diff --git a/Cargo.toml b/Cargo.toml
index 28e1e30f913a09680010a7e0d852972bff807ae2..8ab386045e0f8e12380479442f2efdf72fcb87cb 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -8,7 +8,7 @@ authors = [
edition = "2021"
[dependencies]
-arrayvec = "0.7.4"
+arrayvec = { version = "0.7.4", features = ["serde"] }
clap = { version = "4.5.0", features = ["derive"] }
colored = "2.1.0"
itertools = "0.12.1"
@@ -27,6 +27,7 @@ toml = "0.8.10"
unicode-width = "0.1.11"
float_eq = { version = "1.0.1", features = ["derive"] }
snafu = "0.8.2"
+serde_json = { version = "1.0.127", features = ["preserve_order"] }
[dev-dependencies]
rand = "0.8.5"
diff --git a/src/bin/aphid/main.rs b/src/bin/aphid/main.rs
index 49670787cdbbe7ddf61351a87f150ba016cb0633..a464b6b7e5edbde1414164f1259bcc296b763b1e 100644
--- a/src/bin/aphid/main.rs
+++ b/src/bin/aphid/main.rs
@@ -49,7 +49,7 @@ struct Args {
// Standard output filenames.
mod out {
- pub(super) const CONFIG: &str = "config";
+ pub(super) const CONFIG: &str = "config.json";
}
fn main() {
@@ -150,7 +150,7 @@ fn run() -> Result<(), Error> {
format!("{}", path.display()).blue()
);
let mut file = File::create(path)?;
- writeln!(file, "{:#?}", config.for_display(interner))?;
+ writeln!(file, "{:#}", config.resolve(interner).json())?;
//==============================================================================
// Extract various information from the trees,
diff --git a/src/config.rs b/src/config.rs
index 88f1932fda1c781909af7c9cccd3a159ac0c7652..b5496e9c8bf6cf9369edd946053695418c1a1e83 100644
--- a/src/config.rs
+++ b/src/config.rs
@@ -8,6 +8,8 @@
use std::path::PathBuf;
+use serde::Serialize;
+
use crate::{
gene_tree::MeanNbBases,
interner::SpeciesSymbol,
@@ -50,7 +52,7 @@ pub struct Config {
}
const MAX_UNRESOLVED_LENGTH: f64 = 0.5;
-#[derive(Debug)]
+#[derive(Debug, Serialize)]
pub struct Filters {
// When raised, filter out trees if some species in 'other'
// branche between LCA(outgroup) and the root,
@@ -93,7 +95,7 @@ pub struct SpeciesTriplet {
pub c: SpeciesSymbol,
}
-#[derive(Debug)]
+#[derive(Debug, Serialize)]
pub struct Search {
// Starting point in the search space.
pub init_parms: Parameters<f64>,
diff --git a/src/model/parameters.rs b/src/model/parameters.rs
index bf16c12276a93cf331fc8d62d88ef10b16cb7e92..bc59a80716189e603c0a68824a1eb564c98c03f3 100644
--- a/src/model/parameters.rs
+++ b/src/model/parameters.rs
@@ -4,6 +4,7 @@
use std::fmt::{self, Display};
use arrayvec::ArrayVec;
+use serde::Serialize;
use tch::Tensor;
// The structure is generic among float and tensors
@@ -23,7 +24,7 @@ impl Num for ValGrad {}
// - tau_1 <= tau_2
// - p_* <= 1
// - p_ab + p_ac + p_bc <= 1
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize)]
pub struct Parameters<F: Num> {
// Population size.
pub(crate) theta: F,
@@ -41,7 +42,8 @@ pub struct Parameters<F: Num> {
// Parameters are stack-allocated, so don't overuse possible GF times.
pub(crate) const MAX_N_GF_TIMES: usize = 3;
-#[derive(Debug, Clone, PartialEq, Eq)]
+#[derive(Serialize, Debug, Clone, PartialEq, Eq)]
+#[serde(transparent)]
pub struct GeneFlowTimes<F: Num>(pub(crate) ArrayVec<F, MAX_N_GF_TIMES>);
// Convenience bundle.
diff --git a/src/optim.rs b/src/optim.rs
index b4f9503a5ba7b2813d8904924f5f888fa9285f90..fa7eb1f4a9f33814c86d954c6cac7bd545afc30d 100644
--- a/src/optim.rs
+++ b/src/optim.rs
@@ -10,6 +10,7 @@ pub(crate) mod wolfe_search;
use std::num::NonZeroUsize;
use paste::paste;
+use serde::Serialize;
use snafu::{ensure, Snafu};
use tch::Tensor;
use tensor::Loggable;
@@ -149,7 +150,7 @@ impl History {
// Useful to optimizers using history
// to periodically check slope and stop when it reaches some threshold.
-#[derive(Debug)]
+#[derive(Debug, Serialize)]
pub(crate) struct SlopeTrackingConfig {
history_size: NonZeroUsize,
threshold: f64, // Positive.
diff --git a/src/optim/bfgs.rs b/src/optim/bfgs.rs
index b6cbd151b5fbef7bdfbf2426ed71299577b8d5da..fc006b4cf2a088c50809a441a79f95c4ea4f727d 100644
--- a/src/optim/bfgs.rs
+++ b/src/optim/bfgs.rs
@@ -9,6 +9,7 @@ use std::{
path::PathBuf,
};
+use serde::Serialize;
use snafu::{ensure, ResultExt, Snafu};
use tch::Tensor;
@@ -22,7 +23,7 @@ use crate::optim::{
};
// The exposed config.
-#[derive(Debug)]
+#[derive(Debug, Serialize)]
pub(crate) struct Config {
pub(crate) max_iter: u64,
pub(crate) wolfe: WolfeSearchConfig,
diff --git a/src/optim/gd.rs b/src/optim/gd.rs
index 9c03a6ce7cd68ea2dcdfc14f81f0a6076c0917c9..79e31aa45929182f762ec7ee19cb7f545ee3bdd9 100644
--- a/src/optim/gd.rs
+++ b/src/optim/gd.rs
@@ -4,6 +4,7 @@
// Stops on its own when the mean slope of the history
// becomes flat, provided the history is full.
+use serde::Serialize;
use snafu::Snafu;
use tch::Tensor;
@@ -12,7 +13,7 @@ use crate::optim::{
SlopeTracker, SlopeTrackingConfig,
};
-#[derive(Debug)]
+#[derive(Debug, Serialize)]
pub(crate) struct Config {
pub(crate) max_iter: u64,
pub(crate) step_size: f64, // Above 0.
diff --git a/src/optim/wolfe_search.rs b/src/optim/wolfe_search.rs
index 902356021c98e04643451ecb954445580af5b086..f8657cab0563e249e851e7e891bdc8462f496e83 100644
--- a/src/optim/wolfe_search.rs
+++ b/src/optim/wolfe_search.rs
@@ -28,12 +28,13 @@ use std::{
ops::ControlFlow,
};
+use serde::Serialize;
use snafu::{ensure, Snafu};
use tch::Tensor;
use crate::optim::{tensor::OptimTensor, Best};
-#[derive(Debug)]
+#[derive(Debug, Serialize)]
pub(crate) struct Config {
// 0 < c1 < c2 < 1
pub(crate) c1: f64,
diff --git a/src/output/config.rs b/src/output/config.rs
index 2a0046a9734fc3008237858f21cd2198df2fc56e..83b9b13d4e3ae5a3aad752991fb11092f8ffb8c3 100644
--- a/src/output/config.rs
+++ b/src/output/config.rs
@@ -1,37 +1,116 @@
-// Render config to text, to trace every parameter used if needed.
-// This is basically just pretty-printing of the raw struct,
-// but we cannot simply derive(Debug) for the config
-// because a reference to the interner is necessary
-// to resolve the species symbols into names.
+// Render config to json
+// to trace every parameter used if needed.
+// Serde does most of the job,
+// but a reference to the interner is necessary
+// to resolve species symbols into name strings.
use std::fmt;
+use serde_json::{json, Value as JsValue, Value as Js};
+
use crate::{
config::{SpeciesTriplet, Taxa},
interner::{Interner, ResolvedSymbol},
Config,
};
-pub struct Display<'i> {
+//==================================================================================================
+// 'Resolver' types carry both a reference to their data
+// and to the interner to resolve symbols within them.
+
+pub struct Resolver<'i> {
config: &'i Config,
interner: &'i Interner,
}
-struct TaxaDisplay<'i> {
+struct TaxaResolver<'i> {
taxa: &'i Taxa,
interner: &'i Interner,
}
-struct TripletDisplay<'i> {
+struct TripletResolver<'i> {
triplet: &'i SpeciesTriplet,
interner: &'i Interner,
}
-impl<'i> fmt::Debug for Display<'i> {
+impl Config {
+ pub fn resolve<'d>(&'d self, interner: &'d Interner) -> Resolver<'d> {
+ Resolver { config: self, interner }
+ }
+}
+
+impl Taxa {
+ fn resolve<'d>(&'d self, interner: &'d Interner) -> TaxaResolver<'d> {
+ TaxaResolver { taxa: self, interner }
+ }
+}
+
+impl SpeciesTriplet {
+ fn resolve<'d>(&'d self, interner: &'d Interner) -> TripletResolver<'d> {
+ TripletResolver { triplet: self, interner }
+ }
+}
+
+//==================================================================================================
+// Resolve as json values.
+
+impl Resolver<'_> {
+ pub fn json(&self) -> JsValue {
+ let Resolver { config, interner } = self;
+ let Config { trees, taxa, filters, unresolved_length, search } = config;
+ json!({
+ "trees": trees,
+ "taxa": taxa.resolve(interner).json(),
+ "filters": filters,
+ "unresolved_length": unresolved_length,
+ "search": search,
+ })
+ }
+}
+
+impl TaxaResolver<'_> {
+ pub fn json(&self) -> JsValue {
+ let TaxaResolver { taxa, interner } = self;
+ let Taxa { triplet, outgroup, other } = taxa;
+ let outgroup = Js::Array(
+ outgroup
+ .iter()
+ .map(|&s| json! {interner.resolve(s).unwrap()})
+ .collect(),
+ );
+ let other = Js::Array(
+ other
+ .iter()
+ .map(|&s| json! {interner.resolve(s).unwrap()})
+ .collect(),
+ );
+ json!({
+ "triplet": triplet.resolve(interner).json(),
+ "outgroup": outgroup,
+ "other": other,
+ })
+ }
+}
+
+impl TripletResolver<'_> {
+ pub fn json(&self) -> JsValue {
+ let TripletResolver { triplet, interner } = self;
+ let SpeciesTriplet { a, b, c } = triplet;
+ let [a, b, c] = [a, b, c].map(|&s| interner.resolve(s).unwrap());
+ json! {
+ [[a, b], c]
+ }
+ }
+}
+
+//==================================================================================================
+// Debug displays (same logic without json for informal use within the program).
+
+impl<'i> fmt::Debug for Resolver<'i> {
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
let Config { trees, taxa, filters, unresolved_length, search } = self.config;
f.debug_struct("Config")
.field("trees", trees)
- .field("taxa", &taxa.for_display(self.interner))
+ .field("taxa", &taxa.resolve(self.interner))
.field("filters", filters)
.field("unresolved_length", unresolved_length)
.field("search", search)
@@ -39,7 +118,7 @@ impl<'i> fmt::Debug for Display<'i> {
}
}
-impl<'i> fmt::Debug for TaxaDisplay<'i> {
+impl<'i> fmt::Debug for TaxaResolver<'i> {
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
let Taxa { triplet, outgroup, other } = self.taxa;
let resolve = |slice: &[_]| {
@@ -49,15 +128,14 @@ impl<'i> fmt::Debug for TaxaDisplay<'i> {
.collect::<Vec<_>>()
};
f.debug_struct("Taxa")
- .field("triplet", &triplet.for_display(self.interner))
+ .field("triplet", &triplet.resolve(self.interner))
.field("outgroup", &resolve(outgroup))
.field("other", &resolve(other))
.finish()
}
}
-// Display as [[A, B], C].
-impl<'i> fmt::Debug for TripletDisplay<'i> {
+impl<'i> fmt::Debug for TripletResolver<'i> {
fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
let [a, b, c] = self
.triplet
@@ -67,21 +145,3 @@ impl<'i> fmt::Debug for TripletDisplay<'i> {
f.debug_list().entry(&ab).entry(&c).finish()
}
}
-
-impl Config {
- pub fn for_display<'d>(&'d self, interner: &'d Interner) -> Display<'d> {
- Display { config: self, interner }
- }
-}
-
-impl Taxa {
- fn for_display<'d>(&'d self, interner: &'d Interner) -> TaxaDisplay<'d> {
- TaxaDisplay { taxa: self, interner }
- }
-}
-
-impl SpeciesTriplet {
- fn for_display<'d>(&'d self, interner: &'d Interner) -> TripletDisplay<'d> {
- TripletDisplay { triplet: self, interner }
- }
-}