Merge pull request #408 from ldecicco-USGS/main

ci updates

.Rbuildignore

@@ -96,5 +96,8 @@ vignettes/flags.png
 vignettes/group.png
 vignettes/sites.png
 vignettes/thres.png
+^docker$
+vignettes/update_data.Rmd
+
 
 

.gitlab-ci.yml

@@ -1,7 +1,10 @@
-image: code.usgs.gov:5001/water/wsc/umid/docker_images:latest
-
+workflow:
+ rules:
+ - if: $CI_COMMIT_TAG
+ - if: $CI_COMMIT_BRANCH
+
 stages:
- - getready
+ - build
  - check
  - test
  - end
@@ -24,56 +27,64 @@ variables:
  CONNECT_SERVER: $CONNECT_SERVER
  PAGES_OUTDIR: "$CI_PROJECT_DIR/public"
 
-cache:
- key: ${CI_JOB_NAME}
- paths:
- - $R_LIBS_USER
-
-getready:
- stage: getready
+build-image:
+ stage: build
+ image: ${DEVOPS_REGISTRY}usgs/docker:20
+ services:
+ - name: ${DEVOPS_REGISTRY}usgs/docker:20-dind
+ alias: docker
+ rules:
+ - changes:
+ - docker/Dockerfile
+ - .gitlab-ci.yml
  script:
- - mkdir -p $R_LIBS_USER
- - mkdir -p $APT_CACHE
- - echo "options(Ncpus=$(nproc --all), repos=c(CRAN='$CRAN'))" >> $R_PROFILE
- - Rscript -e "install.packages(c( 'connectapi'))"
- - Rscript -e "devtools::install_deps()"
- cache:
- paths:
- - $R_LIBS_USER
- artifacts:
- paths:
- - $R_LIBS_USER
+ - echo ${CI_REGISTRY_PASSWORD} | docker login -u ${CI_REGISTRY_USER} --password-stdin $CI_REGISTRY
+ - docker pull ${CI_REGISTRY_IMAGE}:latest || true
+ - cd docker
+ - docker build
+ --cache-from ${CI_REGISTRY_IMAGE}:latest
+ -t ${CI_REGISTRY_IMAGE}:BUILD_${CI_COMMIT_SHORT_SHA}
+ -t ${CI_REGISTRY_IMAGE}:latest
+ .
+ # If this is building a git tag, create the corresponding docker tag
+ - if [ -n "${CI_COMMIT_TAG}" ]; then docker tag ${CI_REGISTRY_IMAGE}:BUILD_${CI_COMMIT_SHORT_SHA} ${CI_REGISTRY_IMAGE}:${CI_COMMIT_TAG}; fi
+ - docker push --all-tags ${CI_REGISTRY_IMAGE}
+
 
 buildcheck:
  stage: check
+ image: ${CI_REGISTRY_IMAGE}:latest
+ dependencies:
+ - build-image
  script:
- - mkdir -p $BUILD_LOGS_DIR
- - apt-get update
- - apt-get -o dir::cache::archives=${APT_CACHE} install -y --no-install-recommends qpdf pandoc pandoc-citeproc
  - R CMD build . --no-build-vignettes --no-manual
  - R -e 'devtools::check(document = FALSE, args = "--no-tests", error_on = "error", check_dir = Sys.getenv("BUILD_LOGS_DIR"))'
  artifacts:
+ expire_in: 1 week
  paths:
  - $BUILD_LOGS_DIR
 
 unittests:
  stage: test
+ image: ${CI_REGISTRY_IMAGE}:latest
  dependencies:
- - getready
+ - build-image
  - buildcheck
  script:
  - R -e 'library(testthat); options(testthat.output_file = file.path(Sys.getenv("CI_PROJECT_DIR"), "test-out.xml")); devtools::test(reporter = "junit")'
  artifacts:
  when: always
+ expire_in: 1 week
  paths: 
  - test-out.xml
  reports:
  junit: test-out.xml
 
 covertests:
  stage: test
+ image: ${CI_REGISTRY_IMAGE}:latest
  dependencies:
- - getready
+ - build-image
  - buildcheck
  script:
  - R -e 'x <- covr::package_coverage(); covr::to_cobertura(x); x; '
@@ -82,10 +93,12 @@ covertests:
  coverage_report:
  coverage_format: cobertura
  path: cobertura.xml
+ expire_in: 1 week
  coverage: '/Coverage: \d+.\d+\%/'
 
 pages:
  stage: end
+ image: ${CI_REGISTRY_IMAGE}:latest
  only: 
  - main
  script:

docker/Dockerfile

@@ -0,0 +1,29 @@
+FROM code.chs.usgs.gov:5001/ctek/docker/r-lang/r-base:4.4
+
+# Necessary R libraries
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+ pandoc-citeproc \
+ r-cran-devtools \
+ r-cran-tidyverse \
+ r-cran-checkmate \
+ r-cran-openxlsx \
+ r-cran-here \
+ r-cran-shinydashboard \
+ r-cran-shiny \
+ r-cran-readxl \
+ r-cran-rcolorbrewer \
+ r-cran-shinyace \
+ r-cran-rmarkdown \
+ r-cran-knitr \
+ r-cran-connectapi \
+ r-cran-dt \
+ r-cran-leaflet \
+ r-cran-rmarkdown \
+ r-cran-shinycssloaders \
+ r-cran-covr \
+ r-cran-tcpl \
+ r-cran-rsconnect \
+ && rm -rf /var/lib/apt/lists/*
+
+
+

vignettes/dose_curves.Rmd

@@ -1,6 +1,5 @@
 ---
 title: "Concentration-Response Curves"
-date: "`r format(Sys.time(), '%d %B, %Y')`"
 output: 
  rmarkdown::html_vignette:
  toc: true
@@ -71,21 +70,24 @@ ep <- "NVS_ENZ_hPDE4A1"
 cas <- "1912-24-9"
 
 chem_info <- tcplLoadChem(field = 'casn', val = cas)
-
-assay_info <- tcplLoadAcid(fld = "acnm", val = ep)
-
-mc3 <- tcplLoadData(lvl = 3, type = "mc", 
- fld = c("acid","spid"), 
- val = list(assay_info$acid,
- chem_info$spid))
-
-## Load mc tables from levels of interest
-mc4 <- tcplLoadData(lvl = 4, type = "mc", 
- fld = c("spid", "aeid"), 
- val = list(chem_info$spid,
- unique(mc3$aeid)))
-
-tcplPlotM4ID(mc4, lvl = 5)
+assay_info <- tcplLoadAeid(fld = "acnm", val = ep)
+
+mc5 <- tcplLoadData(lvl = 5, type = "mc",
+ fld = c("aeid","spid"),
+ val = list(assay_info$aeid,
+ chem_info$spid))
+
+plot_out <- tcplPlot(lvl = 5,
+ fld = c("spid","aeid"), # fields to query on
+ val = list(mc5$spid, # sample id's
+ mc5$aeid # assay endpoint id's
+ ),
+ by = "aeid", # parameter to divide files
+ multi = FALSE, # multiple plots per page - output 6 per page if TRUE
+ verbose = TRUE, # output all details if TRUE
+ output = "console") # prefix of the filename
+
+plot_out
 
 ```