Fixes #3

Author: gregorgorjanc

.github/workflows/R-CMD-check.yaml

@@ -42,12 +42,12 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          working-directory: tskitr
+          working-directory: RcppTskit
           extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
-          working-directory: tskitr
+          working-directory: RcppTskit
           upload-snapshots: true
           build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/format-check.yaml

@@ -20,4 +20,4 @@ jobs:
         uses: posit-dev/setup-air@v1
 
       - name: Check
-        run: cd tskitr; air format --check .
+        run: cd RcppTskit; air format --check .

.github/workflows/format-suggest.yaml

@@ -36,7 +36,7 @@ jobs:
         uses: posit-dev/setup-air@v1
 
       - name: Format
-        run: cd tskitr; air format .
+        run: cd RcppTskit; air format .
 
       - name: Suggest
         uses: reviewdog/action-suggester@v1

.github/workflows/jarl-check.yaml

@@ -20,4 +20,4 @@ jobs:
         uses: etiennebacher/setup-jarl@v0.1.0
 
       - name: Check
-        run: cd tskitr; jarl check R/*.R
+        run: cd RcppTskit; jarl check R/*.R

.github/workflows/test-coverage.yaml

@@ -36,12 +36,12 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          working-directory: tskitr
+          working-directory: RcppTskit
           extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
-        working-directory: tskitr
+        working-directory: RcppTskit
         run: |
           cov <- covr::package_coverage(
             quiet = FALSE,
@@ -57,8 +57,8 @@ 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
-          config: tskitr/codecov.yaml
-          files: tskitr/cobertura.xml
+          config: RcppTskit/codecov.yaml
+          files: RcppTskit/cobertura.xml
           plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -4,12 +4,12 @@
 .RData
 .Ruserdata
 .vscode
-tskitr/src/*.o
-tskitr/src/tskit/*.o
-tskitr/src/*.so
-tskitr/src/*.dll*
-tskitr/src/Makevars
-tskitr/src/Makevars.win
+RcppTskit/src/*.o
+RcppTskit/src/tskit/*.o
+RcppTskit/src/*.so
+RcppTskit/src/*.dll*
+RcppTskit/src/Makevars
+RcppTskit/src/Makevars.win
 test.trees
 .DS_Store
 *.html

README.md

@@ -1,4 +1,4 @@
-# tskitr: R access to the `tskit` C API
+# RcppTskit: R access to the `tskit` C API
 
 ## Overview
 
@@ -7,15 +7,15 @@ recombination graphs (ARGs) using succinct tree sequence encoding.
 See https://tskit.dev for project news, documentation, and tutorials.
 Tskit provides Python, C, and Rust APIs. The Python API can be called from R
 via the `reticulate` R package to seamlessly load and analyse a tree sequence,
-as described at https://tskit.dev/tutorials/tskitr.html.
-`tskitr` provides R access to the `tskit` C API for use cases where the
+as described at https://tskit.dev/tutorials/RcppTskit.html.
+`RcppTskit` provides R access to the `tskit` C API for use cases where the
 `reticulate` approach is not optimal. For example, for high-performance and
-low-level work with tree sequences. Currently, `tskitr` provides a very limited
+low-level work with tree sequences. Currently, `RcppTskit` provides a very limited
 number of R functions due to the availability of extensive Python API and
 the `reticulate` approach.
 
 See more details on the state of the tree sequence ecosystem and aims for
-`tskitr` in [tskitr/inst/STATE_and_AIMS.md](tskitr/inst/STATE_and_AIMS.md),
+`RcppTskit` in [RcppTskit/inst/STATE_and_AIMS.md](RcppTskit/inst/STATE_and_AIMS.md),
 including examples on how to use it on its own or to develop new R packages.
 
 TODO: Think how to best point to use cases. Probably best to point to vignette!?
@@ -24,34 +24,34 @@ TODO: Think how to best point to use cases. Probably best to point to vignette!?
 ## Status
 
 <!-- badges: start -->
-  [![R-CMD-check](https://github.com/HighlanderLab/tskitr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/HighlanderLab/tskitr/actions/workflows/R-CMD-check.yaml)
+  [![R-CMD-check](https://github.com/HighlanderLab/RcppTskit/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/HighlanderLab/RcppTskit/actions/workflows/R-CMD-check.yaml)
 
-  [![Codecov test coverage](https://codecov.io/gh/HighlanderLab/tskitr/graph/badge.svg)](https://app.codecov.io/gh/HighlanderLab/tskitr)
+  [![Codecov test coverage](https://codecov.io/gh/HighlanderLab/RcppTskit/graph/badge.svg)](https://app.codecov.io/gh/HighlanderLab/RcppTskit)
 <!-- badges: end -->
 
 TODO: Add R package badges (build status, CRAN version, etc.) to README.md #1
-      https://github.com/HighlanderLab/tskitr/issues/1
+      https://github.com/HighlanderLab/RcppTskit/issues/1
 
 ## Contents
 
-  * `extern` - Git submodule for `tskit` and instructions on obtaining the latest version and copying the `tskit` C code into `tskitr` directory. `extern` is saved outside of the `tskitr` directory because `R CMD CHECK` complains otherwise.
+  * `extern` - Git submodule for `tskit` and instructions on obtaining the latest version and copying the `tskit` C code into `RcppTskit` directory. `extern` is saved outside of the `RcppTskit` directory because `R CMD CHECK` complains otherwise.
 
-  * `tskitr` - R package `tskitr`.
+  * `RcppTskit` - R package `RcppTskit`.
 
 ## License
 
   * See `extern/LICENSE` for `tskit`.
 
-  * See `tskitr/DESCRIPTION` and `tskitr/LICENSE` for `tskitr`.
+  * See `RcppTskit/DESCRIPTION` and `RcppTskit/LICENSE` for `RcppTskit`.
 
 ## Installation
 
 To install the published release from CRAN use:
 
 ```
 # TODO: Publish on CRAN #14
-#       https://github.com/HighlanderLab/tskitr/issues/14
-# install.packages("tskitr")
+#       https://github.com/HighlanderLab/RcppTskit/issues/14
+# install.packages("RcppTskit")
 ```
 
 To install a published release or specific branches from Github use the
@@ -66,33 +66,33 @@ https://mac.r-project.org/tools for macOS tools.
 
 # Release (TODO)
 # TODO: Tag a release #15
-#       https://github.com/HighlanderLab/tskitr/issues/15
-# remotes::install_github("HighlanderLab/tskitr/tskitr")
+#       https://github.com/HighlanderLab/RcppTskit/issues/15
+# remotes::install_github("HighlanderLab/RcppTskit/RcppTskit")
 
 # Main branch
-remotes::install_github("HighlanderLab/tskitr/tskitr")
+remotes::install_github("HighlanderLab/RcppTskit/RcppTskit")
 
 # Development branch
 # TODO: Create a devel branch #16
-#       https://github.com/HighlanderLab/tskitr/issues/16
-# remotes::install_github("HighlanderLab/tskitr/tskitr@devel")
+#       https://github.com/HighlanderLab/RcppTskit/issues/16
+# remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@devel")
 ```
 
 ## Development
 
 First clone the repository:
 
 ```
-git clone https://github.com/HighlanderLab/tskitr.git
+git clone https://github.com/HighlanderLab/RcppTskit.git
 ```
 
 If you plan to update `tskit`, follow instructions in `extern/README.md`.
 
-Then open `tskitr` package directory in your favourite R IDE (Positron, RStudio, text-editor-of-your-choice, etc.), implement your changes and run (in R):
+Then open `RcppTskit` package directory in your favourite R IDE (Positron, RStudio, text-editor-of-your-choice, etc.), implement your changes and run (in R):
 
 ```
-# Note that the tskitr package is in the tskitr sub-directory
-setwd("path/to/tskitr/tskitr")
+# Note that the RcppTskit R package is in the RcppTskit sub-directory
+setwd("path/to/RcppTskit/RcppTskit")
 
 # Run checks of your changes, documentation, etc.
 devtools::check()
@@ -104,15 +104,15 @@ devtools::install()
 Alternatively you can check and install from command line:
 
 ```
-# Note that the tskitr package is in the tskitr sub-directory
-cd path/to/tskitr
+# Note that the RcppTskit package is in the RcppTskit sub-directory
+cd path/to/RcppTskit
 
 # Run checks of your changes, documentation, etc.
-R CMD build tskitr
-R CMD check tskitr_*.tar.gz
+R CMD build RcppTskit
+R CMD check RcppTskit_*.tar.gz
 
 # Install the package
-R CMD INSTALL tskitr_*.tar.gz
+R CMD INSTALL RcppTskit_*.tar.gz
 ```
 
 On Windows, replace `tar.gz` with `zip`.