Merge pull request #86 from neonWhiteout/foot_error_messages

Foot error messages

.appveyor.yml

@@ -13,7 +13,7 @@ matrix:
     - julia_version: nightly
 branches:
   only:
-    - master
+    - main
     - /release-.*/
 notifications:
   - provider: Email

.github/workflows/TagBot.yml

@@ -4,12 +4,27 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          token: ${{ secrets.SERVICE_TOKEN }}

.github/workflows/julia_ci.yml

@@ -4,7 +4,7 @@ on:
   schedule:
     - cron: 0 0 * * *
   push:
-    branches: ["master"]
+    branches: ["main"]
     tags: ["*"]
   pull_request:
   workflow_dispatch:

README.md

@@ -1,81 +1,79 @@
 # AlgebraicStockFlow
 
 [![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://algebraicjulia.github.io/StockFlow.jl/dev/)
-[![Tests](https://github.com/AlgebraicJulia/StockFlow.jl/actions/workflows/tests.yml/badge.svg)](https://github.com/AlgebraicJulia/StockFlow.jl/actions/workflows/tests.yml)
-<!-- TODO: Set up on codecov.io for repo [![codecov](https://codecov.io/github/AlgebraicJulia/StockFlow.jl/branch/maaster/graph/badge.svg)](https://app.codecov.io/github/AlgebraicJulia/StockFlow.jl) -->
+[![CI/CD](https://github.com/AlgebraicJulia/StockFlow.jl/actions/workflows/julia_ci.yml/badge.svg)](https://github.com/AlgebraicJulia/StockFlow.jl/actions/workflows/julia_ci.yml)
+[![Code Coverage](https://codecov.io/gh/AlgebraicJulia/StockFlow.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/AlgebraicJulia/StockFlow.jl)
 
 StockFlow.jl is a Julia library for the creation and execution of [stock and flow modeling diagrams](https://en.wikipedia.org/wiki/System_dynamics#Stock_and_flow_diagrams), designed with model composition and stratification in mind through a [categorical approach](https://arxiv.org/abs/2211.01290).
 
-Stock-flow diagrams are used to represent systems where its population can move between different states, such as tracking how many people have been infected or recovered from a disease.  By providing initial values, and values for the parameters, we can solve the differential equation which the stock-flow diagram represents, which gives us a graph for how the population varies over time.
+Stock-flow diagrams are used to represent systems where its population can move between different states, such as tracking how many people have been infected or recovered from a disease. By providing initial values, and values for the parameters, we can solve the differential equation which the stock-flow diagram represents, which gives us a graph for how the population varies over time.
 
 In this particular schema, stock-flow diagrams consist of stocks, flows, dynamic variables, sum variables, parameters, and the links between them.
 
-* Stocks represent accumulations of a population in a particular state, such as 'susceptible', 'infected', 'recovered', etc.
-* Flows represent transitions between states.  A flow can go from a stock to a stock, from nothing to a stock, or from a stock to nothing, the latter two representing a population entering or leaving a model.  Flows are dependent on a dynamic variable, which determines its rate.
-* Dynamic variables are the equations which determine flow rates.  For instance, if the rate at which people move from uninfected to infected is the uninfected stock S times the parameter c, we can say v\_infectionRate = c * S, and use this as a flow variable.  Dynamic variables can contain stocks, sum variables, parameters and other dynamic variables (but the definition can't be circular; you can't set a dynamic variable equal to itself, for instance).  Currently supports common binary and unary operations such as addition, multiplication, log, exp.
-* Sum variables represent the sum of a subpopulation.  The value of a sum variable is the sum of all the stocks which link to it.  Common examples include the sum of the entire population N, the sum of infected individuals NI, or the sum of a particular subpopulation NS.
-* Parameters are variables for which the particular values are defined outside the model definition.  You can provide parameters and initial values, then solve the differential equation.
+- Stocks represent accumulations of a population in a particular state, such as 'susceptible', 'infected', 'recovered', etc.
+- Flows represent transitions between states. A flow can go from a stock to a stock, from nothing to a stock, or from a stock to nothing, the latter two representing a population entering or leaving a model. Flows are dependent on a dynamic variable, which determines its rate.
+- Dynamic variables are the equations which determine flow rates. For instance, if the rate at which people move from uninfected to infected is the uninfected stock S times the parameter c, we can say v_infectionRate = c \* S, and use this as a flow variable. Dynamic variables can contain stocks, sum variables, parameters and other dynamic variables (but the definition can't be circular; you can't set a dynamic variable equal to itself, for instance). Currently supports common binary and unary operations such as addition, multiplication, log, exp.
+- Sum variables represent the sum of a subpopulation. The value of a sum variable is the sum of all the stocks which link to it. Common examples include the sum of the entire population N, the sum of infected individuals NI, or the sum of a particular subpopulation NS.
+- Parameters are variables for which the particular values are defined outside the model definition. You can provide parameters and initial values, then solve the differential equation.
 
 Stock-flow diagrams can be created and manipulated using the `StockFlow` and `StockFlow.Syntax` modules, the latter of which includes the domain specific language for easier creation.
 
-Stock-flow diagrams can be composed and stratified - that is, combined on stocks and sum variables or split into subpopulations.  One can also do algebraic rewriting for more manual, specific fixes, such as preventing a dynamic variable from unnecessarily being computed twice, or substituting one parameter for another.
-
-Examples of the domain specific language, composition, stratification and algebraic rewriting can be seen in the [examples](examples) folder.  In particular, full\_fledged\_schema\_examples\_new contains examples which use the domain specific language.
-
-
-
- ## Example interpretation of a stock and flow diagram using an ODE solver
-
- From the [SEIR Composition Example](examples/full_fledged_schema_examples_new/composition/SEIR_full_model_measles_chickenpox.ipynb):
-
- ```julia
- seir = @stock_and_flow begin
-     :stocks
-     S
-     E
-     I
-     R
-
-     :parameters
-     μ
-     β
-     tlatent
-     trecovery
-     δ
-
-     :flows
-     ☁ => fbirth(μ * N) => S # dynamic variables can be defined implicitly or with :dynamic_variables
-     S => fincid(β * S * I / N) => E
-     S => fdeathS(S * δ) => ☁
-     E => finf(E / tlatent) => I
-     E => fdeathE(E * δ) => ☁
-     I => frec(I / trecovery) => R
-     I => fdeathI(I * δ) => ☁
-     R => fdeathR(R * δ) => ☁
-
-     :sums
-     N = [S, E, I, R]
-
- end
-
- # define parameter values and initial values of stocks
- # define constant parameters
- p_measles = LVector(
-     β=49.598, μ=0.03/12, δ=0.03/12, tlatent=8.0/30, trecovery=5.0/30
- )
-
- # define initial values for stocks
- u0_measles = LVector(
-     S=90000.0-930.0, E=0.0, I=930.0, R=773545.0
- )
-
- prob_measles = ODEProblem(vectorfield(seir),u0_measles,(0.0,120.0),p_measles);
- sol_measles = solve(prob_measles,Tsit5(),abstol=1e-8);
- plot(sol_measles)
- ```
-
- See the full example for additional comments and the chickenpox model.
- ## Note
-
- This library is under active development and does not yet have an official release.
-
+Stock-flow diagrams can be composed and stratified - that is, combined on stocks and sum variables or split into subpopulations. One can also do algebraic rewriting for more manual, specific fixes, such as preventing a dynamic variable from unnecessarily being computed twice, or substituting one parameter for another.
+
+Examples of the domain specific language, composition, stratification and algebraic rewriting can be seen in the [examples](examples) folder. In particular, full_fledged_schema_examples_new contains examples which use the domain specific language.
+
+## Example interpretation of a stock and flow diagram using an ODE solver
+
+From the [SEIR Composition Example](examples/full_fledged_schema_examples_new/composition/SEIR_full_model_measles_chickenpox.ipynb):
+
+```julia
+seir = @stock_and_flow begin
+    :stocks
+    S
+    E
+    I
+    R
+
+    :parameters
+    μ
+    β
+    tlatent
+    trecovery
+    δ
+
+    :flows
+    ☁ => fbirth(μ * N) => S # dynamic variables can be defined implicitly or with :dynamic_variables
+    S => fincid(β * S * I / N) => E
+    S => fdeathS(S * δ) => ☁
+    E => finf(E / tlatent) => I
+    E => fdeathE(E * δ) => ☁
+    I => frec(I / trecovery) => R
+    I => fdeathI(I * δ) => ☁
+    R => fdeathR(R * δ) => ☁
+
+    :sums
+    N = [S, E, I, R]
+
+end
+
+# define parameter values and initial values of stocks
+# define constant parameters
+p_measles = LVector(
+    β=49.598, μ=0.03/12, δ=0.03/12, tlatent=8.0/30, trecovery=5.0/30
+)
+
+# define initial values for stocks
+u0_measles = LVector(
+    S=90000.0-930.0, E=0.0, I=930.0, R=773545.0
+)
+
+prob_measles = ODEProblem(vectorfield(seir),u0_measles,(0.0,120.0),p_measles);
+sol_measles = solve(prob_measles,Tsit5(),abstol=1e-8);
+plot(sol_measles)
+```
+
+See the full example for additional comments and the chickenpox model.
+
+## Note
+
+This library is under active development and does not yet have an official release.

src/Syntax.jl

@@ -951,8 +951,10 @@ Create a foot with S => N syntax, where S is stock, N is sum variable.
 ```
 """
 macro foot(block::Expr)
-    Base.remove_linenums!(block)
-    return create_foot(block)
+    escaped_block = Expr(:quote, block)
+    quote 
+        create_foot($(escaped_block))
+    end
 end
 
 
@@ -976,14 +978,23 @@ end
 """
 macro feet(block::Expr)
     Base.remove_linenums!(block)
-    @match block begin
-        quote
-          $((block...))
-        end => map(create_foot, block) # also matches empty
-        Expr(e, _...) => [create_foot(block)] # this also matches the above, so it's necessary this comes second.
+    escaped_block = Expr(:quote, block)
+    quote
+        inner_block = $escaped_block
+        @match inner_block begin
+            quote
+              $((inner_block...))
+            end => map(create_foot, inner_block) # also matches empty
+            Expr(e, _...) => [create_foot(inner_block)] # this also matches the above, so it's necessary this comes second.
+        end
     end
 end
 
+macro feet()
+    quote
+        Vector{StockAndFlow0}()
+    end
+end
 
 """
     create_foot(block :: Expr)
@@ -1004,10 +1015,9 @@ multiple_links = @foot A => B, A => B # will have two links from A to B.
 """
 function create_foot(block::Expr)
     @match block.head begin
-
         :tuple => begin
             if isempty(block.args) # case for create_foot(:())
-                error("Cannot create foot with no arguments.")
+                error("Cannot create foot with zero arguments.")
             end
             foot_s = Vector{Symbol}()
             foot_sv = Vector{Symbol}()

test/Syntax.jl

@@ -2,7 +2,7 @@ using Base: is_unary_and_binary_operator
 using Test
 using StockFlow
 using StockFlow.Syntax
-using StockFlow.Syntax: is_binop_or_unary, sum_variables, infix_expression_to_binops, fnone_value_or_vector, extract_function_name_and_args_expr, is_recursive_dyvar, create_foot, apply_flags, substitute_symbols
+using StockFlow.Syntax: is_binop_or_unary, sum_variables, infix_expression_to_binops, fnone_value_or_vector, extract_function_name_and_args_expr, is_recursive_dyvar, create_foot, apply_flags, substitute_symbols, DSLArgument
 
 @testset "Stratification DSL" begin
     include("syntax/Stratification.jl")
@@ -296,16 +296,14 @@ end
 end
 
 @testset "foot syntax disallows invalid feet" begin # note, @feet calls create_foot for each line, so this should apply to both @foot and @feet
-    @test_throws Exception create_foot(:(A => B => C)) # Invalid syntax for second argument of foot: B => C
-    @test_throws Exception create_foot(:(oooo2 + f => C)) # Invalid syntax for first argument of foot: oooo2 + f
-    @test_throws Exception create_foot(:(A + B)) # Invalid syntax function for foot: +
-    @test_throws Exception create_foot(:(=>)) # no method matching create_foot(::Symbol)
-    @test_throws Exception create_foot(:(=>(A, B, C, D)))
-    @test_throws Exception create_foot(:())
-    @test_throws Exception create_foot(:(([]) => ()))
-
-    @test_throws Exception create_foot(:(A => B, P => Q, C))
-    @test_throws Exception create_foot(:(() => E, () => (K,)))
+    @test_throws ErrorException @foot A => B => C # Invalid syntax for second argument of foot: B => C
+    @test_throws ErrorException @foot oooo2 + f => C # Invalid syntax for first argument of foot: oooo2 + f
+    @test_throws ErrorException @foot A + B # Invalid syntax function for foot: +
+    @test_throws ErrorException @foot =>(A, B, C, D)
+    @test_throws ErrorException @foot ()
+    @test_throws ErrorException @foot ([]) => ()
+    @test_throws MethodError @foot A => B, P => Q, C # Issue here is it tries calling match_foot_format with a symbol
+    @test_throws ErrorException @foot () => E, () => (K,)
 
 end
 
@@ -344,12 +342,13 @@ end
         foot(:J, (:K, :Q), (:J => :K, :J => :Q))
     ]
 
+    @test (@feet ) == Vector{StockAndFlow0}();
 end
 
 @testset "feet syntax fails on invalid feet" begin # mostly to check that an exception is thrown even if some of the feet are valid.
-    @test_throws Exception @eval @feet A => B => C # eval required so the errors occur at runtime, rather than at compilation
-    @test_throws Exception @eval @feet begin A => B; =>(D,E,F) end
-    @test_throws Exception @eval @feet begin A => B; 1 => 2; end
+    @test_throws ErrorException @feet A => B => C 
+    @test_throws ErrorException @feet begin A => B; =>(D,E,F) end
+    @test_throws ErrorException @feet begin A => B; 1 => 2; end
 end
 
 ###########################