Refactor "src/dsl.jl" file #985
Conversation
TorkelE
force-pushed
the
src___refactoring___dsl_file
branch
from
3f92a31 to
b6ba044
Compare
src/dsl.jl
Outdated
| variables = vcat(variables_declared, vars_extracted) | ||
|
|
||
| # handle independent variables |
There was a problem hiding this comment.
Part of the organisations so that options are handled together (in two sets, some before and some after the reactions are considered, depending on whichever is possible for which option)
src/dsl.jl
Outdated
| symvec = gensym() | ||
| ex = quote | ||
| $symvec = $ex | ||
| expr = quote |
There was a problem hiding this comment.
in some places we used ex and some expr, here I just made it uniform
TorkelE
changed the title
| (sum(length, [reaction_lines, option_lines]) != length(ex.args)) && | ||
| error("@reaction_network input contain $(length(ex.args) - sum(length.([reaction_lines,option_lines]))) malformed lines.") | ||
| any(!in(option_keys), keys(options)) && | ||
| error("The following unsupported options were used: $(filter(opt_in->!in(opt_in,option_keys), keys(options)))") |
There was a problem hiding this comment.
Step one, read the macro input and check that it is correctly formatted.
| if !allunique(syms_declared) | ||
| nonunique_syms = [s for s in syms_declared if count(x -> x == s, syms_declared) > 1] | ||
| error("The following symbols $(unique(nonunique_syms)) have explicitly been declared as multiple types of components (e.g. occur in at least two of the `@species`, `@parameters`, `@variables`, `@ivs`, `@compounds`, `@differentials`). This is not allowed.") | ||
| end |
There was a problem hiding this comment.
Step 2, read all options that explicitly declares symbols as stuff.
| continuous_events_expr = read_events_option(options, :continuous_events) | ||
| discrete_events_expr = read_events_option(options, :discrete_events) | ||
| default_reaction_metadata = read_default_noise_scaling_option(options) | ||
| combinatoric_ratelaws = read_combinatoric_ratelaws_option(options) |
There was a problem hiding this comment.
Step 4, read the other options.
| spsexpr, spsvar = scalarize_macro(spsexpr_init, "specs") | ||
| vsexpr, vsvar = scalarize_macro(vsexpr_init, "vars") | ||
| cmpsexpr, cmpsvar = scalarize_macro(cmpexpr_init, "comps") | ||
| rxsexprs = get_rxexprs(reactions, equations, all_syms) |
There was a problem hiding this comment.
Step 5, creates the various expressions to put in the macro.
| end | ||
| union!(excluded_syms, species) |
There was a problem hiding this comment.
union! replaces foreach(s -> push!(excluded_syms, s), species)
| syms_inferred = union(sps_inferred, ps_inferred, vs_inferred, diffs_inferred) | ||
| all_syms = union(syms_declared, syms_inferred) | ||
| obsexpr, obs_eqs, obs_syms = read_observed_option(options, ivs, | ||
| union(sps_declared, vs_declared), all_syms; requiredec) |
There was a problem hiding this comment.
Step 3: Read all reactions and equations. Finds all symbols that are inferred as something.
| function escape_equation!(eqexpr::Expr, all_syms) | ||
| eqexpr.args[2] = recursive_escape_functions!(eqexpr.args[2], all_syms) | ||
| eqexpr.args[3] = recursive_escape_functions!(eqexpr.args[3], all_syms) | ||
| eqexpr | ||
| end |
There was a problem hiding this comment.
escape equations is called by get_rxexprs
|
|
||
| # Checks for input errors. | ||
| # Checks for input errors. Needed here but not in `@reaction_network` as `ReactionSystem` perform this check but `Reaction` don't. | ||
| forbidden_symbol_check(union(species, parameters)) |
There was a problem hiding this comment.
For @reaction_network this check is not needed as ReactionSystem does a similar one. We might consider whether Reaction should also perform this type of check (and we remove it from here entirely.
E.g. this works:
@parameters Γ
@species X(t)
Reaction(Γ, [X], [])while this errors:
@reaction Γ, X --> 0
|
This should be ready now. However, Plots fails on precompilation, so have to wait until that is fixed. Not high priority though, doesn't actually change anything (but should make further updates to the DSL easier). Once this PR is merged, I will have a follow-up one which reorders the option handling functions to follow the order with which they are called. |
…to src___refactoring___dsl_file
Also does the "src/expression_utils.jl" file, as that primarily support the dsl file (the other relevant file is the chemistry one).
Primarily four types of changes:
@reaction_networkand@network_componentmacros reuse minimal amount of code (where as previously it the second was basically ctrl+copied versions of the first.I also add some tests of all the various ways to create models via the DSL, mostly stuff that was not tested before.