.Rbuildignore

@@ -2,3 +2,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^Makefile$
+^CODE_OF_CONDUCT\.md$

.gitlab-ci.yml

+services:
+  - name: docker:19.03.6-dind
+    command: ["--mtu=1458"]
+
+variables:
+  DOCKER_DRIVER: overlay2
+  DOCKER_TLS_CERTDIR: ""
+
 stages:
-  - build-image
-  - fit
+  - build
+  - test
 
-build-testing-image:
-  stage: build-image
-  image: docker:19.03.1
-  services:
-    - docker:19.03.1-dind
-  variables:
-    DOCKER_HOST: tcp://docker:2375/
+build docker image:
+  stage: build
+  image: docker:19.03.6
+  tags:
+    - privileged
   before_script:
-    - echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
+    - docker info
+    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
   script:
-    - docker pull $CI_REGISTRY_IMAGE:latest || true
+    - 'docker pull $CI_REGISTRY_IMAGE:latest || true'
     - docker build --cache-from $CI_REGISTRY_IMAGE:latest --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE:latest .
     - docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
     - docker push $CI_REGISTRY_IMAGE:latest
   only:
     changes:
-      - "DESCRIPTION"
-      - "Dockerfile"
-  when: always
-  
-run-drake:
-  stage: fit
+      - Dockerfile
+      - DESCRIPTION
+
+run drake:
+  stage: test
   image: $CI_REGISTRY_IMAGE:latest
   cache:
     key: "$CI_PROJECT_PATH"
@@ -33,11 +39,11 @@ run-drake:
     name: "$CI_JOB_NAME"
     paths:
       - artifacts/
+    reports:
+      metrics: artifacts/metrics.txt
   before_script:
     - Rscript -e "remotes::install_deps()"
   script:
     - ./make.R
+    - zip -r artifacts/drake_cache.zip .drake
   when: always
-
-
-

CODE_OF_CONDUCT.md

+# Contributor Covenant Code of Conduct
+
+[Bosnian](http://contributor-covenant.org/version/1/4/bs/) 
+| [Deutsch](http://contributor-covenant.org/version/1/4/de/) 
+| [ελληνικά](http://contributor-covenant.org/version/1/4/el/) 
+| [English](http://contributor-covenant.org/version/1/4/) 
+| [Español](http://contributor-covenant.org/version/1/4/es/) 
+| [Français](http://contributor-covenant.org/version/1/4/fr/) 
+| [Italiano](http://contributor-covenant.org/version/1/3/0/it/) 
+| [日本語](http://contributor-covenant.org/version/1/3/0/ja/) 
+| [Magyar](http://contributor-covenant.org/version/1/3/0/hu/) 
+| [Nederlands](http://contributor-covenant.org/version/1/4/nl/) 
+| [Polski](http://contributor-covenant.org/version/1/4/pl/) 
+| [Português](http://contributor-covenant.org/version/1/4/pt/) 
+| [Português do Brasil](http://contributor-covenant.org/version/1/4/pt_br/) 
+| [Pусский](http://contributor-covenant.org/version/1/3/0/ru/) 
+| [Română](http://contributor-covenant.org/version/1/4/ro/) 
+| [Svenska](http://contributor-covenant.org/version/1/4/sv/) 
+| [Slovenščina](http://contributor-covenant.org/version/1/4/sl/) 
+| [Türkçe](http://contributor-covenant.org/version/1/4/tr/) 
+| [Українська](http://contributor-covenant.org/version/1/4/uk/) 
+| [한국어](http://contributor-covenant.org/version/1/4/ko/)
+
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at noam.ross@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/
\ No newline at end of file

DESCRIPTION

-Package: repel-drake
+Package: drake-gitlab-docker-example
 Title: Drake pipeline example for model-fitting
 Version: 0.0.0.9000
 Authors@R: 
-    person(given = "Noam",
+    c(person(given = "Noam",
            family = "Ross",
            role = c("aut", "cre"),
            email = "first.last@example.com",
-           comment = c(ORCID = "0000-0002-2136-0000""))
-Description: What the package does (one paragraph).
+           comment = c(ORCID = "0000-0002-2136-0000"")),
+      person("EcoHealth Alliance", role="cph"))  
+Description: Example project repository for building Drake projects
+    with Docker and Gitlab-CI.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports: 
+    txtq,
     drake,
     tidyverse,
     knitr,
     rmarkdown,
     visNetwork,
-    here
+    here,
+    gitlabr
+Remotes:
+    ropensci/drake,
+    wlandau/txtq

Dockerfile

 FROM rocker/verse:3.6.1
 
 RUN apt-get update && apt-get install -y --allow-downgrades --allow-remove-essential --allow-change-held-packages --allow-unauthenticated --no-install-recommends --no-upgrade \
-  curl
+  curl \
+  zip
 
-## Install packages
+## Install packages 
 RUN install2.r -s remotes
 COPY DESCRIPTION /pkg/DESCRIPTION
 RUN Rscript -e "remotes::install_deps(pkgdir = '/pkg/', dependencies=TRUE, upgrade = 'always', force = FALSE, quiet = FALSE)"

Makefile

+CI_REGISTRY_IMAGE ?= registry.gitlab.com/ecohealthalliance/drake-gitlab-docker-example
+
+all: docker
+
+docker:
+	docker build --cache-from $(CI_REGISTRY_IMAGE):latest -t $(CI_REGISTRY_IMAGE):latest . && docker run -v `pwd`:/repo -w /repo $(CI_REGISTRY_IMAGE):latest ./make.R

R/get_cache.R

+import_ci_drake_cache <- function(tag = "master", gitlab_pat = Sys.getenv("GITLAB_PAT"),
+                                  cache_zipfile = "drake_cache.zip",
+                                  project = "14475381",
+                                  job = "run-drake") {
+  td <- tempfile()
+  dir.create(td)
+  zippath <- file.path(td, cache_zipfile)
+  cache_zip <- httr::GET(
+    paste0("https://gitlab.com/api/v4/projects/", project, "/jobs/artifacts/", tag, "/raw/artifacts/", "drake_cache.zip?job=", job),
+    httr::add_headers(`PRIVATE-TOKEN` = Sys.getenv("GITLAB_PAT")),
+    httr::config(followlocation = 1),
+    httr::write_disk(zippath, overwrite = TRUE)
+  )
+  zip::unzip(zippath, exdir = file.path(td))
+  if (!dir.exists(".drake")) drake::new_cache()
+  my_cache <- drake::drake_cache(path = ".drake")
+  ci_cache <- drake::drake_cache(path = file.path(td, ".drake"))
+  my_cache$import(ci_cache)
+  my_cache$history$import(ci_cache$history)
+}
\ No newline at end of file

README.md

+# drake-gitlab-docker-example
 
-# repel-drake
+This is an example/template repository for building `drake` R projects on GitLab CI using Docker. It builds off the drake [`mtcars` example](https://github.com/wlandau/drake-examples/tree/master/mtcars).
 
-Template repo for model-fitting for the REPEL project
+Some key features:
+
+-   The main build script is `make.R`, which builds the project in the local environment.  
+-   The build environment is defined in the project `Dockerfile` and packages required are in `DESCRIPTION`.
+-   Two jobs are defined in `.gitlab-ci.yml`. The first builds or updates the Docker image and is run only when `Dockerfile` or `DESCRIPTION` change.  The image is stored in GitLab's project-level image registry.  The second job builds the drake pipeline.
+-   Outputs from the drake pipeline (model objects, compiled reports, and a drake network graph) go into `artifacts` when built.  This directory is stored as an artifact with each GitLab build job, but `.gitignore`'d.
+-   A [metrics file](https://docs.gitlab.com/ee/ci/metrics_reports.html) is saved
+    on each run which can be read and reported by GitLab.
+-   The `.drake` directory is `.gitignore`'d but cached on GitLab between jobs so as to minimize build times.  It is also stored as a     an artifact (`artifacts/drake_cache.zip) so it may be downloaded and re-used.
+    -   An experimental function in `R/get_cache.R` imports the drake cache from GitLab CI into the local drake cache.  It requires a GitLab access token to be set a `GITLAB_PAT` in the environment (e.g., in `.Renviron`).
+-   A `Makefile` defines a docker command so that `make` builds the Docker environment and runs the `drake` pipeline inside it. This facilitates running the dockerized pipeline locally.
+-   The RStudio project file (`.Rproj`) is configured so that `make.R` is run using "Build All" (Cmd+Shift+B) in the Rstudio build pane.
+
+---
+
+Please note that this project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md).
+By contributing to this project, you agree to abide by its terms.
\ No newline at end of file

_drake.R

+# This file serves the r_*() functions (e.g. r_make()) documented at
+# https://ropenscilabs.github.io/drake-manual/projects.html#safer-interactivity # nolint
+# and
+# https://docs.ropensci.org/drake/reference/r_make.html
+
+# Load your packages and supporting functions into your session.
+# If you use supporting scripts like the ones below,
+# you will need to supply them yourself. Examples:
+# https://github.com/wlandau/drake-examples/tree/master/main/R
+source("R/packages.R")  # Load your packages, e.g. library(drake).
+source("R/functions.R") # Define your custom code as a bunch of functions.
+source("R/plan.R")      # Create your drake plan.
+
+# _drake.R must end with a call to drake_config().
+# The arguments to drake_config() are basically the same as those to make().
+drake_config(my_plan, verbose = 2L)

make.R

 #!/usr/bin/env Rscript
 
-# Walkthrough: https://ropenscilabs.github.io/drake-manual/walkthrough.html
-# Download the code: drake_example("main") # nolint
+library(drake)
+r_make()
 
-# Load your packages and supporting functions into your session.
-# If you use supporting scripts like the ones below,
-# you will need to supply them yourself. Examples:
-# https://github.com/wlandau/drake-examples/tree/master/main/R
-source("R/packages.R")  # Load your packages, e.g. library(drake).
-source("R/functions.R") # Define your custom code as a bunch of functions.
-source("R/plan.R")      # Create your drake plan.
-
-set.seed(42)
-
-# Call make() to run your work.
-# Your targets will be stored in a hidden .drake/ cache,
-# and you can read them back into memory with loadd() and read().
-make(my_plan)
-
-config <- drake_config(my_plan)
-
-my_graph <- drake::vis_drake_graph(config)
-visNetwork::visSave(my_graph, here::here("artifacts", "drake_graph.html"))
+# Save a network graph
+visNetwork::visSave(r_vis_drake_graph(), here::here("artifacts", "drake_graph.html"))
 print(build_times(), n=50)
+
+# Save relevant metrics in OpenMetricc format
+# See https://prometheus.io/docs/instrumenting/exposition_formats/#text-based-format
+# https://docs.gitlab.com/ee/ci/metrics_reports.html
+cat("build_time_seconds ", round(sum(build_times()$elapsed), 2),
+    file = here::here("artifacts", "metrics.txt"))