fixed formatting

docs/make.jl

 using Documenter, COBREXA
 
-# download core model
-download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
-
 makedocs(modules = [COBREXA],
         clean = false,
         sitename = "COBREXA.jl",
@@ -26,5 +23,5 @@ makedocs(modules = [COBREXA],
                 ],
         )
 
-# delete core model
-rm("e_coli_core.json")
\ No newline at end of file
+# delete core model that was downloaded as part of the documentation generation process
+rm("e_coli_core.json")

docs/src/basic_analysis.md

@@ -24,7 +24,8 @@ using COBREXA
 using JuMP
 using Tulip
 
-model = read_model("e_coli_core.json")
+model_location = "e_coli_core.json" # hide
+model = read_model(model_location)
 
 biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
 optimizer = Tulip.Optimizer
@@ -38,6 +39,7 @@ using JSON
 open("fluxes.json", "w") do io
     JSON.print(io, sol)
 end
+rm("fluxes.json") # hide
 ```
 
 ## Solution inspection
@@ -112,7 +114,9 @@ using COBREXA
 using JuMP
 using Tulip
 
-model = read_model("e_coli_core.json")
+model_location = "e_coli_core.json" # hide
+model = read_model(model_location)
+
 cbm, v, mb, ubs, lbs = build_cbm(model)
 glucose_index = model[findfirst(model.reactions, "EX_glc__D_e")]
 set_bound(glucose_index, ubs, lbs; ub=-12.0, lb=-12.0)

docs/src/index.md

@@ -46,17 +46,18 @@ The optimization solvers are implemented through `JuMP` and thus this package sh
 
 ## Quick Example
 Let's perform flux balance analysis on a constraint based model.
-```@example intro
+```@example
 using COBREXA
 using JuMP
 using Tulip
 
+# Download a model from the BIGG database
+download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
+
+# Read that model into Julia
 model = read_model("e_coli_core.json")
 
 biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
 optimizer = Tulip.Optimizer
 sol = fba(model, biomass, optimizer)
 ```
-
-
-

docs/src/io.md

@@ -7,9 +7,13 @@ Currently, JSON and Matlab formatted models can be imported.
 read_model(file_location::String)
 ```
 
-```@example ioexample
+```@example io
 using COBREXA
- 
+
+# Download a model from the BIGG database
+download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")
+
+# Read that model into Julia
 model = read_model("e_coli_core.json")
 model # pretty printing
 ```
@@ -21,10 +25,10 @@ Currently, JSON and Matlab models can be exported.
 save_model(model::CobraModel, file_location::String)
 ```
 
-```@example ioexample
-save_model(model, "e_coli_core2.json")
+```@example io
+save_model(model, "e_coli_core_saved.json")
 rm("e_coli_core2.json") # hide
 ```
 
 ## IO Problems?
-Please let me know when you run into model import/export problems by filing an issue.
\ No newline at end of file
+Please let me know when you run into model import/export problems by filing an issue.

docs/src/sampling_tools.md

@@ -12,7 +12,9 @@ using COBREXA
 using JuMP
 using Tulip
 
-model = read_model("e_coli_core.json")
+model_location = "e_coli_core.json" # hide
+model = read_model(model_location)
+
 optimizer = Tulip.Optimizer
 biomass = findfirst(model.reactions, "BIOMASS_Ecoli_core_w_GAM")
 cons = Dict("EX_glc__D_e" => (-12.0, -12.0))
@@ -20,4 +22,4 @@ sol = fba(model, biomass, optimizer, constraints=cons) # classic flux balance an
 cons["BIOMASS_Ecoli_core_w_GAM"] = (sol["BIOMASS_Ecoli_core_w_GAM"], sol["BIOMASS_Ecoli_core_w_GAM"]*0.99)
 
 samples = hit_and_run(100_000, model, optimizer; keepevery=10, samplesize=5000, constraints=cons)
-```
\ No newline at end of file
+```