Merge pull request #967 from vaerksted/master

fix typos

Author: TorkelE

src/dsl.jl

@@ -269,7 +269,7 @@ function processmult(op, mult, stoich)
     end
 end
 
-# Finds the metadata from a metadata expresion (`[key=val, ...]`) and returns as a Vector{Pair{Symbol,ExprValues}}.
+# Finds the metadata from a metadata expression (`[key=val, ...]`) and returns as a Vector{Pair{Symbol,ExprValues}}.
 function extract_metadata(metadata_line::Expr)
     metadata = :([])
     for arg in metadata_line.args
@@ -471,7 +471,7 @@ function push_reactions!(reactions::Vector{ReactionStruct}, sub_line::ExprValues
             push!(metadata_i.args, :(only_use_rate = $(in(arrow, pure_rate_arrows))))
         end
 
-        # Checks that metadata fields are unqiue.
+        # Checks that metadata fields are unique.
         if !allunique(arg.args[1] for arg in metadata_i.args)
             error("Some reaction metadata fields where repeated: $(metadata_entries)")
         end
@@ -602,7 +602,7 @@ end
 # default metadata value to the `default_reaction_metadata` vector.
 function check_default_noise_scaling!(default_reaction_metadata, options)
     if haskey(options, :default_noise_scaling)
-        if (length(options[:default_noise_scaling].args) != 3) # Becasue of how expressions are, 3 is used.
+        if (length(options[:default_noise_scaling].args) != 3) # Because of how expressions are, 3 is used.
             error("@default_noise_scaling should only have a single input, this appears not to be the case: \"$(options[:default_noise_scaling])\"")
         end
         push!(default_reaction_metadata.args,
@@ -612,7 +612,7 @@ end
 
 # When compound species are declared using the "@compound begin ... end" option, get a list of the compound species, and also the expression that crates them.
 function read_compound_options(opts)
-    # If the compound option is used retrive a list of compound species (need to be added to the reaction system's species), and the option that creates them (used to declare them as compounds at the end).
+    # If the compound option is used retrieve a list of compound species (need to be added to the reaction system's species), and the option that creates them (used to declare them as compounds at the end).
     if haskey(opts, :compounds)
         compound_expr = opts[:compounds]
         # Find compound species names, and append the independent variable.
@@ -625,7 +625,7 @@ function read_compound_options(opts)
     return compound_expr, compound_species
 end
 
-# Read the events (continious or discrete) provided as options to the DSL. Returns an expression which evalutes to these.
+# Read the events (continuous or discrete) provided as options to the DSL. Returns an expression which evaluates to these.
 function read_events_option(options, event_type::Symbol)
     # Prepares the events, if required to, converts them to block form.
     if event_type ∉ [:continuous_events, :discrete_events]
@@ -635,7 +635,7 @@ function read_events_option(options, event_type::Symbol)
                    MacroTools.striplines(:(begin end))
     events_input = option_block_form(events_input)
 
-    # Goes throgh the events, checks for errors, and adds them to the output vector.
+    # Goes through the events, checks for errors, and adds them to the output vector.
     events_expr = :([])
     for arg in events_input.args
         # Formatting error checks.
@@ -646,7 +646,7 @@ function read_events_option(options, event_type::Symbol)
         end
         if (arg isa Expr) && (arg.args[2] isa Expr) && (arg.args[2].head != :vect) &&
            (event_type == :continuous_events)
-            error("The condition part of continious events (the left-hand side) must be a vector. This is not the case for: $(arg).")
+            error("The condition part of continuous events (the left-hand side) must be a vector. This is not the case for: $(arg).")
         end
         if (arg isa Expr) && (arg.args[3] isa Expr) && (arg.args[3].head != :vect)
             error("The affect part of all events (the righ-hand side) must be a vector. This is not the case for: $(arg).")
@@ -661,10 +661,10 @@ end
 
 # Reads the variables options. Outputs:
 # `vars_extracted`: A vector with extracted variables (lhs in pure differential equations only).
-# `dtexpr`: If a differentialequation is defined, the default derrivative (D ~ Differential(t)) must be defined.
+# `dtexpr`: If a differential equation is defined, the default derivative (D ~ Differential(t)) must be defined.
 # `equations`: a vector with the equations provided.
 function read_equations_options(options, variables_declared)
-    # Prepares the equations. First, extracts equations from provided option (converting to block form if requried).
+    # Prepares the equations. First, extracts equations from provided option (converting to block form if required).
     # Next, uses MTK's `parse_equations!` function to split input into a vector with the equations.
     eqs_input = haskey(options, :equations) ? options[:equations].args[3] : :(begin end)
     eqs_input = option_block_form(eqs_input)
@@ -718,12 +718,12 @@ function create_differential_expr(options, add_default_diff, used_syms, tiv)
         (dexpr.args[1] isa Symbol) ||
             error("Differential left-hand side must be a single symbol, instead \"$(dexpr.args[1])\" was given.")
         in(dexpr.args[1], used_syms) &&
-            error("Differential name ($(dexpr.args[1])) is also a species, variable, or parameter. This is ambigious and not allowed.")
+            error("Differential name ($(dexpr.args[1])) is also a species, variable, or parameter. This is ambiguous and not allowed.")
         in(dexpr.args[1], forbidden_symbols_error) &&
             error("A forbidden symbol ($(dexpr.args[1])) was used as a differential name.")
     end
 
-    # If the default differential D has been used, but not pre-declared using the @differenitals
+    # If the default differential D has been used, but not pre-declared using the @differentials
     # options, add this declaration to the list of declared differentials.
     if add_default_diff && !any(diff_dec.args[1] == :D for diff_dec in diffexpr.args)
         push!(diffexpr.args, :(D = Differential($(tiv))))
@@ -732,11 +732,11 @@ function create_differential_expr(options, add_default_diff, used_syms, tiv)
     return diffexpr
 end
 
-# Reads the observables options. Outputs an expression ofr creating the obervable variables, and a vector of observable equations.
+# Reads the observables options. Outputs an expression ofr creating the observable variables, and a vector of observable equations.
 function read_observed_options(options, species_n_vars_declared, ivs_sorted)
     if haskey(options, :observables)
         # Gets list of observable equations and prepares variable declaration expression.
-        # (`options[:observables]` inlucdes `@observables`, `.args[3]` removes this part)
+        # (`options[:observables]` includes `@observables`, `.args[3]` removes this part)
         observed_eqs = make_observed_eqs(options[:observables].args[3])
         observed_vars = Expr(:block, :(@variables))
         obs_syms = :([])
@@ -753,11 +753,11 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
 
             # Error checks.
             if (obs_name in species_n_vars_declared) && is_escaped_expr(obs_eq.args[2])
-                error("An interpoalted observable have been used, which has also been explicitly delcared within the system using eitehr @species or @variables. This is not permited.")
+                error("An interpolated observable have been used, which has also been explicitly declared within the system using either @species or @variables. This is not permitted.")
             end
             if ((obs_name in species_n_vars_declared) || is_escaped_expr(obs_eq.args[2])) &&
                !isnothing(metadata)
-                error("Metadata was provided to observable $obs_name in the `@observables` macro. However, the obervable was also declared separately (using either @species or @variables). When this is done, metadata should instead be provided within the original @species or @variable declaration.")
+                error("Metadata was provided to observable $obs_name in the `@observables` macro. However, the observable was also declared separately (using either @species or @variables). When this is done, metadata should instead be provided within the original @species or @variable declaration.")
             end
 
             # This bits adds the observables to the @variables vector which is given as output.
@@ -789,7 +789,7 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
 
             # Adds the observable to the list of observable names.
             # This is required for filtering away so these are not added to the ReactionSystem's species list.
-            # Again, avoid this check if we have interpoalted the variable.
+            # Again, avoid this check if we have interpolated the variable.
             is_escaped_expr(obs_eq.args[2]) || push!(obs_syms.args, obs_name)
         end
 
@@ -805,7 +805,7 @@ function read_observed_options(options, species_n_vars_declared, ivs_sorted)
 end
 
 # From the input to the @observables options, creates a vector containing one equation for each observable.
-# Checks separate cases for "@obervables O ~ ..." and "@obervables begin ... end". Other cases errors.
+# Checks separate cases for "@observables O ~ ..." and "@observables begin ... end". Other cases errors.
 function make_observed_eqs(observables_expr)
     if observables_expr.head == :call
         return :([$(observables_expr)])

src/expression_utils.jl

@@ -27,7 +27,7 @@ function forbidden_symbol_check(v)
         error("The following symbol(s) are used as species or parameters: " *
               ((map(s -> "'" * string(s) * "', ",
                   intersect(forbidden_symbols_error, v))...)) *
-              "this is not permited.")
+              "this is not permitted.")
     nothing
 end
 
@@ -37,7 +37,7 @@ function forbidden_variable_check(v)
         error("The following symbol(s) are used as variables: " *
               ((map(s -> "'" * string(s) * "', ",
                   intersect(forbidden_variables_error, v))...)) *
-              "this is not permited.")
+              "this is not permitted.")
 end
 
 function unique_symbol_check(syms)

src/network_analysis.jl

@@ -709,7 +709,7 @@ conservedquantities(state, cons_laws) = cons_laws * state
 # If u0s are not given while conservation laws are present, throws an error.
 # Used in HomotopyContinuation and BifurcationKit extensions.
 # Currently only checks if any u0s are given
-# (not whether these are enough for computing conserved quantitites, this will yield a less informative error).
+# (not whether these are enough for computing conserved quantities, this will yield a less informative error).
 function conservationlaw_errorcheck(rs, pre_varmap)
     vars_with_vals = Set(p[1] for p in pre_varmap)
     any(s -> s in vars_with_vals, species(rs)) && return

src/reaction.jl

@@ -445,10 +445,10 @@ end
 """
 getmetadata_dict(reaction::Reaction)
 
-Retrives the `ImmutableDict` containing all of the metadata associated with a specific reaction.
+Retrieves the `ImmutableDict` containing all of the metadata associated with a specific reaction.
 
 Arguments:
-- `reaction`: The reaction for which we wish to retrive all metadata.
+- `reaction`: The reaction for which we wish to retrieve all metadata.
 
 Example:
 ```julia
@@ -482,11 +482,11 @@ end
 """
 getmetadata(reaction::Reaction, md_key::Symbol)
 
-Retrives a certain metadata value from a `Reaction`. If the metadata does not exists, throws an error.
+Retrieves a certain metadata value from a `Reaction`. If the metadata does not exist, throws an error.
 
 Arguments:
-- `reaction`: The reaction for which we wish to retrive a specific metadata value.
-- `md_key`: The metadata for which we wish to retrive.
+- `reaction`: The reaction for which we wish to retrieve a specific metadata value.
+- `md_key`: The metadata for which we wish to retrieve.
 
 Example:
 ```julia
@@ -622,7 +622,7 @@ getmisc(reaction)
 
 Notes:
 - The `misc` field can contain any valid Julia structure. This mean that Catalyst cannot check it
-for symbolci variables that are added here. This means that symbolic variables (e.g. parameters of 
+for symbolic variables that are added here. This means that symbolic variables (e.g. parameters of 
 species) that are stored here are not accessible to Catalyst. This can cause troubles when e.g. 
 creating a `ReactionSystem` programmatically (in which case any symbolic variables stored in the
 `misc` metadata field should also be explicitly provided to the `ReactionSystem` constructor).