@@ -13,3 +13,4 @@ renv*

 ^_pkgdown\.yml$

 ^docs$

 ^pkgdown$

+^\.github$

new file mode 100644

@@ -0,0 +1 @@

+*.html

new file mode 100644

@@ -0,0 +1,70 @@

+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples

+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

+#

+# NOTE: This workflow is overkill for most R packages and

+# check-standard.yaml is likely a better choice.

+# usethis::use_github_action("check-standard") will install it.

+on:

+  push:

+    branches: [devel, master]

+  pull_request:

+    branches: [devel, master]

+

+name: R-CMD-check

+

+jobs:

+  R-CMD-check:

+    runs-on: ${{ matrix.config.os }}

+

+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

+

+    strategy:

+      fail-fast: false

+      matrix:

+        config:

+          - {os: macOS-latest,   r: 'release'}

+          - {os: windows-latest, r: 'release'}

+          - {os: ubuntu-latest, r: 'release'}

+

+    env:

+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

+      R_KEEP_PKG_SOURCE: yes

+

+    steps:

+      - uses: actions/checkout@v2

+

+      - uses: r-lib/actions/setup-pandoc@v1

+

+      - uses: r-lib/actions/setup-r@v1

+        with:

+          r-version: ${{ matrix.config.r }}

+          http-user-agent: ${{ matrix.config.http-user-agent }}

+          use-public-rspm: true

+

+      - name: Install XQuartz on macOS

+        if: runner.os == 'macOS'

+        run: brew install xquartz --cask

+

+      - uses: r-lib/actions/setup-r-dependencies@v1

+        with:

+          extra-packages: rcmdcheck

+

+      - name: Check

+        env:

+          _R_CHECK_CRAN_INCOMING_: false

+        run: |

+          options(crayon.enabled = TRUE)

+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")

+        shell: Rscript {0}

+

+      - name: Show testthat output

+        if: always()

+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true

+        shell: bash

+

+      - name: Upload check results

+        if: failure()

+        uses: actions/upload-artifact@main

+        with:

+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results

+          path: check

new file mode 100644

@@ -0,0 +1,30 @@

+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples

+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help

+on:

+  push:

+    branches: [devel, master]

+  pull_request:

+    branches: [devel, master]

+

+name: test-coverage

+

+jobs:

+  test-coverage:

+    runs-on: ubuntu-latest

+    env:

+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

+

+    steps:

+      - uses: actions/checkout@v2

+

+      - uses: r-lib/actions/setup-r@v1

+        with:

+          use-public-rspm: true

+

+      - uses: r-lib/actions/setup-r-dependencies@v1

+        with:

+          extra-packages: covr

+

+      - name: Test coverage

+        run: covr::codecov()

+        shell: Rscript {0}

deleted file mode 100644

@@ -1,26 +0,0 @@

-language: r

-cache: packages

-sudo: false

-warnings_are_errors: false

-bioc_required: true

-r_build_args: "--no-build-vignettes"

-r_check_args: "--no-vignettes --no-build-vignettes --as-cran"

-notifications:

-  slack:

-    secure: 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

-

-r_github_packages:

-  - r-lib/covr

-  - jimhester/lintr

-  - spatstat/spatstat@v1.64-1

-after_success:

-  - R CMD INSTALL $PKG_TARBALL

-  - Rscript -e 'covr::coveralls()'

-  - Rscript -e 'library(lintr); lint_package(linters = with_defaults(object_length_linter(length = 40L), object_name_linter = NULL, commented_code_linter = NULL, object_usage_linter = NULL, cyclocomp_linter(complexity_limit = 100)), exclusions = list("R/RcppExports.R"))'

-

-addons:

-  apt:

-    sources:

-    - sourceline: 'ppa:opencpu/imagemagick'

-    packages:

-    - libmagick++-dev

@@ -1,5 +1,7 @@

-[![Build Status](https://travis-ci.com/campbio/celda.svg?branch=master)](https://travis-ci.com/campbio/celda)

+<!-- badges: start -->

+[![R-CMD-check](https://github.com/campbio/celda/workflows/R-CMD-check/badge.svg)](https://github.com/campbio/celda/actions)

 [![Coverage Status](https://coveralls.io/repos/github/campbio/celda/badge.svg?branch=master)](https://coveralls.io/github/campbio/celda?branch=master)

+<!-- badges: end -->

 # celda: CEllular Latent Dirichlet Allocation