Merge branch 'develop'

.github/workflows/rust.yml

@@ -12,10 +12,13 @@ env:
 jobs:
   Formatting:
     if: "!contains(github.event.head_commit.message, 'skip ci')"
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v2.4.2
 
       - name: Install stable toolchain
         uses: actions-rs/toolchain@v1
@@ -29,21 +32,26 @@ jobs:
 
   build:
     if: "!contains(github.event.head_commit.message, 'skip ci')"
-    runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v2.4.2
     - name: Build
       run: cargo build --verbose
     - name: Run tests
       run: cargo test --verbose
 
   Linting:
     if: "!contains(github.event.head_commit.message, 'skip ci')"
-    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v2.4.2
 
       - name: Install stable toolchain
         uses: actions-rs/toolchain@v1

.gitignore

@@ -8,3 +8,4 @@ Cargo.lock
 
 # These are backup files generated by rustfmt
 **/*.rs.bk
+.idea/

Cargo.toml

@@ -1,40 +1,51 @@
 [package]
 name = "alevin-fry"
-version = "0.5.0"
-authors = ["Avi Srivastava <[email protected]>", "Hirak Sarkar <[email protected]>", "Dongze He <[email protected]>", "Mohsen Zakeri <[email protected]>", "Rob Patro <[email protected]>"]
-edition = "2018"
+version = "0.5.1"
+authors = [
+  "Avi Srivastava <[email protected]>",
+  "Hirak Sarkar <[email protected]>",
+  "Dongze He <[email protected]>",
+  "Mohsen Zakeri <[email protected]>",
+  "Rob Patro <[email protected]>",
+]
+edition = "2021"
 description = "A suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data."
 license-file = "LICENSE"
-readme= "README.md"
+readme = "README.md"
 repository = "https://github.com/COMBINE-lab/alevin-fry"
 homepage = "https://github.com/COMBINE-lab/alevin-fry"
 documentation = "https://alevin-fry.readthedocs.io/en/latest/"
 include = [
-    "/libradicl/src/*.rs",
-    "/src/*.rs",
-    "/Cargo.toml",
-    "/README.md",
-    "/LICENSE",
-    "/CONTRIBUTING.md",
-    "/CODE_OF_CONDUCT.md"
+  "/libradicl/src/*.rs",
+  "/src/*.rs",
+  "/Cargo.toml",
+  "/README.md",
+  "/LICENSE",
+  "/CONTRIBUTING.md",
+  "/CODE_OF_CONDUCT.md",
+]
+keywords = [
+  "single-cell",
+  "preprocessing",
+  "RNA-seq",
+  "single-nucleus",
+  "RNA-velocity",
 ]
-keywords = ["single-cell", "preprocessing", 
-	    "RNA-seq", "single-nucleus", "RNA-velocity"]
 categories = ["command-line-utilities", "science"]
 
 [workspace]
 
-[dependencies]	
-# for release
-# libradicl = "0.4.4" 
-# for local development
- libradicl = { path = "libradicl", version = "0.4.4" }
+[dependencies]
+# for local development, look in the libradicl directory
+# but when published, pull the specified version
+libradicl = { path = "libradicl", version = "0.4.5" }
+anyhow = "1.0.57"
 arrayvec = "0.7.2"
 ahash = "0.7.6"
 bincode = "1.3.3"
 bstr = "0.2.17"
-crossbeam-channel = "0.5.2"
-crossbeam-queue = "0.3.4"
+crossbeam-channel = "0.5.4"
+crossbeam-queue = "0.3.5"
 indicatif = "0.16.2"
 needletail = "0.4.1"
 petgraph = "0.6.0"
@@ -44,28 +55,30 @@ serde = { version = "1.0.136", features = ["derive"] }
 serde_json = "1.0.79"
 sprs = "0.11.0"
 slog = "2.7.0"
-slog-term = "2.8.1"
+slog-term = "2.9.0"
 slog-async = "2.7.0"
 smallvec = "1.8.0"
-snap = "1"
+snap = "1.0.5"
 rand = "0.8.5"
 chrono = "0.4.19"
 csv = "1.1.6"
-mimalloc = { version = "0.1.26", default-features = false }
+mimalloc = { version = "0.1.29", default-features = false }
 num-format = "0.4.0"
-num_cpus = "1.13.0"
+num_cpus = "1.13.1"
 bio-types = "0.12.1"
-itertools = "0.10.1"
+itertools = "0.10.3"
 thiserror = "1.0.30"
-quickersort = "3.0.1"
-statrs = "0.15.0" 
-rust-htslib = { version = "0.38.2", default-features = false, features = ["bzip2", "lzma"] }
-sce = { git = "https://github.com/parazodiac/SingleCellExperiment", version = "0.1.1" }
+statrs = "0.15.0"
+rust-htslib = { version = "0.39.5", default-features = false, features = [
+  "bzip2",
+  "lzma",
+] }
+sce = { git = "https://github.com/parazodiac/SingleCellExperiment", version = "0.1.2" }
 
-clap = { version = ">=3.1.0", features = ["derive", "wrap_help", "cargo"] }
+clap = { version = ">=3.1.18", features = ["derive", "wrap_help", "cargo"] }
 
 [profile.release]
 #debug = true
-lto="thin"
+lto = "thin"
 #codegen-units=1
-opt-level=3
+opt-level = 3

docs/source/conf.py

@@ -22,7 +22,7 @@
 author = 'Dongze He, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Avi Srivastava, Rob Patro'
 
 # The full version, including alpha/beta/rc tags
-release = '0.4.3'
+release = '0.5.1'
 
 master_doc = 'index'
 

libradicl/Cargo.toml

@@ -1,41 +1,40 @@
 [package]
 name = "libradicl"
-version = "0.4.4"
-authors = ["Avi Srivastava <[email protected]>", "Hirak Sarkar <[email protected]>", "Dongze He <[email protected]>", "Mohsen Zakeri <[email protected]>", "Rob Patro <[email protected]>"]
-edition = "2018"
+version = "0.4.5"
+authors = [
+  "Avi Srivastava <[email protected]>",
+  "Hirak Sarkar <[email protected]>",
+  "Dongze He <[email protected]>",
+  "Mohsen Zakeri <[email protected]>",
+  "Rob Patro <[email protected]>",
+]
+edition = "2021"
 description = "support library for alevin-fry"
 license-file = "LICENSE"
-readme= "README.md"
+readme = "README.md"
 repository = "https://github.com/COMBINE-lab/alevin-fry"
 homepage = "https://github.com/COMBINE-lab/alevin-fry"
 documentation = "https://alevin-fry.readthedocs.io/en/latest/"
-include = [
-    "src/*.rs",
-    "/Cargo.toml",
-    "/README.md",
-    "/LICENSE",
+include = ["src/*.rs", "/Cargo.toml", "/README.md", "/LICENSE"]
+keywords = [
+  "single-cell",
+  "preprocessing",
+  "RNA-seq",
+  "single-nucleus",
+  "RNA-velocity",
 ]
-keywords = ["single-cell", "preprocessing", 
-	    "RNA-seq", "single-nucleus", "RNA-velocity"]
 categories = ["command-line-utilities", "science"]
 
 [dependencies]
 snap = "1"
 scroll = "0.11.0"
 num = "0.4.0"
 ahash = "0.7.6"
-slog = "2.7.0"
-bstr = "0.2.17"
 serde = { version = "1.0.136", features = ["derive"] }
-csv = "1.1.6"
 dashmap = "^5.1.0"
-crossbeam-channel = "0.5.2"
 bio-types = "0.12.1"
-quickersort = "3.0.1"
-needletail = "0.4.1"
-flate2 = "1.0.22"
 smallvec = "1.8.0"
-serde_json = "1.0.79"
-sprs = "0.11.0"
-rust-htslib = { version = "0.38.2", default-features = false, features = ["bzip2", "lzma"] }
-sce = { git = "https://github.com/parazodiac/SingleCellExperiment", version = "0.1.1" }
+rust-htslib = { version = "0.39.5", default-features = false, features = [
+  "bzip2",
+  "lzma",
+] }

libradicl/src/rad_types.rs

@@ -190,25 +190,25 @@ pub fn decode_int_type_tag(type_id: u8) -> Option<RadIntId> {
 
 fn read_into_u64<T: Read>(reader: &mut T, rt: &RadIntId) -> u64 {
     let mut rbuf = [0u8; 8];
-    let v: u64;
-    match rt {
+
+    let v: u64 = match rt {
         RadIntId::U8 => {
             reader.read_exact(&mut rbuf[0..1]).unwrap();
-            v = rbuf.pread::<u8>(0).unwrap() as u64;
+            rbuf.pread::<u8>(0).unwrap() as u64
         }
         RadIntId::U16 => {
             reader.read_exact(&mut rbuf[0..2]).unwrap();
-            v = rbuf.pread::<u16>(0).unwrap() as u64;
+            rbuf.pread::<u16>(0).unwrap() as u64
         }
         RadIntId::U32 => {
             reader.read_exact(&mut rbuf[0..4]).unwrap();
-            v = rbuf.pread::<u32>(0).unwrap() as u64;
+            rbuf.pread::<u32>(0).unwrap() as u64
         }
         RadIntId::U64 => {
             reader.read_exact(&mut rbuf[0..8]).unwrap();
-            v = rbuf.pread::<u64>(0).unwrap();
+            rbuf.pread::<u64>(0).unwrap()
         }
-    }
+    };
     v
 }
 
@@ -290,7 +290,7 @@ impl ReadRecord {
         }
 
         // make sure these are sorted in this step.
-        quickersort::sort(&mut rec.refs[..]);
+        rec.refs.sort_unstable();
         rec
     }
 
@@ -332,7 +332,7 @@ impl ReadRecord {
         }
 
         // make sure these are sorted in this step.
-        quickersort::sort(&mut rec.refs[..]);
+        rec.refs.sort_unstable();
         rec
     }
 }
@@ -374,36 +374,19 @@ impl Chunk {
         let bc_size = bct.bytes_for_type();
 
         let _na = buf.pread::<u32>(0).unwrap();
-        let bc;
-        match bct {
-            RadIntId::U8 => {
-                bc = buf.pread::<u8>(na_size).unwrap() as u64;
-            }
-            RadIntId::U16 => {
-                bc = buf.pread::<u16>(na_size).unwrap() as u64;
-            }
-            RadIntId::U32 => {
-                bc = buf.pread::<u32>(na_size).unwrap() as u64;
-            }
-            RadIntId::U64 => {
-                bc = buf.pread::<u64>(na_size).unwrap();
-            }
-        }
-        let umi;
-        match umit {
-            RadIntId::U8 => {
-                umi = buf.pread::<u8>(na_size + bc_size).unwrap() as u64;
-            }
-            RadIntId::U16 => {
-                umi = buf.pread::<u16>(na_size + bc_size).unwrap() as u64;
-            }
-            RadIntId::U32 => {
-                umi = buf.pread::<u32>(na_size + bc_size).unwrap() as u64;
-            }
-            RadIntId::U64 => {
-                umi = buf.pread::<u64>(na_size + bc_size).unwrap();
-            }
-        }
+
+        let bc = match bct {
+            RadIntId::U8 => buf.pread::<u8>(na_size).unwrap() as u64,
+            RadIntId::U16 => buf.pread::<u16>(na_size).unwrap() as u64,
+            RadIntId::U32 => buf.pread::<u32>(na_size).unwrap() as u64,
+            RadIntId::U64 => buf.pread::<u64>(na_size).unwrap(),
+        };
+        let umi = match umit {
+            RadIntId::U8 => buf.pread::<u8>(na_size + bc_size).unwrap() as u64,
+            RadIntId::U16 => buf.pread::<u16>(na_size + bc_size).unwrap() as u64,
+            RadIntId::U32 => buf.pread::<u32>(na_size + bc_size).unwrap() as u64,
+            RadIntId::U64 => buf.pread::<u64>(na_size + bc_size).unwrap(),
+        };
         (bc, umi)
     }
 }