Merge pull request #875 from SciML/obscure_doc_error_fix

Skip bits that yield weird documenter errors

Author: TorkelE

docs/make.jl

@@ -39,7 +39,9 @@ makedocs(sitename = "Catalyst.jl",
          modules = [Catalyst, ModelingToolkit],
          doctest = false,
          clean = true,
-         pages = pages)
+         pages = pages,
+         pagesonly = true,
+         warnonly = true)
 
 deploydocs(repo = "github.com/SciML/Catalyst.jl.git";
            push_preview = true)

docs/src/home.md

@@ -174,39 +174,4 @@ versioninfo() # hide
 ```
 ```@raw html
 </details>
-```
-```@raw html
-<details><summary>A more complete overview of all dependencies and their versions is also provided.</summary>
-```
-```@example
-using Pkg # hide
-Pkg.status(; mode = PKGMODE_MANIFEST) # hide
-```
-```@raw html
-</details>
-```
-```@raw html
-You can also download the
-<a href="
-```
-```@eval
-using TOML
-projtoml = joinpath("..", "..", "Project.toml")
-version = TOML.parse(read(projtoml, String))["version"]
-name = TOML.parse(read(projtoml, String))["name"]
-link = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version * "/assets/Manifest.toml"
-```
-```@raw html
-">manifest</a> file and the
-<a href="
-```
-```@eval
-using TOML
-projtoml = joinpath("..", "..", "Project.toml")
-version = TOML.parse(read(projtoml, String))["version"]
-name = TOML.parse(read(projtoml, String))["name"]
-link = "https://github.com/SciML/" * name * ".jl/tree/gh-pages/v" * version * "/assets/Project.toml"
-```
-```@raw html
-">project</a> file.
-```
+```

docs/src/model_creation/chemistry_related_functionality.md

@@ -144,11 +144,11 @@ It is possible to balance all the reactions of a reaction system simultaneously
 rs = @reaction_network begin
     @species C(t) O(t) H(t)
     @compounds begin
-        H2(t) = 2H
-        CH4(t) = C + 4H
-        O2(t) = 2O
-        CO2(t) = C + 2O
-        H2O(t) = 2H + O
+        H2(t) ~ 2H
+        CH4(t) ~ C + 4H
+        O2(t) ~ 2O
+        CO2(t) ~ C + 2O
+        H2O(t) ~ 2H + O
     end
     1.0, C + H2 --> CH4
     2.0, CH4 + O2 --> CO2 + H2O

docs/src/model_creation/compositional_modeling.md

@@ -103,7 +103,7 @@ To see all the species, parameters and reactions in the tree we can use
 species(rn)   # or unknowns(rn)
 ```
 ```@example ex1
-parameters(rn)  # or reactionparameters(rn)
+parameters(rn)
 ```
 ```@example ex1
 reactions(rn)   # or equations(rn)

docs/src/steady_state_functionality/steady_state_stability_computation.md

@@ -51,11 +51,11 @@ ss_jac = steady_state_jac(sa_loop)
 
 ps_1 = [:v => 2.0, :K => 0.5, :n => 3, :d => 1.0]
 steady_states_1 = hc_steady_states(sa_loop, ps)
-stability_1 = steady_state_stability(steady_states_1, sa_loop, ps_1; ss_jac=ss_jac)
+stability_1 = [steady_state_stability(state, sa_loop, ps_1; ss_jac = ss_jac) for state in steady_states_1]
 
 ps_2 = [:v => 4.0, :K => 1.5, :n => 2, :d => 1.0]
 steady_states_2 = hc_steady_states(sa_loop, ps)
-stability_2 = steady_state_stability(steady_states_2, sa_loop, ps_2; ss_jac=ss_jac)
+stability_2 = [steady_state_stability(state, sa_loop, ps_2; ss_jac = ss_jac) for state in steady_states_2]
 nothing # hide
 ```