(wip,chore) clippy and deny update

Author: jspaezp

.pre-commit-config.yaml

@@ -1,6 +1,10 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
+-   repo: https://github.com/EmbarkStudios/cargo-deny
+    rev: 0.14.16 # choose your preferred tag
+    hooks:
+    - id: cargo-deny
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.2.0
     hooks:

Cargo.lock

@@ -9,7 +9,7 @@
 # The values provided in this template are the default values that will be used
 # when any section or field is not specified in your own configuration
 
-# Root options
+[graph]
 
 # If 1 or more target triples (and optionally, target_features) are specified,
 # only the specified targets will be checked when running `cargo deny check`.
@@ -50,6 +50,8 @@ no-default-features = false
 # If set, these feature will be enabled when collecting metadata. If `--features`
 # is specified on the cmd line they will take precedence over this option.
 #features = []
+
+[output]
 # When outputting inclusion graphs in diagnostics that include features, this
 # option can be used to specify the depth at which feature edges will be added.
 # This option is included since the graphs can be quite large and the addition
@@ -61,24 +63,18 @@ feature-depth = 1
 # More documentation for the advisories section can be found here:
 # https://embarkstudios.github.io/cargo-deny/checks/advisories/cfg.html
 [advisories]
+version = 2
 # The path where the advisory database is cloned/fetched into
 db-path = "~/.cargo/advisory-db"
 # The url(s) of the advisory databases to use
 db-urls = ["https://github.com/rustsec/advisory-db"]
 # The lint level for security vulnerabilities
-vulnerability = "deny"
-# The lint level for unmaintained crates
-unmaintained = "warn"
-# The lint level for crates that have been yanked from their source registry
 yanked = "warn"
-# The lint level for crates with security notices. Note that as of
-# 2019-12-17 there are no security notice advisories in
-# https://github.com/rustsec/advisory-db
-notice = "warn"
 # A list of advisory IDs to ignore. Note that ignored advisories will still
 # output a note when they are encountered.
 ignore = [
     #"RUSTSEC-0000-0000",
+    "RUSTSEC-2021-0145",  # atty... potential unaligner when using custom allocators.
 ]
 # Threshold for security vulnerabilities, any vulnerability with a CVSS score
 # lower than the range specified will be ignored. Note that ignored advisories
@@ -100,60 +96,28 @@ ignore = [
 # More documentation for the licenses section can be found here:
 # https://embarkstudios.github.io/cargo-deny/checks/licenses/cfg.html
 [licenses]
-# The lint level for crates which do not have a detectable license
-unlicensed = "deny"
+version = 2
 # List of explicitly allowed licenses
 # See https://spdx.org/licenses/ for list of possible licenses
 # [possible values: any SPDX 3.11 short identifier (+ optional exception)].
 allow = [
     "MIT",
     "Apache-2.0",
     "Apache-2.0 WITH LLVM-exception",
-    "CC0-1.0",
     "BSD-3-Clause",
-    "ISC",
     "Unicode-DFS-2016",
     "Zlib",
     # Thank Jesus for rerun that compiled the following for me...
-    "OFL-1.1",                        # https://spdx.org/licenses/OFL-1.1.html
-    "MPL-2.0",                        # https://www.mozilla.org/en-US/MPL/2.0/FAQ/ - see Q11. Used by webpki-roots on Linux.
-    "OpenSSL",                        # https://www.openssl.org/source/license.html - used on Linux
-    "LicenseRef-UFL-1.0",             # See https://github.com/emilk/egui/issues/2321
-]
-# List of explicitly disallowed licenses
-# See https://spdx.org/licenses/ for list of possible licenses
-# [possible values: any SPDX 3.11 short identifier (+ optional exception)].
-deny = [
-    #"Nokia",
 ]
-# Lint level for licenses considered copyleft
-copyleft = "deny"
-# Blanket approval or denial for OSI-approved or FSF Free/Libre licenses
-# * both - The license will be approved if it is both OSI-approved *AND* FSF
-# * either - The license will be approved if it is either OSI-approved *OR* FSF
-# * osi - The license will be approved if it is OSI approved
-# * fsf - The license will be approved if it is FSF Free
-# * osi-only - The license will be approved if it is OSI-approved *AND NOT* FSF
-# * fsf-only - The license will be approved if it is FSF *AND NOT* OSI-approved
-# * neither - This predicate is ignored and the default lint level is used
-allow-osi-fsf-free = "neither"
-# Lint level used when no other predicates are matched
-# 1. License isn't in the allow or deny lists
-# 2. License isn't copyleft
-# 3. License isn't OSI/FSF, or allow-osi-fsf-free = "neither"
-default = "deny"
+
 # The confidence threshold for detecting a license from license text.
 # The higher the value, the more closely the license text must be to the
 # canonical license text of a valid SPDX license file.
 # [possible values: any between 0.0 and 1.0].
 confidence-threshold = 0.95
 # Allow 1 or more licenses on a per-crate basis, so that particular licenses
 # aren't accepted for every possible crate as with the normal allow list
-exceptions = [
-    # Each entry is the crate and version constraint, and its specific allow
-    # list
-    { allow = ["Zlib"], name = "adler32", version = "*" },
-]
+exceptions = []
 
 # Some crates don't have (easily) machine readable licensing information,
 # adding a clarification entry for it allows you to manually specify the
@@ -260,19 +224,12 @@ deny = [
 #exact = true
 
 # Certain crates/versions that will be skipped when doing duplicate detection.
-skip = [
-    # Following line comes from the rerun repo ...https://github.com/rerun-io/rerun/blob/main/deny.toml
-    { name = "webpki-roots" },      # ureq and tungstenite are on different version 😭
-
-    #{ name = "ansi_term", version = "=0.11.0" },
-]
+skip = []
 # Similarly to `skip` allows you to skip certain crates during duplicate
 # detection. Unlike skip, it also includes the entire tree of transitive
 # dependencies starting at the specified crate, up to a certain depth, which is
 # by default infinite.
-skip-tree = [
-    #{ name = "ansi_term", version = "=0.11.0", depth = 20 },
-]
+skip-tree = []
 
 # This section is considered when running `cargo deny check sources`.
 # More documentation about the 'sources' section can be found here:
@@ -288,12 +245,8 @@ unknown-git = "warn"
 # if not specified. If it is specified but empty, no registries are allowed.
 allow-registry = ["https://github.com/rust-lang/crates.io-index"]
 # List of URLs for allowed Git repositories
-allow-git = []
+allow-git = ["https://github.com/lazear/sage"]
 
 [sources.allow-org]
 # 1 or more github.com organizations to allow git sources for
-github = [""]
-# 1 or more gitlab.com organizations to allow git sources for
-gitlab = [""]
-# 1 or more bitbucket.org organizations to allow git sources for
-bitbucket = [""]
+# github = [""]

deny.toml

@@ -1,7 +1,6 @@
 use crate::ms::frames::TimsPeak;
-use crate::space::space_generics::{AsAggregableAtIndex, HasIntensity, IntenseAtIndex};
+use crate::space::space_generics::{AsAggregableAtIndex, HasIntensity};
 use crate::utils;
-use std::ops::Index;
 
 use rayon::prelude::*;
 

src/aggregation/aggregators.rs

@@ -1,14 +1,14 @@
-use crate::aggregation::aggregators::{aggregate_clusters, ClusterAggregator, ClusterLabel};
+use crate::aggregation::aggregators::{aggregate_clusters, ClusterAggregator};
 use crate::space::kdtree::RadiusKDTree;
 use crate::space::space_generics::{
     AsAggregableAtIndex, AsNDPointsAtIndex, DistantAtIndex, HasIntensity, IntenseAtIndex, NDPoint,
     NDPointConverter, QueriableIndexedPoints,
 };
 use crate::utils::{self, ContextTimer};
-use log::{debug, info, trace};
+use log::info;
 use rayon::prelude::*;
 use std::fmt::Debug;
-use std::ops::{Add, Index};
+use std::ops::Add;
 
 use crate::aggregation::dbscan::runner::dbscan_label_clusters;
 
@@ -64,15 +64,13 @@ pub fn reassign_centroid<
         }
 
         // 1/1000 show the first and last neighbor, as well as the centroid
-        if neighbors.len() > 0 {
-            if rand::random::<f32>() < 0.001 {
-                println!(
-                    "Centroid: {:?}, First: {:?}, Last: {:?}",
-                    centroid,
-                    neighbors[0],
-                    neighbors[neighbors.len() - 1]
-                );
-            }
+        if !neighbors.is_empty() && rand::random::<f32>() < 0.001 {
+            println!(
+                "Centroid: {:?}, First: {:?}, Last: {:?}",
+                centroid,
+                neighbors[0],
+                neighbors[neighbors.len() - 1]
+            );
         }
 
         let mut aggregator = def_aggregator();
@@ -149,7 +147,7 @@ where
     let quad_indices = (0..ndpoints.len()).collect::<Vec<_>>();
 
     for (quad_point, i) in ndpoints.iter().zip(quad_indices.iter()) {
-        tree.insert_ndpoint(quad_point.clone(), i);
+        tree.insert_ndpoint(*quad_point, i);
     }
     i_timer.stop(true);
 
@@ -234,13 +232,12 @@ pub fn dbscan_aggregate<
     );
     i_timer.stop(true);
 
-    let centroids = aggregate_clusters(
+    aggregate_clusters(
         cluster_labels.num_clusters,
         cluster_labels.cluster_labels,
         prefiltered_peaks,
         &def_aggregator,
         log_level,
         keep_unclustered,
-    );
-    centroids
+    )
 }

src/aggregation/dbscan/dbscan.rs

@@ -95,15 +95,15 @@ impl AsAggregableAtIndex<TimsPeak> for Vec<TimsPeak> {
 impl DistantAtIndex<f32> for Vec<TimsPeak> {
     fn distance_at_indices(
         &self,
-        index: usize,
-        other: usize,
+        _index: usize,
+        _other: usize,
     ) -> f32 {
         panic!("I dont think this is called ever ...");
-        let mut sum = 0.0;
-        let diff_mz = (self[index].mz - self[other].mz) as f32;
-        sum += diff_mz * diff_mz;
-        let diff_ims = self[index].mobility - self[other].mobility;
-        sum += diff_ims * diff_ims;
-        sum.sqrt()
+        // let mut sum = 0.0;
+        // let diff_mz = (self[index].mz - self[other].mz) as f32;
+        // sum += diff_mz * diff_mz;
+        // let diff_ims = self[index].mobility - self[other].mobility;
+        // sum += diff_ims * diff_ims;
+        // sum.sqrt()
     }
 }

src/aggregation/dbscan/denseframe_dbscan.rs

@@ -5,7 +5,7 @@ use crate::space::space_generics::{
 use crate::utils;
 use core::fmt::Debug;
 use indicatif::ProgressIterator;
-use log::{debug, trace};
+use log::debug;
 use std::marker::PhantomData;
 use std::sync::Arc;
 
@@ -181,10 +181,7 @@ impl DBSCANRunnerState {
     {
         let cluster_labels = ClusterLabels::new(nlabels);
 
-        let filter_fun_cache = match usize_filterfun {
-            Some(_) => Some(FilterFunCache::new(nlabels)),
-            None => None,
-        };
+        let filter_fun_cache = usize_filterfun.map(|_| FilterFunCache::new(nlabels));
         //FilterFunCache::new(Box::new(&usize_filterfun), nlabels);
         let timers = DBScanTimers::new();
         let candidate_metrics = CandidateCountMetrics::new();
@@ -374,8 +371,8 @@ where
                 let cl = |a: &usize, b: &usize| {
                     filterfun(&raw_distance_calculator.distance_at_indices(*a, *b))
                 };
-                let bind = Some(cl);
-                bind
+
+                Some(cl)
             },
             None => None,
         };
@@ -388,7 +385,7 @@ where
 
         let points: DBSCANPoints<N, PP, PE, DAI, D, QIP> = DBSCANPoints {
             raw_elements,
-            intensity_sorted_indices: intensity_sorted_indices,
+            intensity_sorted_indices,
             indexed_points,
             projected_elements,
             raw_dist: raw_distance_calculator,
@@ -591,7 +588,7 @@ where
             .map(|i| points.intensity_at_index(*i))
             .sum::<u64>();
         timers.outer_intensity_calculation.stop(false);
-        return neighbor_intensity_total >= self.min_intensity;
+        neighbor_intensity_total >= self.min_intensity
     }
 
     fn main_loop_expand_cluster<PP, PE, DAI, QIP>(
@@ -661,11 +658,7 @@ where
     {
         timers.inner_loop_nn_timer.reset_start();
         let binding = Arc::clone(&points).get_ndpoint(neighbor_index);
-        let local_neighbors: Vec<usize> = points
-            .query_ndpoint(&binding)
-            .iter()
-            .map(|x| *x)
-            .collect::<Vec<_>>();
+        let local_neighbors: Vec<usize> = points.query_ndpoint(&binding).to_vec();
         // Should I warn if nothing is gotten here?
         // every point should have at least itself as a neighbor ...
         debug_assert!(!local_neighbors.is_empty());
@@ -862,18 +855,16 @@ pub fn dbscan_label_clusters<
         min_n,
         min_intensity,
         progress,
-        filter_fun: filter_fun,
+        filter_fun,
         max_extension_distances,
         _phantom: PhantomData::<D>,
     };
 
-    let cluster_labels = runner.run(
+    runner.run(
         raw_elements,
         intensity_sorted_indices,
         indexed_points,
         projected_elements,
         raw_elements,
-    );
-
-    cluster_labels
+    )
 }