Issues

We use github issues for feature requests, bug reports and developer coordination.

Gitflow workflow

We use the Gitflow workflow. This means we have two main branches:

1. a master branch (master) for stable releases
2. a development branch (develop) where all development takes place

We also use feature branches which branch from the development branch where we can then introduce new features and then pull them back into the development branch.

Code Structure

Directory Structure

├── R # R functions
├── docker # Docker files
│   └── plant-test
├── inst
│   ├── docs # Files for building the documentation
│   │   ├── R
│   │   ├── figure
│   │   ├── figures
│   │   ├── reference
│   │   ├── src
│   ├── include
│   │   ├── plant # .h files for plant.
│   │   └── tk
│   └── reference_plant_ff16 # Reference plant physiology ff16.
│       ├── R
│       └── falster-traitdiversity
├── man # R Documentation ie .Rd files.
├── scripts # R scripts
├── src # C++ files
├── tests # Tests
└── vignettes # Empty until the documentation is built

Building the website:

To build and push the website to the gh-pages branch run make website. This first builds the vignettes from /inst/docs then builds the site with pkgdown. The site is then pushed to the gh-pages branch. (https://traitecoevo.github.io/plant)

Makefile guide:

All

make all

Compiles the package and builds the function documentation to /man.

Test

make test

Runs the test suite.

Install

make install

Installs this package (R CMD INSTALL .).

Build

make build

Builds plant (R CMD build --no-build-vignettes).

Check

make check

Checks plant for common problems.

Clean

make clean

Deletes *.o and *.so files that were produced when compiling the package.

vignettes

make vignettes

Builds the vignettes.

pkgdown

make pkgdown

Makes the pkgdown site.

website

make website

Pushes the site to the gh-pages branch.