Default values are now 'default'. (#87)

* Default values are now 'default'. * Pin extendr. * Correct pins for extendr and libR-sys.
mlondschien · Jan 21, 2022 · e1504e4 · e1504e4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,28 +1,37 @@
 # Changelog
 
+## 0.4.2 - (2021-01-21)
+
+**Other changes:**
+
+- The R-package now makes use of the latest version of `libR-sys`, enabling compilation for Apple silicon on `conda-forge` (#86).
+
+**Bug fixes:**
+
+- Fixed a bug where passing `Control()` to `changeforest` in the Python package overwrote the default value for `random_forest_max_depth` to `None`. Default values for `Control` in the python package are now `"default"` (#87).
+
 ## 0.4.1 - (2021-01-13)
 
 **Bug fixes:**
 
-- Upgrade `biosphere` to `0.2.1` fixing a bug in `RandomForest`.
+- Upgrade `biosphere` to `0.2.1` fixing a bug in `RandomForest` (#84).
 
 **Other changes:**
 
-- New parameter `model_selection_n_permutations`.
+- New parameter `model_selection_n_permutations` (#85).
 
 ## 0.4.0 - (2021-01-11)
 
 **New features:**
 
 - `changeforest` now uses random forests from [`biosphere`](https://github.com/mlondschien/biosphere).
-  This should be faster than `smartcore` used previously and supports parallelization.
+  This should be faster than `smartcore` used previously and supports parallelization (#82).
 
 ## 0.3.0 - (2021-12-15)
 
 **New features:**
 
-- Implemented trait `Display` for `BinarySegmentationResult`. In Python `str(result)`
-  now prints a pretty display (#77).
+- Implemented trait `Display` for `BinarySegmentationResult`. In Python `str(result)` now prints a pretty display (#77).
 
 **Other changes:**
 

diff --git a/Cargo.toml b/Cargo.toml
@@ -3,7 +3,7 @@ name = "changeforest"
 description = "Classifier based non-parametric change point detection."
 authors = ["Malte Londschien <malte@londschien.ch>"]
 repository = "https://github.com/mlondschien/changeforest/"
-version = "0.4.1"
+version = "0.4.2"
 edition = "2021"
 readme = "README.md"
 license = "BSD-3-Clause"

diff --git a/changeforest-py/Cargo.toml b/changeforest-py/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "changeforest_py"
-version = "0.4.1"
+version = "0.4.2"
 edition = "2021"
 
 [lib]

diff --git a/changeforest-py/changeforest/control.py b/changeforest-py/changeforest/control.py
@@ -7,17 +7,17 @@ class Control:
 
     def __init__(
         self,
-        minimal_relative_segment_length=None,
-        minimal_gain_to_split=None,
-        model_selection_alpha=None,
-        model_selection_n_permutations=None,
-        number_of_wild_segments=None,
-        seeded_segments_alpha=None,
-        seed=None,
-        random_forest_n_trees=None,
-        random_forest_max_depth=None,
-        random_forest_mtry=None,
-        random_forest_n_jobs=None,
+        minimal_relative_segment_length="default",
+        minimal_gain_to_split="default",
+        model_selection_alpha="default",
+        model_selection_n_permutations="default",
+        number_of_wild_segments="default",
+        seeded_segments_alpha="default",
+        seed="default",
+        random_forest_n_trees="default",
+        random_forest_max_depth="default",
+        random_forest_mtry="default",
+        random_forest_n_jobs="default",
     ):
         self.minimal_relative_segment_length = _to_float(
             minimal_relative_segment_length
@@ -37,12 +37,16 @@ def __init__(
 def _to_float(value):
     if value is None:
         return None
+    if value == "default":
+        return "default"
     else:
         return float(value)
 
 
 def _to_int(value):
     if value is None:
         return None
+    if value == "default":
+        return "default"
     else:
         return int(value)
diff --git a/changeforest-py/pyproject.toml b/changeforest-py/pyproject.toml
@@ -2,7 +2,7 @@
 name = "changeforest"
 description = "Classifier based non-parametric change point detection"
 readme = "README.md"
-version = "0.4.1"
+version = "0.4.2"
 requires-python = ">=3.7"
 author = "Malte Londschien <malte@londschien.ch>"
 urls = {homepage = "https://github.com/mlondschien/changeforest/"}

diff --git a/changeforest-py/tests/test_changeforest.py b/changeforest-py/tests/test_changeforest.py
@@ -18,9 +18,9 @@ def test_changeforest_repr(iris_dataset):
         == """\
                     best_split max_gain p_value
 (0, 150]                    50   96.322    0.01
- ¦--(0, 50]                 19   -6.524       1
- °--(50, 150]              100   53.855    0.01
-     ¦--(50, 100]           80   -6.793       1
-     °--(100, 150]         123   -7.479       1\
+ ¦--(0, 50]                 23  -10.204       1
+ °--(50, 150]              100   53.822    0.01
+     ¦--(50, 100]           79   -18.63       1
+     °--(100, 150]         134  -10.839       1\
 """
     )
diff --git a/changeforest-py/tests/test_control.py b/changeforest-py/tests/test_control.py
@@ -88,21 +88,24 @@ def test_control_segmentation_parameters(
     assert len(result.segments) == expected_number_of_segments
 
 
-def test_control_seed(iris_dataset):
-    result = changeforest(
-        iris_dataset,
-        "random_forest",
-        "wbs",
-        Control(seed=42, number_of_wild_segments=10),
+@pytest.mark.parametrize(
+    "key, default_value, another_value",
+    [
+        ("random_forest_n_trees", 100, 11),
+        ("minimal_relative_segment_length", 0.1, 0.05),
+        ("seed", 0, 1),
+        ("random_forest_mtry", None, 1),
+        ("random_forest_max_depth", 8, None),
+    ],
+)
+def test_control_defaults(iris_dataset, key, default_value, another_value):
+    result = changeforest(iris_dataset, "random_forest", "bs", Control())
+    default_result = changeforest(
+        iris_dataset, "random_forest", "bs", Control(**{key: default_value})
     )
-    assert result.segments[0].start == 5
-    assert abs(result.segments[0].max_gain - 11.38617) < 1e-5
-
-    result = changeforest(
-        iris_dataset,
-        "random_forest",
-        "wbs",
-        Control(seed=12, number_of_wild_segments=10),
+    another_result = changeforest(
+        iris_dataset, "random_forest", "bs", Control(**{key: another_value})
     )
-    assert result.segments[0].start == 21
-    assert abs(result.segments[0].max_gain - 44.98708) < 1e-5
+
+    assert str(result) == str(default_result)
+    assert str(result) != str(another_result)
diff --git a/changeforest-r/DESCRIPTION b/changeforest-r/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: changeforest
 Type: Package
 Title: Classifier Based Non-Parametric Change Point Detection
-Version: 0.4.1
+Version: 0.4.2
 Author: Malte Londschien
 Maintainer: Malte Londschien <malte@londschien.ch>
 Description: Perform classifier based multivariate, non-parametric change point detection.

diff --git a/changeforest-r/src/rust/Cargo.toml b/changeforest-r/src/rust/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = 'changeforestr'
-version = '0.4.1'
+version = '0.4.2'
 edition = '2021'
 
 [lib]
@@ -13,5 +13,5 @@ changeforest = { path = "../../../" }
 ndarray = "0.15.3"
 
 [patch.crates-io]
-libR-sys = { git = "https://github.com/extendr/libR-sys" }
-extendr-api = { git = 'https://github.com/extendr/extendr'} 
+libR-sys = { git = "https://github.com/extendr/libR-sys", rev = "355cf0de0dd7f28cfa3933a70b29deb247eb2017" }
+extendr-api = { git = "https://github.com/extendr/extendr", rev = "a59d65c50e001810dadba2d8624517a36b4725d2" } 
diff --git a/changeforest-r/tests/testthat/test-control.R b/changeforest-r/tests/testthat/test-control.R
@@ -29,13 +29,12 @@ test_that("control", {
     # seed
     result = changeforest(X_iris, "random_forest", "wbs", Control$new(number_of_wild_segments=10, seed=42))
     expect_equal(result$segments[[1]]$start, 5)
-    expect_equal(result$segments[[1]]$max_gain, 12.28034, tolerance=1e-5)
     result = changeforest(X_iris, "random_forest", "wbs", Control$new(number_of_wild_segments=10, seed=12))
     expect_equal(result$segments[[1]]$start, 21)
     expect_equal(result$segments[[1]]$max_gain, 44.987, tolerance=1e-5)
 
     # random_forest_ntree
-    expect_lists_equal(changeforest(X_iris, "random_forest", "bs", Control$new(random_forest_n_trees=1))$split_points(), c(47, 99))
+    expect_lists_equal(changeforest(X_iris, "random_forest", "bs", Control$new(random_forest_n_trees=1))$split_points(), c(37, 52, 99))
     expect_lists_equal(changeforest(X_iris, "random_forest", "bs", Control$new(random_forest_n_trees=100))$split_points(), c(50, 100))
     expect_lists_equal(changeforest(X, "random_forest", "bs", Control$new(random_forest_n_trees=1))$split_points(), c())
     expect_lists_equal(changeforest(X, "random_forest", "bs", Control$new(random_forest_n_trees=1))$split_points(), c())

diff --git a/src/control.rs b/src/control.rs
@@ -45,7 +45,7 @@ impl Control {
             random_forest_n_trees: 100,
             random_forest_mtry: None,
             random_forest_n_jobs: None,
-            random_forest_max_depth: Some(4),
+            random_forest_max_depth: Some(8),
         }
     }