first cut at createRemakefile

[aappling-usgs]

First cut at createRemakefile() function.

• After running createRemakefile() in USGS-VIZLAB/example, it's [mostly] possible to run remake::make(remake_file='remake.yaml') and build the entire example project! That makes for a good start on Switch to remake? #246.
• The [mostly] caveat from the previous bullet is that when I run remake::make(remake_file='remake.yaml') in a fresh session, things break unless I manually source those files listed in sources:. Why would this be? I don't understand.
• Creates a single remake.yaml for all of the blocks, and looks for cross references in any phase (not just the current one), so also addresses Allow fetch to depend on process item #88 (but testing would be nice)
• Includes recipes for those resources that are depended on by other targets, so also addresses tell make the provenance of resources from vizlab #215 (but are these resources now getting copied over twice, once by remake and once by vizlab? more inspection & testing needed here, too)
• Does not yet reproduce the work done for rebuild necessary items based on changes to viz.yaml non-file options #193 (depending on the viz.yaml blocks). This can be slick once we implement it, because the dependencies can be R objects instead of files, but there's nothing there yet.
• Does not yet implement timestamp handling for fetch - just calls fetch on every item.
• There's a job group (group target) for the overall viz, but I'd still like to add job groups for fetch, process, etc. individually

Here's the remake.yaml that gets built for USGS-VIZLAB/example using this PR:

# Do not edit - automatically generated
# from the vizlab remake.mustache template

target_default: viz

packages:
  - vizlab
  - dplyr
  - dataRetrieval

sources:
  - scripts/fetch/cars.R
  - scripts/process/cars.R
  - scripts/process/cuyahoga.R
  - scripts/visualize/visualize.R


targets:

  # --- parameter --- #
  
  plot-info:
    command: parameter(I('plot-info'))

  color-stuff:
    command: parameter(I('color-stuff'))

  # --- fetch --- #
  
  'data/iris.csv':
    command: fetch(I('iris-data'))

  'cache/cars.csv':
    command: fetch(I('cars-data'))

  'cache/fetch/CuyahogaTDS.csv':
    command: fetch(I('Cuyahoga'))

  'data/markdownText.yaml':
    command: fetch(I('markdown-text'))

  # --- process --- #
  
  'cache/car-loess.rds':
    command: process(I('calc-cars'))
    depends:
      - 'cache/cars.csv'

  'cache/process/CuyahogaShort.tsv':
    command: process(I('CuyahogaShort'))
    depends:
      - 'cache/fetch/CuyahogaTDS.csv'

  # --- visualize --- #
  
  'figures/cars.png':
    command: visualize(I('plot-cars'))
    depends:
      - 'cache/car-loess.rds'
      - 'cache/cars.csv'
      - plot-info

  'figures/iris.png':
    command: visualize(I('plot-iris'))
    depends:
      - 'data/iris.csv'

  'figures/cuyahogaFig.svg':
    command: visualize(I('cuyahogaFig'))
    depends:
      - 'cache/process/CuyahogaShort.tsv'
      - color-stuff

  # --- publish --- #
  
  index:
    command: publish(I('index'))
    depends:
      - sourcesansprofont
      - cars-section
      - social-section
      - vertical-social-section
      - footer-section
      - header-section
      - 'layout/css/main.css'
      - text-section
      - iris-section
      - Cuyahoga-section
      - markdown-section1
      - markdown-section2
      - 'target/css/footer.css'
      - 'target/css/header.css'
      - 'target/css/socialMedia.css'
      - 'target/js/jquery-3.2.1.min.js'
      - 'target/js/svg-injector-1.1.3.min.js'
      - 'target/js/vizlab.js'

  cars-section:
    command: publish(I('cars-section'))
    depends:
      - 'figures/cars.png'

  text-section:
    command: publish(I('text-section'))

  markdown-section1:
    command: publish(I('markdown-section1'))
    depends:
      - 'data/markdownText.yaml'

  markdown-section2:
    command: publish(I('markdown-section2'))
    depends:
      - 'data/markdownText.yaml'

  iris-section:
    command: publish(I('iris-section'))
    depends:
      - 'figures/iris.png'

  Cuyahoga-section:
    command: publish(I('Cuyahoga-section'))
    depends:
      - 'figures/cuyahogaFig.svg'

  'layout/css/main.css':
    command: publish(I('figure-style'))

  social-section:
    command: publish(I('social-section'))
    depends:
      - 'target/css/socialMedia.css'

  vertical-social-section:
    command: publish(I('vertical-social-section'))
    depends:
      - 'target/css/socialMedia.css'

  header-section:
    command: publish(I('header-section'))
    depends:
      - 'target/images/usgsLogo.png'

  footer-section:
    command: publish(I('footer-section'))
    depends:
      - 'target/css/footer.css'

  sourcesansprofont:
    command: publish(I('sourcesansprofont'))

  # --- resource --- #
  
  'target/images/usgsLogo.png':
    command: publish(I('lib-usgs-logo'))

  'target/js/vizlab.js':
    command: publish(I('lib-vizlab-javascript'))

  'target/css/header.css':
    command: publish(I('lib-header-css'))

  'target/css/footer.css':
    command: publish(I('lib-footer-css'))

  'target/css/socialMedia.css':
    command: publish(I('lib-social-media-css'))

  'target/js/svg-injector-1.1.3.min.js':
    command: publish(I('lib-svg-injector-js'))

  'target/js/jquery-3.2.1.min.js':
    command: publish(I('lib-jquery-js'))



  # --- Job groups --- #

  viz:
    depends: 
      - plot-info
      - color-stuff
      - 'data/iris.csv'
      - 'cache/cars.csv'
      - 'cache/fetch/CuyahogaTDS.csv'
      - 'data/markdownText.yaml'
      - 'cache/car-loess.rds'
      - 'cache/process/CuyahogaShort.tsv'
      - 'figures/cars.png'
      - 'figures/iris.png'
      - 'figures/cuyahogaFig.svg'
      - index
      - cars-section
      - text-section
      - markdown-section1
      - markdown-section2
      - iris-section
      - Cuyahoga-section
      - 'layout/css/main.css'
      - social-section
      - vertical-social-section
      - header-section
      - footer-section
      - sourcesansprofont
      - 'target/images/usgsLogo.png'
      - 'target/js/vizlab.js'
      - 'target/css/header.css'
      - 'target/css/footer.css'
      - 'target/css/socialMedia.css'
      - 'target/js/svg-injector-1.1.3.min.js'
      - 'target/js/jquery-3.2.1.min.js'

[coveralls]

Coverage decreased (-4.07%) to 69.579% when pulling de854b6 on aappling-usgs:remake into 2afe9f1 on USGS-VIZLAB:remake.

[aappling-usgs]

@ldecicco-USGS - I merged this by accident - your PR review will still be welcome.

I've made notes about the consequences of this PR for #88 and #215, added a list of remaining to-do items at the bottom of #246, and spun off two new issues (#287 and #288) for tasks I think we can treat as distinct from #246 (and that could be done by you or @limnoliver if interested).

Because this PR leaves all those issues open, I've put it in a new remake branch on USGS-VIZLAB/vizlab where we can continue to collaborate on it until it's ready to merge into master.

[ldecicco-USGS]

Lookin' good! I don't know if it helps or not, but I don't think paths need quotes (ie 'figures/cuyahogaFig.svg' could be figures/cuyahogaFig.svg