Merge branch 'master' into dev_webtest_comptox

Author: stitam

.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 +22,7 @@ README_cache
 ^pkgdown$
 
 .Rmd.orig
+^\.github$
+
+codemeta.json
+^codemeta\.json$

.gitattributes

@@ -0,0 +1,2 @@
+* text=auto
+tests/fixtures/**/* -diff

.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}

.travis.yml

@@ -64,6 +64,8 @@ Some consistency guidelines:
 
 13. SMILES strings may use special characters like "#". `URLencode()` does not encode this as "%23" by default, so use `URLencode(query, reserved = TRUE)` instead. It's important to note that it's the query that has to be encoded like this, not the full url.
 
+14. Print verbose messages. Use `httr::message_for_status()` and `webchem_message()` functions to generate standard messages when possible.
+
 ### Data Sources
 
 You might think all webscraping is perfectly legal but it is unfortunately not that simple.

CONTRIBUTING.md

@@ -7,10 +7,10 @@ Description: Chemical information from around the web. This package interacts
     Flavornet, NIST Chemistry WebBook, OPSIN, PAN Pesticide Database, PubChem,
     SRS, Wikidata.
 Type: Package
-Version: 1.0.0.9000
-Date: 2020-05-27
+Version: 1.1.1
+Date: 2021-02-07
 License: MIT + file LICENSE
-URL: https://docs.ropensci.org/webchem, https://github.com/ropensci/webchem
+URL: https://docs.ropensci.org/webchem/, https://github.com/ropensci/webchem
 BugReports: https://github.com/ropensci/webchem/issues
 Authors@R: c(person("Eduard", "Szöcs", role = "aut"),
     person("Robert", "Allaway", role = "ctb"),    
@@ -19,6 +19,7 @@ Authors@R: c(person("Eduard", "Szöcs", role = "aut"),
     person("Andreas", "Scharmüller", role = "ctb"),        
     person("Eric R", "Scott", role = "ctb"),
     person("Jan", "Stanstrup", role = "ctb"),
+    person("João Vitor", "F Cavalcante", role = "ctb"),
     person("Gordon", "Getzinger", role = "ctb"),
     person("Tamás", "Stirling", email = "stirling.tamas@gmail.com", role = c("ctb", "cre")))
 Maintainer: Tamás Stirling <stirling.tamas@gmail.com>
@@ -31,7 +32,6 @@ Imports:
     xml2,
     httr,
     rvest,
-    RCurl,
     jsonlite,
     stringr,
     methods,
@@ -48,6 +48,10 @@ Suggests:
     robotstxt,
     knitr,
     rmarkdown,
-    plot.matrix
+    plot.matrix,
+    usethis,
+    vcr
 RoxygenNote: 7.1.1
 VignetteBuilder: knitr
+Config/testthat/edition:3
+Config/testthat/parallel:true

DESCRIPTION

@@ -31,12 +31,12 @@ S3method(smiles,pc_prop)
 S3method(smiles,wd_ident)
 export(as.cas)
 export(aw_query)
-export(build_aw_idx)
 export(cas)
 export(chebi_comp_entity)
 export(ci_query)
 export(cid_compinfo)
 export(cir)
+export(cir_img)
 export(cir_query)
 export(cs_check_key)
 export(cs_compinfo)
@@ -90,22 +90,13 @@ import(rvest)
 import(stringr)
 import(tibble)
 import(xml2)
-importFrom(base64enc,base64decode)
 importFrom(data.tree,Do)
 importFrom(data.tree,FindNode)
 importFrom(data.tree,as.Node)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,everything)
-importFrom(dplyr,left_join)
 importFrom(dplyr,select)
-importFrom(httr,GET)
-importFrom(httr,POST)
-importFrom(httr,add_headers)
-importFrom(httr,content)
-importFrom(httr,http_status)
-importFrom(httr,message_for_status)
 importFrom(jsonlite,fromJSON)
-importFrom(jsonlite,toJSON)
 importFrom(methods,is)
 importFrom(purrr,map)
 importFrom(purrr,map2)
@@ -114,16 +105,13 @@ importFrom(purrr,map_dfr)
 importFrom(rlang,as_function)
 importFrom(rlang,fn_fmls)
 importFrom(rvest,html_table)
-importFrom(stats,rexp)
-importFrom(stats,rgamma)
-importFrom(stats,setNames)
+importFrom(stringr,str_trunc)
 importFrom(tibble,as_tibble)
 importFrom(tibble,enframe)
 importFrom(tibble,tibble)
 importFrom(utils,URLdecode)
 importFrom(utils,URLencode)
 importFrom(utils,adist)
 importFrom(utils,globalVariables)
-importFrom(utils,head)
 importFrom(utils,menu)
 importFrom(utils,read.table)