Merge pull request #286 from Aariq/pkgdown

Switch to GH-actions and update website

.Rbuildignore

@@ -6,13 +6,6 @@
 .gitignore
 .github
 
-# Travis
-.travis.yml
-pkg-build.sh
-
-# appveyor
-^appveyor\.yml$
-travis-tool.sh.cmd
 
 # READMES
 README.html
@@ -29,3 +22,6 @@ README_cache
 ^pkgdown$
 
 .Rmd.orig
+^\.github$
+
+codemeta.json

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,87 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - 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: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      _R_CHECK_CRAN_INCOMING_: false
+      RSPM: ${{ matrix.config.rspm }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        run: |
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran","--no-build-vignettes", "--timings", "--no-examples", "--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

.github/workflows/test-coverage.yaml

@@ -0,0 +1,29 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: 'release'
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

README.Rmd

@@ -21,12 +21,11 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 
 [![CRAN](https://www.r-pkg.org/badges/version/webchem)](https://CRAN.R-project.org/package=webchem) 
-[![Travis](https://travis-ci.org/ropensci/webchem.png)](https://travis-ci.org/ropensci/webchem) 
-[![AppVeyor](https://ci.appveyor.com/api/projects/status/8m7wpfnxn41kqjnl?svg=true)](https://ci.appveyor.com/project/ropensci/webchem)
+[![R build status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/webchem/actions)
 [![Coverage](https://codecov.io/github/ropensci/webchem/coverage.svg?branch=master)](https://codecov.io/gh/ropensci/webchem/branch/master) 
 [![Downloads](https://cranlogs.r-pkg.org/badges/webchem)](https://cran.r-project.org/package=webchem)
 [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/webchem?color=blue)](https://cran.r-project.org/package=webchem)
-[![DOI](https://zenodo.org/badge/17223/ropensci/webchem.svg)](https://zenodo.org/badge/latestdoi/17223/ropensci/webchem) 
+[![DOI](https://zenodo.org/badge/17223/ropensci/webchem.svg)](https://zenodo.org/badge/latestdoi/17223/ropensci/webchem)
 
 <!-- badges: end -->
 

README.md

@@ -6,8 +6,8 @@
 <!-- badges: start -->
 
 [![CRAN](https://www.r-pkg.org/badges/version/webchem)](https://CRAN.R-project.org/package=webchem)
-[![Travis](https://travis-ci.org/ropensci/webchem.png)](https://travis-ci.org/ropensci/webchem)
-[![AppVeyor](https://ci.appveyor.com/api/projects/status/8m7wpfnxn41kqjnl?svg=true)](https://ci.appveyor.com/project/ropensci/webchem)
+[![R build
+status](https://github.com/ropensci/webchem/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/webchem/actions)
 [![Coverage](https://codecov.io/github/ropensci/webchem/coverage.svg?branch=master)](https://codecov.io/gh/ropensci/webchem/branch/master)
 [![Downloads](https://cranlogs.r-pkg.org/badges/webchem)](https://cran.r-project.org/package=webchem)
 [![Total

_pkgdown.yml

@@ -8,6 +8,7 @@ reference:
   - cs_convert
   - cts_from
   - cts_to
+  - with_cts
   - wd_ident
   - pc_synonyms
   - opsin_query
@@ -29,6 +30,12 @@ reference:
   - pc_prop
   - pc_sect
   - srs_query
+- title: Molecular structure images
+- contents:
+  - ends_with("_img")
+- title: Cross-data-source functions
+- contents:
+  - find_db
 - title: Data
 - contents:
   - has_keyword("datasets")
@@ -50,3 +57,8 @@ reference:
 - title: Package
 - contents:
   - webchem
+
+# build locally with:
+# template <- list(package = "rotemplate")
+# pkgdown::build_site(devel = FALSE, override = list(template = template))
+

tests/testthat.R

@@ -3,7 +3,7 @@ library('webchem')
 
 # All of the tests rely on the API existing and behaving as documented. However,
 # the API occasionally falls over or stops working which lets to errors on CRAN.
-# Because we use travis CI we will hear about any test failures as soon as they
+# Because we use CI we will hear about any test failures as soon as they
 # happen. So, let's skip all tests on CRAN:
 #
 if (identical(Sys.getenv("NOT_CRAN"), "true")) {