Trying docker

.travis.yml

@@ -1,41 +1,37 @@
-language: r
 cache:
 - packages
 - pip
 sudo: required
 dist: "trusty"
 warnings_are_errors: false
-
-addons:
-  apt:
-    packages:
-      - libgsl0-dbg
-      - libgsl0-dev
-      - libgsl0ldbl
-      - "python3"
-      - "python3-pip"
-    update: true
+services:
+  - docker
 
 before_install:
-  - sudo apt-get update -qq
-  - sudo apt-get install libudunits2-dev
-  - sudo apt-get install python3
-  - sudo pip3 install --upgrade pip
-  - sudo pip3 install git+https://git@github.com/weecology/retriever.git --user
+# Set up environment and create required images
+# If no error don't print output
+-  docker build . -t matss  > /dev/null
+script:
+# Load packages and install the required packages
+# Install retriever from source and run tests 
+# -  docker run matss /bin/sh -c 'Rscript load_and_test.R'
+
+-  docker run matss Rscript load_and_test.R
+
 
-matrix:
-  include:
-  - r: devel
-  - r: release
-    after_success:
-    - R CMD INSTALL .
-    - Rscript -e 'pkgdown::build_site()'
-    - Rscript -e 'covr::codecov()'
-    deploy:
-      provider: pages
-      skip-cleanup: true
-      github-token: $GITHUB_PAT
-      keep-history: true
-      local-dir: docs
-      on:
-        branch: master
+# matrix:
+#   include:
+#   - r: devel
+#   - r: release
+#     after_success:
+#     - R CMD INSTALL .
+#     - Rscript -e 'pkgdown::build_site()'
+#     - Rscript -e 'covr::codecov()'
+#     deploy:
+#       provider: pages
+#       skip-cleanup: true
+#       github-token: $GITHUB_PAT
+#       keep-history: true
+#       local-dir: docs
+#       on:
+#         branch: master

DESCRIPTION

@@ -37,22 +37,25 @@ Imports:
     dplyr,
     tidyr,
     rdataretriever,
+    reticulate,
     RSQLite,
     forecast,
     networkD3,
     here,
     tibble,
-    rlang
+    rlang,
+    usethis (>= 1.4.0.9000)
 Suggests:
     testthat,
     knitr,
-    rmarkdown, 
-    pkgdown, 
-    covr, 
-    reticulate
+    rmarkdown,
+    pkgdown,
+    covr
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr
-Remotes: 
+Remotes:
     weecology/LDATS,
     weecology/portalr,
-    ropensci/drake
+    ropensci/drake,
+    ropensci/rdataretriever,
+    r-lib/usethis

Dockerfile

@@ -0,0 +1,63 @@
+FROM rocker/tidyverse:latest
+
+MAINTAINER Weecology "https://github.com/weecology/rdataretriever"
+
+# Write enviromental options to config files
+RUN echo "options(repos='https://cran.mtu.edu/')" >> ~/.Rprofile
+RUN echo "options(repos='https://cran.mtu.edu/')" >> ~/.Renviron
+RUN echo "R_LIBS=\"/usr/lib/R/library\"">> ~/.Rprofile
+RUN echo "R_LIBS=\"/usr/lib/R/library\"">> ~/.Renviron
+RUN echo "R_LIBS_USER=\"/usr/lib/R/library\"">> ~/.Renviron
+
+RUN apt-get update
+RUN apt-get install -y build-essential  --allow-downgrades --allow-remove-essential --allow-change-held-packages
+RUN apt-get install -y wget git locales locales-all   --allow-downgrades --allow-remove-essential --allow-change-held-packages
+RUN apt-get install  -y postgresql-client mysql-client   --allow-downgrades --allow-remove-essential --allow-change-held-packages
+
+RUN apt-get install -y libgsl0-dbg libgsl0-dev
+RUN apt-get install -y libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev
+
+# RUN apt-get install --allow libgsl0ldbl # not available
+
+# Set encoding
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+
+# Remove python2 and install python3
+RUN apt-get remove -y python && apt-get install -y python3  python3-pip curl
+RUN rm -f /usr/bin/python && ln -s /usr/bin/python3 /usr/bin/python
+RUN rm -f /usr/bin/pip && ln -s /usr/bin/pip3 /usr/bin/pip
+
+
+
+RUN echo "export PATH="/usr/bin/python:$PATH"" >> ~/.profile
+RUN echo "export PYTHONPATH="/usr/bin/python:$PYTHONPATH"" >> ~/.profile
+RUN echo "export PGPASSFILE="~/.pgpass"" >> ~/.profile
+
+# Add permissions to config files
+RUN chmod 0644 ~/.Renviron
+RUN chmod 0644 ~/.Rprofile
+RUN chmod 0644 ~/.profile
+
+# Install retriever python package
+RUN pip install git+https://git@github.com/weecology/retriever.git
+RUN retriever ls > /dev/null
+RUN pip install  psycopg2 pymysql > /dev/null
+RUN R_RETICULATE_PYTHON="/usr/bin/python" | echo $R_RETICULATE_PYTHON >>  ~/.Renviron
+
+COPY . ./MATSS
+# Use entrypoint to run more configurations.
+# set permissions.
+# entrypoint.sh will set out config files
+# RUN chmod 0755 MATSS/cli_tools/entrypoint.sh
+# ENTRYPOINT ["/cli_tools/entrypoint.sh"]
+
+WORKDIR ./MATSS
+
+# Change permissions to config files
+# Do not run these cmds before Entrypoint.
+# RUN chmod 600 cli_tools/.pgpass
+# RUN chmod 600 cli_tools/.my.cnf
+
+CMD ["bash", "-c", "retriever -v"]

cli_tools/.my.cnf

@@ -0,0 +1,5 @@
+[client]
+user="travis"
+password="Password12!"
+host="mysqldb"
+port="3306"

cli_tools/.pgpass

@@ -0,0 +1 @@
+pgdb:*:testdb:postgres:Password12!

cli_tools/entrypoint.sh

@@ -0,0 +1,8 @@
+# #!/bin/sh
+# set -e
+
+# # Copy config files to $HOME
+# cp -r /MATSS/cli_tools/.pgpass  ~/
+# cp -r /MATSS/cli_tools/.my.cnf  ~/
+
+# exec "$@"

load_and_test.R

@@ -0,0 +1,41 @@
+# Used for continous testing platform
+# Install analysis packages using pacman
+# Pacman will load the packages and install
+# the packaes not available
+
+library(devtools)
+# Install pacman if it isn't already installed
+if ("pacman" %in% rownames(installed.packages()) == FALSE) install.packages("pacman")
+# suppressMessages(install.packages("RMariaDB",  quiet = TRUE))
+suppressMessages(
+	pacman::p_load(devtools, RCurl, readr, rmarkdown,
+	testthat, tidyverse, RSQLite,
+	# DBI, RPostgreSQL,
+	magrittr, ggplot2, lubridate,
+ 	dplyr, tidyr, RSQLite, forecast,
+ 	networkD3, here, tibble, rlang)
+)
+
+# Install GitHub packages
+
+devtools::install_github("weecology/portalr")
+devtools::install_github("ropensci/drake")
+devtools::install_github("rstudio/reticulate")
+devtools::install_github("ropensci/rdataretriever")
+devtools::install_github("r-lib/usethis")
+devtools::install_github("weecology/LDATS")
+library(devtools)
+library(portalr)
+library(drake)
+library(reticulate)
+library(rdataretriever)
+library(usethis)
+library(LDATS)
+install.packages(".", repos = NULL, type="source")
+# Test package
+# test_dir("tests/testthat", reporter = c("check", "progress"))
+
+# Try old way
+# This will not work well for reporting and fail/pass 
+devtools::test()
+

tests/testthat/test-02-datasets.R

@@ -15,11 +15,11 @@ test_that("Jornada data is retrievable and works", {
 test_that("Shortgrass Steppe data is retrievable and works", {
     expect_error(sgs_data <- get_sgs_data(), NA)
     expect_true(check_data_format(sgs_data))
-    expect_known_hash(sgs_data, "ccbdc633c1")
+    expect_known_hash(sgs_data, "08c3041cd4")
 })
 
 test_that("Maizuru data is retrievable and works", {
     expect_error(maizuru_data <- get_maizuru_data(), NA)
     expect_true(check_data_format(maizuru_data))
-    expect_known_hash(maizuru_data, "c93bd061db")
-})
+    expect_known_hash(maizuru_data, "ccbdc633c1")
+})

tests/testthat/test-03-retriever-data.R

@@ -25,7 +25,7 @@ test_that("retriever downloading and importing work", {
     expect_error(install_retriever_data("veg-plots-sdl"), NA)
     expect_error(dat <- import_retriever_data("veg-plots-sdl"), NA)
     expect_known_hash(dat$veg_plots_sdl_Count1906, "4f6b34f60a")
-    expect_known_hash(dat$veg_plots_sdl_Photo_info, "5fa488da2a")
+    expect_known_hash(dat$veg_plots_sdl_Photo_info, "5f85a913f4")
     expect_known_hash(dat$veg_plots_sdl_Plot_corners, "53e7e72ee9")
     expect_known_hash(dat$veg_plots_sdl_Plots, "b0c6ec4b6e")
     expect_known_hash(dat$veg_plots_sdl_Seedling_counts, "dd0d14c55a")