From 4aa36fc20dce9c0f447b837ec045ef6e8b02c697 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Thu, 20 Jun 2024 20:24:49 +0000 Subject: [PATCH] build based on 41df8de --- dev/.documenter-siteinfo.json | 2 +- dev/api/index.html | 8 ++++---- dev/equations/index.html | 2 +- dev/generated/literate_example/index.html | 2 +- dev/index.html | 2 +- dev/objects.inv | Bin 1806 -> 1806 bytes 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index c0b5eec..11dd6f6 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T20:15:01","documenter_version":"1.4.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-20T20:24:46","documenter_version":"1.4.1"}} \ No newline at end of file diff --git a/dev/api/index.html b/dev/api/index.html index e836726..94cd237 100644 --- a/dev/api/index.html +++ b/dev/api/index.html @@ -1,11 +1,11 @@ -Library Reference · DiagrammaticEquations.jl
GitHub

Library Reference

Catlab.WiringDiagrams.WiringDiagramAlgebras.oapply — Method
function oapply(relation::RelationDiagram, podes::Vector{D}) where {D<:OpenSummationDecapode}

Compose a list of Decapodes as specified by the given relation diagram.

The Decapodes must be given in the same order as they were specified in the relation.

State variables (such as the (C,V) given in the head of the following @relation) do not affect the result of a composition.

Examples

julia> compose_diff_adv = @relation (C,V) begin
+Library Reference · DiagrammaticEquations.jl
GitHub
Library Reference
Catlab.WiringDiagrams.WiringDiagramAlgebras.oapply — Method
function oapply(relation::RelationDiagram, podes::Vector{D}) where {D<:OpenSummationDecapode}
Compose a list of Decapodes as specified by the given relation diagram.
The Decapodes must be given in the same order as they were specified in the relation.
State variables (such as the (C,V) given in the head of the following @relation) do not affect the result of a composition.
Examples
julia> compose_diff_adv = @relation (C,V) begin
   diffusion(C, ϕ₁)
   advection(C, ϕ₂, V)
   superposition(ϕ₁, ϕ₂, ϕ, C)
 end;
 
 julia> oapply(compose_diff_adv, [(Diffusion, [:C, :ϕ]),
-  (Advection, [:C, :ϕ, :V]), (Superposition, [:ϕ₁, :ϕ₂, :ϕ, :C])]);
source
DiagrammaticEquations.Open — Method
Open(d::SummationDecapode{T,U,V}, names::AbstractVector{Symbol}) where {T,U,V}
creates an OpenSummationDecapode based on named variables rather than variable indices.  See AlgebraicPetri.jl's Open for the analogous verion for LabelledReactionNetworks.
source
DiagrammaticEquations.collate — Method
function collate(equations, boundaries, uwd, symbols)
Create a collage of two Decapodes that simulates with boundary conditions. ```
source
DiagrammaticEquations.contract_operators — Method
function contract_operators(d::SummationDecapode; allowable_ops::Set{Symbol} = Set{Symbol}())
Find chains of Op1s in the given Decapode, and replace them with a single Op1 with a vector of function names. After this process, all Vars that are not a part of any computation are removed.
source
DiagrammaticEquations.dot_rename! — Method
dot_rename!(d::AbstractNamedDecapode)
Rename tangent variables by their depending variable appended with a dot. e.g. If D == ∂ₜ(C), then rename D to Ċ.
If a tangent variable updates multiple vars, choose one arbitrarily. e.g. If D == ∂ₜ(C) and D == ∂ₜ(B), then rename D to either Ċ or B ̇.
source
DiagrammaticEquations.fill_names! — Method
function fill_names!(d::AbstractNamedDecapode; lead_symbol::Symbol = Symbol("•"))
Provide a variable name to all the variables that don't have names.
source
DiagrammaticEquations.find_chains — Method
function findchains(d::SummationDecapode; allowableops::Set{Symbol} = Set{Symbol}())
Find chains of Op1s in the given Decapode. A chain ends when the target of the last Op1 is part of an Op2 or sum, or is a target of multiple Op1s. Only operators with names included in the allowable_ops set are allowed to be contracted. If the set is empty then all operators are allowed.
source
DiagrammaticEquations.find_dep_and_order — Method
find_dep_and_order(d::AbstractNamedDecapode)
Find the order of each tangent variable in the Decapode, and the index of the variable that it is dependent on. Returns a tuple of (dep, order), both of which respecting the order in which incident(d, :∂ₜ, :op1) returns Vars.
source
DiagrammaticEquations.get_valid_op1s — Method
function get_valid_op1s(deca_source::SummationDecapode, varID)
Searches SummationDecapode, deca_source, at the request varID and returns all op1s which are allowed to be averaged. Returns an array of indices of valid op1 sources.
Namely this is meant to exclude ∂ₜ from being included in an average.
source
DiagrammaticEquations.infer_types! — Method
function infer_types!(d::SummationDecapode, op1_rules::Vector{NamedTuple{(:src_type, :tgt_type, :replacement_type, :op), NTuple{4, Symbol}}})
Infer types of Vars given rules wherein one type is known and the other not.
source
DiagrammaticEquations.resolve_overloads! — Method
function resolve_overloads!(d::SummationDecapode, op1_rules::Vector{NamedTuple{(:src_type, :tgt_type, :resolved_name, :op), NTuple{4, Symbol}}})
Resolve function overloads based on types of src and tgt.
source
DiagrammaticEquations.safe_modifytype! — Method
safe_modifytype!(d::SummationDecapode, var_idx::Int, org_type::Symbol, new_type::Symbol)
This function calls safe_modifytype to safely modify a Decapode's variable type.
source
DiagrammaticEquations.safe_modifytype — Method
safe_modifytype(org_type::Symbol, new_type::Symbol)
This function accepts an original type and a new type and determines if the original type   can be safely overwritten by the new type.
source
DiagrammaticEquations.type_check_Decapodes_composition — Method
function type_check_Decapodes_composition(relation::RelationDiagram, decs::Vector{OpenSummationDecapode})
Check that the types of all Vars connected by the same junction match.
This function only throws an error on the first type mismatch found.
source
DiagrammaticEquations.unique_by! — Method
function unique_by!(acset, column_names::Vector{Symbol})
Given column names from the same table, remove duplicate rows.
WARNING: This function does not check if other tables index into the one given. Removal of rows is performed with prejudice.
See also: unique_by.
Examples
julia> unique_by!(parallel_arrows(Graph, 123), :E, [:src,:tgt]) == parallel_arrows(Graph, 1)
-true
source
DiagrammaticEquations.unique_by — Method
function unique_by(acset, column_names::Vector{Symbol})
Given column names from the same table, return a copy of the acset with duplicate rows removed. Removal of rows is performed with prejudice.
WARNING: This function does not check if other tables index into the one given. Removal of rows is performed with prejudice.
See also: unique_by!.
Examples
julia> unique_by(parallel_arrows(Graph, 123), :E, [:src,:tgt]) == parallel_arrows(Graph, 1)
-true
source
Catlab.Graphics.GraphvizGraphs.to_graphviz — Method
Graphics.to_graphviz(F::AbstractDecapode; directed = true, kw...)
Visualize the given Decapode through Graphviz. Ensure that you have called using Catlab.Graphics before-hand, and have a way of visualizing SVG files in your current environment.
source

+  (Advection, [:C, :ϕ, :V]), (Superposition, [:ϕ₁, :ϕ₂, :ϕ, :C])]);
source
DiagrammaticEquations.Open — Method
Open(d::SummationDecapode{T,U,V}, names::AbstractVector{Symbol}) where {T,U,V}

creates an OpenSummationDecapode based on named variables rather than variable indices. See AlgebraicPetri.jl's Open for the analogous verion for LabelledReactionNetworks.

source
DiagrammaticEquations.collate — Method
function collate(equations, boundaries, uwd, symbols)

Create a collage of two Decapodes that simulates with boundary conditions. ```

source
DiagrammaticEquations.contract_operators — Method
function contract_operators(d::SummationDecapode; allowable_ops::Set{Symbol} = Set{Symbol}())

Find chains of Op1s in the given Decapode, and replace them with a single Op1 with a vector of function names. After this process, all Vars that are not a part of any computation are removed.

source
DiagrammaticEquations.dot_rename! — Method
dot_rename!(d::AbstractNamedDecapode)

Rename tangent variables by their depending variable appended with a dot. e.g. If D == ∂ₜ(C), then rename D to Ċ.

If a tangent variable updates multiple vars, choose one arbitrarily. e.g. If D == ∂ₜ(C) and D == ∂ₜ(B), then rename D to either Ċ or B ̇.

source
DiagrammaticEquations.fill_names! — Method
function fill_names!(d::AbstractNamedDecapode; lead_symbol::Symbol = Symbol("•"))

Provide a variable name to all the variables that don't have names.

source
DiagrammaticEquations.find_chains — Method

function findchains(d::SummationDecapode; allowableops::Set{Symbol} = Set{Symbol}())

Find chains of Op1s in the given Decapode. A chain ends when the target of the last Op1 is part of an Op2 or sum, or is a target of multiple Op1s. Only operators with names included in the allowable_ops set are allowed to be contracted. If the set is empty then all operators are allowed.

source
DiagrammaticEquations.find_dep_and_order — Method
find_dep_and_order(d::AbstractNamedDecapode)

Find the order of each tangent variable in the Decapode, and the index of the variable that it is dependent on. Returns a tuple of (dep, order), both of which respecting the order in which incident(d, :∂ₜ, :op1) returns Vars.

source
DiagrammaticEquations.get_valid_op1s — Method
function get_valid_op1s(deca_source::SummationDecapode, varID)

Searches SummationDecapode, deca_source, at the request varID and returns all op1s which are allowed to be averaged. Returns an array of indices of valid op1 sources.

Namely this is meant to exclude ∂ₜ from being included in an average.

source
DiagrammaticEquations.infer_types! — Method
function infer_types!(d::SummationDecapode, op1_rules::Vector{NamedTuple{(:src_type, :tgt_type, :replacement_type, :op), NTuple{4, Symbol}}})

Infer types of Vars given rules wherein one type is known and the other not.

source
DiagrammaticEquations.resolve_overloads! — Method
function resolve_overloads!(d::SummationDecapode, op1_rules::Vector{NamedTuple{(:src_type, :tgt_type, :resolved_name, :op), NTuple{4, Symbol}}})

Resolve function overloads based on types of src and tgt.

source
DiagrammaticEquations.safe_modifytype! — Method
safe_modifytype!(d::SummationDecapode, var_idx::Int, org_type::Symbol, new_type::Symbol)

This function calls safe_modifytype to safely modify a Decapode's variable type.

source
DiagrammaticEquations.safe_modifytype — Method
safe_modifytype(org_type::Symbol, new_type::Symbol)

This function accepts an original type and a new type and determines if the original type can be safely overwritten by the new type.

source
DiagrammaticEquations.type_check_Decapodes_composition — Method
function type_check_Decapodes_composition(relation::RelationDiagram, decs::Vector{OpenSummationDecapode})

Check that the types of all Vars connected by the same junction match.

This function only throws an error on the first type mismatch found.

source
DiagrammaticEquations.unique_by! — Method
function unique_by!(acset, column_names::Vector{Symbol})

Given column names from the same table, remove duplicate rows.

WARNING: This function does not check if other tables index into the one given. Removal of rows is performed with prejudice.

See also: unique_by.

Examples

julia> unique_by!(parallel_arrows(Graph, 123), :E, [:src,:tgt]) == parallel_arrows(Graph, 1)
+true
source
DiagrammaticEquations.unique_by — Method
function unique_by(acset, column_names::Vector{Symbol})

Given column names from the same table, return a copy of the acset with duplicate rows removed. Removal of rows is performed with prejudice.

WARNING: This function does not check if other tables index into the one given. Removal of rows is performed with prejudice.

See also: unique_by!.

Examples

julia> unique_by(parallel_arrows(Graph, 123), :E, [:src,:tgt]) == parallel_arrows(Graph, 1)
+true
source
Catlab.Graphics.GraphvizGraphs.to_graphviz — Method
Graphics.to_graphviz(F::AbstractDecapode; directed = true, kw...)

Visualize the given Decapode through Graphviz. Ensure that you have called using Catlab.Graphics before-hand, and have a way of visualizing SVG files in your current environment.

source
diff --git a/dev/equations/index.html b/dev/equations/index.html index ab4bd25..f25c1a2 100644 --- a/dev/equations/index.html +++ b/dev/equations/index.html @@ -991,4 +991,4 @@ -'/>

Often you will have a linear material where you are scaling by a constant, and a nonlinear version of that material where that scaling is replaced by a generic nonlinear function. This is why we allow Decapodes to represent both of these types of equations.

+'/>

Often you will have a linear material where you are scaling by a constant, and a nonlinear version of that material where that scaling is replaced by a generic nonlinear function. This is why we allow Decapodes to represent both of these types of equations.

diff --git a/dev/generated/literate_example/index.html b/dev/generated/literate_example/index.html index 19a088f..79c8b39 100644 --- a/dev/generated/literate_example/index.html +++ b/dev/generated/literate_example/index.html @@ -1,2 +1,2 @@ -Code Example · DiagrammaticEquations.jl
GitHub
+Code Example · DiagrammaticEquations.jl
GitHub
diff --git a/dev/index.html b/dev/index.html index 1699c7c..522e1dc 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -DiagrammaticEquations.jl · DiagrammaticEquations.jl
GitHub

DiagrammaticEquations.jl

DiagrammaticEquations.jl is a Julia library implementing category-theoretic reasoning about systems of equations with diagrams. This package was extractedd from Decapodes.jl to decouple the representation of systems of equations from the solution of those equations. DiagrammaticEquations will grow to support many flavors of equations, starting with the discrete exterior calculus equations from Decapodes.

+DiagrammaticEquations.jl · DiagrammaticEquations.jl
GitHub

DiagrammaticEquations.jl

DiagrammaticEquations.jl is a Julia library implementing category-theoretic reasoning about systems of equations with diagrams. This package was extractedd from Decapodes.jl to decouple the representation of systems of equations from the solution of those equations. DiagrammaticEquations will grow to support many flavors of equations, starting with the discrete exterior calculus equations from Decapodes.

diff --git a/dev/objects.inv b/dev/objects.inv index 23367b2688788f7b966db6344b6c09d5af99202f..91b71a86ec85a0e96000082c5e1e84cb71b305eb 100644 GIT binary patch delta 12 TcmeC<>*Jdcz-YEHa4#DG8dC%n delta 12 TcmeC<>*Jdcz-YQLa4#DG8cqZh