Expand dev instructions to install the dev tools #114

Author: gregorgorjanc

.github/workflows/test-coverage.yaml

@@ -57,7 +57,7 @@ jobs:
           # Fail if error if not on PR, or if on PR and token is given
           # fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false
-          files: RcppTskit/cobertura.xml
+          files: RcppTskit/cobertura.xml # generated during the process
           plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}

README.md

@@ -128,115 +128,4 @@ vignette("RcppTskit_intro")
 
 ## Development
 
-### Code of Conduct
-
-Please note that the `RcppTskit` project is released with a
-[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html).
-By contributing to this project, you agree to abide by its terms.
-
-### Clone
-
-First clone the repository and step into the directory:
-
-```
-git clone https://github.com/HighlanderLab/RcppTskit.git
-cd RcppTskit
-```
-
-### Pre-commit install
-
-We use [pre-commit](https://pre-commit.com) hooks to ensure code quality.
-Specifically, we use:
-* [air](https://github.com/posit-dev/air) to format `R` code,
-* [jarl](https://github.com/etiennebacher/jarl) to lint `R` code,
-* [clang-format](https://clang.llvm.org/docs/ClangFormat.html) to format `C/C++` code, and
-* [clang-tidy](https://clang.llvm.org/extra/clang-tidy/) to lint `C/C++` code.
-
-To install the hooks, run:
-
-```
-pre-commit install --install-hooks
-pre-commit install --hook-type pre-push
-```
-
-Run these once per clone.
-This enables automatic checks on `commit` and `push`.
-
-### tskit
-
-If you plan to update `tskit`, follow instructions in `extern/README.md`.
-
-### RcppTskit
-
-Then open `RcppTskit` package directory in your favourite `R` editor
-(Positron, RStudio, text-editor-of-your-choice, etc.) and implement your changes.
-
-You should routinely `R CMD check` your changes (in `R`):
-
-```
-# Note that the RcppTskit R package is in the RcppTskit sub-directory
-setwd("path/to/RcppTskit/RcppTskit")
-
-# Check
-devtools::check()
-
-# Install
-devtools::install()
-
-# Test
-devtools::test()
-
-# Test coverage
-cov <- covr::package_coverage(clean = TRUE)
-covr::report(cov)
-```
-
-Alternatively check your changes from the command line:
-
-```
-# Note that the RcppTskit package is in the RcppTskit sub-directory
-cd path/to/RcppTskit/RcppTskit
-
-# Check
-R CMD build RcppTskit
-R CMD check RcppTskit_*.tar.gz
-
-# Install
-R CMD INSTALL RcppTskit_*.tar.gz
-```
-
-On Windows, replace `tar.gz` with `zip`.
-
-### Pre-commit run
-
-When committing your changes,
-`pre-commit` hooks should kick-in automatically
-to ensure code quality.
-Manually, you can run them using:
-
-```
-pre-commit autoupdate # to update the hooks
-pre-commit run # on changed files
-pre-commit run --all-files # on all files
-pre-commit run <hook_id> # just a specific hook
-pre-commit run <hook_id> --all-files # ... on all files
-# see also --hook-stage option
-```
-
-### Continuous integration
-
-We use Github Actions to run continuous integration (CI) checks
-on each push and pull request.
-Specifically, we run:
-* [R CMD check](.github/workflows/R-CMD-check.yaml) on multiple platforms
-  (see curent status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/R-CMD-check.yaml)),
-* [documentation generation](.github/workflows/document.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/document.yaml)),
-* [pre-commit hooks](.github/workflows/pre-commit.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/pre-commit.yaml)), and
-* [test coverage](.github/workflows/test-coverage.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/test-coverage.yaml)).
-
-[R universe for RcppTskit](https://highlanderlab.r-universe.dev/RcppTskit)
-also provides another set of checks - see [here](https://highlanderlab.r-universe.dev/RcppTskit#checktable).
-These are provided after new code is pushed or merged into this repository.
+See [README_DEVEL.md](README_DEVEL.md)