inst/doc/task_plans.R

In aappling-usgs/scipiper: Support functions for ushering data through a scientific workflow

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, cache=FALSE, collapse=TRUE)

library(scipiper)
library(dplyr)

knitr::opts_knit$set(root.dir = tempdir())

## ----step_funs_shhh, echo=FALSE-----------------------------------------------
cat("
## @knitr step_funs

# step 1: prepare some data given the info in prep_name, arg2, file 'A.txt', and R object 'B'
prep <- function(prep_name) {
  message(sprintf('preparing %s', prep_name))
  return(prep_name)
}

# step 2: visualize the data
visualize <- function(plot_name, state_data, state_capital) {
  message(sprintf('visualizing %s - %s', plot_name, state_capital))
  file.create(plot_name, showWarnings=FALSE)
}

# step 3: create the report
report <- function(report_name) {
  message(sprintf('reporting on %s', report_name))
  file.create(report_name, showWarnings=FALSE)
}
", file='script.R')
knitr::read_chunk('script.R')

## ----step_funs----------------------------------------------------------------
# step 1: prepare some data given the info in prep_name, arg2, file 'A.txt', and R object 'B'
prep <- function(prep_name) {
  message(sprintf('preparing %s', prep_name))
  return(prep_name)
}

# step 2: visualize the data
visualize <- function(plot_name, state_data, state_capital) {
  message(sprintf('visualizing %s - %s', plot_name, state_capital))
  file.create(plot_name, showWarnings=FALSE)
}

# step 3: create the report
report <- function(report_name) {
  message(sprintf('reporting on %s', report_name))
  file.create(report_name, showWarnings=FALSE)
}

## ----tasks--------------------------------------------------------------------
task_config <- tibble(
  id=c('WI','AZ','PA'),
  capital=c('Madison','Phoenix','Harrisburg')
)

## ----task_steps---------------------------------------------------------------
# step1 creates recipes like this:
# WI_prep:
#   command: prep(I('WI'))
step1 <- create_task_step(step_name = 'prep')

# step2 creates recipes like this:
# WI_plot.png:
#   command: visualize(
#       plot_name = target_name, 
#       state_data = WI_prep,
#       state_capital = I('Madison'))
step2 <- create_task_step(
  step_name = 'plot',
  target_name = function(task_name, ...) {
    sprintf('%s_plot.png', task_name)
  },
  command = function(target_name, task_name, ...) {
    capital <- task_config[task_config$id == task_name, 'capital']
    psprintf(
      "visualize(",
      "plot_name = target_name,",
      "state_data = %s_prep,"=task_name,
      "state_capital = I('%s'))"=capital
      )
  })

# step3 creates recipes like this:
# WI.pdf:
#   command: report(target_name)
#   depends:
#    - WI_plot.png
step3 <- create_task_step(
  step_name = 'report',
  target_name = function(task_name, ...) {
    sprintf('%s.pdf', task_name)
  },
  depends = function(task_name, ...) {
    sprintf('%s_plot.png', task_name)
  },
  command = function(task_name, step_name, ...) {
    sprintf("report(target_name)", task_name)
  })

## ----plan---------------------------------------------------------------------
task_plan_1 <- create_task_plan(
  task_config$id,
  list(step1, step2, step3),
  final_steps='report',
  ind_dir='states/log')

## ----makefile, results='markup'-----------------------------------------------
create_task_makefile(
  task_plan=task_plan_1,
  makefile='task_plan_1.yml',
  include=c(),
  packages=c('ggplot2','scipiper'),
  sources=c('script.R'),
  file_extensions=c('ind'))

## ----read_makefile, results='markup', comment='', echo=FALSE------------------
cat(readr::read_lines('task_plan_1.yml'), sep='\n')

## ----delete1, echo=FALSE------------------------------------------------------
unlink('.remake')
unlink('build')

## ----loop1a-------------------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml')

## ----scmake_instead-----------------------------------------------------------
scmake('task_plan_1', 'task_plan_1.yml')

## ----try_rebuild_one----------------------------------------------------------
scmake('AZ_plot.png', 'task_plan_1.yml')

## ----delete_one---------------------------------------------------------------
scdel('AZ_plot.png', 'task_plan_1.yml')

## ----rebuild_one--------------------------------------------------------------
scmake('AZ_plot.png', 'task_plan_1.yml')

## ----force_one----------------------------------------------------------------
scmake('AZ_plot.png', 'task_plan_1.yml', force=TRUE)

## ----try_rebuild_all----------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml')

## ----rebuild_all--------------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml',
  force = TRUE)

## ----rebuild_all_scmake-------------------------------------------------------
scmake('task_plan_1', 'task_plan_1.yml', force = TRUE)

## ----delete_all2--------------------------------------------------------------
scdel(target_names=list_all_targets('task_plan_1.yml'), remake_file='task_plan_1.yml')

## ----loop_task_step_only------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml',
  task_names='PA',
  step_names='prep')

## ----loop_steps_only----------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml',
  step_names='plot')

## ----loop_tasks_only----------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml',
  task_names=c('PA','AZ'))

## ----loop_remainder-----------------------------------------------------------
loop_tasks(
  task_plan=task_plan_1,
  task_makefile='task_plan_1.yml')

## ----plan2--------------------------------------------------------------------
task_plan_2 <- create_task_plan(
  task_config$id,
  list(step1, step2, step3),
  final_steps='report',
  add_complete=FALSE)

## ----makefile2, results='markup'----------------------------------------------
create_task_makefile(
  task_plan=task_plan_2,
  makefile='task_plan_2.yml',
  include=c(),
  packages=c('ggplot2'),
  sources=c('script.R'),
  file_extensions=c('ind'),
  finalize_fun = NULL)

## ----read_makefile2, results='markup', comment='', echo=FALSE-----------------
cat(readr::read_lines('task_plan_2.yml'), sep='\n')