From 9a96ce5b88ca97cc7d6ac12500c0b66707ada96c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:00:15 +1000 Subject: [PATCH 1/7] Increment version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 434addcb..17f7776c 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "GenomicFeatures" uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446" authors = ["Kenta Sato ", "Ben J. Ward ", "Ciarán O’Mara "] -version = "2.0.5" +version = "2.1.0" [deps] BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea" From 8f2e96928af36609c049aeeff08c63e718629fd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:01:46 +1000 Subject: [PATCH 2/7] Update authors --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 17f7776c..3e3d72a5 100644 --- a/Project.toml +++ b/Project.toml @@ -1,6 +1,6 @@ name = "GenomicFeatures" uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446" -authors = ["Kenta Sato ", "Ben J. Ward ", "Ciarán O’Mara "] +authors = ["Kenta Sato ", "Sabrina J. Ward ", "Ciarán O’Mara "] version = "2.1.0" [deps] From 84b2d6ef0509a247d55c00fb0db6c2136ff8ef21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:05:17 +1000 Subject: [PATCH 3/7] Update TagBot workflow --- .github/workflows/TagBot.yml | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml index 6d2efc1c..2bacdb87 100644 --- a/.github/workflows/TagBot.yml +++ b/.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' From cd9395b0a4f665a761ed874b9bafab4b44a29729 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:12:22 +1000 Subject: [PATCH 4/7] Update UnitTests workflow Reduces the number of OS tested as there is no need to check third-party software or integrations. --- .github/workflows/UnitTests.yml | 19 +++++++------------ 1 file changed, 7 insertions(+), 12 deletions(-) diff --git a/.github/workflows/UnitTests.yml b/.github/workflows/UnitTests.yml index 90788864..c8144623 100644 --- a/.github/workflows/UnitTests.yml +++ b/.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 From ea7d2ea0abcf8b28273e8275a2bd928d2a89b026 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:19:18 +1000 Subject: [PATCH 5/7] Update Documentation workflow --- .github/workflows/Documentation.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 02e5911e..693e1637 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -10,6 +10,8 @@ on: jobs: Documenter: + permissions: + contents: write name: Documentation runs-on: ubuntu-latest steps: From 751cbd916c84c4d04266bf246934806c15c8c107 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:21:39 +1000 Subject: [PATCH 6/7] Update CompatHelper workflow --- .github/workflows/CompatHelper.yml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index 9fd9f2b3..ca78383f 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.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 From c7f2cb6bbd1d672f9c1db3a0141d8a70f9e43f43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 17 Apr 2023 14:23:17 +1000 Subject: [PATCH 7/7] Improve slack link --- README.md | 2 +- docs/src/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index df77ec83..e4b674de 100644 --- a/README.md +++ b/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). diff --git a/docs/src/index.md b/docs/src/index.md index 45d1d498..13a19536 100644 --- a/docs/src/index.md +++ b/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).