Test PR

.dockerignore

@@ -0,0 +1,5 @@
+.git
+.Rproj.user
+publish
+src
+renv/library

.github/workflows/test_refs_PR.yml

@@ -0,0 +1,25 @@
+name: Env var on PR
+
+on:
+  pull_request:
+    branches:
+     - main
+
+jobs:
+  build-website:
+    runs-on: ubuntu-latest
+    name: "test env var in PR"
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - name: test
+        run: |
+          echo 'GitHub actions:' $GITHUB_ACTIONS
+          echo 'Event name:' $GITHUB_EVENT_NAME
+          echo 'ref:' $GITHUB_REF
+          echo 'ref name:' $GITHUB_REF_NAME
+          echo 'base ref:' $GITHUB_BASE_REF
+          echo 'head ref:' $GITHUB_HEAD_REF
+          echo 'repo:' $GITHUB_REPOSITORY

.github/workflows/update-website-test.yml

@@ -0,0 +1,23 @@
+name: On merge to main, build the protocol and add it to the website "Log RECENT_MERGED_BRANCH_NAME"
+
+on:
+  push:
+    branches:
+     - main
+
+jobs:
+  build-website:
+    runs-on: ubuntu-latest
+    name: "add protocol to website"
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - uses: tonynguyenit18/github-action-custom-vars@v1
+      - name: test
+        run: |
+          echo 'GitHub actions:' $GITHUB_ACTIONS
+          echo 'Event name:' $GITHUB_EVENT_NAME
+          echo 'ref:' $GITHUB_REF
+          echo 'recent merged branch:' $RECENT_MERGED_BRANCH_NAME

.zenodo.json

@@ -1,40 +1,40 @@
 {
-    "title": "Source code of protocols of the Research Institute for Nature and Forest (INBO)",
-    "description": "This archive provides the source code of protocols used at the Research Institute for Nature and Forest (INBO), Brussels, Belgium (<a href=\"https://www.inbo.be/en\">www.inbo.be</a>). The protocols are written in R markdown and are compiled as html using the bookdown package. The website with the compiled protocols (including older versions) is at <a href=\"https://protocols.inbo.be\">https://protocols.inbo.be</a>.",
-    "license": "cc-by",
-    "upload_type": "other",
-    "access_right": "open",
-    "creators": [
-        {
-            "name": "Van Calster, Hans",
-            "affiliation": "Research Institute for Nature and Forest",
-            "orcid": "0000-0001-8595-8426"
-        },
-        {
-            "name": "De Bie, Els",
-            "affiliation": "Research Institute for Nature and Forest",
-            "orcid": "0000-0001-7679-743X"
-        },
-        {
-            "name": "Onkelinx, Thierry",
-            "affiliation": "Research Institute for Nature and Forest",
-            "orcid": "0000-0001-8804-4216"
-        },
-        {
-            "name": "Vanderhaeghe, Floris",
-            "affiliation": "Research Institute for Nature and Forest",
-            "orcid": "0000-0002-6378-6229"
-        }
-    ],
-    "keywords": [
-        "open protocol",
-        "open science",
-        "research institute",
-        "nature",
-        "forest",
-        "environment",
-        "markdown",
-        "Flanders",
-        "Belgium"
-        ]
+  "title": "Source code of protocols of the Research Institute for Nature and Forest (INBO)",
+  "description": "This archive provides the source code of protocols used at the Research Institute for Nature and Forest (INBO), Brussels, Belgium (<a href=\"https://www.inbo.be/en\">www.inbo.be<\/a>). The protocols are written in R markdown and are compiled as html using the bookdown package. The website with the compiled protocols (including older versions) is at <a href=\"https://protocols.inbo.be\">https://protocols.inbo.be<\/a>.",
+  "license": "cc-by",
+  "upload_type": "other",
+  "access_right": "open",
+  "creators": [
+    {
+      "name": "Van Calster, Hans",
+      "affiliation": "Research Institute for Nature and Forest",
+      "orcid": "0000-0001-8595-8426"
+    },
+    {
+      "name": "De Bie, Els",
+      "affiliation": "Research Institute for Nature and Forest",
+      "orcid": "0000-0001-7679-743X"
+    },
+    {
+      "name": "Onkelinx, Thierry",
+      "affiliation": "Research Institute for Nature and Forest",
+      "orcid": "0000-0001-8804-4216"
+    },
+    {
+      "name": "Vanderhaeghe, Floris",
+      "affiliation": "Research Institute for Nature and Forest",
+      "orcid": "0000-0002-6378-6229"
+    }
+  ],
+  "keywords": [
+    "open protocol",
+    "open science",
+    "research institute",
+    "nature",
+    "forest",
+    "environment",
+    "markdown",
+    "Flanders",
+    "Belgium"
+  ]
 }

Dockerfile

@@ -0,0 +1,97 @@
+FROM rocker/verse
+
+ARG BUILD_DATE
+ARG VCS_REF
+LABEL org.label-schema.build-date=$BUILD_DATE \
+org.label-schema.name="RStable" \
+org.label-schema.description="A docker image with stable versions of R and a bunch of packages used to check and publish protocols." \
+org.label-schema.license="MIT" \
+org.label-schema.url="e.g. https://www.inbo.be/" \
+org.label-schema.vcs-ref=$VCS_REF \
+org.label-schema.vcs-url="https://github.com/inbo/protocolsource" \
+org.label-schema.vendor="Research Institute for Nature and Forest" \
+maintainer="Hans Van Calster <hans.vancalster@inbo.be>"
+
+## for apt to be noninteractive
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NONINTERACTIVE_SEEN true
+
+## Install nano
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    nano
+
+COPY docker/Rprofile.site $R_HOME/etc/Rprofile.site
+
+## Install wget
+#RUN  apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    wget
+
+## Install pandoc
+RUN  wget https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-1-amd64.deb \
+  && dpkg -i pandoc-2.7.3-1-amd64.deb \
+  && rm pandoc-2.7.3-1-amd64.deb
+
+## Install git depencencies
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+#    git \
+    openssh-client
+
+## Install curl dependencies
+#RUN  apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    libcurl4-openssl-dev
+
+## Install ggplot2 dependencies
+#RUN  apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    libfreetype6-dev
+
+## Install rgdal dependencies
+RUN apt-get update \
+  && apt-get install -y --no-install-recommends \
+    gdal-bin \
+    libgdal-dev \
+    libproj-dev \
+    proj-bin
+
+## Install openssl dependencies
+#RUN apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    libssl-dev
+
+## Install systemfonts dependencies
+#RUN  apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    libfontconfig1-dev
+
+## Install textshaping dependencies
+#RUN apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    libharfbuzz-dev libfribidi-dev
+
+## Install V8 dependencies
+RUN  apt-get update \
+  && apt-get install -y --no-install-recommends \
+     libv8-dev
+
+## Install xml2 dependencies
+#RUN apt-get update \
+#  && apt-get install -y --no-install-recommends \
+#    libxml2-dev
+
+WORKDIR /github/workspace
+
+RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN R -e "renv::consent(provided = TRUE)"
+COPY renv.lock renv.lock
+RUN R -e "renv::restore()"
+RUN R -e "renv::isolate()"
+
+COPY docker/entrypoint_website.sh /entrypoint_website.sh
+COPY docker/entrypoint_update.sh /entrypoint_update.sh
+COPY docker/entrypoint_check.sh /entrypoint_check.sh
+
+ENTRYPOINT ["/entrypoint_check.sh"]

NEWS.md

@@ -1,3 +1,8 @@
+## Version 2022.01
+
+- Protocol code: sfp-401-nl
+- Title: Klassieke vegetatieopname in een proefvlak aan de hand van visuele inschattingen van bedekking van soorten in (semi-)terrestrische vegetatie
+
 <!--One entry for each release describing the generic changes since the previous release.
 e.g. (sort most recent first)
 
@@ -8,4 +13,4 @@ e.g. (sort most recent first)
     - sfp-402_shorttitle_nl (update)
 - 2020.01
     - sfp-402_shorttitle_nl (first version)
--->
+-->

build_push.sh

@@ -0,0 +1,47 @@
+#to be used on protocolsource (change entrypoint below in Dockerfile to run other parts)
+
+docker build --tag=inbo/protocols .
+
+#entrypoint_check
+docker run --rm --env GITHUB_REPOSITORY="ElsLommelen/protocolsource" --env BRANCH_SOURCE="dockertests" --env PROTOCOL_CODE="sfp-401-nl" --env INPUT_TOKEN inbo/protocols
+#INPUT_TOKEN is als omgevingsvariabele toegevoegd op laptop
+
+#entrypoint_update
+docker run --rm --env GITHUB_REPOSITORY="ElsLommelen/protocolsource" --env BRANCH_SOURCE="dockertests" --env PROTOCOL_CODE="sfp-401-nl" --env INPUT_TOKEN inbo/protocols
+
+#entrypoint_website
+docker run --rm --env GITHUB_REPOSITORY_SOURCE="ElsLommelen/protocolsource" --env BRANCH_SOURCE="dockertests" --env GITHUB_REPOSITORY_DEST="ElsLommelen/protocols" --env INPUT_TOKEN --env GITHUB_ACTIONS=true --env GITHUB_EVENT_NAME=push --env GITHUB_REF=refs/heads/main --env PROTOCOL_CODE="sfp-401-nl" inbo/protocols
+
+
+
+#examples
+docker build --no-cache --tag=inbobmk/checklist .
+
+docker build --tag=inbobmk/checklist .
+
+docker push inbobmk/checklist
+
+# run on branch
+docker run --rm --env GITHUB_REPOSITORY="inbo/checklist" --env GITHUB_SHA=$(git rev-parse HEAD) --env INPUT_TOKEN=$GITHUB_PAT --env INPUT_PATH="." --env ORCID_TOKEN=$ORCID_TOKEN --env CODECOV_TOKEN=$CODECOV_TOKEN inbobmk/checklist
+docker run --rm -it --entrypoint=/bin/bash --env GITHUB_REPOSITORY="inbo/checklist" --env GITHUB_SHA=$(git rev-parse HEAD) --env INPUT_TOKEN=$GITHUB_PAT --env INPUT_PATH="." --env ORCID_TOKEN=$ORCID_TOKEN --env CODECOV_TOKEN=$CODECOV_TOKEN inbobmk/checklist
+
+# run on main
+docker run --rm --env GITHUB_REPOSITORY="inbo/checklist" --env GITHUB_SHA=$(git rev-parse HEAD) --env GITHUB_PAT=$GITHUB_PAT --env INPUT_PATH="." --env ORCID_TOKEN=$ORCID_TOKEN --env CODECOV_TOKEN=$CODECOV_TOKEN --env GITHUB_ACTIONS=true --env GITHUB_EVENT_NAME=push --env GITHUB_REF=refs/heads/main inbobmk/checklist
+
+
+
+#zinvolle env uit github
+GITHUB_BASE_REF: name of target branch of the PR
+GITHUB_EVENT_NAME: name of the event that triggered the workflow run
+GITHUB_HEAD_REF: source branch of the PR
+GITHUB_REF: full ref of branch or tag that triggered the workflow run (best niet gebruiken bij PR)
+GITHUB_REF_NAME: short ref name of branch or tag that triggered the workflow run
+GITHUB_REPOSITORY: owner and repository name, bv. inbo/protocolsource
+
+#aan te passen env
+BRANCH_SOURCE (on PR) -> GITHUB_HEAD_REF
+BRANCH_SOURCE (on push) -> GITHUB_REF_NAME
+PROTOCOL_CODE -> BRANCH_SOURCE (zie hierboven)
+INPUT_TOKEN???
+GITHUB_REPOSITORY_SOURCE -> GITHUB_REPOSITORY
+GITHUB_REPOSITORY_DEST: meegeven als env!

docker/Rprofile.site

@@ -0,0 +1,48 @@
+options(
+  papersize = "a4",
+  tab.width = 2,
+  width = 80,
+  help_type = "html",
+  keep.source.pkgs = TRUE,
+  xpinch = 300,
+  ypinch = 300,
+  yaml.eval.expr = TRUE,
+  repos = c(
+    CRAN = "https://cloud.r-project.org/",
+    INLA = "https://inla.r-inla-download.org/R/stable",
+    inbo = "https://inbo.r-universe.dev"
+  ),
+  install.packages.check.source = "yes",
+  install.packages.compile.from.source = "always",
+  inbo_required = c("checklist", "fortunes", "remotes", "INBOmd", "INBOtheme")
+)
+
+if ("checklist" %in% rownames(utils::installed.packages())) {
+  options(
+    lintr.linter_file = system.file("lintr", package = "checklist")
+  )
+}
+
+if (
+  interactive() &&
+  !all(getOption("inbo_required") %in% rownames(utils::installed.packages()))
+) {
+  warning(
+    c(
+      "\n",
+      rep("^", getOption("width")),
+      "\nThis R installation lacks some required INBO packages.",
+      "\nPlease install them using the code below:\n",
+      "\ninstall.packages(c(",
+      paste0(
+        "\"",
+        getOption("inbo_required")[
+          !getOption("inbo_required") %in% rownames(utils::installed.packages())
+        ],
+        "\"", collapse = ", "
+      ),
+      "))\n\n",
+      rep("^", getOption("width"))
+    )
+  )
+}

docker/check_all.R

@@ -0,0 +1,20 @@
+# bundled checks for protocols
+library(protocolhelper)
+check_all <- function(protocol_code) {
+  #protocol_code <- Sys.getenv("PROTOCOL_CODE")
+  fail <- FALSE
+  tryCatch(
+    protocolhelper::check_frontmatter(protocol_code),
+    error = function(e) e,
+    finally = fail <- TRUE
+  )
+  tryCatch(
+    protocolhelper::check_structure(protocol_code),
+    error = function(e) e,
+    finally = fail <- TRUE
+  )
+  if (fail) {
+    stop("\nThe source code failed some checks. Please check the error message above.\n")
+  }
+}
+check_all(Sys.getenv("PROTOCOL_CODE"))