diff --git a/.DS_Store b/.DS_Store index e7e1dbb..9219ffe 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml index 623860f..f389611 100644 --- a/.github/workflows/TagBot.yml +++ b/.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' @@ -12,4 +17,4 @@ jobs: - uses: JuliaRegistries/TagBot@v1 with: token: ${{ secrets.GITHUB_TOKEN }} - ssh: ${{ secrets.DOCUMENTER_KEY }} \ No newline at end of file + ssh: ${{ secrets.DOCUMENTER_KEY }} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..3511a5e --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,50 @@ +name: CI +on: + pull_request: + push: + branches: [main] + tags: ['*'] +jobs: + test: + name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + version: + - '1' # automatically expands to the latest stable 1.x release of Julia + - 'nightly' + os: + - ubuntu-latest + arch: + - x64 + include: + - os: windows-latest + version: '1' + arch: x86 + steps: + - uses: actions/checkout@v2 + - uses: julia-actions/setup-julia@v1 + with: + version: ${{ matrix.version }} + arch: ${{ matrix.arch }} + - uses: julia-actions/cache@v1 + - uses: julia-actions/julia-buildpkg@v1 + - uses: julia-actions/julia-runtest@v1 + env: + JULIA_NUM_THREADS: 4 + - uses: julia-actions/julia-processcoverage@v1 + - uses: codecov/codecov-action@v1 + with: + file: lcov.info + docs: + name: Documentation + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: julia-actions/cache@v1 + - uses: julia-actions/julia-buildpkg@latest + - uses: julia-actions/julia-docdeploy@latest + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} diff --git a/.gitignore b/.gitignore index 62a1f41..c0b58e7 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ *.cov docs/build/ docs/site/ +.DS_Store diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 0e5a84d..0000000 --- a/.travis.yml +++ /dev/null @@ -1,26 +0,0 @@ -language: julia - -os: - - linux - - osx - -julia: - - 1.6 - - nightly - -notifications: - email: false - -matrix: - allow_failures: - - julia: nightly - -script: - - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi - - julia --color=yes -e 'using Pkg; Pkg.build()' - - julia --check-bounds=yes --color=yes -e 'using Pkg; Pkg.add("Test"); Pkg.test("RLEVectors"; coverage=true)' - -after_success: - - julia -e 'using Pkg; cd(Pkg.dir("RLEVectors")); Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())' - - julia -e 'using Pkg; Pkg.add("Documenter")' - - julia -e 'using Pkg; cd(Pkg.dir("RLEVectors")); include(joinpath("docs", "make.jl"))' diff --git a/docs/src/index.md b/docs/src/index.md index b535fe8..bb8e5b6 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -1,7 +1,7 @@ # RLEVectors -`RLEVectors` is an alternate implementation of the Rle type from +`RLEVectors` is an alternate implementation of the `Rle` type from Bioconductor's IRanges package by H. Pages, P. Aboyoun and -M. Lawrence. RLEVectors represent a vector with repeated values as the +M. Lawrence. `RLEVectors` represent a vector with repeated values as the ordered set of values and repeat extents. In the field of genomics, data of various types are measured across the ~3 billion letters in the human genome can often be represented in a few thousand runs. It