feat: Cell Ranger 10.1.0

Author: 10x Genomics

Cargo.lock

@@ -27,6 +27,72 @@ opt-level = 3
 [profile.test]
 opt-level = 3
 
+[workspace.lints.rust]
+# Lint groups
+future_incompatible = "deny"
+nonstandard_style = "deny"
+rust_2018_idioms = "deny"
+unused = "deny"
+warnings = "deny"
+# Individual lints
+unused_qualifications = "deny"
+
+[workspace.lints.clippy]
+complexity = "deny"
+perf = "deny"
+style = "deny"
+suspicious = "deny"
+comparison_chain = { level = "allow", priority = 1 }
+
+# nursery
+needless_collect = "deny"
+or_fun_call = "deny"
+
+# pedantic
+borrow_as_ptr = "deny"
+cloned_instead_of_copied = "deny"
+enum_glob_use = "deny"
+explicit_deref_methods = "deny"
+explicit_into_iter_loop = "deny"
+explicit_iter_loop = "deny"
+filter_map_next = "deny"
+flat_map_option = "deny"
+from_iter_instead_of_collect = "deny"
+ignored_unit_patterns = "deny"
+implicit_clone = "deny"
+inefficient_to_string = "deny"
+manual_assert = "deny"
+manual_instant_elapsed = "deny"
+manual_is_variant_and = "deny"
+manual_let_else = "deny"
+manual_ok_or = "deny"
+manual_string_new = "deny"
+map_unwrap_or = "deny"
+match_wildcard_for_single_variants = "deny"
+mut_mut = "deny"
+needless_bitwise_bool = "deny"
+needless_continue = "deny"
+needless_for_each = "deny"
+needless_raw_string_hashes = "deny"
+option_as_ref_cloned = "deny"
+ptr_as_ptr = "deny"
+ptr_cast_constness = "deny"
+redundant_closure_for_method_calls = "deny"
+redundant_else = "deny"
+ref_as_ptr = "deny"
+semicolon_if_nothing_returned = "deny"
+single_char_pattern = "deny"
+unchecked_time_subtraction = "deny"
+unicode_not_nfc = "deny"
+uninlined_format_args = "deny"
+unnecessary_join = "deny"
+unnecessary_wraps = "deny"
+unnested_or_patterns = "deny"
+unused_self = "deny"
+used_underscore_binding = "deny"
+wildcard_imports = "deny"
+
 [workspace.dependencies]
 itertools = ">=0.10"
-rand = { version = "0.9", default-features = false, features = ["small_rng"] }
+rand = { version = "0.10", default-features = false }
+rand_distr = "0.6"

Cargo.toml

@@ -20,6 +20,9 @@ include = [
     "contrib/tsne/tsne/bh_sne_src/vptree.h",
 ]
 
+[lints]
+workspace = true
+
 [dependencies]
 ndarray = "0.16"
 smart-default = "*"

bhtsne/Cargo.toml

@@ -7,7 +7,6 @@ fn main() {
     build
         .cpp(true)
         .warnings(false)
-        .static_flag(true)
         .pic(true)
         .flag_if_supported("-std=c++17")
         .flag_if_supported("/std:c++17")
@@ -42,9 +41,6 @@ fn main() {
             build.flag("-mcmpxchg16b");
         }
     }
-    if cfg!(target_feature = "fma4") {
-        build.flag("-mfma4");
-    }
     if cfg!(target_feature = "avx") {
         build.flag("-mavx");
     }

bhtsne/build.rs

@@ -1,5 +1,4 @@
-#![allow(non_snake_case, clippy::upper_case_acronyms)]
-#![deny(warnings)]
+#![expect(non_snake_case, clippy::upper_case_acronyms)]
 
 #[macro_use]
 extern crate smart_default;
@@ -68,7 +67,7 @@ impl BarnesHutTSNE {
                 self.n_dims as c_int,
                 self.perplexity,
                 self.theta,
-                self.seed.map(|x| x as c_int).unwrap_or(RANDOM_STATE),
+                self.seed.map_or(RANDOM_STATE, |x| x as c_int),
                 false,
                 std::ptr::null_mut(),
                 false,

bhtsne/src/lib.rs

@@ -6,6 +6,9 @@ license-file = "../LICENSE"
 edition = "2021"
 include = ["src/lib.rs"]
 
+[lints]
+workspace = true
+
 [target.'cfg(target_os = "macos")'.dependencies]
 accelerate-src = "0.3.2"
 

blas-src/Cargo.toml

@@ -1,7 +1,7 @@
-#[allow(unused_extern_crates)]
+#[expect(unused_extern_crates)]
 #[cfg(target_os = "macos")]
 extern crate accelerate_src;
 
-#[allow(unused_extern_crates)]
+#[expect(unused_extern_crates)]
 #[cfg(not(target_os = "macos"))]
 extern crate intel_mkl_src;

blas-src/src/lib.rs

@@ -6,5 +6,8 @@ license-file = "../LICENSE"
 edition = "2021"
 include = ["src/**/*", "LICENSE", "!**/tests/**/*"]
 
+[lints]
+workspace = true
+
 [dev-dependencies]
 approx = "0.5"

cephes/Cargo.toml

@@ -8,20 +8,20 @@ const MAXGAM: f64 = 171.624_376_956_302_7;
 pub fn beta(a: f64, b: f64) -> f64 {
     if a <= 0.0 && a == a.floor() {
         let ai = a as i32;
-        if a == ai as f64 {
-            return beta_negint(ai, b);
+        return if a == ai as f64 {
+            beta_negint(ai, b)
         } else {
-            return f64::INFINITY;
-        }
+            f64::INFINITY
+        };
     }
 
     if b <= 0.0 && b == b.floor() {
         let bi = b as i32;
-        if a == bi as f64 {
-            return beta_negint(bi, a);
+        return if a == bi as f64 {
+            beta_negint(bi, a)
         } else {
-            return f64::INFINITY;
-        }
+            f64::INFINITY
+        };
     }
 
     let (a, b) = if a.abs() < b.abs() { (b, a) } else { (a, b) };
@@ -77,20 +77,20 @@ fn beta_negint(a: i32, b: f64) -> f64 {
 pub fn betaln(a: f64, b: f64) -> f64 {
     if a <= 0.0 && a == a.floor() {
         let ai = a as i32;
-        if a == ai as f64 {
-            return betaln_negint(ai, b);
+        return if a == ai as f64 {
+            betaln_negint(ai, b)
         } else {
             return f64::INFINITY;
-        }
+        };
     }
 
     if b <= 0.0 && b == b.floor() {
         let bi = b as i32;
-        if b == bi as f64 {
-            return betaln_negint(bi, a);
+        return if b == bi as f64 {
+            betaln_negint(bi, a)
         } else {
-            return f64::INFINITY;
-        }
+            f64::INFINITY
+        };
     }
 
     let (a, b) = if a.abs() < b.abs() { (b, a) } else { (a, b) };

cephes/src/beta.rs

@@ -61,20 +61,15 @@ pub fn betaincinv(aa: f64, bb: f64, yy0: f64) -> f64 {
         let d = 2.0 * d;
         if d < MINLOG {
             // underflow, x <- 0.0
-            if rflg {
-                return 1.0 - MACHEP;
-            } else {
-                return 0.0;
-            }
+            return if rflg { 1.0 - MACHEP } else { 0.0 };
+        }
+        x = a / (a + b * d.exp());
+        y = betainc(a, b, x);
+        let yp = (y - y0) / y0;
+        if yp.abs() < 0.2 {
+            state = NewT;
         } else {
-            x = a / (a + b * d.exp());
-            y = betainc(a, b, x);
-            let yp = (y - y0) / y0;
-            if yp.abs() < 0.2 {
-                state = NewT;
-            } else {
-                state = IHalve;
-            }
+            state = IHalve;
         }
     }
 
@@ -232,7 +227,6 @@ pub fn betaincinv(aa: f64, bb: f64, yy0: f64) -> f64 {
                 }
                 dithresh = 256.0 * MACHEP;
                 state = IHalve;
-                continue 'outer;
             }
         }
     }