Pkg dev tools

Author: gregorgorjanc

README.md

@@ -18,6 +18,12 @@ See more details on the state of the tree sequence ecosystem and aims for
 
 ## 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)
+
+  [![Codecov test coverage](https://codecov.io/gh/HighlanderLab/tskitr/graph/badge.svg)](https://app.codecov.io/gh/HighlanderLab/tskitr)
+<!-- badges: end -->
+
 TODO: Add R package badges (build status, CRAN version, etc.) to README.md #1
       https://github.com/HighlanderLab/tskitr/issues/1
 

tskitr/.Rbuildignore

@@ -2,7 +2,10 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^[.]?air[.]toml$
+^[.]?jarl[.]toml$
 ^test\.trees$
 ^.*\.o$
 ^.*\.so$
 ^\.github$
+pkg_dev_notes.md
+^codecov\.yml$

tskitr/.github/workflows/jarl-check.yaml

@@ -0,0 +1,23 @@
+# Workflow derived from https://github.com/posit-dev/setup-air/tree/main/examples
+
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+
+name: jarl-check.yaml
+
+permissions: read-all
+
+jobs:
+  jarl-check:
+    name: jarl-check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install
+        uses: etiennebacher/setup-jarl@v0.1.0
+
+      - name: Check
+        run: jarl check --fix

tskitr/codecov.yml

@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true

tskitr/jarl.toml

@@ -0,0 +1,6 @@
+[lint]
+# Set the default assignment operator to report cases where "=" is used.
+assignment = "<-"
+# Use the default set of excluded files (mostly files that are automatically
+# generated by other tools).
+default-exclude = true

tskitr/src/tskitr_minimal.cpp

@@ -37,6 +37,7 @@ Rcpp::IntegerVector tskit_version() {
         Rcpp::_["patch"] = TSK_VERSION_PATCH);
 }
 
+// # nocov start
 // TODO: Decide what tskit functionality we want to expose as R functions #21
 //       https://github.com/HighlanderLab/tskitr/issues/21
 int table_collection_num_nodes_zero_check() {
@@ -50,6 +51,7 @@ int table_collection_num_nodes_zero_check() {
     tsk_table_collection_free(&tables);
     return n;
 }
+// # nocov end
 
 // Finaliser function to free tsk_treeseq_t when it is garbage collected
 //
@@ -282,6 +284,7 @@ Rcpp::String ts_time_units(SEXP ts) {
     return Rcpp::String(std::string(p, p + n));
 }
 
+// # nocov start
 // This is how we would get metadata, but it will be raw bytes,
 // so would have to work with schema and codes ...
 // ts_file <- system.file("examples/test.trees", package = "tskitr")
@@ -294,6 +297,7 @@ Rcpp::String ts_metadata(SEXP ts) {
     tsk_size_t n = tsk_treeseq_get_metadata_length(xptr);
     return Rcpp::String(std::string(p, p + n));
 }
+// # nocov end
 
 //' @name ts_metadata_length
 //' @title Get the length of metadata in a tree sequence and its tables