Cm/docs canon #193

quffaro · 2024-01-31T14:55:58Z

Docs broken.

src/canon/docs_test.jl may have a working macro defined but it should be moved to src/canon.jl and applied to the other examples.
Literate is commented out in docs/make.jl because of rogue formatting obstacles in the examples.

jpfairbanks · 2024-01-31T15:52:11Z

src/canon/docs_test.jl

+
+macro create_pode(modelname,source,variable,pode) 
+  quote 
+    local v1 = $(esc(modelname))


I think you don’t need the local on this.

jpfairbanks · 2024-01-31T15:53:18Z

src/canon/docs_test.jl

+
+    $v3
+
+    """


After the “”” you want to have const $modelname = @decapode begin $pode end

jpfairbanks · 2024-01-31T15:54:29Z

src/canon/docs_test.jl

+end 
+
+for (modelname,link,variable,pode) ∈ db
+    @eval @create_pode $modelname $link $variable $pode


If you replace @create_pode with a function create_pode then the line here can be

eval(create_pode(modelname, link, variable, pode))

jpfairbanks · 2024-01-31T15:55:28Z

src/canon/docs_test.jl

+     ,("Oscillator", "https://www.archlinux.org", "oscillator", quote y="BBBB" end)]
+
+macro create_pode(modelname,source,variable,pode) 
+  quote 


For auto docs, you will need to add export @modelname to the expr that you are generating.

jpfairbanks · 2024-02-05T16:31:53Z

src/canon/canon.jl

+
+  $desc
+
+  ### Model


promote to ## Model

jpfairbanks · 2024-02-05T16:32:01Z

src/canon/canon.jl

+                  " end, "\n")
+
+  docstring = "
+  ## $modelname


Promote to # $modelname

jpfairbanks · 2024-02-05T16:32:49Z

src/canon/canon.jl

+
+  ### Model
+
+  $modeldef 


$modeldef

jpfairbanks · 2024-02-08T18:33:28Z

I think we should use the Markdown stdlib to get the formatting right.

https://github.com/JuliaLang/julia/blob/master/stdlib/Markdown/src/Markdown.jl

a="a"; using Markdown; Markdown.catdoc(md"# h1", md"$a", md"$a", md"paragraph")
works for me.

jpfairbanks

This is almost there. We have 3 changes in 1 PR, which we should try to avoid, but I don't want to delay by starting over here. See inline comments

jpfairbanks · 2024-02-13T13:09:19Z

.buildkite/toolbox/dryrun.sh

+# check if we are in a valid git repository 
+REPO=`git rev-parse --show-toplevel`
+if [[ ! $REPO ]]; then 
+  echo "badness"  


echo "We are not in a valid git repo $(pwd)"

jpfairbanks · 2024-02-13T13:10:56Z

.buildkite/toolbox/srun.sh

@@ -0,0 +1,6 @@
+srun --cpus-per-task=32 \
+  --mem=8G \


16G by default might be safer.

jpfairbanks · 2024-02-13T13:13:14Z

examples/chemistry/brusselator_bounded.jl

 using Decapodes
 using MultiScaleArrays
 using MLStyle
 using OrdinaryDiffEq
 using LinearAlgebra
-using GLMakie
+using CairoMakie


Maybe we should use

using CairoMakie import CairoMakie: wireframe [all the other methods we use]

and then we won't have to use the CairoMakie namespace in the code. Then if we switch back to GL, we can just change it at the top of the file.

jpfairbanks · 2024-02-13T13:14:31Z

src/canon/Physics.jl

+  end
+ )
+
+# @docapode(:OutgoingLongwaveRadiation


why commented out?

jpfairbanks · 2024-02-13T13:14:50Z

src/canon/Physics.jl

+
+
+
+# Diffusion = @decapode DiffusionQuantities begin


why commented out?

jpfairbanks · 2024-02-13T13:16:12Z

Also squash all this history into 1-3 commits before merging.

jpfairbanks · 2024-02-14T15:07:16Z

Project.toml

@@ -32,7 +33,6 @@ Catlab = "0.15, 0.16"
 CombinatorialSpaces = "0.5, 0.6"
 ComponentArrays = "0.15"
 DataStructures = "0.18.13"
-DiagrammaticEquations = "0.1.2"


This seems important. Why delete?

jpfairbanks · 2024-02-14T15:09:09Z

examples/chemistry/brusselator.jl

 Brusselator = @decapode begin
-  # Values living on vertices.


Can these comments get the ## coment treatment that we discovered in the literate docs?

…akie but we should not expect these docs to work until the pmap branch is completed

jpfairbanks · 2024-02-26T22:14:20Z

the commit that got lost in being bad at git

diff --git a/examples/chemistry/brusselator_bounded.jl b/examples/chemistry/brusselator_bounded.jl
index b2cf391..4b72fb0 100644
--- a/examples/chemistry/brusselator_bounded.jl
+++ b/examples/chemistry/brusselator_bounded.jl
@@ -65,7 +65,7 @@ resolve_overloads!(Brusselator)
 to_graphviz(Brusselator)

 # TODO: Create square domain of approximately 32x32 vertices.
-s = loadmesh(Rectangle_30x10())
+s = triangulated_grid(30,10,2,2)
 scaling_mat = Diagonal([1/maximum(x->x[1], s[:point]),
                         1/maximum(x->x[2], s[:point]),
                         1.0])
@@ -230,7 +230,7 @@ constants_and_parameters = (
   R = R,
   F = t -> t ≥ 1.1 ? F₂ : F₁)

-tₑ = 21.5e4
+tₑ = 21.5e2

 @info("Precompiling Solver")
 prob = ODEProblem(fₘ, u₀, (0, 1e-4), constants_and_parameters)

quffaro requested a review from jpfairbanks January 31, 2024 14:55

jpfairbanks requested changes Jan 31, 2024

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quffaro mentioned this pull request Feb 2, 2024

Feature buildkite #186

Merged

jpfairbanks reviewed Feb 5, 2024

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jpfairbanks requested changes Feb 13, 2024

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quffaro force-pushed the cm/docs-canon branch 2 times, most recently from ac6bd73 to fcc53d1 Compare February 14, 2024 15:08

jpfairbanks reviewed Feb 14, 2024

View reviewed changes

quffaro force-pushed the cm/docs-canon branch from fcc53d1 to fe85847 Compare February 14, 2024 15:12

lukem12345 and others added 10 commits February 26, 2024 16:06

Add canon of models

66754e5

trying to add docstrings to Canon

fdd8d40

swapped link for source

7d6da10

Cite environment Decapodes, and update Halfar

2511a4e

Cite Jordan, Kinderlehrer, and Otto

7dad903

Testing autodocs with @docapodes macro

f47bd29

addressed feedback from PR

61077a9

the examples are currently being refactored. I addressed using CairoM…

f05c803

…akie but we should not expect these docs to work until the pmap branch is completed

intending to resolve branch. pmapping examples on cm/pmap branch

db20377

un-underscored things

e6fd11b

olynch force-pushed the cm/docs-canon branch from 20c20ef to e6fd11b Compare February 26, 2024 22:06

jpfairbanks closed this Feb 26, 2024

olynch reopened this Feb 26, 2024

olynch added 2 commits February 27, 2024 10:55

shrunk model for docs build

32f12ba

removed manifests

3792b6e

jpfairbanks merged commit 0c37b8b into main Feb 27, 2024
7 of 8 checks passed

jpfairbanks deleted the cm/docs-canon branch February 27, 2024 17:49

lukem12345 mentioned this pull request Mar 3, 2024

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Cm/docs canon #193

Cm/docs canon #193

quffaro commented Jan 31, 2024

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jpfairbanks commented Feb 26, 2024

Cm/docs canon #193

Cm/docs canon #193

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quffaro commented Jan 31, 2024

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jpfairbanks commented Feb 8, 2024

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jpfairbanks commented Feb 13, 2024

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jpfairbanks commented Feb 26, 2024