Merge pull request #50 from natverse/dev/actions

.Rbuildignore

@@ -6,3 +6,4 @@
 ^\.github$
 ^sample$
 ^pkgdown$
+^codecov\.yml$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,53 @@
+# 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.yaml
+
+permissions: read-all
+
+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
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.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]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# 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.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - 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, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 inst/doc
+docs

DESCRIPTION

@@ -11,7 +11,7 @@ Authors@R: c(
     )
 Description: Extends package 'nat' (NeuroAnatomy Toolbox) by providing a
     collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).
-URL: https://natverse.org/nat.nblast/
+URL: https://natverse.org/nat.nblast/, http://natverse.org/nat.nblast/
 BugReports: https://github.com/natverse/nat.nblast/issues
 Depends:
     R (>= 2.15.1),
@@ -33,6 +33,6 @@ Suggests:
 License: GPL-3
 LazyData: yes
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Language: en-GB
 Encoding: UTF-8

R/nat.nblast.r

@@ -89,10 +89,9 @@
 #'
 #' @name nat.nblast-package
 #' @aliases nat.nblast
-#' @docType package
 #' @import methods
 #' @keywords package
 #' @seealso \code{\link{nblast}}, \code{\link{smat.fcwb}},
 #'   \code{\link{nhclust}}, \code{\link{sub_dist_mat}},
 #'   \code{\link{sub_score_mat}}, \code{\link{create_scoringmatrix}}
-NULL
+"_PACKAGE"

README.md

@@ -3,8 +3,10 @@
 [![natverse](https://img.shields.io/badge/natverse-Part%20of%20the%20natverse-a241b6)](https://natverse.org/)
 [![Release Version](https://img.shields.io/github/release/natverse/nat.nblast.svg)](https://github.com/natverse/nat.nblast/releases/latest) 
 [![CRAN status](https://www.r-pkg.org/badges/version/nat.nblast)](https://CRAN.R-project.org/package=nat.nblast)
-[![Build Status](https://travis-ci.org/natverse/nat.nblast.svg?branch=master)](https://app.travis-ci.com/natverse/nat.nblast)
 [![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://natverse.org/nat.nblast/reference/)
+[![R-CMD-check](https://github.com/natverse/nat.nblast/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/natverse/nat.nblast/actions/workflows/R-CMD-check.yaml)
+[![codecov](https://codecov.io/gh/natverse/nat.nblast/graph/badge.svg?token=VqX3HEdELo)](https://codecov.io/gh/natverse/nat.nblast)
+
 <!-- badges: end -->
 
 **nat.nblast** is part of the [NeuroAnatomy Toolbox](https://jefferislab.github.io/)

_pkgdown.yml

@@ -1,3 +1,6 @@
+url: https://natverse.org/nat.nblast/
+template:
+  bootstrap: 5
 navbar:
   structure:
     left:
@@ -80,4 +83,3 @@ reference:
   - '['
   - fill_in_sparse_score_mat
   - fill_pairs_sparse_score_mat
-

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