Browse Source

Add Travis CI

pull/95/head
kaguillera 2 years ago
committed by JulioV
parent
commit
7f6448c431
  1. 2
      .Rprofile
  2. 4
      .gitignore
  3. 91
      .travis.yml
  4. 2
      environment.yml
  5. 678
      renv.lock
  6. 3
      renv/.gitignore
  7. 341
      renv/activate.R
  8. 4
      rules/renv.snakefile
  9. 2
      tests/data/processed/test01/sms_sent_daily.csv

2
.Rprofile

@ -0,0 +1,2 @@
source("renv/activate.R")
options(renv.settings.snapshot.type = "all")

4
.gitignore

@ -85,7 +85,6 @@ target/
# Mypy cache
.mypy_cache/
.Rprofile
packrat/lib*/
packrat/*
!packrat/packrat.lock
@ -108,5 +107,4 @@ reports/
.RData
.Rhistory
sn_profile_*/
renv/
settings.dcf

91
.travis.yml

@ -1,44 +1,61 @@
services:
- mysql
os: linux
language: python # this works for Linux but is an error on macOS or Windows
dist: xenial
language: python
python:
- '3.7'
cache:
directories:
- /home/linuxbrew/.linuxbrew
- $HOME/.local/share/renv
- $TRAVIS_BUILD_DIR/renv/library
before_install:
- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
- export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
- source ~/.bashrc
- sudo apt-get install linuxbrew-wrapper
- brew install r
# - sudo chmod ugo+rw /usr/local/lib/R/site-library
- R -e 'install.packages(c( "rmarkdown"), repos = "http://cran.us.r-project.org")'
- R --version
jobs:
include:
- name: "Python 3.7 on Xenial Linux"
os: linux
language: python
python: 3.7
before_install:
- /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
- export PATH=/home/linuxbrew/.linuxbrew/bin:$PATH
- source ~/.bashrc
- sudo apt-get install linuxbrew-wrapper
- brew tap --shallow linuxbrew/xorg
- brew install r
- R --version
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- bash miniconda.sh -b -p $HOME/miniconda
- source "$HOME/miniconda/etc/profile.d/conda.sh"
- hash -r
- conda config --set always_yes yes --set changeps1 no
cache:
directories:
- /home/travis/.linuxbrew
- $HOME/.local/share/renv
- $TRAVIS_BUILD_DIR/renv/library
- name: "Python 3.7 on macOS"
os: osx
osx_image: xcode11.3 # Python 3.7 running on macOS 10.14.4
language: generic # 'language: python' is an error on Travis CI macOS
before_install:
- brew install mysql
- brew services start mysql
- brew install r
- R --version
- brew cask install miniconda
- eval "$(/usr/local/bin/conda shell.bash hook)"
env:
- RENV_PATHS_ROOT="$HOME/renv/cache"
cache:
directories:
- /usr/local/lib/R
- $RENV_PATHS_ROOT
- $TRAVIS_BUILD_DIR/renv/library
install:
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- bash miniconda.sh -b -p $HOME/miniconda
- source "$HOME/miniconda/etc/profile.d/conda.sh"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
- conda info -a
- conda init
- conda update -q --all --yes conda
- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
- conda activate test-environment
- snakemake renv_install
- snakemake renv_init
- snakemake renv_restore
- R -e 'renv::settings$use.cache(FALSE)'
- snakemake renv_restore
script:
- cp -r tests/data/raw/* data/raw
- snakemake --profile tests/settings -R sms_features
@ -47,16 +64,10 @@ script:
notifications:
email: false
slack:
# if: branch = travis_test
secure: 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
on_success: always
template:
- "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
- "Execution time: *%{duration}*"
- "Message: %{message}"
branches:
except:
- master
only:
- travis_test
- "Message: %{message}"

2
environment.yml

@ -1,8 +1,8 @@
name: moshi-env
channels:
- anaconda
- defaults
- conda-forge
- defaults
dependencies:
- appdirs=1.4.3
- arrow=0.15.2

678
renv.lock
File diff suppressed because it is too large
View File

3
renv/.gitignore

@ -0,0 +1,3 @@
library/
python/
staging/

341
renv/activate.R

@ -0,0 +1,341 @@
local({
# the requested version of renv
version <- "0.10.0"
# the project directory
project <- getwd()
# avoid recursion
if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA)))
return(invisible(TRUE))
# signal that we're loading renv during R startup
Sys.setenv("RENV_R_INITIALIZING" = "true")
on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE)
# signal that we've consented to use renv
options(renv.consent = TRUE)
# load the 'utils' package eagerly -- this ensures that renv shims, which
# mask 'utils' packages, will come first on the search path
library(utils, lib.loc = .Library)
# check to see if renv has already been loaded
if ("renv" %in% loadedNamespaces()) {
# if renv has already been loaded, and it's the requested version of renv,
# nothing to do
spec <- .getNamespaceInfo(.getNamespace("renv"), "spec")
if (identical(spec[["version"]], version))
return(invisible(TRUE))
# otherwise, unload and attempt to load the correct version of renv
unloadNamespace("renv")
}
# load bootstrap tools
bootstrap <- function(version, library) {
# fix up repos
repos <- getOption("repos")
on.exit(options(repos = repos), add = TRUE)
repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
options(repos = repos)
# attempt to download renv
tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
if (inherits(tarball, "error"))
stop("failed to download renv ", version)
# now attempt to install
status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
if (inherits(status, "error"))
stop("failed to install renv ", version)
}
renv_bootstrap_download_impl <- function(url, destfile) {
mode <- "wb"
# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
fixup <-
Sys.info()[["sysname"]] == "Windows" &&
substring(url, 1L, 5L) == "file:"
if (fixup)
mode <- "w+b"
download.file(
url = url,
destfile = destfile,
mode = mode,
quiet = TRUE
)
}
renv_bootstrap_download <- function(version) {
methods <- list(
renv_bootstrap_download_cran_latest,
renv_bootstrap_download_cran_archive,
renv_bootstrap_download_github
)
for (method in methods) {
path <- tryCatch(method(version), error = identity)
if (is.character(path) && file.exists(path))
return(path)
}
stop("failed to download renv ", version)
}
renv_bootstrap_download_cran_latest <- function(version) {
# check for renv on CRAN matching this version
db <- as.data.frame(available.packages(), stringsAsFactors = FALSE)
if (!"renv" %in% rownames(db))
stop("renv is not available on your declared package repositories")
entry <- db["renv", ]
if (!identical(entry$Version, version))
stop("renv is not available on your declared package repositories")
message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
info <- tryCatch(
download.packages("renv", destdir = tempdir()),
condition = identity
)
if (inherits(info, "condition")) {
message("FAILED")
return(FALSE)
}
message("OK")
info[1, 2]
}
renv_bootstrap_download_cran_archive <- function(version) {
name <- sprintf("renv_%s.tar.gz", version)
repos <- getOption("repos")
urls <- file.path(repos, "src/contrib/Archive/renv", name)
destfile <- file.path(tempdir(), name)
message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE)
for (url in urls) {
status <- tryCatch(
renv_bootstrap_download_impl(url, destfile),
condition = identity
)
if (identical(status, 0L)) {
message("OK")
return(destfile)
}
}
message("FAILED")
return(FALSE)
}
renv_bootstrap_download_github <- function(version) {
enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
if (!identical(enabled, "TRUE"))
return(FALSE)
# prepare download options
pat <- Sys.getenv("GITHUB_PAT")
if (nzchar(Sys.which("curl")) && nzchar(pat)) {
fmt <- "--location --fail --header \"Authorization: token %s\""
extra <- sprintf(fmt, pat)
saved <- options("download.file.method", "download.file.extra")
options(download.file.method = "curl", download.file.extra = extra)
on.exit(do.call(base::options, saved), add = TRUE)
} else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
fmt <- "--header=\"Authorization: token %s\""
extra <- sprintf(fmt, pat)
saved <- options("download.file.method", "download.file.extra")
options(download.file.method = "wget", download.file.extra = extra)
on.exit(do.call(base::options, saved), add = TRUE)
}
message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
name <- sprintf("renv_%s.tar.gz", version)
destfile <- file.path(tempdir(), name)
status <- tryCatch(
renv_bootstrap_download_impl(url, destfile),
condition = identity
)
if (!identical(status, 0L)) {
message("FAILED")
return(FALSE)
}
message("Done!")
return(destfile)
}
renv_bootstrap_install <- function(version, tarball, library) {
# attempt to install it into project library
message("* Installing renv ", version, " ... ", appendLF = FALSE)
dir.create(library, showWarnings = FALSE, recursive = TRUE)
# invoke using system2 so we can capture and report output
bin <- R.home("bin")
exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
r <- file.path(bin, exe)
args <- c("--vanilla", "CMD", "INSTALL", "-l", shQuote(library), shQuote(tarball))
output <- system2(r, args, stdout = TRUE, stderr = TRUE)
message("Done!")
# check for successful install
status <- attr(output, "status")
if (is.numeric(status) && !identical(status, 0L)) {
header <- "Error installing renv:"
lines <- paste(rep.int("=", nchar(header)), collapse = "")
text <- c(header, lines, output)
writeLines(text, con = stderr())
}
status
}
renv_bootstrap_prefix <- function() {
# construct version prefix
version <- paste(R.version$major, R.version$minor, sep = ".")
prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
# include SVN revision for development versions of R
# (to avoid sharing platform-specific artefacts with released versions of R)
devel <-
identical(R.version[["status"]], "Under development (unstable)") ||
identical(R.version[["nickname"]], "Unsuffered Consequences")
if (devel)
prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
# build list of path components
components <- c(prefix, R.version$platform)
# include prefix if provided by user
prefix <- Sys.getenv("RENV_PATHS_PREFIX")
if (nzchar(prefix))
components <- c(prefix, components)
# build prefix
paste(components, collapse = "/")
}
renv_bootstrap_library_root <- function(project) {
path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
if (!is.na(path))
return(path)
path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
if (!is.na(path))
return(file.path(path, basename(project)))
file.path(project, "renv/library")
}
renv_bootstrap_validate_version <- function(version) {
loadedversion <- utils::packageDescription("renv", fields = "Version")
if (version == loadedversion)
return(TRUE)
# assume four-component versions are from GitHub; three-component
# versions are from CRAN
components <- strsplit(loadedversion, "[.-]")[[1]]
remote <- if (length(components) == 4L)
paste("rstudio/renv", loadedversion, sep = "@")
else
paste("renv", loadedversion, sep = "@")
fmt <- paste(
"renv %1$s was loaded from project library, but renv %2$s is recorded in lockfile.",
"Use `renv::record(\"%3$s\")` to record this version in the lockfile.",
"Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
sep = "\n"
)
msg <- sprintf(fmt, loadedversion, version, remote)
warning(msg, call. = FALSE)
FALSE
}
renv_bootstrap_load <- function(project, libpath, version) {
# try to load renv from the project library
if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
return(FALSE)
# warn if the version of renv loaded does not match
renv_bootstrap_validate_version(version)
# load the project
renv::load(project)
TRUE
}
# construct path to library root
root <- renv_bootstrap_library_root(project)
# construct library prefix for platform
prefix <- renv_bootstrap_prefix()
# construct full libpath
libpath <- file.path(root, prefix)
# attempt to load
if (renv_bootstrap_load(project, libpath, version))
return(TRUE)
# load failed; attempt to bootstrap
bootstrap(version, libpath)
# try again to load
if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
message("Successfully installed and loaded renv ", version, ".")
return(renv::load())
}
# failed to download or load renv; warn the user
msg <- c(
"Failed to find an renv installation: the project will not be loaded.",
"Use `renv::activate()` to re-initialize the project."
)
warning(paste(msg, collapse = "\n"), call. = FALSE)
})

4
rules/renv.snakefile

@ -1,12 +1,12 @@
## renv_install: installs renv onto machine
rule renv_install:
shell:
"R -e 'install.packages(\"renv\", repos=\"http://cran.us.r-project.org\")'"
"R -e 'if (!requireNamespace(\"renv\", quietly = TRUE)) install.packages(\"renv\", repos=\"http://cran.us.r-project.org\")'"
## renv_install: initialize a renv environment for this project
rule renv_init:
shell:
"R -e 'options(renv.consent = TRUE)' && R -e 'renv::init()'"
"R -e 'renv::init()'"
## renv_snap : Look for new R packages in files & archives them
rule renv_snap:

2
tests/data/processed/test01/sms_sent_daily.csv

@ -1,2 +1,2 @@
"local_date","sms_sent_daily_countmostfrequentcontact","sms_sent_daily_count","sms_sent_daily_distinctcontacts","sms_sent_daily_timefirstsms","sms_sent_daily_timelastsms"
"2017-05-14",1,1,1,18.10,18.45
"2017-05-14",1,1,1,18.45,18.45
Loading…
Cancel
Save