Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/kinto-b/makepipe
Tools for constructing simple make-like pipelines in R.
https://github.com/kinto-b/makepipe
make pipeline r
Last synced: 26 days ago
JSON representation
Tools for constructing simple make-like pipelines in R.
- Host: GitHub
- URL: https://github.com/kinto-b/makepipe
- Owner: kinto-b
- License: gpl-3.0
- Created: 2021-04-04T06:36:27.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2022-12-07T22:06:39.000Z (almost 2 years ago)
- Last Synced: 2024-09-30T02:43:21.414Z (about 1 month ago)
- Topics: make, pipeline, r
- Language: R
- Homepage: https://kinto-b.github.io/makepipe/
- Size: 1.25 MB
- Stars: 30
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# makepipe 
[](https://app.codecov.io/gh/kinto-b/makepipe?branch=master)
[](https://CRAN.R-project.org/package=makepipe)
[](https://github.com/kinto-b/makepipe/actions/workflows/R-CMD-check.yaml)
The goal of `makepipe` is to allow for the construction of make-like pipelines in R with very minimal overheads. In contrast to `targets` (and its predecessor `drake`) which offers an opinionated pipeline framework that demands highly functionalised code, `makepipe` is easy-going, being adaptable to a wide range of data science workflows.
A minimal example can be found here: https://github.com/kinto-b/makepipe_example
## Installation
You can install the released version of `makepipe` from [CRAN](https://CRAN.R-project.org) with:
``` r
install.packages("makepipe")
```
And the development version from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("kinto-b/makepipe")
```
## Building a pipeline
To construct a pipeline, one simply needs to chain together a number of `make_with_*()` statements. When the pipeline is run through, each `make_with_*()` block is evaluated if and only if the `targets` are out-of-date with respect to the `dependencies` (and `source` file). But, whether or not the block is evaluated, a segment will be added to the Pipeline object behind the scenes. At the end of the script, once the entire pipeline has been run through, one can display the accumulated Pipeline object to produce a flow-chart visualisation of the pipeline. For example:
``` r
make_with_source(
note = "Clean raw survey data and do derivations",
source = "one.R",
targets = "data/1 data.Rds",
dependencies = c("data/raw.Rds", "lookup/concordance.csv")
)
make_with_recipe(
label = "Merge it!",
note = "Merge demographic variables from population data into survey data",
recipe = {
dat <- readRDS("data/1 data.Rds")
pop <- readRDS("data/pop.Rds")
merged_dat <- merge(dat, pop, by = "id")
saveRDS(merged_dat, "data/2_data.Rds")
},
targets = c("data/2 data.Rds"),
dependencies = c("data/1 data.Rds", "data/pop.Rds")
)
make_with_source(
note = "Convert data from 'wide' to 'long' format",
source = "three.R",
targets = "data/3 data.Rds",
dependencies = "data/2 data.Rds"
)
show_pipeline()
```
```{r out.width = "75%", echo = FALSE, fig.align = "center"}
knitr::include_graphics("man/figures/pipeline_nomnoml_uptodate.png")
```
We can also get an interactive visNetwork widget:
```r
show_pipeline(as = "visnetwork")
```
```{r out.width = "75%", echo = FALSE, fig.align = "center"}
knitr::include_graphics("man/figures/pipeline_visnetwork_uptodate.png")
```
Or a text summary (which can be saved to a .md file),
```r
show_pipeline(as = "text")
#> # Pipeline
#>
#> ## one.R
#>
#> Clean raw survey data and do derivations
#>
#> * Source: 'one.R'
#> * Targets: 'data/1 data.Rds'
#> * File dependencies: 'data/raw.Rds', 'lookup/concordance.csv'
#> * Executed: FALSE
#> * Environment: 0x0000015399acfeb8
#>
#> ## Merge it!
#>
#> Merge demographic variables from population data into survey data
#>
#> * Recipe:
#>
#> {
#> dat <- readRDS("data/1 data.Rds")
#> pop <- readRDS("data/pop.Rds")
#> saveRDS(dat, "data/2_data.Rds")
#> }
#>
#> * Targets: 'data/2 data.Rds'
#> * File dependencies: 'data/1 data.Rds', 'data/pop.Rds'
#> * Executed: TRUE
#> * Execution time: 0.00103879 secs
#> * Result: 0 object(s)
#> * Environment: 0x0000015390c6c568
#>
#> ## three.R
#>
#> Convert data from 'wide' to 'long' format
#>
#> * Source: 'three.R'
#> * Targets: 'data/3 data.Rds'
#> * File dependencies: 'data/2 data.Rds'
#> * Executed: FALSE
#> * Environment: 0x00000153928570f8
```
Once you've constructed a pipeline, you can 'clean' it (i.e. delete all registered targets):
```r
p <- get_pipeline()
p$clean()
```
Then, when you look again at the visualisation, the target nodes will be red not green since they're out-of-date:
```r
show_pipeline()
```
```{r out.width = "75%", echo = FALSE, fig.align = "center"}
knitr::include_graphics("man/figures/pipeline_nomnoml_outofdate.png")
```
And then you can 'rebuild' to re-execute the entire pipeline and re-create the cleaned targets:
```r
p <- get_pipeline()
p$build()
```
Another way to build a pipeline is to add a roxygen header into your .R scripts containing a special `@makepipe` tag along with the `@targets`, `@dependencies`,
and so on. For example, at the top of script `one.R` you might have
```r
#'@title Load
#'@description Clean raw survey data and do derivations
#'@dependencies "data/raw.Rds", "lookup/concordance.csv"
#'@targets "data/1 data.Rds"
#'@makepipe
NULL
```
You can then call `make_with_dir()`, which will construct a pipeline using all
the scripts it finds in the provided directory containing the `@makepipe`
tag.