From c432960b65afc33e70bfebf21792452d989571cb Mon Sep 17 00:00:00 2001 From: Zachary Kurtz Date: Fri, 18 Nov 2022 20:30:17 -0500 Subject: [PATCH 1/4] add github actions workflow --- .github/workflows/test_build.R | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 .github/workflows/test_build.R diff --git a/.github/workflows/test_build.R b/.github/workflows/test_build.R new file mode 100644 index 0000000..c43d31f --- /dev/null +++ b/.github/workflows/test_build.R @@ -0,0 +1,33 @@ +name: test + +on: + push: + branches: [ "master" ] + pull_request: + branches: [ "master" ] + workflow_dispatch: + +permissions: + contents: read + +jobs: + build: + runs-on: ubuntu-latest + strategy: + matrix: + r-version: ['3.6.3', '4.1.1'] + + steps: + - uses: actions/checkout@v3 + - name: Set up R ${{ matrix.r-version }} + uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.r-version }} + - name: Install dependencies + run: | + install.packages(c("remotes", "rcmdcheck")) + remotes::install_deps(dependencies = TRUE) + shell: Rscript {0} + - name: Check + run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") + shell: Rscript {0} \ No newline at end of file From b9f2d2d965102f4106fcc8c4c1644331ebb17b07 Mon Sep 17 00:00:00 2001 From: Zachary Kurtz Date: Sat, 14 Oct 2023 13:34:36 -0400 Subject: [PATCH 2/4] try caching r-dependencies --- .github/workflows/test_build.R | 40 +++++++++++++++++++--------------- 1 file changed, 23 insertions(+), 17 deletions(-) diff --git a/.github/workflows/test_build.R b/.github/workflows/test_build.R index c43d31f..6bd13df 100644 --- a/.github/workflows/test_build.R +++ b/.github/workflows/test_build.R @@ -2,7 +2,7 @@ name: test on: push: - branches: [ "master" ] + branches: [ "master", "gh-actions" ] pull_request: branches: [ "master" ] workflow_dispatch: @@ -13,21 +13,27 @@ permissions: jobs: build: runs-on: ubuntu-latest - strategy: - matrix: - r-version: ['3.6.3', '4.1.1'] + # strategy: + # matrix: + # r-version: ['3.6.3', '4.1.1'] + steps: - - uses: actions/checkout@v3 - - name: Set up R ${{ matrix.r-version }} - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.r-version }} - - name: Install dependencies - run: | - install.packages(c("remotes", "rcmdcheck")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - name: Check - run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") - shell: Rscript {0} \ No newline at end of file + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + cache: true + cache-version: 1 + extra-packages: | + any::rcmdcheck + any::remotes + any::devtools + any::pulsar + local::. + needs: check + - uses: r-lib/actions/check-r-package@v2 + with: + args: 'c("--no-manual", "--as-cran")' + error-on: '"error"' + check-dir: '"check"' From 6f565dfce722e200ee80a490a9886d2eaab5439a Mon Sep 17 00:00:00 2001 From: Zachary Kurtz Date: Sat, 14 Oct 2023 13:36:55 -0400 Subject: [PATCH 3/4] remove extra file --- .github/workflows/test_build.R | 39 ------------------------------- .github/workflows/test_build.yml | 40 ++++++++++++++++++-------------- 2 files changed, 23 insertions(+), 56 deletions(-) delete mode 100644 .github/workflows/test_build.R diff --git a/.github/workflows/test_build.R b/.github/workflows/test_build.R deleted file mode 100644 index 6bd13df..0000000 --- a/.github/workflows/test_build.R +++ /dev/null @@ -1,39 +0,0 @@ -name: test - -on: - push: - branches: [ "master", "gh-actions" ] - pull_request: - branches: [ "master" ] - workflow_dispatch: - -permissions: - contents: read - -jobs: - build: - runs-on: ubuntu-latest - # strategy: - # matrix: - # r-version: ['3.6.3', '4.1.1'] - - - steps: - - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v2 - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - cache: true - cache-version: 1 - extra-packages: | - any::rcmdcheck - any::remotes - any::devtools - any::pulsar - local::. - needs: check - - uses: r-lib/actions/check-r-package@v2 - with: - args: 'c("--no-manual", "--as-cran")' - error-on: '"error"' - check-dir: '"check"' diff --git a/.github/workflows/test_build.yml b/.github/workflows/test_build.yml index c43d31f..6bd13df 100644 --- a/.github/workflows/test_build.yml +++ b/.github/workflows/test_build.yml @@ -2,7 +2,7 @@ name: test on: push: - branches: [ "master" ] + branches: [ "master", "gh-actions" ] pull_request: branches: [ "master" ] workflow_dispatch: @@ -13,21 +13,27 @@ permissions: jobs: build: runs-on: ubuntu-latest - strategy: - matrix: - r-version: ['3.6.3', '4.1.1'] + # strategy: + # matrix: + # r-version: ['3.6.3', '4.1.1'] + steps: - - uses: actions/checkout@v3 - - name: Set up R ${{ matrix.r-version }} - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.r-version }} - - name: Install dependencies - run: | - install.packages(c("remotes", "rcmdcheck")) - remotes::install_deps(dependencies = TRUE) - shell: Rscript {0} - - name: Check - run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error") - shell: Rscript {0} \ No newline at end of file + - uses: actions/checkout@v3 + - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + cache: true + cache-version: 1 + extra-packages: | + any::rcmdcheck + any::remotes + any::devtools + any::pulsar + local::. + needs: check + - uses: r-lib/actions/check-r-package@v2 + with: + args: 'c("--no-manual", "--as-cran")' + error-on: '"error"' + check-dir: '"check"' From 8e812b5a2e99d594a358addf234387e8a8ea9c2f Mon Sep 17 00:00:00 2001 From: Zachary Kurtz Date: Sat, 14 Oct 2023 14:35:22 -0400 Subject: [PATCH 4/4] remove travis badges --- README.Rmd | 1 - README.md | 1 - 2 files changed, 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index fbc1909..008ab8e 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,6 @@ if (!runchunks) load('.README.RData') ``` SpiecEasi ========= -[![Build Status](https://app.travis-ci.com/zdk123/SpiecEasi.svg?branch=master)](https://app.travis-ci.com/zdk123/SpiecEasi) Sparse InversE Covariance estimation for Ecological Association and Statistical Inference diff --git a/README.md b/README.md index ed717f1..a63ca77 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,6 @@ SpiecEasi ========= -[![Build Status](https://app.travis-ci.com/zdk123/SpiecEasi.svg?branch=master)](https://app.travis-ci.com/zdk123/SpiecEasi) Sparse InversE Covariance estimation for Ecological Association and Statistical Inference