Skip to content

Commit

Permalink
Merge pull request #1019 from isaacsas/fix_bad_formatting
Browse files Browse the repository at this point in the history
cleanup reaction getmetadata function and fix error mesg bug
  • Loading branch information
isaacsas authored Aug 13, 2024
2 parents 7a52aa7 + 739051b commit d2d05ad
Showing 1 changed file with 10 additions and 11 deletions.
21 changes: 10 additions & 11 deletions src/reaction.jl
Original file line number Diff line number Diff line change
Expand Up @@ -351,7 +351,7 @@ MT.is_alg_equation(rx::Reaction) = false
"""
get_symbolics(set, rx::Reaction)
Returns all symbolic variables that are part of a reaction. This includes all variables
Returns all symbolic variables that are part of a reaction. This includes all variables
encountered in:
- Rates.
- Among substrates and products.
Expand All @@ -365,7 +365,7 @@ end
"""
get_variables!(set, rx::Reaction)
Adds all symbolic variables that are part of a reaction to set. This includes all variables
Adds all symbolic variables that are part of a reaction to set. This includes all variables
encountered in:
- Rates.
- Among substrates and products.
Expand Down Expand Up @@ -412,7 +412,7 @@ function MT.modified_unknowns!(munknowns, rx::Reaction, sts::AbstractVector)
munknowns
end

### `Reaction`-specific Functions ###
### `Reaction`-specific Functions ###

"""
isbcbalanced(rx::Reaction)
Expand Down Expand Up @@ -495,12 +495,11 @@ getmetadata(reaction, :description)
```
"""
function getmetadata(reaction::Reaction, md_key::Symbol)
if !hasmetadata(reaction, md_key)
error("The reaction does not have a metadata field $md_key. It does have the following metadata fields: $(keys(getmetadata_dict(reaction))).")
end
metadata = getmetadata_dict(reaction)
return metadata[findfirst(isequal(md_key, entry[1])
for entry in getmetadata_dict(reaction))][2]
idx = findfirst(isequal(md_key, entry[1]) for entry in metadata)
(idx === nothing) &&
error("The reaction does not have a metadata field $md_key. It does have the following metadata fields: $(first.(values(metadata))).")
return metadata[idx][2]
end

### Implemented Reaction Metadata ###
Expand Down Expand Up @@ -622,10 +621,10 @@ getmisc(reaction)
Notes:
- The `misc` field can contain any valid Julia structure. This mean that Catalyst cannot check it
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.
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).
`misc` metadata field should also be explicitly provided to the `ReactionSystem` constructor).
"""
function getmisc(reaction::Reaction)
Expand Down

0 comments on commit d2d05ad

Please sign in to comment.