omicser: NDCN Omics Browser

# Building a Prod-Ready, Robust Shiny Application.
#
# README: each step of the dev files is optional, and you don't have to
# fill every dev scripts before getting started.
# 01_start.R should be filled at start.
# 02_dev.R should be used to keep track of your development during the project.
# 03_deploy.R should be used once you need to deploy your app.
#
#
###################################
#### CURRENT FILE: DEV SCRIPT #####
###################################

# Engineering
usethis::use_pipe()
## Dependencies ----
## Add one line by package you want to add as dependency
#usethis::use_package( "thinkr" )
usethis::use_package( "golem" )

# add more?
usethis::use_package("shiny")
usethis::use_package("shinyjs")

usethis::use_package("shinyBS")

# usethis::use_package("shinyWidgets") # might not need?
# usethis::use_package("shinydashboard") # might not need?
usethis::use_package("shinydashboardPlus") #maybe automatically get shinydashboard?


usethis::use_package("data.table")
usethis::use_package("DT")
usethis::use_package("Matrix")
usethis::use_package("configr")

usethis::use_package("ggplot2")
usethis::use_package("gridExtra")
usethis::use_package("ggdendro")
usethis::use_package("markdown")
usethis::use_package("rmarkdown")
#devtools::install_github("jokergoo/ComplexHeatmap")
#usethis::use_dev_package("ComplexHeatmap",remote='jokergoo/ComplexHeatmap')

#remotes::install_bioc("3.14/ComplexHeatmap")
#usethis::use_dev_package("ComplexHeatmap",remote='bioc::3.13/ComplexHeatmap')
#usethis::use_package("ComplexHeatmap")
remotes::install_github("jokergoo/ComplexHeatmap")
usethis::use_dev_package("ComplexHeatmap",remote="github::jokergoo/ComplexHeatmap")
usethis::use_package("plotly")

usethis::use_package("anndata")
usethis::use_package("magick")
usethis::use_package("Cairo")

usethis::use_package("waiter")

usethis::use_package("shinyFiles")

# # DISABLED for now
# usethis::use_package("BiocManager")
# # usethis::use_package("SingleCellExperiment")
# #usethis::use_dev_package('bioc::3.14/ComplexHeatmap')
# # remotes::install_bioc("3.14/SingleCellExperiment")
# # remotes::install_bioc("3.14/LoomExperiment")
# # remotes::install_github("cellgeni/sceasy")
# usethis::use_dev_package("SingleCellExperiment",remote="bioc::3.14/SingleCellExperiment")
# usethis::use_dev_package("sceasy",remote="cellgeni/sceasy")
# usethis::use_dev_package("LoomExperiment",remote="bioc::3.14/LoomExperiment")

usethis::use_package("dplyr")
#usethis::use_package("tidyr") # called by dplyr as dependency?
#usethis::use_package("magrittr")  # use_pipe()
usethis::use_package("broom")


## Add modules ----
## Create a module infrastructure in R/
golem::add_module( name = "ingestor" ) # Name of the module
golem::add_module( name = "playground" ) # Name of the module
golem::add_module( name = "pg_vis_raw" ) # Name of the module
golem::add_module( name = "pg_vis_comp" ) # Name of the module
golem::add_module( name = "pg_table" ) # Name of the module
golem::add_module( name = "side_selector" ) # Name of the module
golem::add_module( name = "welcome" ) # Name of the module
golem::add_module( name = "side_info" ) # Name of the module
golem::add_module( name = "additional_info") # Name of the module
golem::add_module( name = "omic_selector") # Name of the module
golem::add_module( name = "subset_selector") # Name of the module
golem::add_module( name = "help") # Name of the module

# DEPRICATE?
golem::add_module( name = "pg_vis_qc") # Name of the module
golem::add_module( name = "export" ) # Name of the module

## Add helper functions ----
## Creates fct_* and utils_*
# golem::add_fct( "module" ) # NOTE: `fct` are server helpers
# golem::add_utils( "module" ) #   'utils` are ui helpers

# ## External resources
# TODO: ADD THESE JS/CSS resources
# ## Creates .js and .css files at inst/app/www
# golem::add_js_file( "script" )
# golem::add_js_handler( "handlers" )
# golem::add_css_file( "custom" )

# TODO:  add tests ASAP
## Tests ----
## Add one line by test you want to create
#usethis::use_test( "app" )

# Documentation
## Vignette ----
usethis::use_vignette("omicser")
devtools::build_vignettes()

# ## Code Coverage----
# ## Set the code coverage service ("codecov" or "coveralls")
# usethis::use_coverage()
#
# # Create a summary readme for the testthat subdirectory
# covrpage::covrpage()
#
# ## CI ----
# ## Use this part of the script if you need to set up a CI
# ## service for your application
# ##
# ## (You'll need GitHub there)
# usethis::use_github()
#
# # # GitHub Actions
# usethis::use_github_action()
# # Chose one of the three
# # See https://usethis.r-lib.org/reference/use_github_action.html
# usethis::use_github_action_check_release()
# usethis::use_github_action_check_standard()
# usethis::use_github_action_check_full()
# # Add action for PR
# usethis::use_github_action_pr_commands()
#
# # Travis CI
# usethis::use_travis()
# usethis::use_travis_badge()
#
# # AppVeyor
# usethis::use_appveyor()
# usethis::use_appveyor_badge()
#
# # Circle CI
# usethis::use_circleci()
# usethis::use_circleci_badge()
#
# # Jenkins
# usethis::use_jenkins()
#
# # GitLab CI
# usethis::use_gitlab_ci()

# You're now set! ----
# go to dev/03_deploy.R
rstudioapi::navigateToFile("dev/03_deploy.R")