Fix jarl complaints about capture.output(p<-ts$print())

.github/workflows/pre-commit.yaml

@@ -0,0 +1,45 @@
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+
+name: pre-commit.yaml
+
+permissions: read-all
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install Rcpp
+        run: Rscript -e 'install.packages("Rcpp")'
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install --yes clang-format clang-tidy
+
+      - name: Install Air
+        uses: posit-dev/setup-air@v1
+
+      - name: Install Jarl
+        run: |
+          curl --proto '=https' --tlsv1.2 -LsSf \
+            https://github.com/etiennebacher/jarl/releases/latest/download/jarl-installer.sh | sh
+          echo "$HOME/.local/bin" >> "$GITHUB_PATH"
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: --all-files --show-diff-on-failure

README.md

@@ -197,11 +197,13 @@ 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)),
-* [covr test coverage](.github/workflows/covr.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/test-coverage.yaml)), and
-* [Roxygen documentation generation](.github/workflows/document.yaml)
-  (see current status [here](https://github.com/HighlanderLab/RcppTskit/actions/workflows/document.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 once the code is merged into this repository.
+These are provided after new code is pushed or merged into this repository.

RcppTskit/tests/testthat/test_TableCollection.R

@@ -131,6 +131,7 @@ test_that("TableCollection and TreeSequence round-trip works", {
 
   tc <- ts$dump_tables()
   expect_true(is(tc, "TableCollection"))
+  # jarl-ignore implicit_assignment:  it's just a test
   tmp <- capture.output(p <- tc$print())
   expect_equal(
     p,
@@ -177,7 +178,9 @@ test_that("TableCollection and TreeSequence round-trip works", {
 
   ts2 <- tc$tree_sequence()
   expect_true(is(ts2, "TreeSequence"))
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(ts_print <- ts$print())
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(ts2_print <- ts2$print())
   expect_equal(ts_print, ts2_print)
 

RcppTskit/tests/testthat/test_load_summary_and_dump.R

@@ -13,6 +13,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   )
   expect_no_error(tc_load(ts_file, skip_tables = TRUE))
   check_empty_tables <- function(ts) {
+    # jarl-ignore implicit_assignment: it's just a test
     tmp <- capture.output(p <- ts$print())
     expect_true(all(p$tables$number == 0))
   }
@@ -50,6 +51,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   )
   expect_no_error(tc_load(ts_file, skip_tables = TRUE))
   check_empty_tables <- function(tc) {
+    # jarl-ignore implicit_assignment:  it's just a test
     tmp <- capture.output(p <- tc$print())
     expect_true(all(p$tables$number == 0))
   }
@@ -225,6 +227,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
     regexp = "ts must be an object of externalptr class!"
   )
   p_ptr <- ts_ptr_print(ts_ptr)
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(p <- ts$print())
   expect_equal(
     p,
@@ -276,6 +279,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
     regexp = "tc must be an object of externalptr class!"
   )
   p_ptr <- tc_ptr_print(tc_ptr)
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(p <- tc$print())
   expect_equal(
     p,
@@ -549,6 +553,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   expect_equal(m_ptr, m)
 
   p_ptr <- ts_ptr_print(ts_ptr)
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(p <- ts$print())
   expect_equal(
     p_ptr,
@@ -630,6 +635,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   expect_equal(m_ptr_tc, m_ptr_ts)
 
   p_ptr <- tc_ptr_print(tc_ptr)
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(p <- tc$print())
   expect_equal(
     p_ptr,

RcppTskit/tests/testthat/test_misc.R

@@ -11,13 +11,18 @@ test_that("tskit_version() works", {
 })
 
 test_that("tsk_bug_assert() works", {
+  # jarl-ignore internal_function:  it's just a test
   expect_error(RcppTskit:::test_tsk_bug_assert_c())
+  # jarl-ignore internal_function:  it's just a test
   expect_error(RcppTskit:::test_tsk_bug_assert_cpp())
 })
 
 test_that("tsk_trace_error() works", {
   t <- "You have to compile with -DTSK_TRACE_ERRORS to run these tests. See src/Makevars.in."
+  # jarl-ignore internal_function:  it's just a test
   skip_if_not(RcppTskit:::tsk_trace_errors_defined(), t)
+  # jarl-ignore internal_function:  it's just a test
   expect_warning(RcppTskit:::test_tsk_trace_error_c())
+  # jarl-ignore internal_function:  it's just a test
   expect_warning(RcppTskit:::test_tsk_trace_error_cpp())
 })

RcppTskit/tests/testthat/test_r_to_py_and_py_to_r.R

@@ -142,7 +142,9 @@ test_that("ts_r_to_py() and ts_py_to_r() work", {
   expect_equal(length(ts2_py$tables$mutations$metadata), m2$mutations)
 
   expect_true(is(ts2_r, "TreeSequence"))
+  # jarl-ignore implicit_assignment:  it's just a test
   tmp <- capture.output(ts2_r_print <- ts2_r$print())
+  # jarl-ignore implicit_assignment:  it's just a test
   tmp <- capture.output(ts_ptr2_r_print <- ts_ptr_print(ts_ptr2_r))
   expect_equal(ts2_r_print, ts_ptr2_r_print)
 })
@@ -264,7 +266,9 @@ test_that("tc_r_to_py() and tc_py_to_r() work", {
   expect_equal(length(tc2_py$mutations$metadata), m2$mutations)
 
   expect_true(is(tc2_r, "TableCollection"))
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(tc2_r_print <- tc2_r$print())
+  # jarl-ignore implicit_assignment: it's just a test
   tmp <- capture.output(tc_ptr2_r <- tc_ptr_print(tc_ptr2_r))
   expect_equal(tc2_r_print, tc_ptr2_r)
 })