWiringDiagrams, and CPortGraphs in this document.
-using Catlab.GATs, Catlab.Theories
+using GATlab, Catlab.Theories
 using Catlab.CategoricalAlgebra
 using Catlab.WiringDiagrams
 using Catlab.Programs

diff --git a/docs/literate/wiring_diagrams/wiring_diagram_basics.jl b/docs/literate/wiring_diagrams/wiring_diagram_basics.jl
@@ -2,7 +2,7 @@
 #
 #md # [![](https://img.shields.io/badge/show-nbviewer-579ACA.svg)](@__NBVIEWER_ROOT_URL__/generated/wiring_diagrams/wiring_diagram_basics.ipynb)
 # 
-# using Catlab.GATs, you can create, manipulate, serialize, and visualize *wiring
+# using GATlab, you can create, manipulate, serialize, and visualize *wiring
 # diagrams*, also known as [string
 # diagrams](https://ncatlab.org/nlab/show/string+diagram). The flexible data
 # structure for wiring diagrams allows arbitrary data to be attached to boxes,

diff --git a/docs/make.jl b/docs/make.jl
@@ -76,7 +76,6 @@ makedocs(
       ],
     ],
     "Modules" => Any[
-      "apis/gats.md",
       "apis/theories.md",
       "apis/categorical_algebra.md",
       "apis/graphs.md",

diff --git a/docs/src/apis/categorical_algebra.md b/docs/src/apis/categorical_algebra.md
@@ -63,7 +63,7 @@ We can also add equations to this presentation, but we currently do nothing with
 We will now give an example of how this all works in practice.
 
 ```@example
-using Catlab.GATs, Catlab.CategoricalAlgebra
+using GATlab, Catlab.CategoricalAlgebra
 
 # Write down the schema for a weighted graph
 @present SchWeightedGraph(FreeSchema) begin