Merge pull request #44 from mrc-ide/pipeline

Continuous Integration

.buildkite/Dockerfile

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+FROM rocker/r-ver:4
+
+RUN Rscript -e 'install.packages("pak")'
+
+# For some reason pak fails to install urltools
+RUN Rscript -e 'install.packages("urltools")'
+
+COPY .buildkite/pkgdepends.txt /src/.buildkite/pkgdepends.txt
+RUN Rscript -e 'pak::pkg_install(readLines("/src/.buildkite/pkgdepends.txt"))'
+
+COPY . /src

.buildkite/pipeline.R

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+library(orderly2)
+
+orderly_init()
+orderly_location_add(
+    "packit.dide",
+    type = "packit", 
+    args = list(
+        url = "https://packit.dide.ic.ac.uk/priority-pathogens",
+        token = Sys.getenv("GITHUB_TOKEN"))
+)
+
+orderly_location_pull_metadata("packit.dide")
+orderly_location_pull_packet("latest(name == 'db_extraction' && parameter:pathogen == 'LASSA')",
+                             options = list(location="packit.dide"))
+
+ids <- c(
+    orderly_run("db_double", parameters = list(pathogen = "LASSA")),
+    orderly_run("db_compilation", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_serology", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_severity", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_delays", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_transmission", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_summary", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_latex_tables", parameters = list(pathogen = "LASSA")),
+    orderly_run("lassa_collate", parameters = list(pathogen = "LASSA")))
+
+orderly_location_push(ids, "packit.dide")

.buildkite/pipeline.sh

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+#!/usr/bin/env bash
+
+set -eux
+
+PACKAGE_ORG=mrc-ide
+PACKAGE_NAME=priority-pathogen
+GIT_SHA=${BUILDKITE_COMMIT:0:7}
+TAG_SHA=$PACKAGE_ORG/$PACKAGE_NAME:$GIT_SHA
+
+docker build -t $TAG_SHA --progress=plain -f .buildkite/Dockerfile .
+docker run -e GITHUB_TOKEN --rm -w /src $TAG_SHA Rscript /src/.buildkite/pipeline.R

.buildkite/pipeline.yml

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+steps:
+  - command: .buildkite/pipeline.sh
+    agents:
+      queue: "paul"

.buildkite/pkgdepends.txt

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+mrc-ide/orderly2
+mrc-ide/orderly.sharedfile
+mrc-ide/epireview
+cowplot
+doconv
+dplyr
+epitrix
+estmeansd
+flextable
+ftExtra
+ggbreak
+ggforce
+ggplot2
+ggrepel
+ggsci
+ggspatial
+grid
+gridExtra
+gt
+harrypotter
+ids
+janitor
+meta
+metafor
+mixdist
+odbc
+officer
+optparse
+patchwork
+png
+purrr
+ragg
+readr
+readxl
+rio
+rnaturalearth
+rnaturalearthdata
+scales
+sf
+snakecase
+splitstackshape
+stringr
+tibble
+tidyr
+tidyverse
+tm
+writexl
+zip

.dockerignore

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+archive
+draft
+.outpack