Release v0.2.0

.Rbuildignore

@@ -13,3 +13,4 @@
 ^index\.md$
 ^README\.md$
 ^R/\.setup\.R
+^\.github$

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

@@ -0,0 +1,81 @@
+on:
+  push:
+    branches:
+      - master
+      - main
+      - dev
+  pull_request:
+    branches:
+      - master
+      - main
+      - dev
+
+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: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}      
+          - {os: windows-latest, r: 'devel'}          
+          - {os: windows-latest, r: 'oldrel'}
+          - {os: windows-latest, r: 'release'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      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), "depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-3-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        env:
+          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+        run: |
+          Rscript -e "remotes::install_github('r-hub/sysreqs')"
+          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+          sudo -s eval "$sysreqs"
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Check
+        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+      - dev
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        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 dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          install.packages("pkgdown", type = "binary")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/pr-commands.yaml

@@ -0,0 +1,51 @@
+on:
+  issue_comment:
+    types: [created]
+name: Commands
+jobs:
+  document:
+    if: startsWith(github.event.comment.body, '/document')
+    name: document
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@master
+      - name: Install dependencies
+        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+      - name: commit
+        run: |
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+      - uses: r-lib/actions/pr-push@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+  style:
+    if: startsWith(github.event.comment.body, '/style')
+    name: style
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+      - uses: r-lib/actions/pr-fetch@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: r-lib/actions/setup-r@master
+      - name: Install dependencies
+        run: Rscript -e 'install.packages("styler")'
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+      - name: commit
+        run: |
+          git add \*.R
+          git commit -m 'Style'
+      - uses: r-lib/actions/pr-push@master
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -0,0 +1,48 @@
+on:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches:
+      - master
+      - main
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        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 dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: kwb.endnote
 Title: Helper Functions for Analysing KWB Endnote Library
     (Exported as .xml)
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: 
     c(person(given = "Michael",
              family = "Rustler",
@@ -13,6 +13,8 @@ Authors@R:
              role = "ctb",
              email = "hauke.sonnenberg@kompetenz-wasser.de",
              comment = c(ORCID = "0000-0001-9134-2871")),
+      person(given = "FAKIN",
+             role = "fnd"),
       person(given = "Kompetenzzentrum Wasser Berlin gGmbH (KWB)",
              role = "cph"))
 Description: Helper Functions For Analysing KWB Endnote Library
@@ -35,7 +37,8 @@ Imports:
     tibble,
     tidyr,
     wordcloud2,
-    xml2
+    xml2, 
+    plotly
 Suggests: 
     covr,
     knitr,
@@ -46,5 +49,5 @@ Remotes:
     github::kwb-r/kwb.utils
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 VignetteBuilder: knitr

NEWS.md

@@ -1,5 +1,6 @@
 # kwb.endnote 0.0.0.9000
 
+* Move to GitHub Actions as CI (from Travis/Appveyor)
 * Added a `NEWS.md` file to track changes to the package.
 
 * see https://style.tidyverse.org/news.html for writing a good `NEWS.md`

R/check_for_differences.R

@@ -17,8 +17,8 @@
 #' ### Check differences between two different versions of "KWB_documents.xml"
 #' ############################################################################
 #'
-#' old_xml <- extdata_file("2019-01-14_KWB_documents.xml")
-#' new_xml <- extdata_file("2019-07-09_KWB_documents.xml")
+#' old_xml <- extdata_file("2020-05-25_KWB-documents.xml")
+#' new_xml <- extdata_file("2020-06-17_KWB-documents.xml")
 #' old_list <- kwb.endnote::create_endnote_list(old_xml)
 #' new_list <- kwb.endnote::create_endnote_list(new_xml)
 #' old_df <- kwb.endnote::create_references_df(old_list)

R/create_references_df_from_list.R

@@ -1,3 +1,17 @@
+# colbind: Wrapper around dplyr::bind_cols(). Makes sure that no rows get lost
+# if the data frame to add has no rows.
+colbind <- function(df, df_2) {
+  if (nrow(df_2) == 0L) {
+    # Return the original data frame if the data frame to add has no columns
+    if (ncol(df_2) == 0L) {
+      return(df)
+    }
+    # Give the data frame to add one empty row (full of NA)
+    df_2 <- df_2[1L, ]
+  }
+  dplyr::bind_cols(df, df_2)
+}
+
 #' @noRd
 #' @keywords internal
 null_to_na <- function(x, na_fill = NA_character_) {
@@ -154,6 +168,11 @@ record_list_to_df <- function(record_list, collapse = FALSE) {
                     collapse_val = "",
                     element = 1)
   }
+
+  replace_newline_with_semicolon <- function(text) {
+    gsub("\r", ", ", text)
+  }
+
   get_titles_style <- function(path) get_style(c("titles", path))
   get_period_style <- function(path) get_style(c("periodical", path))
   get_dates_style <- function(path) get_style(c("dates", path))
@@ -164,11 +183,11 @@ record_list_to_df <- function(record_list, collapse = FALSE) {
     ref_type_name = attr(get_record_entry("ref-type"), which = "name"),
     abstract = get_abstract(record_list, collapse)
   ) %>%
-    dplyr::bind_cols(get_keywords(record_list, collapse = collapse)) %>%
-    dplyr::bind_cols(get_authors(record_list, collapse = collapse)) %>%
-    dplyr::bind_cols(get_secondary_authors(record_list, collapse = collapse)) %>%
-    dplyr::bind_cols(get_tertiary_authors(record_list, collapse = collapse)) %>%
-    dplyr::bind_cols(
+    colbind(get_keywords(record_list, collapse = collapse)) %>%
+    colbind(get_authors(record_list, collapse = collapse)) %>%
+    colbind(get_secondary_authors(record_list, collapse = collapse)) %>%
+    colbind(get_tertiary_authors(record_list, collapse = collapse)) %>%
+    colbind(
       tibble::tibble(
         database_name = get_record_entry("database")[[1]],
         database_path = attr(get_record_entry("database"), which = "path"),
@@ -191,13 +210,13 @@ record_list_to_df <- function(record_list, collapse = FALSE) {
         authaddress = get_style("auth-address"),
         edition = get_style("edition"),
         worktype = get_style("work-type"),
-        label = get_style("label"),
+        label = replace_newline_with_semicolon(get_style("label")),
         isbn = get_style("isbn"),
-        language = get_style("language")
+        language = replace_newline_with_semicolon(get_style("language"))
       )
     ) %>%
-    dplyr::bind_cols(get_pdfurls(record_list, collapse = collapse)) %>%
-    dplyr::bind_cols(tibble::tibble(
+    colbind(get_pdfurls(record_list, collapse = collapse)) %>%
+    colbind(tibble::tibble(
       urls_related = get_style(c("urls", "related-urls", "url")),
       electronic_resource_num = get_style("electronic-resource-num"),
       custom1 = get_style("custom1"),

R/helper.R

@@ -20,7 +20,7 @@ colname_i <- function(name, i) {
 #' @export
 #'
 default_xml <- function() {
-  extdata_file("2019-07-09_KWB_documents.xml")
+  extdata_file("2020-06-17_KWB-documents.xml")
 }
 
 # first_of_element -------------------------------------------------------------