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use thiserror::Error;
use crate::specification::Graph;
use crate::specification::GraphDefaults;
use crate::specification::UnresolvedDeme;
use crate::specification::UnresolvedDemeHistory;
use crate::specification::UnresolvedEpoch;
use crate::specification::UnresolvedGraph;
use crate::DemesError;
use crate::InputGenerationTime;
use crate::InputProportion;
use crate::InputTime;
use crate::TimeUnits;
use crate::UnresolvedMigration;
/// Error type raised by [`GraphBuilder`]
#[derive(Error, Debug)]
#[non_exhaustive]
pub enum BuilderError {
/// Error type when defaults fail to serialize
#[error(transparent)]
SerdeYamlError(#[from] serde_yaml::Error),
}
/// This type allows building a [`Graph`](crate::Graph) using code
/// rather then using text input.
///
/// # Notes
///
/// * A "builder" in rust will never be as convenient
/// as one in, say, Python or Juilia.
/// The lack of a rust REPL and the strong type checking
/// are the primary reasons.
/// * All error checks are delayed until resolution.
pub struct GraphBuilder {
graph: UnresolvedGraph,
metadata: Option<crate::Metadata>,
}
impl GraphBuilder {
/// Constructor
///
/// # Returns
///
/// This function returns an "builder" containing an unresolved
/// [`Graph`](crate::Graph).
pub fn new(
time_units: TimeUnits,
generation_time: Option<InputGenerationTime>,
defaults: Option<GraphDefaults>,
) -> Self {
Self {
graph: UnresolvedGraph::new(time_units, generation_time, defaults),
metadata: None,
}
}
/// Construct a builder with time units in generations.
///
/// This function works by calling [`GraphBuilder::new`](crate::GraphBuilder::new).
pub fn new_generations(defaults: Option<GraphDefaults>) -> Self {
Self {
graph: UnresolvedGraph::new(TimeUnits::Generations, None, defaults),
metadata: None,
}
}
/// Add a [`Deme`](crate::Deme) to the graph.
///
/// # Examples
///
/// ```
/// let start_size = demes::InputDemeSize::from(100.);
/// let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
/// let history = demes::UnresolvedDemeHistory::default();
/// let mut b = demes::GraphBuilder::new_generations(None);
/// b.add_deme("A", vec![epoch], history, Some("this is deme A"));
/// b.resolve().unwrap();
/// ```
///
/// # Notes
pub fn add_deme<I: IntoIterator<Item = UnresolvedEpoch>>(
&mut self,
name: &str,
epochs: I,
history: UnresolvedDemeHistory,
description: Option<&str>,
) {
let epochs = epochs.into_iter().collect::<Vec<_>>();
let ptr = UnresolvedDeme::new_via_builder(name, epochs, history, description);
self.graph.add_deme(ptr);
}
/// Add a migration to the graph.
///
/// # Examples
///
/// ## Adding an asymmetric migration
///
/// See [`UnresolvedMigration`].
///
/// ```
/// let start_size = demes::InputDemeSize::from(100.);
/// let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
/// let history = demes::UnresolvedDemeHistory::default();
/// let mut b = demes::GraphBuilder::new_generations(None);
/// b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
/// b.add_deme("B", vec![epoch], history, Some("this is deme B"));
/// let migration = demes::UnresolvedMigration::default().set_source("A").set_dest("B").set_rate(1e-4);
/// b.add_migration(migration);
/// b.resolve().unwrap();
/// ```
///
/// ## Adding a symmetric migration
///
/// See [`UnresolvedMigration`].
///
/// ```
/// let start_size = demes::InputDemeSize::from(100.);
/// let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
/// let history = demes::UnresolvedDemeHistory::default();
/// let mut b = demes::GraphBuilder::new_generations(None);
/// b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
/// b.add_deme("B", vec![epoch], history, Some("this is deme B"));
/// let migration = demes::UnresolvedMigration::default().set_demes(["A","B"].as_slice()).set_rate(1e-4);
/// b.add_migration(migration);
/// b.resolve().unwrap();
/// ```
///
/// We can also use a `Vec` instead of an array:
///
/// ```
/// # let start_size = demes::InputDemeSize::from(100.);
/// # let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
/// # let history = demes::UnresolvedDemeHistory::default();
/// # let mut b = demes::GraphBuilder::new_generations(None);
/// # b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
/// # b.add_deme("B", vec![epoch], history, Some("this is deme B"));
/// let migration = demes::UnresolvedMigration::default().set_demes(vec!["A","B"]).set_rate(1e-4);
/// b.add_migration(migration);
/// # b.resolve().unwrap();
/// ```
pub fn add_migration(&mut self, migration: UnresolvedMigration) {
self.graph.add_migration(migration);
}
/// Add an [`UnresolvedPulse`](crate::UnresolvedPulse) to the graph.
///
/// # Examples
///
/// ```
/// let start_size = demes::InputDemeSize::from(100.);
/// let epoch = demes::UnresolvedEpoch{start_size: Some(start_size), ..Default::default()};
/// let history = demes::UnresolvedDemeHistory::default();
/// let mut b = demes::GraphBuilder::new_generations(None);
/// b.add_deme("A", vec![epoch], history.clone(), Some("this is deme A"));
/// b.add_deme("B", vec![epoch], history, Some("this is deme B"));
/// b.add_pulse(Some(&["A"]),
/// Some("B"),
/// Some(50.0),
/// Some([0.5].as_slice()));
/// b.resolve().unwrap();
/// ```
pub fn add_pulse<T: Into<InputTime>, P: Into<InputProportion>, I: IntoIterator<Item = P>>(
&mut self,
sources: Option<&[&str]>,
dest: Option<&str>,
time: Option<T>,
proportions: Option<I>,
) {
let sources = sources.map(|value| value.iter().map(|v| v.to_string()).collect::<Vec<_>>());
let dest = dest.map(|value| value.to_string());
let time = time.map(|t| t.into());
let proportions = proportions.map(|s| {
s.into_iter()
.map(|p| p.into())
.collect::<Vec<InputProportion>>()
});
self.graph.add_pulse(sources, dest, time, proportions);
}
/// Generate and return a resolved [`Graph`](crate::Graph).
///
/// # Errors
///
/// Returns [`DemesError'](crate::DemesError) if any
/// of the data are invalid.
pub fn resolve(self) -> Result<Graph, DemesError> {
let mut builder = self;
match builder.metadata {
None => (),
Some(m) => builder.graph.set_metadata(m),
}
builder.graph.resolve()?;
builder.graph.try_into()
}
/// Set top-level metadata
///
/// # Parameters
///
/// * `metadata`: the metadata type
///
/// # Note
///
/// Repeated calls will overwrite existing metadata.
///
/// # Errors
///
/// * [`BuilderError`] if serialization to YAML fails.
///
/// # Example
///
/// ```
/// #[derive(serde::Serialize, serde::Deserialize)]
/// struct MyMetaData {
/// foo: i32,
/// bar: String
/// }
/// # let mut builder = demes::GraphBuilder::new_generations(None);
/// builder.set_toplevel_metadata(&MyMetaData{foo: 3, bar: "string".to_owned()}).unwrap();
/// ```
pub fn set_toplevel_metadata<T: serde::Serialize>(
&mut self,
metadata: &T,
) -> Result<(), BuilderError> {
let yaml = serde_yaml::to_string(metadata)?;
let metadata: crate::Metadata = serde_yaml::from_str(&yaml)?;
self.metadata = Some(metadata);
Ok(())
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::specification::DemeDefaults;
use crate::InputDemeSize;
#[test]
#[should_panic]
fn new_builder() {
let b = GraphBuilder::new(TimeUnits::Generations, None, None);
b.resolve().unwrap();
}
#[test]
fn add_deme_with_epochs() {
let mut b = GraphBuilder::new_generations(Some(GraphDefaults::default()));
let edata = UnresolvedEpoch {
start_size: Some(InputDemeSize::from(100.0)),
..Default::default()
};
b.add_deme("CEU", vec![edata], UnresolvedDemeHistory::default(), None);
let _graph = b.resolve().unwrap();
}
#[test]
fn use_proportion_for_proportions() {
let p = InputProportion::from(0.5);
let _ = UnresolvedDemeHistory {
proportions: Some(vec![p, p]),
..Default::default()
};
}
#[test]
fn builder_deme_defaults() {
let defaults = DemeDefaults {
epoch: UnresolvedEpoch {
end_size: Some(InputDemeSize::from(100.)),
..Default::default()
},
};
let history = UnresolvedDemeHistory {
defaults,
..Default::default()
};
let mut b = GraphBuilder::new_generations(None);
b.add_deme("YRB", vec![], history, None);
b.resolve().unwrap();
}
}