scimesh Development Information

Required system dev dependencies

To build and check the R package, you will need these:

sudo apt install build-essential qpdf tidy pandoc libuv1-dev libharfbuzz-dev libfribidi-dev

You must also install all R packages which are suggested by scimesh, see the package DESCRIPTION.

Also make sure you have the basics, in R:

install.packages(c("devtools", "knitr", "remotes"))

And finally, install tinytex for vignette building:

install.packages("tinytex")
tinytex::install_tinytex()

Running the C++ unit tests

The C++ tests use Catch2 (amalgamated) and are in cpp_tests/:

cd cpp_tests
cmake -B build
cmake --build build
./build/scimesh_tests

Running the R unit tests

devtools::test()

Or via R CMD check:

R CMD build . && R CMD check scimesh_*.tar.gz

Generating C++ API documentation

The C++ API documentation is generated with Doxygen. The configuration is in Doxyfile at the repository root.

Prerequisites: Install Doxygen (and optionally Graphviz for diagrams):

sudo apt install doxygen graphviz

Generate locally:

# From the repository root:
doxygen Doxyfile

This produces HTML output in docs/cpp_api/html/. Open docs/cpp_api/html/index.html in a browser to view the docs.

The published API documentation is available at: https://dfsp-spirit.github.io/scimesh/

It is built and deployed automatically via GitHub Actions (.github/workflows/docs.yml) on every push to main.

Making a release

• bump version in all of these files:
  • DESCRIPTION (R package version)
  • CMakeLists.txt — the project(scimesh VERSION ...) line (C++ version, single source of truth)
    • The C++ header version.h is auto-generated by CMake from this value — no need to edit it manually.
  • Doxyfile — the PROJECT_NUMBER field (version shown in published C++ API docs)
• make sure new additions have proper doc strings and tests, then build/refresh all docs. In R, run devtools::document() to re-generate docs.
• REQUIRED: Re-run Doxygen so the published C++ API docs pick up the new version in PROJECT_NUMBER:

  doxygen Doxyfile

  Do not skip this step — the online API documentation at https://dfsp-spirit.github.io/scimesh/ will show a stale or empty version otherwise.

• run all tests and make sure they are green:

  C++ unit tests:

  cd cpp_tests && cmake -B build && cmake --build build && ./build/scimesh_tests

  R unit tests:

  devtools::test()

• make sure to run all examples:

  ./examples/cpp/run_all_cpp.sh
  ./examples/R/run_all_R.sh

• run R CMD build . to build new package version
• run R CMD check scimesh_0.1.0.tar.gz, or whatever version you are testing. This must pass without errors/warnings/notes.
• run the even stricter R CMD check scimesh_0.1.0.tar.gz --as-cran and see what you can do to get as little notes and warnings as possible. Stuff in downstream code is not our problem though, but you may have to discuss that with CRAN team on submit, hf.
• test package on winbuilder
• submit to CRAN when green
• when it's accepted at CRAN, tag it in git and publish release on github, with artefact attached