From d86968e4bc65e1e98a1023503edd11afed473b3a Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Sat, 18 Nov 2023 16:25:28 +0000
Subject: [PATCH] standard check and covr

---
 .github/workflows/R-CMD-check.yaml   | 49 +++++++++++++++++++++++++++
 .github/workflows/test-coverage.yaml | 50 ++++++++++++++++++++++++++++
 README.md                            |  4 +--
 3 files changed, 101 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .github/workflows/test-coverage.yaml

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..a3ac618
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..27d4528
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/README.md b/README.md
index da72e6c..19e5071 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,9 @@
 <!-- badges: start -->
-[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.github.io)
+[![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.org)
 [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
-[![Travis build status](https://travis-ci.org/natverse/nat.h5reg.svg?branch=master)](https://travis-ci.org/natverse/nat.h5reg)
 [![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://natverse.github.io/nat.h5reg/reference/)
 <img src="man/figures/logo.svg" align="right" height="139" /> 
+[![R-CMD-check](https://github.com/natverse/nat.h5reg/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/natverse/nat.h5reg/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 # nat.h5reg