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
 
 ```