Merge pull request #464 from LCSB-BioCore/mo-docstring-fixes

Fix some small docstring issues + small readme changes

README.md

@@ -118,22 +118,21 @@ Dict{String,Float64} with 95 entries:
 #### Model variant processing
 
 The main feature of COBREXA.jl is the ability to easily specify and process
-many analyses at once, in parallel. Let's see how the organism would perform if
-some reactions were disabled:
+many analyses in parallel. To demonstrate, let's see how the organism would perform if
+some reactions were disabled independently:
 
 ```julia
-# convert to a model type that is easy to modify
+# convert to a model type that is efficient to modify
 m = convert(StandardModel, m)
 
-# find the model objective value if oxygen and carbon dioxide transports are disabled
-screen(m,
-    # this specifies how to generate the desired model variants
-    variants=[
-        [], # one with no modifications
+# find the model objective value if oxygen or carbon dioxide transports are disabled
+screen(m, # the base model
+    variants=[ # this specifies how to generate the desired model variants
+        [], # one with no modifications, i.e. the base case
         [with_changed_bound("O2t", lower=0.0, upper=0.0)], # disable oxygen
         [with_changed_bound("CO2t", lower=0.0, upper=0.0)], # disable CO2
         [with_changed_bound("O2t", lower=0.0, upper=0.0),
-	 with_changed_bound("CO2t", lower=0.0, upper=0.0)], # disable both
+	        with_changed_bound("CO2t", lower=0.0, upper=0.0)], # disable both
     ],
     # this specifies what to do with the model variants (received as the argument `x`)
     analysis = x ->
@@ -151,8 +150,10 @@ biomass production much harder:
 ```
 
 Most importantly, such analyses can be easily specified by automatically
-generating long lists of the modifications to apply to the model, and
-parallelized:
+generating long lists of modifications to be applied to the model, and
+parallelized.
+
+Knocking out each reaction in the model is efficiently accomplished:
 
 ```julia
 # load the task distribution package, add several worker nodes, and load

src/analysis/parsimonious_flux_balance_analysis.jl

@@ -36,7 +36,7 @@ finds a minimal total flux through the model that still satisfies the (slightly
 relaxed) optimum. This is done using a quadratic problem optimizer. If the
 original optimizer does not support quadratic optimization, it can be changed
 using the callback in `qp_modifications`, which are applied after the FBA. See
-the documentation of flux_balance_analysis for usage examples of modifications.
+the documentation of [`flux_balance_analysis`](@ref) for usage examples of modifications.
 
 Thhe optimum relaxation sequence can be specified in `relax` parameter, it
 defaults to multiplicative range of `[1.0, 0.999999, ..., 0.99]` of the

src/base/types/abstract/MetabolicModel.jl

@@ -217,7 +217,7 @@ function metabolite_formula(
 end
 
 """
-metabolite_charge(model::MetabolicModel, metabolite_id::String)::Maybe{Int}
+    metabolite_charge(model::MetabolicModel, metabolite_id::String)::Maybe{Int}
 
 Return the charge associated with metabolite `metabolite_id` in `model`.
 Returns `nothing` if charge not present.