https://github.com/mrc-ide/orderly2
https://github.com/mrc-ide/orderly2
Last synced: 9 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/mrc-ide/orderly2
- Owner: mrc-ide
- License: other
- Created: 2023-03-29T14:59:34.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-01-06T09:15:46.000Z (about 1 year ago)
- Last Synced: 2025-03-22T14:05:01.766Z (12 months ago)
- Language: R
- Homepage: https://mrc-ide.github.io/orderly2/
- Size: 9.25 MB
- Stars: 8
- Watchers: 2
- Forks: 2
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-reproducible-research - orderly - R package that automates writing reproducible analyses (Development Resources)
README
# orderly2
[](https://www.repostatus.org/#wip)
[](https://github.com/mrc-ide/orderly2/actions)
[](https://www.codefactor.io/repository/github/mrc-ide/orderly2)
[](https://codecov.io/github/mrc-ide/orderly2?branch=main)
> 1. an attendant in a hospital responsible for the non-medical care of patients and the maintenance of order and cleanliness.
> 2. a soldier who carries orders or performs minor tasks for an officer.
`orderly2` is a package designed to help make analysis more reproducible. Its principal aim is to automate a series of basic steps in the process of writing analyses, making it easy to:
* track all inputs into an analysis (packages, code, and data resources)
* store multiple versions of an analysis where it is repeated
* track outputs of an analysis
* create analyses that depend on the outputs of previous analyses
## Get started
Two vignettes provide an overview of the package, depending on your tastes:
* `vignette("orderly2")` describes the problem that `orderly2` tries to solve ([read on package website](https://mrc-ide.github.io/orderly2/articles/orderly2.html))
* `vignette("introduction")` describes `orderly2` by example, walking through the basic features ([read on package website](https://mrc-ide.github.io/orderly2/articles/introduction.html))
## Roadmap
This package is a ground-up rewrite of our [`orderly`](https://vaccineimpact.org/orderly) package, which is now ready for use on new projects or by adventurous users of the original package.
Over the next few months `orderly` will be renamed `orderly1`, and we will finalise the API for this package. Once stable, we will rename it back from `orderly2` to `orderly` and release to CRAN to replace the existing package. A migration path for existing users is described in `vignette("migrating")` and will be updated based on our experience migrating people.
The web framework [`OrderlyWeb`](https://github.com/vimc/orderly-web) is being rewritten in parallel (to [`packit`](https://github.com/mrc-ide/packit)) and we will provide a migration path here too.
## Installation
Please install from our [r-universe](https://mrc-ide.r-universe.dev/):
```r
install.packages(
"orderly2",
repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))
```
If you prefer, you can install from GitHub with `remotes`:
```r
remotes::install_github("mrc-ide/orderly2")
```
## Testing
To run all tests, you need to have [`outpack_server`](https://github.com/mrc-ide/outpack_server) available on your system path. One way to achieve this is to run
```
cargo install --git https://github.com/mrc-ide/outpack_server
```
For all tests we also require development versions of [`gert`](https://github.com/r-lib/gert/) and [`jsonvalidate`](https://github.com/ropensci/jsonvalidate/). These can be installed from the [rOpenSci r-universe](https://ropensci.r-universe.dev), with:
```r
install.packages(
c("gert", "jsonvalidate"),
repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))
```
Without these, some tests will be skipped, but the suite will still run.
If you want to force validation of schemas during testing, set the R option `outpack.schema_validate` to `TRUE`. This will automatically be set on CI (as detected by the `CI` environment variable) and will be enabled if `jsonvalidate` is installed. Set the option `outpack.schema_validate` as `FALSE` to disable checking.
## Licence
MIT © Imperial College of Science, Technology and Medicine