README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# INCLUDE Shiny Template

<!-- badges: start -->
[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
<!-- badges: end -->

Welcome to INCLUDE. This repository will serve as a guide for developing
shiny applications and contains the most basic golem shiny application
structure.

## Installation

You can install the released version of includeshinytemplate from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("includeshinytemplate")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("include-dcc/include-shiny-template")
```
## Example

This is a basic example which shows you how to solve a common problem:

```{r example}
library(includeshinytemplate)
## basic example code
```


## Using this template

1. After copying this template, these are the files that must be updated with your repository name.

    - README.Rmd
    - docker-compose.yml
    - CONTRIBUTING.md
    - dev/01_start.R
    - dev/02_dev.R
1. After updating these files, please make sure to run the functions in `dev/01_start.R` to update this repository.
1. If you want to push this shiny application to CAVATICA, add a github secret with your CAVATICA_AUTH_TOKEN. Make sure you also create a CAVATICA project. Comment the `deploy` section of the `.github/workflows/ci.yaml`.


## Developmental Guide

In this shiny application template we try to follow the guidelines described by Engineering Production-Grade Shiny Apps: https://engineering-shiny.org/index.html.  In particular we utilize tools such as `golem` and `renv` to build our shiny application.  The steps described below can all be found in more detail in  the shiny engineering link above.

1. Create Golem Shiny App: `golem::create_golem()` as documented [here](https://engineering-shiny.org/setting-up-for-success.html#create-a-golem)
1. Utilize [renv](https://engineering-shiny.org/build-yourself-safety-net.html#renv) to set up your R environment
1. Update readme by modifying README.Rmd (not README.md):

    ```
    devtools::build_readme()
    ```

1. Add golem modules. You will most likely want to remove `mod_hello_world.R` and add your own golem module. Be sure to add to `app_ui.R` and `app_ui.R` to use your module. More information [here](https://engineering-shiny.org/build-app-golem.html#submodules-and-utility-functions)

    ```
    golem::add_module( name = "hello_world" )
    ```

1. Add tests. More information [here](https://engineering-shiny.org/build-app-golem.html#add-tests)

    ```
    usethis::use_test( "app" )
    ```

1.  Need to use Python?  Use [reticulate](https://rstudio.github.io/reticulate/)  Be sure to use either `conda` or `pipenv` to manage your Python dependencies.
1. The CI/CD for this repository is done through github actions and consists of 3 major steps.  The file is located at .github/workflows/ci.yaml
    * test: Testing of the shiny package
    * docker: This section is commented out ci.yaml but you can choose to un-comment it out if you want to use this.
    * deploy: Upload this to CAVATICA project so it can be used in data cruncher.