Merge pull request #1 from smartcorelib/development

update

.circleci/config.yml

@@ -6,6 +6,8 @@ workflows:
     jobs:
       - build
       - clippy
+      - coverage
+
 jobs:
   build:
     docker:
@@ -21,10 +23,10 @@ jobs:
           command: cargo fmt -- --check
       - run:
           name: Stable Build
-          command: cargo build --features "nalgebra-bindings ndarray-bindings"
+          command: cargo build --all-features
       - run:
           name: Test
-          command: cargo test --features "nalgebra-bindings ndarray-bindings"
+          command: cargo test --all-features
       - save_cache:
           key: project-cache
           paths:
@@ -41,3 +43,17 @@ jobs:
       - run:
           name: Run cargo clippy
           command: cargo clippy --all-features -- -Drust-2018-idioms -Dwarnings
+
+  coverage:
+    machine: true
+    steps:
+      - checkout
+      - run:
+          name: Generate report
+          command: >
+            docker run --security-opt seccomp=unconfined -v $PWD:/volume
+            xd009642/tarpaulin:latest-nightly cargo tarpaulin -v --ciserver circle-ci
+            --out Lcov --all-features -- --test-threads 1
+      - run:
+          name: Upload
+          command: bash <(curl -s https://codecov.io/bash) -Z -f

Cargo.toml

@@ -2,7 +2,7 @@
 name = "smartcore"
 description = "The most advanced machine learning library in rust."
 homepage = "https://smartcorelib.org"
-version = "0.1.0"
+version = "0.2.0"
 authors = ["SmartCore Developers"]
 edition = "2018"
 license = "Apache-2.0"
@@ -19,14 +19,13 @@ nalgebra-bindings = ["nalgebra"]
 datasets = []
 
 [dependencies]
-ndarray = { version = "0.13", optional = true }
-nalgebra = { version = "0.22.0", optional = true }
+ndarray = { version = "0.14", optional = true }
+nalgebra = { version = "0.23.0", optional = true }
 num-traits = "0.2.12"
 num = "0.3.0"
 rand = "0.7.3"
 rand_distr = "0.3.0"
-serde = { version = "1.0.115", features = ["derive"] }
-serde_derive = "1.0.115"
+serde = { version = "1.0.115", features = ["derive"], optional = true }
 
 [dev-dependencies]
 criterion = "0.3"
@@ -35,4 +34,9 @@ bincode = "1.3.1"
 
 [[bench]]
 name = "distance"
-harness = false
+harness = false
+
+[[bench]]
+name = "naive_bayes"
+harness = false
+required-features = ["ndarray-bindings", "nalgebra-bindings"]

benches/naive_bayes.rs

@@ -0,0 +1,73 @@
+use criterion::BenchmarkId;
+use criterion::{black_box, criterion_group, criterion_main, Criterion};
+
+use nalgebra::DMatrix;
+use ndarray::Array2;
+use smartcore::linalg::naive::dense_matrix::DenseMatrix;
+use smartcore::linalg::BaseMatrix;
+use smartcore::linalg::BaseVector;
+use smartcore::naive_bayes::gaussian::GaussianNB;
+
+pub fn gaussian_naive_bayes_fit_benchmark(c: &mut Criterion) {
+    let mut group = c.benchmark_group("GaussianNB::fit");
+
+    for n_samples in [100_usize, 1000_usize, 10000_usize].iter() {
+        for n_features in [10_usize, 100_usize, 1000_usize].iter() {
+            let x = DenseMatrix::<f64>::rand(*n_samples, *n_features);
+            let y: Vec<f64> = (0..*n_samples)
+                .map(|i| (i % *n_samples / 5_usize) as f64)
+                .collect::<Vec<f64>>();
+            group.bench_with_input(
+                BenchmarkId::from_parameter(format!(
+                    "n_samples: {}, n_features: {}",
+                    n_samples, n_features
+                )),
+                n_samples,
+                |b, _| {
+                    b.iter(|| {
+                        GaussianNB::fit(black_box(&x), black_box(&y), Default::default()).unwrap();
+                    })
+                },
+            );
+        }
+    }
+    group.finish();
+}
+
+pub fn gaussian_naive_matrix_datastructure(c: &mut Criterion) {
+    let mut group = c.benchmark_group("GaussianNB");
+    let classes = (0..10000).map(|i| (i % 25) as f64).collect::<Vec<f64>>();
+
+    group.bench_function("DenseMatrix", |b| {
+        let x = DenseMatrix::<f64>::rand(10000, 500);
+        let y = <DenseMatrix<f64> as BaseMatrix<f64>>::RowVector::from_array(&classes);
+
+        b.iter(|| {
+            GaussianNB::fit(black_box(&x), black_box(&y), Default::default()).unwrap();
+        })
+    });
+
+    group.bench_function("ndarray", |b| {
+        let x = Array2::<f64>::rand(10000, 500);
+        let y = <Array2<f64> as BaseMatrix<f64>>::RowVector::from_array(&classes);
+
+        b.iter(|| {
+            GaussianNB::fit(black_box(&x), black_box(&y), Default::default()).unwrap();
+        })
+    });
+
+    group.bench_function("ndalgebra", |b| {
+        let x = DMatrix::<f64>::rand(10000, 500);
+        let y = <DMatrix<f64> as BaseMatrix<f64>>::RowVector::from_array(&classes);
+
+        b.iter(|| {
+            GaussianNB::fit(black_box(&x), black_box(&y), Default::default()).unwrap();
+        })
+    });
+}
+criterion_group!(
+    benches,
+    gaussian_naive_bayes_fit_benchmark,
+    gaussian_naive_matrix_datastructure
+);
+criterion_main!(benches);

src/algorithm/neighbour/bbd_tree.rs

@@ -44,10 +44,7 @@ impl<T: RealNumber> BBDTree<T> {
 
         let (n, _) = data.shape();
 
-        let mut index = vec![0; n];
-        for i in 0..n {
-            index[i] = i;
-        }
+        let index = (0..n).collect::<Vec<_>>();
 
         let mut tree = BBDTree {
             nodes,
@@ -64,7 +61,7 @@ impl<T: RealNumber> BBDTree<T> {
 
     pub(in crate) fn clustering(
         &self,
-        centroids: &Vec<Vec<T>>,
+        centroids: &[Vec<T>],
         sums: &mut Vec<Vec<T>>,
         counts: &mut Vec<usize>,
         membership: &mut Vec<usize>,
@@ -92,8 +89,8 @@ impl<T: RealNumber> BBDTree<T> {
     fn filter(
         &self,
         node: usize,
-        centroids: &Vec<Vec<T>>,
-        candidates: &Vec<usize>,
+        centroids: &[Vec<T>],
+        candidates: &[usize],
         k: usize,
         sums: &mut Vec<Vec<T>>,
         counts: &mut Vec<usize>,
@@ -117,15 +114,15 @@ impl<T: RealNumber> BBDTree<T> {
             let mut new_candidates = vec![0; k];
             let mut newk = 0;
 
-            for i in 0..k {
+            for candidate in candidates.iter().take(k) {
                 if !BBDTree::prune(
                     &self.nodes[node].center,
                     &self.nodes[node].radius,
                     centroids,
                     closest,
-                    candidates[i],
+                    *candidate,
                 ) {
-                    new_candidates[newk] = candidates[i];
+                    new_candidates[newk] = *candidate;
                     newk += 1;
                 }
             }
@@ -166,9 +163,9 @@ impl<T: RealNumber> BBDTree<T> {
     }
 
     fn prune(
-        center: &Vec<T>,
-        radius: &Vec<T>,
-        centroids: &Vec<Vec<T>>,
+        center: &[T],
+        radius: &[T],
+        centroids: &[Vec<T>],
         best_index: usize,
         test_index: usize,
     ) -> bool {
@@ -285,8 +282,8 @@ impl<T: RealNumber> BBDTree<T> {
         }
 
         let mut mean = vec![T::zero(); d];
-        for i in 0..d {
-            mean[i] = node.sum[i] / T::from(node.count).unwrap();
+        for (i, mean_i) in mean.iter_mut().enumerate().take(d) {
+            *mean_i = node.sum[i] / T::from(node.count).unwrap();
         }
 
         node.cost = BBDTree::node_cost(&self.nodes[node.lower.unwrap()], &mean)
@@ -295,11 +292,11 @@ impl<T: RealNumber> BBDTree<T> {
         self.add_node(node)
     }
 
-    fn node_cost(node: &BBDTreeNode<T>, center: &Vec<T>) -> T {
+    fn node_cost(node: &BBDTreeNode<T>, center: &[T]) -> T {
         let d = center.len();
         let mut scatter = T::zero();
-        for i in 0..d {
-            let x = (node.sum[i] / T::from(node.count).unwrap()) - center[i];
+        for (i, center_i) in center.iter().enumerate().take(d) {
+            let x = (node.sum[i] / T::from(node.count).unwrap()) - *center_i;
             scatter += x * x;
         }
         node.cost + T::from(node.count).unwrap() * scatter

src/algorithm/neighbour/cover_tree.rs

@@ -6,6 +6,7 @@
 //! use smartcore::algorithm::neighbour::cover_tree::*;
 //! use smartcore::math::distance::Distance;
 //!
+//! #[derive(Clone)]
 //! struct SimpleDistance {} // Our distance function
 //!
 //! impl Distance<i32, f64> for SimpleDistance {
@@ -23,6 +24,7 @@
 //! ```
 use std::fmt::Debug;
 
+#[cfg(feature = "serde")]
 use serde::{Deserialize, Serialize};
 
 use crate::algorithm::sort::heap_select::HeapSelection;
@@ -31,7 +33,8 @@ use crate::math::distance::Distance;
 use crate::math::num::RealNumber;
 
 /// Implements Cover Tree algorithm
-#[derive(Serialize, Deserialize, Debug)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug)]
 pub struct CoverTree<T, F: RealNumber, D: Distance<T, F>> {
     base: F,
     inv_log_base: F,
@@ -55,7 +58,8 @@ impl<T, F: RealNumber, D: Distance<T, F>> PartialEq for CoverTree<T, F, D> {
     }
 }
 
-#[derive(Debug, Serialize, Deserialize)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug)]
 struct Node<F: RealNumber> {
     idx: usize,
     max_dist: F,
@@ -64,7 +68,7 @@ struct Node<F: RealNumber> {
     scale: i64,
 }
 
-#[derive(Debug, Serialize, Deserialize)]
+#[derive(Debug)]
 struct DistanceSet<F: RealNumber> {
     idx: usize,
     dist: Vec<F>,
@@ -436,7 +440,7 @@ impl<T: Debug + PartialEq, F: RealNumber, D: Distance<T, F>> CoverTree<T, F, D>
         }
     }
 
-    fn max(&self, distance_set: &Vec<DistanceSet<F>>) -> F {
+    fn max(&self, distance_set: &[DistanceSet<F>]) -> F {
         let mut max = F::zero();
         for n in distance_set {
             if max < n.dist[n.dist.len() - 1] {
@@ -453,7 +457,8 @@ mod tests {
     use super::*;
     use crate::math::distance::Distances;
 
-    #[derive(Debug, Serialize, Deserialize)]
+    #[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+    #[derive(Debug, Clone)]
     struct SimpleDistance {}
 
     impl Distance<i32, f64> for SimpleDistance {
@@ -499,6 +504,7 @@ mod tests {
     }
 
     #[test]
+    #[cfg(feature = "serde")]
     fn serde() {
         let data = vec![1, 2, 3, 4, 5, 6, 7, 8, 9];
 

src/algorithm/neighbour/linear_search.rs

@@ -5,6 +5,7 @@
 //! use smartcore::algorithm::neighbour::linear_search::*;
 //! use smartcore::math::distance::Distance;
 //!
+//! #[derive(Clone)]
 //! struct SimpleDistance {} // Our distance function
 //!
 //! impl Distance<i32, f64> for SimpleDistance {
@@ -21,6 +22,7 @@
 //!
 //! ```
 
+#[cfg(feature = "serde")]
 use serde::{Deserialize, Serialize};
 use std::cmp::{Ordering, PartialOrd};
 use std::marker::PhantomData;
@@ -31,7 +33,8 @@ use crate::math::distance::Distance;
 use crate::math::num::RealNumber;
 
 /// Implements Linear Search algorithm, see [KNN algorithms](../index.html)
-#[derive(Serialize, Deserialize, Debug)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug)]
 pub struct LinearKNNSearch<T, F: RealNumber, D: Distance<T, F>> {
     distance: D,
     data: Vec<T>,
@@ -137,6 +140,8 @@ mod tests {
     use super::*;
     use crate::math::distance::Distances;
 
+    #[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+    #[derive(Debug, Clone)]
     struct SimpleDistance {}
 
     impl Distance<i32, f64> for SimpleDistance {

src/algorithm/neighbour/mod.rs

@@ -1,3 +1,4 @@
+#![allow(clippy::ptr_arg)]
 //! # Nearest Neighbors Search Algorithms and Data Structures
 //!
 //! Nearest neighbor search is a basic computational tool that is particularly relevant to machine learning,
@@ -34,6 +35,7 @@ use crate::algorithm::neighbour::linear_search::LinearKNNSearch;
 use crate::error::Failed;
 use crate::math::distance::Distance;
 use crate::math::num::RealNumber;
+#[cfg(feature = "serde")]
 use serde::{Deserialize, Serialize};
 
 pub(crate) mod bbd_tree;
@@ -44,15 +46,17 @@ pub mod linear_search;
 
 /// Both, KNN classifier and regressor benefits from underlying search algorithms that helps to speed up queries.
 /// `KNNAlgorithmName` maintains a list of supported search algorithms, see [KNN algorithms](../algorithm/neighbour/index.html)
-#[derive(Serialize, Deserialize, Debug, Clone)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug, Clone)]
 pub enum KNNAlgorithmName {
     /// Heap Search algorithm, see [`LinearSearch`](../algorithm/neighbour/linear_search/index.html)
     LinearSearch,
     /// Cover Tree Search algorithm, see [`CoverTree`](../algorithm/neighbour/cover_tree/index.html)
     CoverTree,
 }
 
-#[derive(Serialize, Deserialize, Debug)]
+#[cfg_attr(feature = "serde", derive(Serialize, Deserialize))]
+#[derive(Debug)]
 pub(crate) enum KNNAlgorithm<T: RealNumber, D: Distance<Vec<T>, T>> {
     LinearSearch(LinearKNNSearch<Vec<T>, T, D>),
     CoverTree(CoverTree<Vec<T>, T, D>),