feat!: Update strum and ordered-float dependencies and change From<LogProb> into TryFrom<LogProb> for NotNan<f64>.

CHANGELOG.md

@@ -2,6 +2,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+
+## [0.42.0](https://www.github.com/rust-bio/rust-bio/compare/v0.42.0...v0.41.0) (2022-05-03)
+
+* Change `impl From<LogProb> for NotNan<f64>` to `impl TryFrom<LogProb> for NotNan<f64>` to indicate the conversion can fail.
+* Upgrade `strum` to version `0.24`
+* Upgrade `ordered-float` to `2.0`
+
 ## [0.41.0](https://www.github.com/rust-bio/rust-bio/compare/v0.40.0...v0.41.0) (2022-03-30)
 
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bio"
-version = "0.41.0"
+version = "0.42.0"
 authors = ["Johannes Köster <johannes.koester@tu-dortmund.de>"]
 description = "A bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields."
 homepage = "https://rust-bio.github.io"
@@ -37,16 +37,16 @@ serde_derive = "1.0"
 approx = ">=0.3, <0.6"
 custom_derive = "0.1"
 newtype_derive = "0.1"
-ordered-float = "1.0"
+ordered-float = "2.0"
 regex = { version = "1.3", default-features = false, features = ["std", "perf"] }
 multimap = ">=0.6, <0.9"
 fxhash = "0.2"
 statrs = ">= 0.11, < 0.16"
 bio-types = ">=0.11.0"
 pest = { version = "2", optional = true }
 pest_derive = { version = "2", optional = true }
-strum = ">= 0.16, < 0.24"
-strum_macros = ">= 0.16, < 0.24"
+strum = "0.24"
+strum_macros = "0.24"
 getset = ">=0.0.9, <0.2"
 enum-map = ">=0.6.4, <2"
 triple_accel = ">=0.3, <0.5"

src/pattern_matching/pssm/mod.rs

@@ -296,7 +296,7 @@ pub trait Motif {
         let bits = Self::get_bits();
         let scores = self.get_scores();
         let mut tot = 0.0;
-        for row in scores.genrows() {
+        for row in scores.rows() {
             tot += bits - ent(row.iter());
         }
         tot

src/stats/probs/adaptive_integration.rs

@@ -5,7 +5,7 @@
 
 use std::cmp;
 use std::collections::HashMap;
-use std::convert::Into;
+use std::convert::{Into, TryFrom};
 use std::hash::Hash;
 use std::{
     fmt::Debug,
@@ -43,7 +43,7 @@ use ordered_float::NotNan;
 /// );
 /// abs_diff_eq!(integral.exp(), 0.682, epsilon=0.01);
 /// ```
-pub fn ln_integrate_exp<T, F>(
+pub fn ln_integrate_exp<T, F, E>(
     mut density: F,
     min_point: T,
     max_point: T,
@@ -57,10 +57,11 @@ where
         + Div<NotNan<f64>, Output = T>
         + Mul<Output = T>
         + Into<f64>
-        + From<f64>
+        + TryFrom<f64, Error = E>
         + Ord
         + Debug
         + Hash,
+    E: Debug,
     F: FnMut(T) -> LogProb,
     f64: From<T>,
 {
@@ -112,7 +113,7 @@ where
     // METHOD additionally investigate small interval around the optimum
     for point in linspace(
         cmp::max(
-            middle.unwrap() - (max_resolution.into() * 3.0).into(),
+            middle.unwrap() - T::try_from(max_resolution.into() * 3.0).unwrap(),
             min_point,
         )
         .into(),
@@ -124,23 +125,23 @@ where
         linspace(
             middle.unwrap().into(),
             cmp::min(
-                middle.unwrap() + (max_resolution.into() * 3.0).into(),
+                middle.unwrap() + T::try_from(max_resolution.into() * 3.0).unwrap(),
                 max_point,
             )
             .into(),
             4,
         )
         .skip(1),
     ) {
-        grid_point(point.into(), &mut probs);
+        grid_point(T::try_from(point).unwrap(), &mut probs);
     }
 
     let sorted_grid_points: Vec<f64> = probs.keys().sorted().map(|point| (*point).into()).collect();
 
     // METHOD:
     // Step 2: integrate over grid points visited during the binary search.
     LogProb::ln_trapezoidal_integrate_grid_exp::<f64, _>(
-        |_, g| *probs.get(&T::from(g)).unwrap(),
+        |_, g| *probs.get(&T::try_from(g).unwrap()).unwrap(),
         &sorted_grid_points,
     )
 }

src/stats/probs/mod.rs

@@ -10,6 +10,7 @@ pub mod adaptive_integration;
 pub mod cdf;
 pub mod errors;
 
+use std::convert::TryFrom;
 use std::f64;
 use std::iter;
 use std::mem;
@@ -18,7 +19,7 @@ use std::ops::{Add, AddAssign, Div, Mul, Sub, SubAssign};
 use itertools::Itertools;
 use itertools_num::linspace;
 use num_traits::{Float, Zero};
-use ordered_float::NotNan;
+use ordered_float::{FloatIsNan, NotNan};
 
 use crate::utils::FastExp;
 
@@ -401,9 +402,10 @@ impl From<NotNan<f64>> for LogProb {
     }
 }
 
-impl From<LogProb> for NotNan<f64> {
-    fn from(p: LogProb) -> NotNan<f64> {
-        NotNan::from(*p)
+impl TryFrom<LogProb> for NotNan<f64> {
+    type Error = FloatIsNan;
+    fn try_from(p: LogProb) -> Result<Self, Self::Error> {
+        NotNan::new(*p)
     }
 }