Merge branch 'master' into master

.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "cargo"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      # Prefix all commit messages with "deps: ", which should be
+      # accepted as a conventional commit and trigger release-please
+      prefix: "deps"

.github/workflows/rust.yml

@@ -86,7 +86,7 @@ jobs:
     needs: Formatting
     runs-on: ubuntu-latest
     env:
-      MSRV_VERSION: 1.62.0
+      MSRV_VERSION: 1.65.0
     steps:
       - name: Checkout repository
         uses: actions/checkout@v2
@@ -100,40 +100,39 @@ jobs:
       - name: check if README matches MSRV defined here
         run: grep $MSRV_VERSION README.md
 
-      - name: pin dependency versions for MSRV
-        run: |
-          cargo update -p indexmap --precise 1.8.2
-
       - name: Run tests
         uses: actions-rs/cargo@v1
         with:
           command: test
           args: --all --no-fail-fast
 
-  Coverage:
-    needs: Formatting
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v2
-        with:
-          submodules: recursive
-
-      - name: Install nightly toolchain
-        uses: actions-rs/toolchain@v1
-        with:
-          toolchain: nightly
-          override: true
-
-      - name: Install and run cargo-tarpaulin
-        uses: actions-rs/tarpaulin@v0.1
-        with:
-          # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
-          version: "0.22.0"
-          args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 300"
-
-      - name: Upload coverage
-        uses: coverallsapp/github-action@v1
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: ./lcov.info
+  # TODO re-enable coverage estimation once we have removed the simd-dependency which is incompatible
+  # with nightly. We need to wait for the stdlib simd implementation to stabilize, see
+  # https://github.com/rust-lang/rust/issues/86656
+  # Coverage:
+  #   needs: Formatting
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Checkout repository
+  #       uses: actions/checkout@v2
+  #       with:
+  #         submodules: recursive
+
+  #     - name: Install nightly toolchain
+  #       uses: actions-rs/toolchain@v1
+  #       with:
+  #         toolchain: nightly
+  #         override: true
+
+  #     - name: Install and run cargo-tarpaulin
+  #       uses: actions-rs/tarpaulin@v0.1
+  #       with:
+  #         # TODO: update to latest tarpaulin once artefact download is fixed: https://github.com/actions-rs/tarpaulin/pull/23
+  #         version: "0.22.0"
+  #         args: "--workspace --all-features --run-types Tests,Doctests --out Lcov --timeout 300"
+
+  #     - name: Upload coverage
+  #       uses: coverallsapp/github-action@v1
+  #       with:
+  #         github-token: ${{ secrets.GITHUB_TOKEN }}
+  #         path-to-lcov: ./lcov.info

CHANGELOG.md

@@ -3,6 +3,19 @@ All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 
+## [1.4.0](https://www.github.com/rust-bio/rust-bio/compare/v1.3.1...v1.4.0) (2023-09-12)
+
+
+### Features
+
+* memory efficient banded poa ([#532](https://www.github.com/rust-bio/rust-bio/issues/532)) ([f03ee1c](https://www.github.com/rust-bio/rust-bio/commit/f03ee1cdf6d4a9b36f125bd72fcf5b6191324f0b))
+
+
+### Bug Fixes
+
+* include `doctests` in the test coverage of code that tarpaulin calculates ([#533](https://www.github.com/rust-bio/rust-bio/issues/533)) ([29cf0f5](https://www.github.com/rust-bio/rust-bio/commit/29cf0f59daf9377e218b62b118f209afe5fe3615))
+* make dependabot commit message follow conventional commits ([#542](https://www.github.com/rust-bio/rust-bio/issues/542)) ([bb88281](https://www.github.com/rust-bio/rust-bio/commit/bb882814395a172de48f670cd316429ea2e50864))
+
 ### [1.3.1](https://www.github.com/rust-bio/rust-bio/compare/v1.3.0...v1.3.1) (2023-06-23)
 
 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bio"
-version = "1.3.1"
+version = "1.4.0"
 authors = ["Johannes Köster <johannes.koester@tu-dortmund.de>"]
 description = "A bioinformatics library for Rust. This library provides implementations of many algorithms and data structures that are useful for bioinformatics, but also in other fields."
 homepage = "https://rust-bio.github.io"
@@ -40,7 +40,7 @@ custom_derive = "0.1"
 newtype_derive = "0.1"
 ordered-float = "3.1"
 regex = { version = "1.3", default-features = false, features = ["std", "perf"] }
-multimap = ">=0.6, <0.9"
+multimap = ">=0.6, <0.10"
 fxhash = "0.2"
 statrs = ">= 0.11, < 0.17"
 bio-types = ">=1.0.0"
@@ -49,7 +49,7 @@ pest_derive = { version = "2", optional = true }
 strum = ">= 0.16, < 0.26"
 strum_macros = ">= 0.16, < 0.26"
 getset = ">=0.0.9, <0.2"
-enum-map = ">=0.6.4, <2"
+enum-map = ">=0.6.4, <3"
 triple_accel = ">=0.3, <0.5"
 thiserror = "1"
 anyhow = "1"

README.md

@@ -57,7 +57,7 @@ For extra credit, feel free to familiarize yourself with:
 
 ## Minimum supported Rust version
 
-Currently the minimum supported Rust version is 1.62.0.
+Currently the minimum supported Rust version is 1.65.0.
 
 ## License