From eaf5c73eb5af325ac97a46c18dd3d539fa9cb41a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 25 May 2020 14:08:07 +1000 Subject: [PATCH] Update CI and documentation for the general registry - Update documentation workflow. - Update CompatHelper workflow. - Update TagBot workflow. - Update unit test workflow. - Update codecov. --- .github/workflows/CompatHelper.yml | 33 +++++------------------ .github/workflows/Documentation.yml | 40 +++++++++++---------------- .github/workflows/TagBot.yml | 3 +-- .github/workflows/UnitTests.yml | 42 ++++++++++++++++++++++------- Project.toml | 2 +- README.md | 13 +++------ ci_prep.jl | 3 --- coverage/Project.toml | 2 -- coverage/coverage.jl | 11 -------- docs/src/index.md | 15 +++-------- 10 files changed, 62 insertions(+), 102 deletions(-) delete mode 100644 ci_prep.jl delete mode 100644 coverage/Project.toml delete mode 100644 coverage/coverage.jl diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index 36f1665..98d1792 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.github/workflows/CompatHelper.yml @@ -2,37 +2,16 @@ name: CompatHelper on: schedule: - - cron: '00 * * * *' + - cron: '0 0 * * *' jobs: CompatHelper: - runs-on: ${{ matrix.os }} - strategy: - matrix: - julia-version: [1.3.0] - julia-arch: [x86] - 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 + run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")' + - name: Run CompatHelper env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run: julia -e ' - using CompatHelper, Pkg; - my_registries = [ - Pkg.RegistrySpec( - name = "BioJuliaRegistry", - uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca", - url = "https://github.com/BioJulia/BioJuliaRegistry.git" - ), - Pkg.RegistrySpec( - name = "General", - uuid = "23338594-aafe-5451-b93e-139f81909106", - url = "https://github.com/JuliaRegistries/General.git" - ) - ]; - CompatHelper.main(; registries = my_registries, master_branch = "master");' + COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }} + run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")' diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml index 9610301..85a6cd9 100644 --- a/.github/workflows/Documentation.yml +++ b/.github/workflows/Documentation.yml @@ -1,34 +1,26 @@ -name: Documentation +name: Build Documentation on: - push: - branches: - - 'master' - - 'develop' - - 'release/.*' - tags: '*' - pull_request: + push: + branches: + - master + - develop + - release/* + tags: '*' + pull_request: jobs: build: - runs-on: ${{ matrix.os }} - strategy: - matrix: - julia-version: [1.3.0] - julia-arch: [x86] - os: [ubuntu-latest] + runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1.0.0 - - uses: julia-actions/setup-julia@latest + - uses: actions/checkout@v2 + - uses: julia-actions/setup-julia@v1 with: - version: ${{ matrix.julia-version }} - - name: Install dependencies - run: | - julia ci_prep.jl; - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' - - name: Build and deploy + version: '1' + - name: Install Dependencies + run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' + - name: Build and Deploy env: - # https://github.com/JuliaDocs/Documenter.jl/issues/1177 # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key - run: julia --project=docs/ --color=yes docs/make.jl + run: julia --color=yes --project=docs/ docs/make.jl diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml index e65374b..086a8e5 100644 --- a/.github/workflows/TagBot.yml +++ b/.github/workflows/TagBot.yml @@ -1,7 +1,7 @@ name: TagBot on: schedule: - - cron: '0 * * * *' + - cron: '0 0 * * *' jobs: TagBot: runs-on: ubuntu-latest @@ -10,4 +10,3 @@ jobs: with: token: ${{ secrets.GITHUB_TOKEN }} ssh: ${{ secrets.TAGBOT_KEY }} - registry: BioJulia/BioJuliaRegistry \ No newline at end of file diff --git a/.github/workflows/UnitTests.yml b/.github/workflows/UnitTests.yml index cbaf083..9d5c078 100644 --- a/.github/workflows/UnitTests.yml +++ b/.github/workflows/UnitTests.yml @@ -1,22 +1,44 @@ -name: Unit tests +name: Unit Tests -on: [push, pull_request] +on: + - push + - pull_request jobs: test: runs-on: ${{ matrix.os }} + continue-on-error: ${{ matrix.experimental }} strategy: + fail-fast: false matrix: - julia-version: ['1.1', '1.2', '1.3'] - julia-arch: [x64] + julia-version: + - '1.0' # LTS + - '1' + julia-arch: [x64, x86] os: [ubuntu-latest, windows-latest, macOS-latest] + experimental: [false] + include: + - julia-version: nightly + julia-arch: x64 + os: ubuntu-latest + experimental: true steps: - - uses: actions/checkout@v1.0.0 - - uses: julia-actions/setup-julia@v1 + - name: Checkout Repository + uses: actions/checkout@v2 + - name: Setup Julia + uses: julia-actions/setup-julia@v1 with: version: ${{ matrix.julia-version }} - arch: ${{ matrix.julia-arch }} - - name: Install dependencies - run: julia ci_prep.jl - - uses: julia-actions/julia-runtest@master + - name: Run Tests + uses: julia-actions/julia-runtest@latest + - name: Create CodeCov + uses: julia-actions/julia-processcoverage@v1 + - name: Upload CodeCov + uses: codecov/codecov-action@v1 + with: + file: ./lcov.info + flags: unittests + name: codecov-umbrella + fail_ci_if_error: false + token: ${{ secrets.CODECOV_TOKEN }} diff --git a/Project.toml b/Project.toml index 1f031ee..f5a56c2 100644 --- a/Project.toml +++ b/Project.toml @@ -23,7 +23,7 @@ BioSequences = "2" GenomicFeatures = "2" Indexes = "0.1" TranscodingStreams = "0.6, 0.7, 0.8, 0.9" -julia = "1.1" +julia = "1" [extras] FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd" diff --git a/README.md b/README.md index 850a435..951c649 100644 --- a/README.md +++ b/README.md @@ -11,18 +11,11 @@ blog post"). ## Description -XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files. +The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files. ## Installation -The latest version of XAM is made available to install through BioJulia's package registry. -By default, Julia's package manager only includes the "General" package registry. - -To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command: -```julia -registry add https://github.com/BioJulia/BioJuliaRegistry.git -``` - -Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following: +You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/). +Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command: ```julia add XAM ``` diff --git a/ci_prep.jl b/ci_prep.jl deleted file mode 100644 index f3a7535..0000000 --- a/ci_prep.jl +++ /dev/null @@ -1,3 +0,0 @@ -using Pkg.Registry -Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git")) -Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git")) diff --git a/coverage/Project.toml b/coverage/Project.toml deleted file mode 100644 index 4fbdc47..0000000 --- a/coverage/Project.toml +++ /dev/null @@ -1,2 +0,0 @@ -[deps] -Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037" diff --git a/coverage/coverage.jl b/coverage/coverage.jl deleted file mode 100644 index 3d33ed9..0000000 --- a/coverage/coverage.jl +++ /dev/null @@ -1,11 +0,0 @@ -get(ENV, "TRAVIS_OS_NAME", "") == "linux" || exit() -get(ENV, "TRAVIS_JULIA_VERSION", "") == "1.3" || exit() - -using Pkg -Pkg.instantiate() - -using Coverage - -cd(joinpath(@__DIR__, "..")) do - Codecov.submit(Codecov.process_folder()) -end diff --git a/docs/src/index.md b/docs/src/index.md index a3bbf39..de6ee30 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -10,20 +10,11 @@ > This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/). ## Description - -XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files. - +The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files. ## Installation -The latest version of XAM is made available to install through BioJulia's package registry. -By default, Julia's package manager only includes the "General" package registry. - -To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command: -```julia -registry add https://github.com/BioJulia/BioJuliaRegistry.git -``` - -Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following: +You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/). +Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command: ```julia add XAM ```