Update deps

CHANGELOG.md

@@ -1,6 +1,12 @@
 
 # Changelog
 
+## 2.0.0 - (2025-12-11)
+
+**Breaking changes:**
+
+- Update `ndarray` to 0.17.1, `biosphere` to 0.4.2, `numpy` and `pyo3` to 0.27.1, `r-extendr` to 0.8.1, and `rand` from 0.8 to 0.9. As the rust crate `rand` changed the algorithm for the `Uniform` distribution, this breaks backwards reproducibility.
+
 ## 1.2.1 - (2025-09-22)
 
 **Bug fixes:**

Cargo.toml

@@ -3,7 +3,7 @@ name = "changeforest"
 description = "Random Forests for Change Point Detection"
 authors = ["Malte Londschien <malte@londschien.ch>"]
 repository = "https://github.com/mlondschien/changeforest/"
-version = "1.2.1"
+version = "2.0.0"
 edition = "2021"
 readme = "README.md"
 license = "BSD-3-Clause"
@@ -13,14 +13,14 @@ exclude = ["/.github", "/changeforest-py", "/changeforest-r", "/testdata", ".pre
 name = "changeforest"
 
 [dependencies]
-ndarray = "0.16"
-rand = "0.8"
-biosphere = "0.4.0"
+ndarray = "0.17.1"
+rand = "0.9"
+biosphere = "0.4.2"
 
 [dev-dependencies]
 rstest = "0.26"
 assert_approx_eq = "1.1"
-ndarray-rand = "0.15"
-ndarray = { version = "0.16", features = ["approx"] }
-ndarray-csv = "^0.5"
+ndarray-rand = "0.16"
+ndarray = { version = "0.17.1", features = ["approx"] }
+ndarray-csv = "0.5.4"
 csv = "^1"

changeforest-py/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "changeforest_py"
-version = "1.2.1"
+version = "2.0.0"
 edition = "2021"
 readme = "README.md" 
 
@@ -12,8 +12,8 @@ crate-type = ["cdylib"]
 name = "changeforest"
 
 [dependencies]
-numpy = "0.26"
+numpy = "0.27.1"
 changeforest = { path = "../" }
-ndarray = "0.16"
-pyo3 = {version = "0.26", features = ["extension-module"]}
-biosphere = "0.4.0"
+ndarray = "0.17.1"
+pyo3 = {version = "0.27", features = ["extension-module"]}
+biosphere = "0.4.2"

changeforest-py/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "changeforest"
 description = "Random Forests for Change Point Detection"
-version = "1.2.1"
+version = "2.0.0"
 readme = "README.md"
 requires-python = ">=3.8"
 author = "Malte Londschien <malte@londschien.ch>"

changeforest-py/src/control.rs

@@ -1,9 +1,9 @@
 use biosphere::MaxFeatures;
 use changeforest::Control;
 use pyo3::exceptions;
-use pyo3::prelude::{pyclass, Bound, FromPyObject, PyAny, PyErr, PyResult};
+use pyo3::prelude::{pyclass, FromPyObject, PyAny, PyErr, PyResult};
 use pyo3::prelude::{Py, Python};
-use pyo3::types::PyAnyMethods;
+use pyo3::Borrowed;
 
 pub fn control_from_pyobj(py: Python, obj: Option<Py<PyAny>>) -> PyResult<Control> {
     let mut control = Control::default();
@@ -109,8 +109,10 @@ impl PyMaxFeatures {
     }
 }
 
-impl FromPyObject<'_> for PyMaxFeatures {
-    fn extract_bound(ob: &Bound<'_, PyAny>) -> PyResult<Self> {
+impl<'py> FromPyObject<'_, 'py> for PyMaxFeatures {
+    type Error = PyErr;
+
+    fn extract(ob: Borrowed<'_, 'py, PyAny>) -> PyResult<Self> {
         if let Ok(value) = ob.extract::<usize>() {
             Ok(PyMaxFeatures::new(MaxFeatures::Value(value)))
         } else if let Ok(value) = ob.extract::<f64>() {

changeforest-py/tests/test_changeforest.py

@@ -22,11 +22,11 @@ def test_changeforest_repr(iris_dataset):
         result.__repr__()
         == """\
                     best_split max_gain p_value
-(0, 150]                    50   96.233   0.005
- ¦--(0, 50]                  2  -14.191       1
- °--(50, 150]              100   52.799   0.005
-     ¦--(50, 100]           53     5.44   0.245
-     °--(100, 150]         136   -2.398   0.875\
+(0, 150]                    50   95.867   0.005
+ ¦--(0, 50]                  2   -14.37       1
+ °--(50, 150]              100   52.853   0.005
+     ¦--(50, 100]           53    5.152    0.27
+     °--(100, 150]         102   -6.981     0.9\
 """
     )
 
@@ -42,12 +42,12 @@ def test_changeforest_repr_segments(iris_dataset):
         result.__repr__()
         == """\
                     best_split max_gain p_value
-(0, 150]                    50     95.1   0.005
+(0, 150]                    50   94.844   0.005
  ¦--(0, 50]                                    
- °--(50, 150]              100   52.799   0.005
-     ¦--(50, 100]           53    6.892   0.315
-     °--(100, 150]         136   -3.516    0.68\
-"""  # noqa: W291
+ °--(50, 150]              100   52.853   0.005
+     ¦--(50, 100]           53    5.152    0.28
+     °--(100, 150]         147  -12.303   0.975\
+"""  # noqa W291
     )
 
 
@@ -62,10 +62,10 @@ def test_changeforest_repr_segments2(iris_dataset):
         result.__repr__()
         == """\
                     best_split max_gain p_value
-(0, 150]                    49   87.462   0.005
- ¦--(0, 49]                  2   -8.889   0.995
- °--(49, 150]              102   41.237   0.005
+(0, 150]                    49   87.437   0.005
+ ¦--(0, 49]                  2   -13.76    0.96
+ °--(49, 150]              102   34.621   0.005
      ¦--(49, 102]                              
-     °--(102, 150]         136    1.114    0.36\
-"""  # noqa: W291
+     °--(102, 150]         138    0.301   0.475\
+"""  # noqa W291
     )

changeforest-py/tests/test_control.py

@@ -27,26 +27,25 @@
             "change_in_mean",
             {"minimal_gain_to_split": None},
             [50, 100],
-        ),  # log(150) * 4 / 150
+        ),
         # model_selection_alpha
         ("iris", "bs", "knn", {"model_selection_alpha": 0.001}, []),
         ("iris", "bs", "knn", {"model_selection_alpha": 0.05}, [50, 100]),
         # random_forest_n_estimators
-        # This is impressive and unexpected.
-        ("iris", "bs", "random_forest", {"random_forest_n_estimators": 1}, [47, 99]),
+        ("iris", "bs", "random_forest", {"random_forest_n_estimators": 1}, [48]),
         ("iris", "bs", "random_forest", {"random_forest_n_estimators": 100}, [50, 100]),
         # Use X_test instead
         ("X_test", "bs", "random_forest", {"random_forest_n_estimators": 1}, []),
         ("X_test", "bs", "random_forest", {"random_forest_n_estimators": 1.0}, []),
-        ("X_test", "bs", "random_forest", {"random_forest_n_estimators": 100}, [5]),
+        ("X_test", "bs", "random_forest", {"random_forest_n_estimators": 100}, [3, 5]),
         ("X_correlated", "bs", "random_forest", {"random_forest_max_depth": 1}, []),
-        ("X_correlated", "bs", "random_forest", {"random_forest_max_depth": 2}, [49]),
+        ("X_correlated", "bs", "random_forest", {"random_forest_max_depth": 2}, [50]),
         (
             "X_correlated",
             "bs",
             "random_forest",
             {"random_forest_max_features": "sqrt"},
-            [49],
+            [50],
         ),
         ("iris", "bs", "random_forest", {"model_selection_n_permutations": 10}, []),
     ],

changeforest-r/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: changeforest
 Type: Package
 Title: Random Forests for Change Point Detection
-Version: 1.2.1
+Version: 2.0.0
 Author: Malte Londschien
 Maintainer: Malte Londschien <malte@londschien.ch>
 Description:

changeforest-r/src/rust/Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = 'changeforestr'
 publish = false
-version = '1.2.1'
+version = '2.0.0'
 edition = '2021'
 
 [lib]
@@ -11,5 +11,5 @@ name = 'changeforestr'
 [dependencies]
 extendr-api = { version="0.8", features = ["ndarray"] }
 changeforest = { path = "../../../" }
-ndarray = "0.16"
-biosphere = "0.4.0"
+ndarray = "0.17.1"
+biosphere = "0.4.2"

src/segmentation.rs

@@ -2,7 +2,7 @@ use crate::optimizer::OptimizerResult;
 use crate::ModelSelectionResult;
 use crate::Optimizer;
 use rand::{
-    distributions::{Distribution, Uniform},
+    distr::{Distribution, Uniform},
     rngs::StdRng,
     SeedableRng,
 };
@@ -68,7 +68,7 @@ impl<'a> Segmentation<'a> {
             }
             SegmentationType::WBS => {
                 let mut rng = StdRng::seed_from_u64(optimizer.control().seed);
-                let dist = Uniform::from(0..(optimizer.n() + 1));
+                let dist = Uniform::new(0, optimizer.n() + 1).unwrap();
 
                 let mut start: usize;
                 let mut stop: usize;
@@ -181,11 +181,11 @@ mod tests {
         (50, 100, 62, 3000.0)
     ])]
     #[case(SegmentationType::WBS, vec![
-        (73, 78, 74, 415.0),
-        (2, 59, 16, 684.0),
-        (26, 77, 38, 1836.0),
-        (22, 80, 36, 1856.0),
-        (75, 97, 80, 1870.0)
+        (56, 78, 61, 1452.0),
+        (12, 77, 28, 1430.0),
+        (7, 22, 10, 255.0),
+        (79, 80, 79, 89.0),
+        (62, 75, 65, 936.0)
     ])]
     fn test_generate_segments(
         #[case] segmentation_type: SegmentationType,
@@ -212,7 +212,7 @@ mod tests {
     #[rstest]
     #[case(SegmentationType::BS, (25, 1000.))]
     #[case(SegmentationType::SBS, (62, 3000.))]
-    #[case(SegmentationType::WBS, (60, 2900.))]
+    #[case(SegmentationType::WBS, (60, 2958.))]
     fn test_optimizer(#[case] segmentation_type: SegmentationType, #[case] expected: (usize, f64)) {
         let control = Control::default();
         let optimizer = testing::TrivialOptimizer { control: &control };

src/testing.rs

@@ -209,7 +209,7 @@ pub fn array() -> Array2<f64> {
     X.slice_mut(s![25..40, 2]).fill(3.);
     X.slice_mut(s![25..80, 1]).fill(-2.);
 
-    X + Array::random_using((100, 5), Uniform::new(0., 1.), &mut rng)
+    X + Array::random_using((100, 5), Uniform::new(0., 1.).unwrap(), &mut rng)
 }
 
 #[cfg(test)]