• Stars
    star
    153
  • Rank 243,368 (Top 5 %)
  • Language
    R
  • Created about 8 years ago
  • Updated 5 months ago

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

Tasks Integrating Continuously: CI-Agnostic Workflow Definitions

tic

tic CircleCI CRAN status codecov Lifecycle: stable tic status badge

The goal of tic is to enhance and simplify working with continuous integration (CI) systems.

The following providers are supported:

Provider R package Platforms Info
Circle CI {circle} Linux via Docker images from rocker
Github Actions {ghactions} Linux, macOS, Windows

In addition there is partial support for Drone CI via class DRONE_CI. This means that {tic} recognizes Drone CI as a CI platform and does not exit early or requires setting a fake env var to mimic another CI provider. However, there is neither an R client package for Drone CI currently nor {tic} templates available for bootstrapping CI configuration via tic::use_tic().

To learn more about CI, read our Getting Started vignette.

The most important improvements over existing solutions are:

  1. Deployment to a Git repository is greatly simplified. Update your repository with results from the CI build.

  2. Support for R packages and other kinds of projects (bookdown, blogdown, etc.), with predefined templates. Set up your project to deploy rendered versions of your book or blog with a single push to Git.

  3. Workflow specification in a single .R file, regardless of CI system used. Forget about .yml files or web browser configurations.

Installation

{tic} can be installed from GitHub with:

remotes::install_github("ropensci/tic")

Setup

By calling tic::use_tic() a production ready CI setup is initialized, tailored to your specific R project. The created templates will use the providers Circle CI and Github Actions.

If only the CI YAML templates from {tic} are desired, the use_<provider>_yml() functions can be used. Refer to the complete list of options.

For an R package, the following steps will be set up for the CI workflow:

  • Installation of required dependencies for the project (dependencies are scraped from the DESCRIPTION file*)
  • Satisfying build-time dependencies of steps to be run in all CI stages (by scraping pkg::fun calls in tic.R)
  • Checking of package via rcmdcheck::rcmdcheck()
  • Creation of a pkgdown site including Github deployment
  • Running a code coverage and upload to codecov.io

See the Getting Started vignette for more information and links to minimal example repositories for various R projects (package, blogdown, bookdown and more).

Quickstart

If you are a new user, run

tic::use_tic()

If you already use {tic} and want to configure a new CI provider, do one of the following (depending on your preferred CI provider)

### Circle CI ------------------------------------------------------------------

circle::use_circle_deploy() # (optional for deployment)
tic::use_circle_yml() # optional: Change `type` arg to your liking
tic::use_tic_r("package", deploy_on = "circle")
# (all of the above in one call)
# tic::use_tic(wizard = FALSE, linux = "circle", mac = "none", windows = "none",
#              matrix = "circle", deploy = "circle")
tic::use_update_tic()

### GitHub Actions -------------------------------------------------------------

tic::use_ghactions_deploy() # (optional for deployment)
tic::use_ghactions_yml() # optional: Change `type` arg to your liking
tic::use_tic_r("package", deploy_on = "ghactions")
# (all of the above in one call)
# tic::use_tic(wizard = FALSE, linux = "ghactions", mac = "ghactions",
#              windows = "ghactions", matrix = "ghactions", deploy = "ghactions")

tic::use_tic_badge("ghactions")
tic::use_update_tic()

Good to know

We would like to mention that {tic} is a choice and sits on top of existing community efforts providing R support for various CI providers. While {tic} will prevent you from dealing/learning every CIs YAML syntax, you will have to learn {tic}'s way of specifying your tasks on CI systems.

Also, there is no way around familiarizing yourself with the basics of CI systems in general. Without this knowledge, you will also have a hard way understanding {tic}.

We also recommend to take a look at the projects providing the direct R support for each CI system (which {tic} builds upon) to gain a deeper understanding of the whole concept.

Keeping CI templates up-to-date

{tic} is refreshing its template every few months. There are two ways to stay up-to-date and have a functional CI YAML definition:

  1. Manual updates: You can keep {tic} up-to-date by rerunning the use_*_() function which you have used to init {tic} the first time. If you have forgotten which settings you have chosen back then, you can have a look at the first line of your YAML file.

  2. Automatic updates via GHA: If you're using GitHub actions, you can use tic::use_update_tic(). This will initialize a new workflow which checks daily for new template updates. Important: This workflow requires a personal access token with "workflow" scopes. After creation, you can add it via tic::gha_add_secret() to your repo account. Hint: If you're operating in an organization, you can set this GHA secret organization-wide which saves you adding it to multiple single repos.

See vignette "Updating Templates" for more information.

Vignettes

Limitations

The setup functions in this package assume Git as version control system, and GitHub as platform. Automated setup works best if the project under test is located in the root of the Git repository. Multi-project repositories are not supported, see the comment by @jwijffels for guidance to work around this limitation.

The DESCRIPTION files needs to live in the project root. To simplify its creation have a look at usethis::use_package() or usethis::use_description().

More Repositories

1

drake

An R-focused pipeline toolkit for reproducibility and high-performance computing
R
1,339
star
2

skimr

A frictionless, pipeable approach to dealing with summary statistics
HTML
1,108
star
3

targets

Function-oriented Make-like declarative workflows for R
R
912
star
4

rtweet

🐦 R client for interacting with Twitter's [stream and REST] APIs
R
785
star
5

tabulizer

Bindings for Tabula PDF Table Extractor Library
R
518
star
6

pdftools

Text Extraction, Rendering and Converting of PDF Documents
C++
489
star
7

magick

Magic, madness, heaven, sin
R
440
star
8

visdat

Preliminary Exploratory Visualisation of Data
R
439
star
9

stplanr

Sustainable transport planning with R
R
417
star
10

RSelenium

An R client for Selenium Remote WebDriver
R
332
star
11

rnoaa

R interface to many NOAA data APIs
R
328
star
12

osmdata

R package for downloading OpenStreetMap data
R
315
star
13

charlatan

Create fake data in R
R
291
star
14

software-review

rOpenSci Software Peer Review.
R
279
star
15

iheatmapr

Complex, interactive heatmaps in R
R
259
star
16

taxize

A taxonomic toolbelt for R
R
250
star
17

rrrpkg

Use of an R package to facilitate reproducible research
248
star
18

elastic

R client for the Elasticsearch HTTP API
R
244
star
19

tesseract

Bindings to Tesseract OCR engine for R
R
236
star
20

git2r

R bindings to the libgit2 library
R
216
star
21

qualtRics

Download ⬇️ Qualtrics survey data directly into R!
R
215
star
22

biomartr

Genomic Data Retrieval with R
R
212
star
23

writexl

Portable, light-weight data frame to xlsx exporter for R
C
202
star
24

googleLanguageR

R client for the Google Translation API, Google Cloud Natural Language API and Google Cloud Speech API
HTML
194
star
25

rnaturalearth

An R package to hold and facilitate interaction with natural earth map data 🌍
R
191
star
26

textreuse

Detect text reuse and document similarity
R
188
star
27

piggyback

📦 for using large(r) data files on GitHub
R
182
star
28

tokenizers

Fast, Consistent Tokenization of Natural Language Text
R
179
star
29

rentrez

talk with NCBI entrez using R
R
178
star
30

rcrossref

R client for various CrossRef APIs
R
166
star
31

osmextract

Download and import OpenStreetMap data from Geofabrik and other providers
R
166
star
32

dataspice

🌶️ Create lightweight schema.org descriptions of your datasets
R
159
star
33

rgbif

Interface to the Global Biodiversity Information Facility API
R
155
star
34

webchem

Chemical Information from the Web
R
149
star
35

geojsonio

Convert many data formats to & from GeoJSON & TopoJSON
R
148
star
36

tsbox

tsbox: Class-Agnostic Time Series in R
R
148
star
37

MODIStsp

An "R" package for automatic download and preprocessing of MODIS Land Products Time Series
R
147
star
38

ghql

GraphQL R client
R
145
star
39

DataPackageR

An R package to enable reproducible data processing, packaging and sharing.
R
145
star
40

dev_guide

rOpenSci Packages: Development, Maintenance, and Peer Review
R
141
star
41

osfr

R interface to the Open Science Framework (OSF)
R
140
star
42

jqr

R interface to jq
R
139
star
43

tarchetypes

Archetypes for targets and pipelines
R
130
star
44

osmplotr

Data visualisation using OpenStreetMap objects
R
130
star
45

opencv

R bindings for OpenCV
C++
130
star
46

ssh

Native SSH client in R based on libssh
C
126
star
47

RefManageR

R package RefManageR
R
114
star
48

ezknitr

Avoid the typical working directory pain when using 'knitr'
R
112
star
49

spocc

Species occurrence data toolkit for R
R
109
star
50

hunspell

High-Performance Stemmer, Tokenizer, and Spell Checker for R
C++
106
star
51

weathercan

R package for downloading weather data from Environment and Climate Change Canada
R
102
star
52

crul

R6 based http client for R (for developers)
R
102
star
53

UCSCXenaTools

📦 An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
R
102
star
54

gistr

Interact with GitHub gists from R
R
101
star
55

spelling

Tools for Spell Checking in R
R
101
star
56

rfishbase

R interface to the fishbase.org database
R
100
star
57

gutenbergr

Search and download public domain texts from Project Gutenberg
R
99
star
58

git2rdata

An R package for storing and retrieving data.frames in git repositories.
R
99
star
59

openalexR

Getting bibliographic records from OpenAlex
R
98
star
60

bib2df

Parse a BibTeX file to a tibble
R
97
star
61

ckanr

R client for the CKAN API
R
97
star
62

nasapower

API Client for NASA POWER Global Meteorology, Surface Solar Energy and Climatology in R
R
96
star
63

rsvg

SVG renderer for R based on librsvg2
C
95
star
64

EML

Ecological Metadata Language interface for R: synthesis and integration of heterogenous data
R
94
star
65

FedData

Functions to Automate Downloading Geospatial Data Available from Several Federated Data Sources
R
94
star
66

cyphr

:shipit: Humane encryption
R
93
star
67

GSODR

API Client for Global Surface Summary of the Day (GSOD) Weather Data Client in R
R
90
star
68

mapscanner

R package to print maps, draw on them, and scan them back in
R
88
star
69

av

Working with Video in R
C
88
star
70

opencage

🌐 R package for the OpenCage API -- both forward and reverse geocoding 🌐
R
87
star
71

gittargets

Data version control for reproducible analysis pipelines in R with {targets}.
R
85
star
72

tidync

NetCDF exploration and data extraction
R
85
star
73

historydata

Datasets for Historians
R
83
star
74

rzmq

R package for ZMQ
C++
82
star
75

CoordinateCleaner

Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.
HTML
79
star
76

rebird

Wrapper to the eBird API
R
79
star
77

smapr

An R package for acquisition and processing of NASA SMAP data
R
79
star
78

bikedata

🚲 Extract data from public hire bicycle systems
R
79
star
79

dittodb

dittodb: A Test Environment for DB Queries in R
R
78
star
80

arkdb

Archive and unarchive databases as flat text files
R
78
star
81

fingertipsR

R package to interact with Public Health England’s Fingertips data tool
R
78
star
82

vcr

Record HTTP calls and replay them
R
77
star
83

nodbi

Document DBI connector for R
R
76
star
84

opentripplanner

An R package to set up and use OpenTripPlanner (OTP) as a local or remote multimodal trip planner.
R
73
star
85

nlrx

nlrx NetLogo R
R
71
star
86

slopes

Package to calculate slopes of roads, rivers and trajectories
R
70
star
87

tidyhydat

An R package to import Water Survey of Canada hydrometric data and make it tidy
R
70
star
88

rb3

A bunch of downloaders and parsers for data delivered from B3
R
69
star
89

robotstxt

robots.txt file parsing and checking for R
R
68
star
90

codemetar

an R package for generating and working with codemeta
R
66
star
91

tradestatistics

R package to access Open Trade Statistics API
R
65
star
92

unconf17

Website for 2017 rOpenSci Unconf
JavaScript
64
star
93

roadoi

Use Unpaywall with R
R
64
star
94

terrainr

Get DEMs and orthoimagery from the USGS National Map, georeference your images and merge rasters, and visualize with Unity 3D
R
64
star
95

tiler

Generate geographic and non-geographic map tiles from R
R
64
star
96

comtradr

Functions for Interacting with the UN Comtrade API
R
64
star
97

NLMR

📦 R package to simulate neutral landscape models 🏔
R
63
star
98

parzer

Parse geographic coordinates
R
63
star
99

rWBclimate

R interface for the World Bank climate data
R
62
star
100

stats19

R package for working with open road traffic casualty data from Great Britain
R
61
star