feat: save subset of variables

python/rebop/__init__.py

@@ -1,9 +1,14 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import xarray as xr
 
 from .rebop import Gillespie, __version__  # type: ignore[attr-defined]
 
+if TYPE_CHECKING:
+    from collections.abc import Sequence
+
 __all__ = ("Gillespie", "__version__")
 
 og_run = Gillespie.run
@@ -17,13 +22,22 @@ def run_xarray(  # noqa: PLR0913 too many parameters in function definition
     seed: int | None = None,
     *,
     sparse: bool = False,
+    var_names: Sequence[str] | None = None,
 ) -> xr.Dataset:
     """Run the system until `tmax` with `nb_steps` steps.
 
     The initial configuration is specified in the dictionary `init`.
     Returns an xarray Dataset.
     """
-    times, result = og_run(self, init, tmax, nb_steps, seed, sparse=sparse)
+    times, result = og_run(
+        self,
+        init,
+        tmax,
+        nb_steps,
+        seed,
+        sparse=sparse,
+        var_names=var_names,
+    )
     ds = xr.Dataset(
         data_vars={
             name: xr.DataArray(values, dims="time", coords={"time": times})

python/rebop/rebop.pyi

@@ -1,3 +1,5 @@
+from collections.abc import Sequence
+
 import xarray
 
 class Gillespie:
@@ -32,6 +34,7 @@ class Gillespie:
         seed: int | None = None,
         *,
         sparse: bool = False,
+        var_names: Sequence[str] | None = None,
     ) -> xarray.Dataset:
         """Run the system until `tmax` with `nb_steps` steps.
 

src/lib.rs

@@ -303,14 +303,15 @@ impl Gillespie {
     /// values at the given time points.  One can specify a random `seed` for reproducibility.
     /// If `nb_steps` is `0`, then returns all reactions, ending with the first that happens at
     /// or after `tmax`.
-    #[pyo3(signature = (init, tmax, nb_steps, seed=None, sparse=false))]
+    #[pyo3(signature = (init, tmax, nb_steps, seed=None, sparse=false, var_names=None))]
     fn run(
         &self,
         init: HashMap<String, usize>,
         tmax: f64,
         nb_steps: usize,
         seed: Option<u64>,
         sparse: bool,
+        var_names: Option<Vec<String>>,
     ) -> PyResult<(Vec<f64>, HashMap<String, Vec<isize>>)> {
         let mut x0 = vec![0; self.species.len()];
         for (name, &value) in &init {
@@ -322,6 +323,13 @@ impl Gillespie {
             Some(seed) => gillespie::Gillespie::new_with_seed(x0, sparse, seed),
             None => gillespie::Gillespie::new(x0, sparse),
         };
+        let save_indices: Vec<_> = match &var_names {
+            Some(x) => x
+                .iter()
+                .map(|key| self.species.get(key).unwrap().clone())
+                .collect(),
+            None => (0..self.species.len()).collect(),
+        };
 
         for (rate, reactants, products) in self.reactions.iter() {
             let mut vreactants = vec![0; self.species.len()];
@@ -340,34 +348,43 @@ impl Gillespie {
         }
         let mut times = Vec::new();
         // species.shape = (species, nb_steps)
-        let mut species = vec![Vec::new(); self.species.len()];
+        let mut species = vec![Vec::new(); save_indices.len()];
         if nb_steps > 0 {
             for i in 0..=nb_steps {
                 let t = tmax * i as f64 / nb_steps as f64;
                 times.push(t);
                 g.advance_until(t);
-                for s in 0..self.species.len() {
-                    species[s].push(g.get_species(s));
+                for (i, s) in save_indices.iter().enumerate() {
+                    species[i].push(g.get_species(*s));
                 }
             }
         } else {
             // nb_steps = 0: we return every step
             let mut rates = vec![f64::NAN; g.nb_reactions()];
             times.push(g.get_time());
-            for s in 0..self.species.len() {
-                species[s].push(g.get_species(s));
+            for (i, s) in save_indices.iter().enumerate() {
+                species[i].push(g.get_species(*s));
             }
             while g.get_time() < tmax {
                 g._advance_one_reaction(&mut rates);
                 times.push(g.get_time());
-                for s in 0..self.species.len() {
-                    species[s].push(g.get_species(s));
+                for (i, s) in save_indices.iter().enumerate() {
+                    species[i].push(g.get_species(*s));
                 }
             }
         }
         let mut result = HashMap::new();
-        for (name, &id) in &self.species {
-            result.insert(name.clone(), species[id].clone());
+        match var_names {
+            Some(x) => {
+                for (id, name) in x.iter().enumerate() {
+                    result.insert(name.clone(), species[id].clone());
+                }
+            }
+            None => {
+                for (name, &id) in &self.species {
+                    result.insert(name.clone(), species[id].clone());
+                }
+            }
         }
         Ok((times, result))
     }

tests/test_rebop.py

@@ -55,7 +55,33 @@ def test_all_reactions(seed: int) -> None:
 def test_dense_vs_sparse() -> None:
     sir = sir_model()
     init = {"S": 999, "I": 1}
-    kwargs = {"tmax": 250, "nb_steps": 250, "seed": 42}
-    ds_dense = sir.run(init, **kwargs, sparse=False)
-    ds_sparse = sir.run(init, **kwargs, sparse=True)
+    tmax = 250
+    nb_steps = 250
+    seed = 42
+    ds_dense = sir.run(init, tmax=tmax, nb_steps=nb_steps, seed=seed, sparse=False)
+    ds_sparse = sir.run(init, tmax=tmax, nb_steps=nb_steps, seed=seed, sparse=True)
     assert (ds_dense == ds_sparse).all()
+
+
+@pytest.mark.parametrize("nb_steps", [0, 250])
+def test_var_names(nb_steps: int) -> None:
+    all_variables = {"S", "I", "R"}
+    subset_to_save = ["S", "I"]
+    remaining = all_variables.difference(subset_to_save)
+
+    sir = sir_model()
+    init = {"S": 999, "I": 1}
+    tmax = 250
+    seed = 0
+
+    ds_all = sir.run(init, tmax=tmax, nb_steps=nb_steps, seed=seed, var_names=None)
+    ds_subset = sir.run(
+        init, tmax=tmax, nb_steps=nb_steps, seed=seed, var_names=subset_to_save
+    )
+
+    for s in subset_to_save:
+        assert s in ds_subset
+    for s in remaining:
+        assert s not in ds_subset
+
+    assert ds_all[subset_to_save] == ds_subset