Merge pull request #3 from onecodex/vp_cleanup

Remove legacy feature & update bincode

Author: Keats

.github/workflows/ci.yml

@@ -0,0 +1,97 @@
+name: CI
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: 1.40.0
+          override: true
+
+      - name: create SSH key
+        uses: webfactory/ssh-agent@v0.2.0
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+
+      - name: version info
+        run:  rustc --version; cargo --version;
+
+      - name: Run all tests
+        run: cargo test
+
+  tests-prefetching:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: nightly
+          override: true
+
+      - name: create SSH key
+        uses: webfactory/ssh-agent@v0.2.0
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+
+      - name: version info
+        run:  rustc --version; cargo --version;
+
+      - name: Run all tests
+        run: cargo test --all-features
+
+  fmt:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+
+      - name: create SSH key
+        uses: webfactory/ssh-agent@v0.2.0
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+
+      - uses: actions-rs/cargo@v1
+        with:
+          command: fmt
+          args: --all -- --check
+
+  clippy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@master
+
+      - uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          override: true
+
+      - name: create SSH key
+        uses: webfactory/ssh-agent@v0.2.0
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+
+      - uses: actions-rs/cargo@v1
+        with:
+          command: clippy
+          args:  -- -D warnings

.gitignore

@@ -2,3 +2,4 @@
 **/*.rs.bk
 Cargo.lock
 .DS_Store
+.idea/

Cargo.toml

@@ -1,18 +1,15 @@
 [package]
 name = "bfield"
-version = "0.2.0"
+version = "0.2.1"
 authors = ["Roderick Bovee <roderick@onecodex.com>"]
 edition = "2018"
 
 [dependencies]
-bincode = "0.9.2"
-mmap-bitvec = { git="ssh://git@github.com/onecodex/mmap-bitvec.git", tag="v0.3.0" }
+bincode = "1"
+mmap-bitvec = { git="ssh://git@github.com/onecodex/mmap-bitvec.git", tag="v0.3.1" }
 murmurhash3 = "0.0.5"
 serde = "1.0.15"
 serde_derive = "1.0.15"
-serde_json = { version = "1.0.4", optional = true}
 
 [features]
-marker_lookup = ["mmap-bitvec/rank_lookup"]
 prefetching = []
-legacy = ["mmap-bitvec/backward_bytes", "serde_json"]

src/bfield.rs

@@ -13,8 +13,7 @@ pub struct BField<T> {
 }
 
 impl<'a, T: Clone + DeserializeOwned + Serialize> BField<T> {
-    // the hashing is different, so we don't want to accidentally create file in legacy mode
-    #[cfg(not(feature = "legacy"))]
+    #[allow(clippy::too_many_arguments)]
     pub fn create<P>(
         filename: P,
         size: usize,
@@ -67,7 +66,6 @@ impl<'a, T: Clone + DeserializeOwned + Serialize> BField<T> {
         })
     }
 
-    #[cfg(not(feature = "legacy"))]
     pub fn from_file<P>(filename: P, read_only: bool) -> Result<Self, io::Error>
     where
         P: AsRef<Path>,
@@ -95,32 +93,6 @@ impl<'a, T: Clone + DeserializeOwned + Serialize> BField<T> {
         Ok(BField { members, read_only })
     }
 
-    #[cfg(feature = "legacy")]
-    pub fn from_file<P>(filename: P, _: bool) -> Result<Self, io::Error>
-    where
-        P: AsRef<Path>,
-    {
-        let first_member = BFieldMember::open_legacy(&filename)?;
-        let mut members = vec![first_member];
-        let mut n = 1;
-        loop {
-            let member_filename = Path::with_extension(
-                Path::file_stem(filename.as_ref()).unwrap().as_ref(),
-                format!("mmap.secondary.{:03}", n),
-            );
-            if !member_filename.exists() {
-                break;
-            }
-            let member = BFieldMember::open_legacy(&member_filename)?;
-            members.push(member);
-            n += 1;
-        }
-        Ok(BField {
-            members,
-            read_only: true,
-        })
-    }
-
     pub fn build_params(&self) -> (u8, u8, u8, Vec<usize>) {
         let (_, n_hashes, marker_width, n_marker_bits) = self.members[0].info();
         let sizes = self.members.iter().map(|i| i.info().0).collect();
@@ -189,12 +161,3 @@ impl<'a, T: Clone + DeserializeOwned + Serialize> BField<T> {
         self.members.iter().map(|m| m.info()).collect()
     }
 }
-
-#[cfg(feature = "legacy")]
-#[test]
-fn test_legacy() {
-    let bf: BField<usize> = BField::from_file("./test_data/legacy/test_bfield.mmap", true).unwrap();
-    assert_eq!(bf.get(b"Hello"), Some(0));
-    assert_eq!(bf.get(b"Not here."), None);
-    assert_eq!(bf.get(b"Hello again"), Some(0));
-}