Merge pull request #44 from cjneely10/development

Better error handling

CHANGELOG.md

@@ -0,0 +1,27 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+
+## [Unreleased]
+
+### Python bindings
+- [PyO3](https://github.com/PyO3/pyo3)-derived bindings for use within Python
+
+## [0.2.0] - 2022-07-24
+### Added
+- Better stderr messages on file-parsing errors
+  - Line/col numbers and kind of error
+  - Disallow `nan` values in input per Affinity Propagation algorithm requirements
+
+### Changed
+- Small edits to pass-by-value instead of by-reference
+
+### Fixed
+- `nan` values were accepted as valid input.
+  - No valid similarity calculation is present for `nan` values
+
+## [0.1.1] - 2022-02-15
+First release of `affinityprop`

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "affinityprop"
-version = "0.1.1"
+version = "0.2.0"
 edition = "2021"
 authors = ["Chris Neely <[email protected]>"]
 license = "GPL-3.0"

README.md

@@ -1,6 +1,6 @@
 [![Rust](https://github.com/cjneely10/affinityprop/actions/workflows/rust.yml/badge.svg?branch=main)](https://github.com/cjneely10/affinityprop/actions/workflows/rust.yml)
 [![affinityprop crate](https://img.shields.io/crates/v/affinityprop?color=blue&style=flat)](https://crates.io/crates/affinityprop)
-[![affinityprop docs](https://img.shields.io/docsrs/affinityprop)](https://docs.rs/affinityprop/0.1.1/affinityprop/)
+[![affinityprop docs](https://img.shields.io/docsrs/affinityprop)](https://docs.rs/affinityprop/0.2.0/affinityprop/)
 [![GitHub](https://img.shields.io/github/license/cjneely10/affinityprop)](https://www.gnu.org/licenses/gpl-3.0.html)
 [![affinityprop: rustc 1.58](https://img.shields.io/badge/affinityprop-rustc__1.58-blue)](https://doc.rust-lang.org/rustc/what-is-rustc.html)
 ![coverage](https://img.shields.io/badge/coverage-95%25-success)
@@ -48,7 +48,7 @@ with `rustc >=1.58`
 ## In Rust code
 ```toml
 [dependencies]
-affinityprop = "0.1.1"
+affinityprop = "0.2.0"
 ndarray = "0.15.4"
 ```
 
@@ -146,7 +146,7 @@ IDs will automatically be assigned by zero-based index.
 
 ### Help Menu
 ```text
-affinityprop 0.1.1
+affinityprop 0.2.0
 Chris N. <[email protected]>
 Vectorized and Parallelized Affinity Propagation
 

src/algorithm.rs

@@ -176,7 +176,7 @@ where
         Zip::from(self.tmp.axis_iter_mut(Axis(0)))
             .and(self.similarity.axis_iter(Axis(0)))
             .and(&max1)
-            .par_for_each(|mut t, s, m| t.iter_mut().zip(s.iter()).for_each(|(t, s)| *t = *s - *m));
+            .par_for_each(|mut t, s, &m| t.iter_mut().zip(s.iter()).for_each(|(t, s)| *t = *s - m));
 
         // tmp[ind, I] = S[ind, I] - Y2
         Zip::from(self.tmp.axis_iter_mut(Axis(0)))
@@ -203,7 +203,7 @@ where
         // np.maximum(R, 0, tmp)
         Zip::from(&mut self.tmp)
             .and(&self.responsibility)
-            .par_for_each(|t, r| *t = *r);
+            .par_for_each(|t, &r| *t = r);
         self.tmp.par_map_inplace(|v| {
             if *v < self.zero {
                 *v = self.zero;
@@ -248,9 +248,9 @@ where
     fn max_argmax(data: ArrayView<F, Dim<[usize; 1]>>) -> (usize, F) {
         let mut max_pos = 0;
         let mut max: F = data[0];
-        data.iter().enumerate().for_each(|(idx, val)| {
-            if *val > max {
-                max = *val;
+        data.iter().enumerate().for_each(|(idx, &val)| {
+            if val > max {
+                max = val;
                 max_pos = idx;
             }
         });
@@ -313,9 +313,6 @@ mod test {
             assert!(
                 actual.len() == exemplars.len()
                     && actual.iter().all(|(idx, values)| {
-                        if !exemplars.contains_key(idx) {
-                            return false;
-                        }
                         let v: HashSet<usize> =
                             HashSet::from_iter(values.iter().map(|v| v.clone()));
                         let a: HashSet<usize> = HashSet::from_iter(

src/bin/affinityprop/main.rs

@@ -17,7 +17,7 @@ mod ops;
 #[cfg(not(tarpaulin_include))]
 fn main() {
     let matches = clap_app!(affinityprop =>
-        (version: "0.1.1")
+        (version: "0.2.0")
         (author: "Chris N. <[email protected]>")
         (about: "Vectorized and Parallelized Affinity Propagation")
         (@arg INPUT: -i --input +takes_value +required "Path to input file")
@@ -166,20 +166,11 @@ fn predict<F>(
         Some(pref) => Preference::Value(pref),
         None => Preference::Median,
     };
-    let a: (bool, HashMap<usize, Vec<usize>>);
-    match similarity {
-        1 => {
-            a = ap.predict(&x, NegCosine::default(), preference);
-        }
-        2 => {
-            a = ap.predict(&x, LogEuclidean::default(), preference);
-        }
-        3 => {
-            a = ap.predict_precalculated(x, preference);
-        }
-        _ => {
-            a = ap.predict(&x, NegEuclidean::default(), preference);
-        }
-    }
+    let a: (bool, HashMap<usize, Vec<usize>>) = match similarity {
+        1 => ap.predict(&x, NegCosine::default(), preference),
+        2 => ap.predict(&x, LogEuclidean::default(), preference),
+        3 => ap.predict_precalculated(x, preference),
+        _ => ap.predict(&x, NegEuclidean::default(), preference),
+    };
     display_results(a.0, &a.1, y);
 }