new_project.sh

#!/usr/bin/env bash
# Little script to create a new data analysis project directory
# Requires a single cmdline argument for the new project name
# With inspiration from https://github.com/chendaniely/computational-project-cookie-cutter
# Time-stamp: <2019-03-05 13:43:54 (slane)>

# Don't kill files
set -o noclobber

# Exit if no arguments were provided.
[ $# -eq 0 ] && { echo "Usage: $0 [target directory]"; exit 1; }

# Create the base project directory
mkdir $1

# Create the extra required directories
cd $1
mkdir data data-raw figs manuscripts R Rmd scripts

# Add a README.md
cat > README.md <<EOF
# $1

## Project description

Add some description here.
EOF

# Add a basic .gitignore
cat > .gitignore <<EOF
# Git ignore file
*.pdf
*.png
*.doc
*.docx
*.xls
*.xlsx
*.aux
*.log
*.lot
*.ttt
*.out
*.bbl
*.Rhistory
*.html
*.RData
*.rds
*.rda
*.tex
*.fdb_latexmk
*.fls
*.toc
*.lof
*.fff
*.blg
*.bcf
*.rec
*.run.xml
*.zip
*.txt
*~
manuscripts/cache/*
manuscripts/auto/*
.DS_Store
EOF

# Add a basic Makefile
cat > Makefile <<EOF
# Makefile
# Time-stamp: <>
.PHONY: all install-packages clean-manuscripts clobber

all: install-packages data/data.rds manuscripts/manuscript.pdf

# Set the directory of the Makefile.
ROOT_DIR:=\$(shell dirname \$(realpath \$(lastword \$(MAKEFILE_LIST))))

################################################################################
# Build docker container for reproducible environment
# .PHONY: build-docker
# build-docker: .build.docker
# .build.docker: docker/Dockerfile
# 	docker build --rm -t container-name docker/ \\
# 	&& touch .build.docker

################################################################################
# Rules to make data
# data/data.rds: R/clean-data.R data-raw/data.csv
# 	cd \$(<D) \\
# 	&& Rscript --no-save --no-restore \$(<F)

################################################################################
# Rules to make manuscripts
# manuscripts/manuscript.tex: manuscripts/manuscript.Rnw data/data.rds
# 	cd \$(<D) \\
# 	&& Rscript --no-save --no-restore -e "knitr::knit('\$(<F)')"

# manuscripts/manuscript.pdf: manuscripts/manuscript.tex
# 	cd \$(<D) \\
# 	&& latexmk -pdf \$(<F)

# manuscripts/manuscript.html: manuscripts/manuscript.Rmd
# 	cd \$(<D) \\
# 	&& Rscript --no-save --no-restore -e "rmarkdown::render('\$(<F)')"

################################################################################
# Cleaning up
clean-manuscripts:
	cd manuscripts/ \\
	&& rm -f *.aux *.bbl *.bcf *.blg *.fdb_latexmk *.fls *.lof *.log \\
		*.lot *.code *.loe *.toc *.rec *.out *.run.xml *~ *.tex

clobber: clean-manuscripts
	cd manuscripts/ \\
	&& rm -rf auto/ cache/ figure/

################################################################################
# Rule to install packages (from script extraction).
# This has been provided for the case where library/require calls are made in
# separate scripts. If the packages are not installed, make should return an
# error, saying that the packages are not available. This is politic; don't
# assume the user wants to install stuff without asking.
install-packages: scripts/installs.txt
scripts/installs.txt: scripts/strip-libs.sh R/ipak.R
	cd scripts; \\
	chmod u+x strip-libs.sh; \\
	./strip-libs.sh ../R/ installs.txt; \\
	./strip-libs.sh ../Rmd/ installs.txt; \\
	./strip-libs.sh ../manuscripts/ installs.txt; \\
	Rscript --no-save --no-restore ../R/ipak.R insts=installs.txt

################################################################################
# Show help on important targets.
.PHONY: help
help: Makefile
	@echo '\\nHelp on $1 Targets\\n----';
	@sed -n "s/^#' //p" \$(<F);
	@echo '----';

################################################################################
# Rule to create dependency graph.
deps-png:
	docker run -v \$\$(pwd):/tmp/graph stevelane/makedeps-graph \\
	&& mv deps.* figs/
EOF

# Add install packages scripts
cat > scripts/strip-libs.sh <<EOF
#!/usr/bin/env bash
# Strips libraries from .R/.r scripts and creates a text file with a list of them.
# Requires first argument as folder where scripts are stored, and second as the
# text file it is stored in.
folder=\$1
inst=\$2
for filename in \$folder/*.{r,R}{md,nw,}; do
    if [ -f \$filename ]; then
	awk -F '[(]|[)]' '/^library|^require/{print \$2;}' \$filename >> \$inst
	grep -oE '\b[a-zA-Z0-9]*::' $filename | awk -F '::' '{print $1;}' >> $inst
    fi
done
sort < \$inst > \$inst.bk
uniq < \$inst.bk > \$inst
rm \$inst.bk
EOF

cat > R/ipak.R <<EOF
#!/usr/bin/env Rscript
args <- commandArgs(trailingOnly = TRUE)
################################################################################
################################################################################
## Title: ipak
## Author: Steve Lane
## Synopsis: Script to test for installed packages, and if not installed,
## install them.
################################################################################
################################################################################
if(length(args) == 0){
    stop("A single argument must be passed to ipak.R: insts.\ninsts is the location of a newline separated list of required packages:\n\tRscript ipak.R insts=path/to/installs.txt\nA repository may be passed using the repos option:\n\tRscript ipak.R insts=path/to/installs.txt repos=REPOS",
         call. = FALSE)
} else {
    hasOpt <- grepl("=", args)
    argLocal <- strsplit(args[hasOpt], "=")
    for(i in seq_along(argLocal)){
        value <- NA
        tryCatch(value <- as.double(argLocal[[i]][2]), warning = function(e){})
        if(!is.na(value)){
            ## Assume int/double
            assign(argLocal[[i]][1], value, inherits = TRUE)
        } else {
            assign(argLocal[[i]][1], argLocal[[i]][2], inherits = TRUE)
        }
    }
}
if(exists("repos")){
    options(repos = c(CRAN = repos))
} else {
    ## Set default cran repository.
    ## Use the one set from .Rprofile if given, else set.
    if(getOption("repos") == "@CRAN@" | is.null(getOption("repos"))){
        options(repos = c(CRAN = "https://cran.rstudio.com"))
    }
}   
## Check if packages installed
pkg <- scan(insts, "character")
new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
## Install if not already installed (including dependencies).
if(length(new.pkg) > 0){
    install.packages(new.pkg, dependencies = TRUE)
} else {
    message("All packages currently installed.")
}
EOF