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Contributing to ImmuneSpaceR

Opening issues

Please briefly describe your problem and what output you expect and include a minimal reprex.

The goal of a reprex is to make it as easy as possible for me to recreate your problem so that I can fix it. If you've never heard of a reprex before, start by reading this.

Brief description of the problem

# insert reprex here

Issue labels

  • bug: found something that's giving you a headache? use this flag!
  • question: not sure how to use or what is going on? Ask away
  • enhancement: new feature? refactor? optimization?
  • infrastructure: tests, ci, codecov, bioconductor, pkgdown
  • help wanted: maybe you are stuck? need some help? use this flag to get attention

General development guidelines

If you'd like to contribute changes to ImmuneSpaceR, we use the GitHub flow for proposing, submitting, reviewing, and accepting changes. If you haven't done this before, Hadley Wickham provides a nice overview of git, as well as best practices for submitting pull requests. We also recommend using his style guide when writing code.

Development Flow

New Feature

fb_newFeature -> Code Review -> dev -> main -> Bioconductor Submission

For example:

  1. Run into a problem or come up with an idea for a new feature or optimization/enhancement
  2. Create an issue to address the problem or propose the new feature
  3. Create a new branch from dev
  4. Make changes in the new branch
  5. Build and install
  6. Manually test out your changes
  7. Make a commit
  8. If you have more changes to make, repeat steps from #4 to #8
  9. Run R CMD check and BiocCheck
  10. If you get an error or warning, repeat steps from #4 to #10
  11. Push your commit(s) to GitHub. This will kick off Travis build
  12. Wait for Travis build to be done and repeat steps from #4 to #12 if there are errors or you'd like to make more changes
  13. When the new branch is ready to merge, create a Pull Request. The maintainer will assign reviewers for your PR
  14. Reviewers will go through the PR checklist and give you feedback. Repeat steps from #4 to #13 accordingly
  15. Once the reviewers approve your PR, the maintainer will merge your branch to dev branch

Hot Fix

dev -> main -> Bioconductor Submission

Package Structure (WIP)

ImmuneSpaceR.R

  • Package description
  • Declare global variables for data.table scoping

CreateConnection.R

  • CreateConnection(): constructor for ISCon class

ISCon.R

  • ISCon definition and documentation
    • self$study
    • self$config
    • self$availableDatasets
    • self$cache
    • private$.constants
  • self$initialize()
  • .check_internet()
  • .get_host()
  • .check_portal()
  • .get_url_base()
  • .get_user_email()
  • .get_url_path()
  • .set_curl_options()
  • .check_credential()

ISCon-cytometry.R

  • self$listWorkspaces()
  • self$listGatingSets()
  • self$summarizeCyto()
  • self$summarizeGatingSet()
  • self$loadGatingSet()
  • private$.openWorkspace()
  • private$.downloadCytoData()
  • private$.mergePD()
  • .isRstudioDocker()
  • .assertRstudio()
  • .buildGSPath()

ISCon-dataset.R

  • self$listDatasets()
  • self$getDataset()
  • private()$.setAvailableDatasets()
  • private$.getColnames()
  • private$.checkFilter()
  • .extractNames()
  • .fixColFilter()
  • .transformData()

ISCon-geneExpression.R

  • self$listGEMatrices()
  • self$listGEAnalysis()
  • self$getGEMatrix()
  • self$getGEAnalysis()
  • self$getGEInputs()
  • self$getGEFiles()
  • self$downloadGEFiles()
  • self$addTreatment()
  • self$mapSampleNames()
  • private$.downloadMatrix()
  • private$.getGEFeatures()
  • private$.constructExpressionSet()
  • private$.mungeFeatureId()
  • .setCacheName()
  • .combineEMs()

ISCon-participantGroup.R

  • self$listParticipantGroups()
  • self$getParticipantData()
  • private.assertAllStudyConnection()

ISCon-plot.R

  • self$plot()
  • .plot()
  • .standardize_time()
  • .qpHeatmap2()
  • .qpBoxplotViolin()
  • .qpLineplot()
  • .getDataToPlot()
  • .heatmapAnnotations()
  • .format_lab()

ISCon-utils.R

  • self$print()
  • self$clearCache()
  • private$.checkStudy()
  • private$.munge()
  • private$.isProject()
  • private$.isRunningLocally()
  • private$.localStudyPath()
  • private$.listISFiles()
  • .getLKtbl()
  • .mixedsort()

netrc.R

  • interactive_netrc()
  • write_netrc()
  • check_netrc()
  • .get_env_netrc()
  • .get_env_url()
  • .get_path()
  • .check_con()

template.R

  • template_IS()

theme.R

  • theme_IS()
  • ISpalette()
  • .override_scale()

utils.R

  • loadConnection()
  • saveConnection()

zzz.R

  • .onAttach()

ISCon-*.R Structure (WIP)

#' @include ISCon.R
NULL



# PUBLIC -----------------------------------------------------------------------
# (fields and methods that will be public)
# (they should be documented in ISCon.R file)

# (comment what/how this method is doing)
ISCon$set(
  which = "public",
  name = "aPublicMethod",
  value = function() {
  
  }
)


# (comment about the method)
ISCon$set(
  which = "public",
  name = "anotherPublicMethod",
  value = function() {

  }
)



# PRIVATE -----------------------------------------------------------------------

# (comment about this method)
ISCon$set(
  which = "private",
  name = ".aPrivateMethod",
  value = function() {
  
  }
)


# (comment)
ISCon$set(
  which = "private",
  name = ".anotherPrivateMethod",
  value = function() {
  
  }
)



# HELPERS -----------------------------------------------------------------------

# (comment)
.aHelper <- function(x) {

}


# (comment)
.anotherHelper <- function() {

}
  • ISCon-*.R files are divided into four sections: PURPOSE, PUBLIC, PRIVATE, HELPERS
  • PURPOSE section
    • Describes the purpose of this .R file and functions/methods as group
  • PUBLIC section
    • For functions that require fields or methods in self
    • These methods should be documented in ISCon.R file
  • PRIVATE section
    • Like public methods, this section are for functions that require fields or methods in self, not accessible to the user
    • The name of a PRIVATE method should start with a dot (.)
  • HELPER section
    • Contains helper functions exclusively used in public/private methods in this .R file
    • The name of a HELPER function should start with a dot (.)
  • Spacing
    • Two new lines between methods/functions in the same section
    • Three new lines between the sections

Package Development Guide

Functional Code Guide

  • Use data.table::data.table() instead of data.frame()
  • Use data.table::fread() instead of read.csv() or read.table()
  • Use TRUE or FALSE instead of T or F
  • Avoid sapply(), use vapply() instead
  • Use message() and warning() to communicate with the user in your functions
  • Use fieldname for colNameOpt argument if you decide to use labkey.selectRows() or labkey.executeSql()
  • Use the profvis package to test the performance of your code

Style Guide

  • We are mainly following the tidyverse style guide except for the object naming convention
  • Run styler::style_pkg() for convenience
  • The maximum line length is 80 characters
  • Use <- not = for assignment
  • When indenting your code, use two spaces. Never use tabs or mix tabs and spaces
  • Use common sense and BE CONSISTENT

Naming Things

  • Use lowerCamelCase for variables, functions, methods, arguments
  • Use snake_case for column names in tables
  • Use specific words or look up shorthands in the glossary table
  • Avoid generic names
  • Use verbs for functions and methods

Commenting Things

  • Comment every functions and methods
  • Comments should explain the why, not the what

Versioning

  • Bump version in only dev branch after hot fixes and/or feature branch merge
  • We follow Sementic Verioning 2.0.0: MAJOR.MINOR.PATCH
    • MAJOR: when making incompatible API changes
    • MINOR: when adding functionality in a backwards compatible manner
    • PATH: when making backwards compatible bug fixes
  • For ImmuneSpaceR, we follow Bioconductor's Verion Numbering

Notes

  • Even a smallest change can break the package and the portal, so be mindful about the changes you make
  • Check out ImmuneSpace Glossary for commonly used Acronyms, symbols, abbreviations, and terms

Maintainer Guide

Merge to main Branch Checklist

  • Is the version bumped?
  • Is the documentation up to date?
  • Is the pkgdown site up to date?
  • Is it passing BiocCheck::BiocCheck()?
  • Is it passing against the production?

Bioconductor Submission Checklist

  • Is the version valid?
  • Is it passing BiocCheck?
  • Does it need to be merged to the release branch of BiocConductor?

FAQ (WIP)

What is the point of this?

  • The point of having these guidelines is "to have a common vocabulary of coding so people can concentrate on what you are saying, rather than on how you are saying it" (Google's R Style Guide).

How does ImmuneSpaceR work?

  • Well

How do I setup my machine for ImmuneSpaceR development?

Further Readings

R related

General coding best practices