first attempts at writing the serializers for the new types PhylogeneticModel and GroupBasedPhylogeneticModel #4010
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…ticModel and GroupBasedPhylogeneticModel
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #4010 +/- ##
==========================================
- Coverage 84.58% 84.10% -0.48%
==========================================
Files 596 613 +17
Lines 81969 83133 +1164
==========================================
+ Hits 69336 69923 +587
- Misses 12633 13210 +577
|
| save_object(s, graph(pm), :tree) # already implemented | ||
| save_object(s, number_states(pm), :states) # already implemented | ||
| save_object(s, probability_ring(pm), :probability_ring) # already implemented | ||
| save_object(s, root_distribution(pm), :root_distribution) # needs to be implemented, or we change the entry type to QQFieldElem |
There was a problem hiding this comment.
you can using save_typed_object here if the type isn't always know, or if your using a vector any because not all entries are the same type you'll need to use a tuple
src/Serialization/Combinatorics.jl
Outdated
| @@ -19,6 +20,19 @@ function load_object(s::DeserializerState, g::Type{Graph{T}}) where T <: Union{D | |||
| return g(smallobj) | |||
| end | |||
|
|
|||
| function save_object(s::SerializerState, e::Edge) | |||
| save_data_dict(s) do | |||
There was a problem hiding this comment.
this can be done using save_data_array instead, it'll make file sizes smaller
…d object Co-authored-by: antonydellavecchia <antonydellavecchia@gmail.com>
…zation of dicts to catch the case where the key is not serialized with params
|
|
||
|
|
||
| function load_object(s::DeserializerState, g::Type{PhylogeneticModel}) | ||
| graph = load_object(s, Graph{Directed}, :tree) |
There was a problem hiding this comment.
here you would need to use
Suggested change
| graph = load_object(s, Graph{Directed}, :tree) | |
| graph = load_typed_object(s, :tree) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
I am currently trying to serialize the new data types introduced in the algebraic statistics (sub)project on algebraic phylogenetics by @marinagarrote et al (cf. #3812). Following the documentation and writing the code as naive as possible, I got problems when testing the functions by trying to save an instance of GroupPhylogeneticModel, with the following error message:
Unsupported type 'GroupBasedPhylogeneticModel' for encoding.