Merge branch 'master' into develop

.github/workflows/CompatHelper.yml

@@ -3,10 +3,23 @@ on:
   schedule:
     - cron: 0 0 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
       - name: "Add the General registry via Git"
         run: |
           import Pkg

.github/workflows/Documentation.yml

@@ -10,6 +10,8 @@ on:
 
 jobs:
   Documenter:
+    permissions:
+      contents: write
     name: Documentation
     runs-on: ubuntu-latest
     steps:

.github/workflows/TagBot.yml

@@ -1,11 +1,25 @@
 name: TagBot
-
 on:
   issue_comment:
     types:
       - created
   workflow_dispatch:
-
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

.github/workflows/UnitTests.yml

@@ -8,24 +8,18 @@ jobs:
   test:
     name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.julia-arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
-    continue-on-error: ${{ matrix.experimental }}
+    continue-on-error: ${{ matrix.julia-version == 'nightly' }}
     strategy:
       fail-fast: false
       matrix:
         julia-version:
           - '1.0' # LTS
+          - '1.6' # LTS
           - '1'
-        julia-arch: [x64, x86]
-        os: [ubuntu-latest, windows-latest, macOS-latest]
-        exclude:
-          - os: macOS-latest
-            julia-arch: x86
-        experimental: [false]
-        include:
-          - julia-version: nightly
-            julia-arch: x64
-            os: ubuntu-latest
-            experimental: true
+          - 'nightly'
+        julia-arch:
+            - x64
+        os: [ubuntu-latest]
 
     steps:
       - name: Checkout Repository
@@ -34,6 +28,7 @@ jobs:
         uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-arch }}
       - name: Run Tests
         uses: julia-actions/julia-runtest@v1
       - name: Create CodeCov

Project.toml

@@ -1,7 +1,7 @@
 name = "GenomicFeatures"
 uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446"
-authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <benjward@protonmail.com>", "Ciarán O’Mara <[email protected]>"]
-version = "2.0.5"
+authors = ["Kenta Sato <[email protected]>", "Sabrina J. Ward <sabrinajward@protonmail.com>", "Ciarán O’Mara <[email protected]>"]
+version = "2.1.0"
 
 [deps]
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"

README.md

@@ -70,4 +70,4 @@ 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 [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).
+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.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/src/index.md

@@ -69,4 +69,4 @@ 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 [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).
+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.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).