Merge branch 'dev' into master

.github/workflows/ci.yml

@@ -0,0 +1,17 @@
+name: CI
+on: [push, pull_request]
+
+jobs:
+  test:
+    uses: aschampion/gh-actions/.github/workflows/rust-test.yml@v0
+    with:
+      msrv: 1.56
+
+  semver-checks:
+    uses: aschampion/gh-actions/.github/workflows/rust-semver-checks.yml@v0
+
+  publish:
+    uses: aschampion/gh-actions/.github/workflows/rust-publish.yml@v0
+    needs: [test]
+    if: github.event_name == 'push' && contains(github.ref, 'refs/tags/v')
+    secrets: inherit

.rustfmt.toml

@@ -0,0 +1 @@
+imports_layout = "Vertical"

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+<!-- next-header -->
+
+## [Unreleased]
+### Changed
+- Increase MSRV 1.39 -> 1.56 for tool and dependency upgrades.
 
 ## [0.7.6] - 2020-10-26
 ### Added
@@ -180,3 +185,23 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 
 ## [0.1.0] - 2018-02-28
+
+
+<!-- next-url -->
+[Unreleased]: https://github.com/aschampion/rust-n5/compare/0.7.6...HEAD
+[0.7.6]: https://github.com/aschampion/rust-n5/compare/0.7.5...0.7.6
+[0.7.5]: https://github.com/aschampion/rust-n5/compare/0.7.4...0.7.5
+[0.7.4]: https://github.com/aschampion/rust-n5/compare/0.7.3...0.7.4
+[0.7.3]: https://github.com/aschampion/rust-n5/compare/0.7.2...0.7.3
+[0.7.2]: https://github.com/aschampion/rust-n5/compare/0.7.1...0.7.2
+[0.7.1]: https://github.com/aschampion/rust-n5/compare/0.7.0...0.7.1
+[0.7.0]: https://github.com/aschampion/rust-n5/compare/0.6.1...0.7.0
+[0.6.1]: https://github.com/aschampion/rust-n5/compare/0.6.0...0.6.1
+[0.6.0]: https://github.com/aschampion/rust-n5/compare/0.5.0...0.6.0
+[0.5.0]: https://github.com/aschampion/rust-n5/compare/0.4.0...0.5.0
+[0.4.0]: https://github.com/aschampion/rust-n5/compare/0.3.0...0.4.0
+[0.3.0]: https://github.com/aschampion/rust-n5/compare/0.2.3...0.3.0
+[0.2.3]: https://github.com/aschampion/rust-n5/compare/0.2.2...0.2.3
+[0.2.2]: https://github.com/aschampion/rust-n5/compare/0.2.1...0.2.2
+[0.2.1]: https://github.com/aschampion/rust-n5/compare/0.2.0...0.2.1
+[0.2.0]: https://github.com/aschampion/rust-n5/compare/0.1.0...0.2.0

Cargo.toml

@@ -2,6 +2,7 @@
 name = "n5"
 version = "0.7.6"
 edition = "2018"
+rust-version = "1.39"
 license = "MIT/Apache-2.0"
 authors = ["Andrew Champion <[email protected]>"]
 description = "Rust implementation of the N5 tensor file system format"

README.md

@@ -1,4 +1,4 @@
-# N5 [![Build Status](https://travis-ci.org/aschampion/rust-n5.svg?branch=master)](https://travis-ci.org/aschampion/rust-n5) [![Coverage](https://codecov.io/gh/aschampion/rust-n5/branch/master/graph/badge.svg)](https://codecov.io/gh/aschampion/rust-n5)
+# N [![Build Status](https://github.com/aschampion/rust-n5/actions/workflows/ci.yml/badge.svg)](https://github.com/aschampion/rust-n5/actions/workflows/ci.yml/) [![Coverage](https://codecov.io/gh/aschampion/rust-n5/branch/master/graph/badge.svg)](https://codecov.io/gh/aschampion/rust-n5)
 
 A (mostly pure) rust implementation of the [N5 "Not HDF5" n-dimensional tensor file system storage format](https://github.com/saalfeldlab/n5) created by the Saalfeld lab at Janelia Research Campus.
 
@@ -10,7 +10,7 @@ Compatible with Java N5 Version 2.1.3.
 
 ## Minimum supported Rust version (MSRV)
 
-Stable 1.39
+Stable 1.56
 
 ## Quick start
 

benches/parallel_write.rs

@@ -12,10 +12,8 @@
 //! will take several hours to run.
 #![feature(test)]
 
-
 extern crate test;
 
-
 use std::fs::File;
 use std::io::BufReader;
 
@@ -38,7 +36,6 @@ use tiff::decoder::{
 use n5::prelude::*;
 use n5::smallvec::smallvec;
 
-
 lazy_static! {
     static ref TEST_IMAGE: Vec<i8> = {
         let mut pixels = Vec::with_capacity(163 * 163 * 93);
@@ -54,7 +51,7 @@ lazy_static! {
                     for p in img {
                         pixels.push(p as i8);
                     }
-                },
+                }
             }
 
             decoder.next_image().unwrap();
@@ -66,15 +63,12 @@ lazy_static! {
 const BLOCK_DIM: u32 = 64;
 const N_BLOCKS: u64 = 5;
 
-fn write<T, N5>(
-        n: &N5,
-        compression: &CompressionType,
-        block_data: &[T],
-        pool_size: usize,
-) where T: 'static + std::fmt::Debug + ReflectedType + PartialEq + Default + Sync + Send,
-        N5: N5Writer + Sync + Send + Clone + 'static,
-        SliceDataBlock<T, std::sync::Arc<[T]>>: n5::WriteableDataBlock {
-
+fn write<T, N5>(n: &N5, compression: &CompressionType, block_data: &[T], pool_size: usize)
+where
+    T: 'static + std::fmt::Debug + ReflectedType + PartialEq + Default + Sync + Send,
+    N5: N5Writer + Sync + Send + Clone + 'static,
+    SliceDataBlock<T, std::sync::Arc<[T]>>: n5::WriteableDataBlock,
+{
     let block_size = smallvec![BLOCK_DIM; 3];
     let data_attrs = DatasetAttributes::new(
         smallvec![u64::from(BLOCK_DIM) * N_BLOCKS; 3],
@@ -83,9 +77,11 @@ fn write<T, N5>(
         compression.clone(),
     );
 
-    let path_name = format!("dataset.{:?}.{}",
+    let path_name = format!(
+        "dataset.{:?}.{}",
         data_attrs.get_data_type(),
-        data_attrs.get_compression());
+        data_attrs.get_compression()
+    );
 
     n.create_dataset(&path_name, &data_attrs)
         .expect("Failed to create dataset");
@@ -104,10 +100,7 @@ fn write<T, N5>(
                 let pn = path_name.clone();
                 let da = data_attrs.clone();
                 all_jobs.push(pool.spawn_fn(move || {
-                    let block_in = SliceDataBlock::new(
-                        bs,
-                        smallvec![x, y, z],
-                        bd);
+                    let block_in = SliceDataBlock::new(bs, smallvec![x, y, z], bd);
                     ni.write_block(&pn, &da, &block_in)
                         .expect("Failed to write block");
                     Ok(0)
@@ -120,30 +113,36 @@ fn write<T, N5>(
 }
 
 fn bench_write_dtype_compression<T, C>(b: &mut Bencher, pool_size: usize)
-        where
-            T: 'static + ReflectedType + Default + PartialEq + std::fmt::Debug +
-                std::convert::From<i8> + Sync + Send,
-            C: compression::Compression,
-            CompressionType: std::convert::From<C>,
-            SliceDataBlock<T, std::sync::Arc<[T]>>: n5::WriteableDataBlock {
-
+where
+    T: 'static
+        + ReflectedType
+        + Default
+        + PartialEq
+        + std::fmt::Debug
+        + std::convert::From<i8>
+        + Sync
+        + Send,
+    C: compression::Compression,
+    CompressionType: std::convert::From<C>,
+    SliceDataBlock<T, std::sync::Arc<[T]>>: n5::WriteableDataBlock,
+{
     let dir = tempdir::TempDir::new("rust_n5_integration_tests").unwrap();
 
-    let n = N5Filesystem::open_or_create(dir.path())
-        .expect("Failed to create N5 filesystem");
+    let n = N5Filesystem::open_or_create(dir.path()).expect("Failed to create N5 filesystem");
     let compression = CompressionType::new::<C>();
     // TODO: load the test image data.
     // let block_data: Vec<T> = vec![T::default(); (BLOCK_DIM * BLOCK_DIM * BLOCK_DIM) as usize];
-    let block_data = TEST_IMAGE.iter().take((BLOCK_DIM * BLOCK_DIM * BLOCK_DIM) as usize)
+    let block_data = TEST_IMAGE
+        .iter()
+        .take((BLOCK_DIM * BLOCK_DIM * BLOCK_DIM) as usize)
         .map(|&v| T::from(v))
         .collect::<Vec<T>>();
 
     b.iter(|| write(&n, &compression, &block_data, pool_size));
 
-    b.bytes =
-        (BLOCK_DIM * BLOCK_DIM * BLOCK_DIM) as u64 *
-        (N_BLOCKS * N_BLOCKS * N_BLOCKS) as u64 *
-        std::mem::size_of::<T>() as u64;
+    b.bytes = (BLOCK_DIM * BLOCK_DIM * BLOCK_DIM) as u64
+        * (N_BLOCKS * N_BLOCKS * N_BLOCKS) as u64
+        * std::mem::size_of::<T>() as u64;
 }
 
 // 1 Thread. Can't macro this because of the concat_idents! limitation.

benches/simple.rs

@@ -1,33 +1,28 @@
 //! # Simple In-memory Read/Write Benchmarks
 #![feature(test)]
 
-
 extern crate test;
 
-
 use rand::{
     distributions::Standard,
     Rng,
 };
 use test::Bencher;
 
 use n5::prelude::*;
+use n5::smallvec::smallvec;
 use n5::{
     DefaultBlock,
     DefaultBlockReader,
     DefaultBlockWriter,
 };
-use n5::smallvec::smallvec;
 
-
-fn test_block_compression_rw<T>(
-        compression: compression::CompressionType,
-        b: &mut Bencher
-) where T: 'static + std::fmt::Debug + ReflectedType + PartialEq + Default,
-        rand::distributions::Standard: rand::distributions::Distribution<T>,
-        VecDataBlock<T>: n5::ReadableDataBlock + n5::WriteableDataBlock,
+fn test_block_compression_rw<T>(compression: compression::CompressionType, b: &mut Bencher)
+where
+    T: 'static + std::fmt::Debug + ReflectedType + PartialEq + Default,
+    rand::distributions::Standard: rand::distributions::Distribution<T>,
+    VecDataBlock<T>: n5::ReadableDataBlock + n5::WriteableDataBlock,
 {
-
     let data_attrs = DatasetAttributes::new(
         smallvec![1024, 1024, 1024],
         smallvec![64, 64, 64],
@@ -41,20 +36,20 @@ fn test_block_compression_rw<T>(
     let block_in = VecDataBlock::new(
         data_attrs.get_block_size().into(),
         smallvec![0, 0, 0],
-        block_data.clone());
+        block_data.clone(),
+    );
 
     let mut inner: Vec<u8> = Vec::new();
 
     b.iter(|| {
-        DefaultBlock::write_block(
-            &mut inner,
-            &data_attrs,
-            &block_in).expect("write_block failed");
+        DefaultBlock::write_block(&mut inner, &data_attrs, &block_in).expect("write_block failed");
 
         let _block_out = <DefaultBlock as DefaultBlockReader<T, _>>::read_block(
             &inner[..],
             &data_attrs,
-            smallvec![0, 0, 0]).expect("read_block failed");
+            smallvec![0, 0, 0],
+        )
+        .expect("read_block failed");
     });
 
     b.bytes = (data_attrs.get_block_num_elements() * data_attrs.get_data_type().size_of()) as u64;

release.toml

@@ -0,0 +1,11 @@
+publish = false
+pre-release-commit-message = "Version {{version}}"
+pre-release-replacements = [
+  {file="CHANGELOG.md", search="^## \\[Unreleased\\]", replace="## [{{version}}] - {{date}}", exactly=1},
+  {file="CHANGELOG.md", search="\\[Unreleased\\]", replace="[{{version}}]", min=1},
+  {file="CHANGELOG.md", search="\\.\\.\\.HEAD", replace="...{{tag_name}}", exactly=1},
+]
+post-release-replacements = [
+  {file="CHANGELOG.md", search="<!-- next-header -->", replace="<!-- next-header -->\n## [Unreleased]\n\n", exactly=1},
+  {file="CHANGELOG.md", search="<!-- next-url -->", replace="<!-- next-url -->\n[Unreleased]: https://github.com/aschampion/rust-n5/compare/{{tag_name}}...HEAD", exactly=1},
+]