Recology

R/etc.

gistr - R client for GitHub gists

    R github
 Source: .Rmd/.md

GitHub has this site https://gist.github.com/ in which we can share code, text, images, maps, plots, etc super easily, without having to open up a repo, etc. GitHub gists are a great way to throw up an example use case to show someone, or show code that’s throwing errors to a support person, etc. In addition, there’s API access, which means we can interact with Gists not just from their web interface, but from the command line, or any programming language. There are clients for Node.js, Ruby, Python, and on and on. But AFAIK there wasn’t one for R. Along with Ramnath and others, we’ve been working on an R client for gists. v0.1 is now on CRAN. Below is an overview.

One useful thing about this package in terms of other R packages is that you can now depend on gistr to easily share results as Gists. For example, you can share maps as gists (via geojson, rendered as interactive map), or code, or plots, etc. That is, you don’t have to re-write an interface to Github Gists yourself. We plan on using gistr in a few rOpenSci packages.

Installation

Installation

Install from CRAN

install.packages("gistr")

Or the development version from GitHub

install.packages("devtools")
devtools::install_github("ropensci/gistr")
library("gistr")

Authentication

There are two ways to authorise gistr to work with your GitHub account:

Using the PAT is recommended.

Using the gist_auth() function you can authenticate seperately first, or if you’re not authenticated, this function will run internally with each functionn call. If you have a PAT, that will be used, if not, OAuth will be used.

gist_auth()

Workflow

In gistr you can use pipes to pass outputs from one function to another. If you have used dplyr with pipes you can see the difference, and perhaps the utility, of this workflow over the traditional workflow in R. You can use a non-piping or a piping workflow with gistr. Examples below use a mix of both workflows. Here is an example of a piping wofklow (with some explanation):

gists(what = "minepublic")[[6]] %>% # List my public gists, and index 1st
  add_files("~/alm_othersources.md") %>% # Add new file to that gist
  update() # update sends a PATCH command to Gists API to add file to your gist

And a non-piping workflow that does the same exact thing:

g <- gists(what = "minepublic")[[1]]
g <- add_files(g, "~/alm_othersources.md")
update(g)

Or you could string them all together in one line (but it’s rather difficult to follow what’s going on because you have to read from the inside out)

update(add_files(gists(what = "minepublic")[[1]], "~/alm_othersources.md"))

Rate limit information

rate_limit()
#> Rate limit: 5000
#> Remaining:  4948
#> Resets in:  46 minutes

List gists

Limiting to a few results here to keep it brief

gists(per_page = 2)
#> [[1]]
#> <gist>575fd0342ae15f89645f
#>   URL: https://gist.github.com/575fd0342ae15f89645f
#>   Description: Script to disable the mouse acceleration on Ubuntu (and probably also other distributions). Read the 'usage' section.
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:41:49Z / 2015-01-04T17:41:50Z
#>   Files: disable-mouse-accel.sh
#> 
#> [[2]]
#> <gist>1ebff1af906f214f98cd
#>   URL: https://gist.github.com/1ebff1af906f214f98cd
#>   Description: Ladda
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:41:45Z / 2015-01-04T17:41:45Z
#>   Files: Ladda.markdown, index.html, script.js, style.css

Since a certain date/time

gists(since='2014-05-26T00:00:00Z', per_page = 2)
#> [[1]]
#> <gist>575fd0342ae15f89645f
#>   URL: https://gist.github.com/575fd0342ae15f89645f
#>   Description: Script to disable the mouse acceleration on Ubuntu (and probably also other distributions). Read the 'usage' section.
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:41:49Z / 2015-01-04T17:41:50Z
#>   Files: disable-mouse-accel.sh
#> 
#> [[2]]
#> <gist>1ebff1af906f214f98cd
#>   URL: https://gist.github.com/1ebff1af906f214f98cd
#>   Description: Ladda
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:41:45Z / 2015-01-04T17:41:45Z
#>   Files: Ladda.markdown, index.html, script.js, style.css

Request different types of gists, one of public, minepublic, mineall, or starred.

gists('minepublic', per_page = 2)
#> [[1]]
#> <gist>588921d4111e00551bcf
#>   URL: https://gist.github.com/588921d4111e00551bcf
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:33:47Z / 2015-01-04T17:33:56Z
#>   Files: code.R
#> 
#> [[2]]
#> <gist>54c0195ee8753c7aaf9f
#>   URL: https://gist.github.com/54c0195ee8753c7aaf9f
#>   Description: a new cool gist
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:33:47Z / 2015-01-04T17:33:47Z
#>   Files: stuff.md

List a single gist

gist(id = 'f1403260eb92f5dfa7e1')
#> <gist>f1403260eb92f5dfa7e1
#>   URL: https://gist.github.com/f1403260eb92f5dfa7e1
#>   Description: Querying bitly from R 
#>   Public: TRUE
#>   Created/Edited: 2014-10-15T20:40:12Z / 2014-10-15T21:54:29Z
#>   Files: bitly_r.md

Create gist

You can pass in files

First, get a file to work with

stuffpath <- system.file("examples", "stuff.md", package = "gistr")
gist_create(files=stuffpath, description='a new cool gist')
gist_create(files=stuffpath, description='a new cool gist', browse = FALSE)
#> <gist>aa391404638f2f368b99
#>   URL: https://gist.github.com/aa391404638f2f368b99
#>   Description: a new cool gist
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:42:37Z / 2015-01-04T17:42:37Z
#>   Files: stuff.md

Or, wrap gist_create() around some code in your R session/IDE, like so, with just the function name, and a {' at the start and a }' at the end.

gist_create(code={'
x <- letters
numbers <- runif(8)
numbers

[1] 0.3229318 0.5933054 0.7778408 0.3898947 0.1309717 0.7501378 0.3206379 0.3379005
'}, browse=FALSE)
#> <gist>85158117880f197df422
#>   URL: https://gist.github.com/85158117880f197df422
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:42:37Z / 2015-01-04T17:42:37Z
#>   Files: code.R

You can also knit an input file before posting as a gist:

file <- system.file("examples", "stuff.Rmd", package = "gistr")
gist_create(file, description='a new cool gist', knit=TRUE)
#> <gist>4162b9c53479fbc298db
#>   URL: https://gist.github.com/4162b9c53479fbc298db
#>   Description: a new cool gist
#>   Public: TRUE
#>   Created/Edited: 2014-10-27T16:07:31Z / 2014-10-27T16:07:31Z
#>   Files: stuff.md

Or code blocks before (note that code blocks without knitr block demarcations will result in unexecuted code):

gist_create(code={'
x <- letters
(numbers <- runif(8))
'}, knit=TRUE)
#> <gist>ec45c396dee4aa492139
#>   URL: https://gist.github.com/ec45c396dee4aa492139
#>   Description:
#>   Public: TRUE
#>   Created/Edited: 2014-10-27T16:09:09Z / 2014-10-27T16:09:09Z
#>   Files: file81720d1ceff.md

knit code from file path, code block, or gist file

knit a local file

file <- system.file("examples", "stuff.Rmd", package = "gistr")
run(file, knitopts = list(quiet=TRUE)) %>% gist_create(browse = FALSE)
#> <gist>d5d86e11964c36cb4f1e
#>   URL: https://gist.github.com/d5d86e11964c36cb4f1e
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:42:38Z / 2015-01-04T17:42:38Z
#>   Files: stuff.md

knit a code block (knitr code block notation missing, do add that in) (result not shown)

run({'
x <- letters
(numbers <- runif(8))
'}) %>% gist_create

knit a file from a gist, has to get file first (result not shown)

gists('minepublic')[[1]] %>% run() %>% update()

List commits on a gist

gists()[[1]] %>% commits()
#> [[1]]
#> <commit>
#>   Version: faa7a40f4b55aa7914be7685c75d5c80731971bb
#>   User: sckott
#>   Commited: 2015-01-04T17:42:37Z
#>   Commits [total, additions, deletions]: [5,5,0]

Star a gist

Star

gist('7ddb9810fc99c84c65ec') %>% star()
#> <gist>7ddb9810fc99c84c65ec
#>   URL: https://gist.github.com/7ddb9810fc99c84c65ec
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2014-06-27T17:50:37Z / 2014-06-27T17:50:37Z
#>   Files: code.R, manifest.yml, rrt_manifest.yml

Unstar

gist('7ddb9810fc99c84c65ec') %>% unstar()
#> <gist>7ddb9810fc99c84c65ec
#>   URL: https://gist.github.com/7ddb9810fc99c84c65ec
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2014-06-27T17:50:37Z / 2014-06-27T17:50:37Z
#>   Files: code.R, manifest.yml, rrt_manifest.yml

Update a gist

Add files

First, path to file

file <- system.file("examples", "alm_othersources.md", package = "gistr")
gists(what = "minepublic")[[1]] %>%
  add_files(file) %>%
  update()
#> <gist>85158117880f197df422
#>   URL: https://gist.github.com/85158117880f197df422
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:42:37Z / 2015-01-04T17:42:42Z
#>   Files: alm_othersources.md, code.R

Delete files

gists(what = "minepublic")[[1]] %>%
  delete_files(file) %>%
  update()
#> <gist>85158117880f197df422
#>   URL: https://gist.github.com/85158117880f197df422
#>   Description: 
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:42:37Z / 2015-01-04T17:42:42Z
#>   Files: code.R

Open a gist in your default browser

gists()[[1]] %>% browse()

Opens the gist in your default browser

Get embed script

gists()[[1]] %>% embed()
#> [1] "<script src=\"https://gist.github.com/sckott/85158117880f197df422.js\"></script>"

List forks

Returns a list of gist objects, just like gists()

gist(id='1642874') %>% forks(per_page=2)
#> [[1]]
#> <gist>1642989
#>   URL: https://gist.github.com/1642989
#>   Description: Spline Transition
#>   Public: TRUE
#>   Created/Edited: 2012-01-19T21:45:20Z / 2014-12-10T03:25:19Z
#>   Files: 
#> 
#> [[2]]
#> <gist>1643051
#>   URL: https://gist.github.com/1643051
#>   Description: Line Transition (Broken)
#>   Public: TRUE
#>   Created/Edited: 2012-01-19T21:51:30Z / 2014-04-09T03:11:36Z
#>   Files:

Fork a gist

Returns a gist object

g <- gists()
(forked <- g[[ sample(seq_along(g), 1) ]] %>% fork())
#> <gist>62b05dd4ebc2d29add15
#>   URL: https://gist.github.com/62b05dd4ebc2d29add15
#>   Description: Solution to level 1 in Untrusted: http://alex.nisnevich.com/untrusted/
#>   Public: TRUE
#>   Created/Edited: 2015-01-04T17:42:43Z / 2015-01-04T17:42:43Z
#>   Files: untrusted-lvl1-solution.js

Example use case

Working with the Mapzen Pelias geocoding API

The API is described at https://github.com/pelias/pelias, and is still in alpha they say. The steps: get data, make a gist. The data is returned from Mapzen as geojson, so all we have to do is literally push it up to GitHub gists and we’re done b/c GitHub renders the map.

library('httr')
base <- "http://pelias.mapzen.com/search"
res <- GET(base, query = list(input = 'coffee shop', lat = 45.5, lon = -122.6))
json <- content(res, as = "text")
gist_create(code = json, filename = "pelias_test.geojson")
#> <gist>017214637bcfeb198070
#>   URL: https://gist.github.com/017214637bcfeb198070
#>   Description:
#>   Public: TRUE
#>   Created/Edited: 2014-10-28T14:42:36Z / 2014-10-28T14:42:36Z
#>   Files: pelias_test.geojson

And here’s that gist: https://gist.github.com/sckott/017214637bcfeb198070

image

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