build: fix clippy lints and MSRV check

.github/workflows/python.yml

@@ -57,7 +57,7 @@ jobs:
 
       - name: Start Redis
         if: startsWith(runner.os, 'Linux') && (matrix.py == '3.9')
-        uses: supercharge/redis-github-action@f63fe516254d0af5df91755a4488274c2e71e38c
+        uses: supercharge/redis-github-action@1.5.0
         with:
           redis-version: 6
 

.github/workflows/rust.yml

@@ -268,17 +268,17 @@ jobs:
 
       - uses: actions-rs/toolchain@v1
         with:
-          toolchain: "1.60.0"
+          toolchain: "1.64.0"
           override: true
 
       - name: check if README matches MSRV defined here
-        run: grep '1.60.0' src/core/README.md
+        run: grep '1.64.0' src/core/README.md
 
       - name: Check if it builds properly
         uses: actions-rs/cargo@v1
         with:
           command: build
-          args: --all-features
+          args: --all-features --tests
 
   check_cbindgen:
     name: "Check if cbindgen runs cleanly for generating the C headers"

Cargo.toml

@@ -3,6 +3,7 @@ members = [
   "src/core",
 ]
 default-members = ["src/core"]
+resolver = "2"
 
 [profile.test]
 opt-level = 1

flake.nix

@@ -37,11 +37,11 @@
           rustc = rustVersion;
         };
         naersk-lib = naersk.lib."${system}".override {
-          cargo = rustPlatform.rust.cargo;
-          rustc = rustPlatform.rust.rustc;
+          cargo = rustVersion;
+          rustc = rustVersion;
         };
 
-        python = pkgs.python310Packages;
+        python = pkgs.python311Packages;
 
       in
 
@@ -104,8 +104,8 @@
 
             git
             stdenv.cc.cc.lib
-            (python310.withPackages (ps: with ps; [ virtualenv tox cffi ]))
-            (python311.withPackages (ps: with ps; [ virtualenv ]))
+            (python311.withPackages (ps: with ps; [ virtualenv tox cffi ]))
+            (python310.withPackages (ps: with ps; [ virtualenv ]))
             (python39.withPackages (ps: with ps; [ virtualenv ]))
             (python38.withPackages (ps: with ps; [ virtualenv ]))
 

src/core/Cargo.toml

@@ -11,7 +11,7 @@ edition = "2021"
 readme = "README.md"
 autoexamples = false
 autobins = false
-rust-version = "1.60.0"
+rust-version = "1.64.0"
 
 [lib]
 name = "sourmash"
@@ -31,6 +31,7 @@ cfg-if = "1.0"
 counter = "0.5.7"
 finch = { version = "0.5.0", optional = true }
 fixedbitset = "0.4.0"
+getrandom = { version = "0.2", features = ["js"] }
 getset = "0.1.1"
 log = "0.4.19"
 md5 = "0.7.0"
@@ -57,7 +58,6 @@ criterion = "0.5.1"
 needletail = { version = "0.5.1", default-features = false }
 proptest = { version = "1.2.0", default-features = false, features = ["std"]}
 rand = "0.8.2"
-getrandom = { version = "0.2", features = ["js"] }
 tempfile = "3.6.0"
 
 [[bench]]

src/core/README.md

@@ -38,4 +38,4 @@ Development happens on github at
 
 ## Minimum supported Rust version
 
-Currently the minimum supported Rust version is 1.60.0.
+Currently the minimum supported Rust version is 1.64.0.

src/core/src/ffi/cmd/compute.rs

@@ -52,7 +52,7 @@
     if ptr.is_null() {
         return;
     }
-    Vec::from_raw_parts(ptr as *mut u32, insize, insize);
+    Vec::from_raw_parts(ptr, insize, insize);
 }
 
 ffi_fn! {
@@ -65,7 +65,7 @@
 
     let ksizes = {
         assert!(!ksizes_ptr.is_null());
-        slice::from_raw_parts(ksizes_ptr as *const u32, insize)
+        slice::from_raw_parts(ksizes_ptr, insize)
     };
 
     cp.set_ksizes(ksizes.into());

src/core/src/ffi/minhash.rs

@@ -39,7 +39,7 @@
     if ptr.is_null() {
         return;
     }
-    Vec::from_raw_parts(ptr as *mut u64, insize, insize);
+    Vec::from_raw_parts(ptr, insize, insize);
 }
 
 ffi_fn! {
@@ -232,7 +232,7 @@
     // FIXME: make a SourmashSlice_u64 type?
     let hashes = {
         assert!(!hashes_ptr.is_null());
-        slice::from_raw_parts(hashes_ptr as *const u64, insize)
+        slice::from_raw_parts(hashes_ptr, insize)
     };
 
     for hash in hashes {
@@ -277,13 +277,13 @@
     // FIXME: make a SourmashSlice_u64 type?
     let hashes = {
         assert!(!hashes_ptr.is_null());
-        slice::from_raw_parts(hashes_ptr as *const u64, insize)
+        slice::from_raw_parts(hashes_ptr, insize)
     };
 
     // FIXME: make a SourmashSlice_u64 type?
     let abunds = {
         assert!(!abunds_ptr.is_null());
-        slice::from_raw_parts(abunds_ptr as *const u64, insize)
+        slice::from_raw_parts(abunds_ptr, insize)
     };
 
     let mut pairs: Vec<_> = hashes.iter().cloned().zip(abunds.iter().cloned()).collect();

src/core/src/ffi/nodegraph.rs

@@ -29,7 +29,7 @@
     if ptr.is_null() {
         return;
     }
-    Vec::from_raw_parts(ptr as *mut u8, insize, insize);
+    Vec::from_raw_parts(ptr, insize, insize);
 }
 
 #[no_mangle]

src/core/src/ffi/storage.rs

@@ -64,7 +64,7 @@
     // FIXME: use the ForeignObject trait, maybe define new method there...
     let ptr_sigs: Vec<*mut SourmashStr> = sbts
         .into_iter()
-        .map(|x| Box::into_raw(Box::new(SourmashStr::from_string(x))) as *mut SourmashStr)
+        .map(|x| Box::into_raw(Box::new(SourmashStr::from_string(x))))
         .collect();
 
     let b = ptr_sigs.into_boxed_slice();
@@ -86,7 +86,7 @@
     // FIXME: use the ForeignObject trait, maybe define new method there...
     let ptr_sigs: Vec<*mut SourmashStr> = files
         .into_iter()
-        .map(|x| Box::into_raw(Box::new(SourmashStr::from_string(x))) as *mut SourmashStr)
+        .map(|x| Box::into_raw(Box::new(SourmashStr::from_string(x))))
         .collect();
 
     let b = ptr_sigs.into_boxed_slice();

src/core/src/sketch/minhash.rs

@@ -1655,7 +1655,7 @@
         let mins: BTreeSet<u64> = other.mins.into_iter().collect();
         let abunds = other
             .abunds
-            .map(|abunds| mins.iter().cloned().zip(abunds.into_iter()).collect());
+            .map(|abunds| mins.iter().cloned().zip(abunds).collect());
 
         new_mh.mins = mins;
         new_mh.abunds = abunds;

src/core/src/storage.rs

@@ -3,7 +3,8 @@ use std::ffi::OsStr;
 use std::fs::{DirBuilder, File};
 use std::io::{BufReader, BufWriter, Read, Write};
 use std::path::{Path, PathBuf};
-use std::sync::{Arc, Mutex};
+use std::rc::Rc;
+use std::sync::RwLock;
 
 use serde::{Deserialize, Serialize};
 use thiserror::Error;
@@ -24,11 +25,11 @@ pub trait Storage {
 }
 
 #[derive(Clone)]
-pub struct InnerStorage(Arc<Mutex<dyn Storage>>);
+pub struct InnerStorage(Rc<RwLock<dyn Storage>>);
 
 impl InnerStorage {
     pub fn new(inner: impl Storage + 'static) -> InnerStorage {
-        InnerStorage(Arc::new(Mutex::new(inner)))
+        InnerStorage(Rc::new(RwLock::new(inner)))
     }
 }
 
@@ -85,20 +86,20 @@ impl From<&StorageArgs> for FSStorage {
     }
 }
 
-impl<L> Storage for Mutex<L>
+impl<L> Storage for RwLock<L>
 where
     L: ?Sized + Storage,
 {
     fn save(&self, path: &str, content: &[u8]) -> Result<String, Error> {
-        self.lock().unwrap().save(path, content)
+        self.read().unwrap().save(path, content)
     }
 
     fn load(&self, path: &str) -> Result<Vec<u8>, Error> {
-        self.lock().unwrap().load(path)
+        self.read().unwrap().load(path)
     }
 
     fn args(&self) -> StorageArgs {
-        self.lock().unwrap().args()
+        self.read().unwrap().args()
     }
 }
 

tox.ini

@@ -79,7 +79,7 @@ commands = pytest \
 [testenv:khmer_master]
 basepython = python3.8
 deps =
-  -e git+https://github.com/dib-lab/khmer.git#egg=khmer
+  -e git+https://github.com/dib-lab/khmer.git\#egg=khmer
 commands = pytest \
            --cov "{envsitepackagesdir}/sourmash" \
            --cov-config "{toxinidir}/tox.ini" \