Hotfix/2.2.0

.github/workflows/CompatHelper.yml

@@ -1,24 +1,35 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '00 * * * *'
-
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1]
-        julia-arch: [x64]
-        os: [ubuntu-latest]
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: ${{ matrix.julia-version }}
-      - name: Add CompatHelper
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e 'using CompatHelper; CompatHelper.main(;);'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Downstream.yml

@@ -0,0 +1,53 @@
+name: Downstream
+on:
+  push:
+    branches: [master, develop]
+    tags: [v*]
+  pull_request:
+
+jobs:
+  test:
+    name: ${{ matrix.package.repo }}/${{ matrix.package.group }}
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.package.group }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: [1]
+        os: [ubuntu-latest]
+        package:
+          - {user: BioJulia, repo: BioStructures.jl, group: BioAlignments}
+          - {user: BioJulia, repo: BioTools.jl, group: BioAlignments}
+          - {user: BioJulia, repo: XAM.jl, group: BioAlignments}
+          - {user: JuliaHealth, repo: CAOS.jl, group: BioAlignments}
+          - {user: phaverty, repo: GenomicVectors.jl, group: BioAlignments}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - uses: julia-actions/julia-buildpkg@latest
+      - name: Clone Downstream
+        uses: actions/checkout@v2
+        with:
+          repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
+          path: downstream
+      - name: Load this and run the downstream tests
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          try
+            # force it to use this PR's version of the package
+            Pkg.develop(PackageSpec(path="."))  # resolver may fail with main deps
+            Pkg.update()
+            Pkg.test()  # resolver may fail with test time deps
+          catch err
+            err isa Pkg.Resolve.ResolverError || rethrow()
+            # If we can't resolve that means this is incompatible by SemVer and this is fine.
+            # It means we marked this as a breaking change, so we don't need to worry about.
+            # Mistakenly introducing a breaking change, as we have intentionally made one.
+            @info "Not compatible with this release. No problem." exception=err
+            exit(0)  # Exit immediately, as a success
+          end

.github/workflows/TagBot.yml

@@ -4,6 +4,11 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  contents: write
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -12,3 +17,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/ci.yml

@@ -1,12 +1,9 @@
 name: CI
+
 on:
-  pull_request:
-    branches:
-      - master
   push:
-    branches:
-      - master
-    tags: '*'
+  pull_request:
+
 jobs:
   test:
     name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
@@ -16,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.0'
+          - '1.6'
           - '1'
           - 'nightly'
         os:
@@ -50,19 +47,14 @@ jobs:
         with:
           file: lcov.info
   docs:
+    permissions:
+      contents: write
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          version: '1'
-      - run: |
-          julia --project=docs -e '
-            using Pkg
-            Pkg.develop(PackageSpec(path=pwd()))
-            Pkg.instantiate()'
-      - run: julia --project=docs docs/make.jl
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

CHANGELOG.md

@@ -1,11 +1,60 @@
 # Changelog
+
 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).
 
 ## [Unreleased]
 
+## [2.2.0]
+
+### Added
+- Compact printing of alignments (#53)
+- More SubstitutionMatrix operations (#60)
+- Downstream tests (#70)
+- SSH secret to TagBot.yml (#71)
+- Doctests as part of the unit tests (#78)
+
+### Changed
+- Updated chat links (#ebea200c)
+- Expanded test matrix, adding julia v1.6 (#77)
+- Incremented BioSequences compatibility to v3 (#72)
+- Incremented BioSymbols compatibility to v5 (#72)
+- Adjusted test matrix for minimum compatibility (#72)
+- Updated doctests (#72)
+
+### Removed
+- :exclamation: Removed Gitter chat links (#ebea200c)
+- :exclamation: Dropped support for julia less than v1.6 (#72)
+- :exclamation: Removed alignment position support, as it was a breaking change (#44, #76)
+
+### Fixed
+- Doctests (#78)
+
+## [2.1.0] - 2022-02-10 [YANKED]
+
+### Added
+- Zenodo badge (#c49bb0a3)
+
+### Removed
+- :exclamation: Dropped support for julia less than v1 (#50)
+
+### Changed
+
+## [2.0.1] - 2022-02-08 [UNREGISTERED]
+
+### Added
+- Alignment position support (#44)
+
+### Changed
+- Updated CI to use GitHub actions (#47)
+- *master* set as the main development branch (#49, #50)
+
+### Removed
+- :exclamation: Reverted the use of *BioJulia* registry,
+  the package switched to [General Julia Registry](https://github.com/JuliaRegistries/General) (#48)
+
 ## [2.0.0]
 
 ### Added
@@ -57,7 +106,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ## [0.1.0] - 2017-06-30
 - This initial release extracted the alignment utilities out from Bio.jl into this dedicated package.
 
-[Unreleased]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.0.0...HEAD
+[Unreleased]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.2.0...HEAD
+[2.2.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.1.0...v2.2.0
+[2.1.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.0.1...v2.1.0
+[2.0.1]: https://github.com/BioJulia/BioAlignments.jl/compare/v2.0.0...v2.0.1
 [2.0.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v1.0.1...v2.0.0
 [1.0.1]: https://github.com/BioJulia/BioAlignments.jl/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/BioJulia/BioAlignments.jl/compare/v0.3.0...v1.0.0

Project.toml

@@ -1,24 +1,25 @@
 name = "BioAlignments"
 uuid = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
-authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <benjward@protonmail.com>"]
-version = "2.0.0"
+authors = ["Kenta Sato <bicycle1885@gmail.com>", "Sabrina J. Ward <sabrinajward@protonmail.com>"]
+version = "2.2.0"
 
 [deps]
-BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea" # Note: required for distance function.
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [compat]
-julia = "0.7,1"
 BioGenerics = "0.1"
-BioSequences = "2"
-BioSymbols = "4"
+BioSequences = "3"
+BioSymbols = "5"
 IntervalTrees = "1"
+julia = "1"
 
 [extras]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Documenter", "Test"]

README.md

@@ -1,11 +1,12 @@
 # <img src="./sticker.svg" width="30%" align="right" /> BioAlignments.jl
 
+[![DOI](https://zenodo.org/badge/94387480.svg)](https://zenodo.org/badge/latestdoi/94387480)
+
 [![Latest release](https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg)](https://github.com/BioJulia/BioAlignments.jl/releases/latest)
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/BioAlignments.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/BioAlignments.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/BioAlignments.jl/dev)
 [![Project Status: Active](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![Gitter](https://badges.gitter.im/BioJulia/BioAlignments.jl.svg)](https://gitter.im/BioJulia/BioAlignments.jl?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 ## Description
 
@@ -19,17 +20,18 @@ You can install *BioAlignments.jl* from Julia REPL in [pkg mode](https://docs.ju
 pkg> add BioAlignments
 ```
 
-If you are interested in the cutting edge of the development, please check out the [develop branch](https://github.com/BioJulia/BioAlignments.jl/tree/develop) to try new features before release.
+If you are interested in the cutting edge of the development, please check out the [*master* branch](https://github.com/BioJulia/BioAlignments.jl/tree/master) to try new features before release.
 
 ## Testing
 
 BioAlignments is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 
-[![Build Status](https://travis-ci.org/BioJulia/BioAlignments.jl.svg?branch=master)](https://travis-ci.org/BioJulia/BioAlignments.jl)
+[![Build Status](https://github.com/BioJulia/BioAlignments.jl/workflows/CI/badge.svg)](https://github.com/BioJulia/BioAlignments.jl/actions)
 [![appveyor](https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true)](https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master)
 [![codecov](https://codecov.io/gh/BioJulia/BioAlignments.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/BioAlignments.jl)
+[![Downstream](https://github.com/BioJulia/BioAlignments.jl/actions/workflows/Downstream.yml/badge.svg)](https://github.com/BioJulia/BioAlignments.jl/actions/workflows/Downstream.yml)
 
 ## Contributing
 
@@ -72,4 +74,4 @@ Your logo will show up here with a link to your website.
 
 ## Questions?
 
-If you have a question about contributing or using BioJulia software, come on over and chat to us on [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/make.jl

@@ -22,6 +22,6 @@ makedocs(
 
 deploydocs(
     repo = "github.com/BioJulia/BioAlignments.jl.git",
-    devbranch = "develop",
+    devbranch = "master",
     push_preview = true
 )

docs/src/alignments.md

@@ -118,7 +118,7 @@ julia> convert(Operation, 'M')  # Char => Operation
 OP_MATCH
 
 julia> convert(Char, OP_MATCH)  # Operation => Char
-'M': ASCII/Unicode U+004d (category Lu: Letter, uppercase)
+'M': ASCII/Unicode U+004D (category Lu: Letter, uppercase)
 
 julia> ismatchop(OP_MATCH)
 true

docs/src/index.md

@@ -5,7 +5,6 @@
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/BioAlignments.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/BioAlignments.jl/dev)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
-[![Gitter](https://badges.gitter.im/BioJulia/BioAlignments.jl.svg)](https://gitter.im/BioJulia/BioAlignments.jl?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 ## Description
 
@@ -19,17 +18,18 @@ You can install *BioAlignments.jl* from Julia REPL in [pkg mode](https://docs.ju
 pkg> add BioAlignments
 ```
 
-If you are interested in the cutting edge of the development, please check out the [develop branch](https://github.com/BioJulia/BioAlignments.jl/tree/develop) to try new features before release.
+If you are interested in the cutting edge of the development, please check out the [*master* branch](https://github.com/BioJulia/BioAlignments.jl/tree/master) to try new features before release.
 
 ## Testing
 
 *BioAlignments.jl* is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 
-[![Build Status](https://travis-ci.org/BioJulia/BioAlignments.jl.svg?branch=master)](https://travis-ci.org/BioJulia/BioAlignments.jl)
+[![Build Status](https://github.com/BioJulia/BioAlignments.jl/workflows/CI/badge.svg)](https://github.com/BioJulia/BioAlignments.jl/actions)
 [![appveyor](https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true)](https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master)
 [![codecov](https://codecov.io/gh/BioJulia/BioAlignments.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/BioAlignments.jl)
+[![Downstream](https://github.com/BioJulia/BioAlignments.jl/actions/workflows/Downstream.yml/badge.svg)](https://github.com/BioJulia/BioAlignments.jl/actions/workflows/Downstream.yml)
 
 ## Contributing
 
@@ -67,4 +67,4 @@ Your logo will show up here with a link to your website.
 
 ## Questions?
 
-If you have a question about contributing or using BioJulia software, come on over and chat to us on [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).