tskit tree format integration

Cargo.toml

@@ -15,6 +15,7 @@ members = [
     "necsim/plugins/metacommunity",
     "necsim/plugins/statistics",
     "necsim/plugins/species",
+    "necsim/plugins/tskit",
 
     "necsim/partitioning/core",
     "necsim/partitioning/monolithic",
@@ -39,6 +40,7 @@ default-members = [
     "necsim/plugins/metacommunity",
     "necsim/plugins/statistics",
     "necsim/plugins/species",
+    "necsim/plugins/tskit",
 ]
 
 [profile.release]

necsim/core/src/lineage.rs

@@ -19,6 +19,20 @@ use crate::{
 #[repr(transparent)]
 pub struct GlobalLineageReference(NonZeroOneU64);
 
+impl GlobalLineageReference {
+    #[doc(hidden)]
+    #[must_use]
+    pub unsafe fn into_inner(self) -> NonZeroOneU64 {
+        self.0
+    }
+
+    #[doc(hidden)]
+    #[must_use]
+    pub unsafe fn from_inner(inner: NonZeroOneU64) -> Self {
+        Self(inner)
+    }
+}
+
 impl fmt::Display for GlobalLineageReference {
     fn fmt(&self, f: &mut fmt::Formatter) -> fmt::Result {
         write!(f, "{}", self.0.get() - 2)

necsim/impls/no-std/Cargo.toml

@@ -26,6 +26,7 @@ serde = { version = "1.0", default-features = false, features = ["alloc", "deriv
 log = "0.4"
 displaydoc = { version = "0.2", default-features = false, features = [] }
 final = { git = "https://github.com/MomoLangenstein/final", rev = "a2dbfd6" }
+fnv = { version = "1.0", default-features = false, features = [] }
 
 [target.'cfg(target_os = "cuda")'.dependencies]
 rust-cuda = { git = "https://github.com/MomoLangenstein/rust-cuda", branch = "main", features = ["derive"], optional = true }

necsim/impls/no-std/src/cogs/active_lineage_sampler/alias/dynamic/indexed/mod.rs

@@ -5,6 +5,7 @@ use core::{
     hash::Hash,
     num::{NonZeroU128, NonZeroUsize},
 };
+use fnv::FnvBuildHasher;
 
 use hashbrown::HashMap;
 
@@ -26,7 +27,7 @@ struct RejectionSamplingGroup<E: Eq + Hash> {
 pub struct DynamicAliasMethodIndexedSampler<E: Eq + Hash + Clone> {
     exponents: Vec<i16>,
     groups: Vec<RejectionSamplingGroup<E>>,
-    lookup: HashMap<E, EventLocation>,
+    lookup: HashMap<E, EventLocation, FnvBuildHasher>,
     min_exponent: i16,
     total_weight: u128,
 }
@@ -47,7 +48,7 @@ impl<E: Eq + Hash> RejectionSamplingGroup<E> {
 
     unsafe fn sample_pop_inplace<M: MathsCore, G: RngCore<M>>(
         &mut self,
-        lookup: &mut HashMap<E, EventLocation>,
+        lookup: &mut HashMap<E, EventLocation, FnvBuildHasher>,
         rng: &mut G,
     ) -> (Option<&mut Self>, E) {
         if let [event] = &self.events[..] {
@@ -86,7 +87,7 @@ impl<E: Eq + Hash> RejectionSamplingGroup<E> {
     #[cfg(test)]
     fn sample_pop<M: MathsCore, G: RngCore<M>>(
         mut self,
-        lookup: &mut HashMap<E, EventLocation>,
+        lookup: &mut HashMap<E, EventLocation, FnvBuildHasher>,
         rng: &mut G,
     ) -> (Option<Self>, E) {
         match unsafe { self.sample_pop_inplace(lookup, rng) } {
@@ -98,7 +99,7 @@ impl<E: Eq + Hash> RejectionSamplingGroup<E> {
     unsafe fn remove_inplace(
         &mut self,
         index: usize,
-        lookup: &mut HashMap<E, EventLocation>,
+        lookup: &mut HashMap<E, EventLocation, FnvBuildHasher>,
     ) -> Option<&mut Self> {
         self.events.swap_remove(index);
         let weight = self.weights.swap_remove(index);
@@ -119,7 +120,11 @@ impl<E: Eq + Hash> RejectionSamplingGroup<E> {
     }
 
     #[cfg(test)]
-    fn remove(mut self, index: usize, lookup: &mut HashMap<E, EventLocation>) -> Option<Self> {
+    fn remove(
+        mut self,
+        index: usize,
+        lookup: &mut HashMap<E, EventLocation, FnvBuildHasher>,
+    ) -> Option<Self> {
         if unsafe { self.remove_inplace(index, lookup) }.is_some() {
             Some(self)
         } else {
@@ -158,7 +163,7 @@ impl<E: Eq + Hash + Clone> DynamicAliasMethodIndexedSampler<E> {
         Self {
             exponents: Vec::new(),
             groups: Vec::new(),
-            lookup: HashMap::new(),
+            lookup: HashMap::default(),
             min_exponent: 0_i16,
             total_weight: 0_u128,
         }
@@ -172,7 +177,7 @@ impl<E: Eq + Hash + Clone> DynamicAliasMethodIndexedSampler<E> {
         Self {
             exponents: Vec::with_capacity(capacity_log2_approx),
             groups: Vec::with_capacity(capacity_log2_approx),
-            lookup: HashMap::with_capacity(capacity),
+            lookup: HashMap::with_capacity_and_hasher(capacity, FnvBuildHasher::default()),
             min_exponent: 0_i16,
             total_weight: 0_u128,
         }

necsim/impls/no-std/src/cogs/active_lineage_sampler/alias/dynamic/indexed/tests.rs

@@ -22,15 +22,15 @@ fn singular_event_group() {
     assert_eq!(&group.weights, &[1_u64]);
     assert_eq!(group.total_weight, 1_u128);
 
-    assert!(group.remove(0, &mut HashMap::new()).is_none());
+    assert!(group.remove(0, &mut HashMap::default()).is_none());
 }
 
 #[test]
 #[allow(clippy::too_many_lines)]
 fn add_remove_event_group() {
     let mut group = RejectionSamplingGroup::new(0_u8, 1_u64);
 
-    let mut lookup = HashMap::new();
+    let mut lookup = HashMap::default();
     lookup.insert(
         0_u8,
         EventLocation {
@@ -137,7 +137,7 @@ fn add_remove_event_group() {
     );
 
     assert_eq!(
-        group.sample_pop(&mut HashMap::new(), &mut DummyRng::new(vec![0.0, 0.0])),
+        group.sample_pop(&mut HashMap::default(), &mut DummyRng::new(vec![0.0, 0.0])),
         (None, 2_u8)
     );
 }
@@ -151,7 +151,7 @@ fn sample_single_group() {
         decompose_weight(PositiveF64::new(6.0 / 12.0).unwrap()).mantissa,
     );
 
-    let mut lookup = HashMap::new();
+    let mut lookup = HashMap::default();
 
     for i in 1..6 {
         assert_eq!(

necsim/impls/no-std/src/cogs/lineage_store/coherent/globally/almost_infinite/mod.rs

@@ -1,5 +1,6 @@
 use core::{marker::PhantomData, ops::Index};
 
+use fnv::FnvBuildHasher;
 use hashbrown::hash_map::HashMap;
 use slab::Slab;
 
@@ -20,7 +21,7 @@ mod store;
 #[derive(Debug)]
 pub struct AlmostInfiniteLineageStore<M: MathsCore> {
     lineages_store: Slab<Lineage>,
-    location_to_lineage_reference: HashMap<Location, InMemoryLineageReference>,
+    location_to_lineage_reference: HashMap<Location, InMemoryLineageReference, FnvBuildHasher>,
     _marker: PhantomData<M>,
 }
 
@@ -46,7 +47,8 @@ impl<M: MathsCore> AlmostInfiniteLineageStore<M> {
         let lineages_amount_hint = origin_sampler.full_upper_bound_size_hint() as usize;
 
         let mut lineages_store = Slab::with_capacity(lineages_amount_hint);
-        let mut location_to_lineage_references = HashMap::with_capacity(lineages_amount_hint);
+        let mut location_to_lineage_references =
+            HashMap::with_capacity_and_hasher(lineages_amount_hint, FnvBuildHasher::default());
 
         for lineage in origin_sampler {
             location_to_lineage_references.insert(

necsim/impls/no-std/src/cogs/lineage_store/coherent/globally/gillespie/mod.rs

@@ -2,6 +2,7 @@ use core::{marker::PhantomData, ops::Index};
 
 use alloc::vec::Vec;
 
+use fnv::FnvBuildHasher;
 use hashbrown::hash_map::HashMap;
 use slab::Slab;
 
@@ -21,7 +22,7 @@ pub struct GillespieLineageStore<M: MathsCore, H: Habitat<M>> {
     lineages_store: Slab<Lineage>,
     location_to_lineage_references: Array2D<Vec<InMemoryLineageReference>>,
     indexed_location_to_lineage_reference:
-        HashMap<IndexedLocation, (GlobalLineageReference, usize)>,
+        HashMap<IndexedLocation, (GlobalLineageReference, usize), FnvBuildHasher>,
     _marker: PhantomData<(M, H)>,
 }
 
@@ -55,7 +56,7 @@ impl<'h, M: MathsCore, H: 'h + Habitat<M>> GillespieLineageStore<M, H> {
         );
 
         let mut indexed_location_to_lineage_reference =
-            HashMap::with_capacity(lineages_amount_hint);
+            HashMap::with_capacity_and_hasher(lineages_amount_hint, FnvBuildHasher::default());
 
         let x_from = landscape_extent.x();
         let y_from = landscape_extent.y();

necsim/impls/no-std/src/cogs/lineage_store/coherent/locally/classical/mod.rs

@@ -1,5 +1,6 @@
 use core::{marker::PhantomData, ops::Index};
 
+use fnv::FnvBuildHasher;
 use hashbrown::hash_map::HashMap;
 use slab::Slab;
 
@@ -17,7 +18,8 @@ mod store;
 #[derive(Debug)]
 pub struct ClassicalLineageStore<M: MathsCore, H: Habitat<M>> {
     lineages_store: Slab<Lineage>,
-    indexed_location_to_lineage_reference: HashMap<IndexedLocation, InMemoryLineageReference>,
+    indexed_location_to_lineage_reference:
+        HashMap<IndexedLocation, InMemoryLineageReference, FnvBuildHasher>,
     _marker: PhantomData<(M, H)>,
 }
 
@@ -43,7 +45,7 @@ impl<'h, M: MathsCore, H: 'h + Habitat<M>> ClassicalLineageStore<M, H> {
         let mut lineages_store = Slab::with_capacity(lineages_amount_hint);
 
         let mut indexed_location_to_lineage_reference =
-            HashMap::with_capacity(lineages_amount_hint);
+            HashMap::with_capacity_and_hasher(lineages_amount_hint, FnvBuildHasher::default());
 
         for lineage in origin_sampler {
             let indexed_location = lineage.indexed_location.clone();

necsim/plugins/metacommunity/Cargo.toml

@@ -17,3 +17,4 @@ necsim-plugins-core = { path = "../core", features = ["export"] }
 serde = { version = "1.0", features = ["derive"] }
 log = { version = "0.4" }
 rand = "0.8"
+fnv = "1.0"

necsim/plugins/metacommunity/src/lib.rs

@@ -5,6 +5,7 @@ extern crate log;
 
 use std::{collections::HashSet, fmt, num::NonZeroU64};
 
+use fnv::FnvBuildHasher;
 use rand::{rngs::StdRng, Rng, SeedableRng};
 use serde::{Deserialize, Serialize};
 
@@ -102,7 +103,8 @@ impl Reporter for MetacommunityMigrationReporter {
 
         let mut rng = StdRng::seed_from_u64(self.seed);
 
-        let mut unique_migration_targets = HashSet::new();
+        let mut unique_migration_targets =
+            HashSet::with_capacity_and_hasher(self.migrations, FnvBuildHasher::default());
 
         for _ in 0..self.migrations {
             unique_migration_targets.insert(rng.gen_range(0..metacommunity_size.get()));

necsim/plugins/species/Cargo.toml

@@ -18,3 +18,4 @@ necsim-plugins-core = { path = "../core", features = ["export"] }
 serde = { version = "1.0", features = ["derive"] }
 log = { version = "0.4" }
 rusqlite = "0.26"
+fnv = "1.0"

necsim/plugins/species/src/species/mod.rs

@@ -1,5 +1,6 @@
 use std::{collections::HashMap, convert::TryFrom, fmt, path::PathBuf};
 
+use fnv::FnvBuildHasher;
 use rusqlite::Connection;
 use serde::{Deserialize, Serialize};
 
@@ -26,9 +27,9 @@ pub struct SpeciesLocationsReporter {
     // Original (present-time) locations of all lineages
     origins: Vec<(GlobalLineageReference, IndexedLocation)>,
     // Child -> Parent lineage mapping
-    parents: HashMap<GlobalLineageReference, GlobalLineageReference>,
+    parents: HashMap<GlobalLineageReference, GlobalLineageReference, FnvBuildHasher>,
     // Species originator -> Species identities mapping
-    species: HashMap<GlobalLineageReference, SpeciesIdentity>,
+    species: HashMap<GlobalLineageReference, SpeciesIdentity, FnvBuildHasher>,
 
     output: PathBuf,
     table: String,
@@ -79,8 +80,8 @@ impl TryFrom<SpeciesLocationsReporterArgs> for SpeciesLocationsReporter {
             last_dispersal_event: None,
 
             origins: Vec::new(),
-            parents: HashMap::new(),
-            species: HashMap::new(),
+            parents: HashMap::default(),
+            species: HashMap::default(),
 
             output: args.output,
             table: args.table,

necsim/plugins/tskit/Cargo.toml

@@ -0,0 +1,31 @@
+[package]
+name = "necsim-plugins-tskit"
+version = "0.1.0"
+authors = ["Momo Langenstein <momo.langenstein17@imperial.ac.uk>"]
+license = "MIT OR Apache-2.0"
+edition = "2018"
+
+[lib]
+crate-type = ["cdylib"]
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+necsim-core = { path = "../../core" }
+necsim-core-bond = { path = "../../core/bond" }
+necsim-plugins-core = { path = "../core", features = ["export"] }
+
+serde = { version = "1.0", features = ["derive"] }
+serde_json = "1.0"
+tskit = { version = "0.5", features = ["provenance"] }
+uname = "0.1"
+findshlibs = "0.10"
+fnv = "1.0"
+
+rustc_version = "0.4"
+semver = { version = "1.0", features = ["serde"] }
+git-version = "0.3"
+
+[build-dependencies]
+rustc_version = "0.4"
+semver = "1.0"