From aee0896a0013af87b438788130b4fe16d34d75d3 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 17 Sep 2024 15:25:48 -0600 Subject: [PATCH 01/18] updated pkgdown action --- .github/workflows/pkgdown.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 087f0b05..c9f0165d 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -11,6 +11,8 @@ on: name: pkgdown +permissions: read-all + jobs: pkgdown: runs-on: ubuntu-latest @@ -19,8 +21,10 @@ jobs: group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + permissions: + contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -39,7 +43,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages From cd9cd9b1b887ac4de85dd5fdc7e0eab13ecc976f Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 17 Sep 2024 15:29:09 -0600 Subject: [PATCH 02/18] updated test-coverage action --- .github/workflows/test-coverage.yaml | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2c5bb502..98822609 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -6,7 +6,9 @@ on: pull_request: branches: [main, master] -name: test-coverage +name: test-coverage.yaml + +permissions: read-all jobs: test-coverage: @@ -15,7 +17,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -23,28 +25,37 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::covr + extra-packages: any::covr, any::xml2 needs: coverage - name: Test coverage run: | - covr::codecov( + cov <- covr::package_coverage( quiet = FALSE, clean = FALSE, - install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") + 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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package From f9189345e6b4c7689016a8848f173d0a1c708597 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 17 Sep 2024 15:30:00 -0600 Subject: [PATCH 03/18] updated R-CMD-check action --- .github/workflows/R-CMD-check.yaml | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index e74976f5..6faed846 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,5 +1,9 @@ # 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 +# +# NOTE: This workflow is overkill for most R packages and +# check-standard.yaml is likely a better choice. +# usethis::use_github_action("check-standard") will install it. on: push: branches: [main, master] @@ -8,6 +12,8 @@ on: name: R-CMD-check +permissions: read-all + jobs: R-CMD-check: runs-on: ${{ matrix.config.os }} @@ -19,17 +25,24 @@ jobs: 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'} + # use 4.0 or 4.1 to check with rtools40's older compiler + - {os: windows-latest, r: 'oldrel-4'} + + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + - {os: ubuntu-latest, r: 'oldrel-2'} + - {os: ubuntu-latest, r: 'oldrel-3'} + - {os: ubuntu-latest, r: 'oldrel-4'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -61,3 +74,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' From 720a3a5079bfd235111589cd9151b6b498a1ea43 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 17 Sep 2024 15:30:18 -0600 Subject: [PATCH 04/18] updated README badges --- README.Rmd | 2 +- README.md | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index cfee7009..0491fe0a 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,7 +15,7 @@ knitr::opts_chunk$set( [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![R-CMD-check](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml) -[![codecov](https://codecov.io/github/poissonconsulting/embr/branch/main/graph/badge.svg?token=RSs3t4kgR0)](https://codecov.io/github/poissonconsulting/mbr) +[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/embr/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/embr) [![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) diff --git a/README.md b/README.md index 1552f95d..55c91bc4 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,8 @@ [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) [![R-CMD-check](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/embr/actions/workflows/R-CMD-check.yaml) -[![codecov](https://codecov.io/github/poissonconsulting/embr/branch/main/graph/badge.svg?token=RSs3t4kgR0)](https://codecov.io/github/poissonconsulting/mbr) +[![Codecov test +coverage](https://codecov.io/gh/poissonconsulting/embr/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/embr) [![License: MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) From 8f9bda10d1c2293310ed4b440e3422a13af4ad03 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 17 Sep 2024 15:31:34 -0600 Subject: [PATCH 05/18] updated R-CMD-check action --- .github/workflows/R-CMD-check.yaml | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 6faed846..c59e56fe 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,9 +1,5 @@ # 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 -# -# NOTE: This workflow is overkill for most R packages and -# check-standard.yaml is likely a better choice. -# usethis::use_github_action("check-standard") will install it. on: push: branches: [main, master] @@ -25,17 +21,10 @@ jobs: matrix: config: - {os: macos-latest, r: 'release'} - - {os: windows-latest, r: 'release'} - # use 4.0 or 4.1 to check with rtools40's older compiler - - {os: windows-latest, r: 'oldrel-4'} - - - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} - - {os: ubuntu-latest, r: 'oldrel-2'} - - {os: ubuntu-latest, r: 'oldrel-3'} - - {os: ubuntu-latest, r: 'oldrel-4'} + - {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 }} From 6cd9bbbb01a4bee525f8b337e585616f439cc518 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Fri, 20 Sep 2024 15:32:57 -0600 Subject: [PATCH 06/18] reverted dependency back to R >= 4.0 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3137b69a..2f5dd050 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ License: MIT + file LICENSE URL: https://github.com/poissonconsulting/embr BugReports: https://github.com/poissonconsulting/embr/issues Depends: - R (>= 4.1) + R (>= 4.0) Imports: beepr, chk, From 53d60f290ebb14557fca3584becacf4e7cb0ad7c Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Fri, 20 Sep 2024 15:43:31 -0600 Subject: [PATCH 07/18] ignore this and last commit --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 2f5dd050..3137b69a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ License: MIT + file LICENSE URL: https://github.com/poissonconsulting/embr BugReports: https://github.com/poissonconsulting/embr/issues Depends: - R (>= 4.0) + R (>= 4.1) Imports: beepr, chk, From 999dd5df915b33879ffe184173c20371a88534de Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Thu, 3 Oct 2024 16:09:06 -0600 Subject: [PATCH 08/18] updated S3 tag for `pars.character()` --- R/pars.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/pars.R b/R/pars.R index b7c6fc2a..256d1117 100644 --- a/R/pars.R +++ b/R/pars.R @@ -1,3 +1,4 @@ +#' @exportS3Method NULL pars.character <- function(x, ...) { check_dots_empty() if (is.null(x)) { From 95e62e93c0c3cc9e6ae4279aebae7044663f8ee5 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Sun, 15 Dec 2024 11:25:59 -0700 Subject: [PATCH 09/18] IGNORE: empty commit --- R/pars.R | 1 - README.md | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/R/pars.R b/R/pars.R index 256d1117..b7c6fc2a 100644 --- a/R/pars.R +++ b/R/pars.R @@ -1,4 +1,3 @@ -#' @exportS3Method NULL pars.character <- function(x, ...) { check_dots_empty() if (is.null(x)) { diff --git a/README.md b/README.md index 55c91bc4..bb97e21f 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h [![Codecov test coverage](https://codecov.io/gh/poissonconsulting/embr/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/embr) [![License: -MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) +MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/license/mit/) # embr From 1dc0150d5a784d1734c3f5a07b5790c4a0767743 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Sun, 15 Dec 2024 11:26:34 -0700 Subject: [PATCH 10/18] updated S3 methods tag --- R/pars.R | 1 + README.md | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/R/pars.R b/R/pars.R index b7c6fc2a..256d1117 100644 --- a/R/pars.R +++ b/R/pars.R @@ -1,3 +1,4 @@ +#' @exportS3Method NULL pars.character <- function(x, ...) { check_dots_empty() if (is.null(x)) { diff --git a/README.md b/README.md index bb97e21f..55c91bc4 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](h [![Codecov test coverage](https://codecov.io/gh/poissonconsulting/embr/graph/badge.svg)](https://app.codecov.io/gh/poissonconsulting/embr) [![License: -MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/license/mit/) +MIT](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) # embr From b9f96fd1e6fa574159f8a29366b1d22f198d88cb Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 12:45:03 -0700 Subject: [PATCH 11/18] updated documentation check action --- embr.Rproj | 1 + 1 file changed, 1 insertion(+) diff --git a/embr.Rproj b/embr.Rproj index 30e02be1..1c3bcdd7 100644 --- a/embr.Rproj +++ b/embr.Rproj @@ -1,4 +1,5 @@ Version: 1.0 +ProjectId: 2d8840dd-7990-4d4a-ae0f-b9292df991df RestoreWorkspace: No SaveWorkspace: No From d40f07902f32cb0cba175835736023f18911c00f Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 12:58:07 -0700 Subject: [PATCH 12/18] added macOS libomp install --- .github/workflows/R-CMD-check.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c59e56fe..07f5dad1 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -37,7 +37,9 @@ jobs: - name: Install JAGS macOS if: runner.os == 'macOS' - run: brew install jags + run: | + brew install jags + brew install libomp - name: Download JAGS Windows if: runner.os == 'Windows' From a7f67641653cd29b8e67e7c076d873bb72ecc3f2 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 13:03:20 -0700 Subject: [PATCH 13/18] link macos jags --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 07f5dad1..41e231e6 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -39,7 +39,7 @@ jobs: if: runner.os == 'macOS' run: | brew install jags - brew install libomp + brew link --overwrite jags - name: Download JAGS Windows if: runner.os == 'Windows' From 6b788bcfb47eafebd4adfea1590818679473aa1b Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 13:10:23 -0700 Subject: [PATCH 14/18] added jags location --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 41e231e6..790fbe74 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -40,6 +40,7 @@ jobs: run: | brew install jags brew link --overwrite jags + ls -l /usr/local/lib/libjags.4.dylib - name: Download JAGS Windows if: runner.os == 'Windows' From da785d66a7dfffa9e5021d48866197383bc3c4b8 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 13:11:36 -0700 Subject: [PATCH 15/18] removed jags link --- .github/workflows/R-CMD-check.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 790fbe74..a4316755 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -39,7 +39,6 @@ jobs: if: runner.os == 'macOS' run: | brew install jags - brew link --overwrite jags ls -l /usr/local/lib/libjags.4.dylib - name: Download JAGS Windows From 36b840962ebea7b5fb57baaf81d5acc8d62154e5 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 14:29:02 -0700 Subject: [PATCH 16/18] install rjags package --- .github/workflows/R-CMD-check.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a4316755..74acb995 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -37,9 +37,11 @@ jobs: - name: Install JAGS macOS if: runner.os == 'macOS' - run: | - brew install jags - ls -l /usr/local/lib/libjags.4.dylib + run: brew install jags + + - name: Install rjags on macOS + if: runner.os == 'macOS' + run: R -e "install.packages('rjags')" - name: Download JAGS Windows if: runner.os == 'Windows' From c75e074c5a24dee871bceee65fb84d3d766e5a92 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Tue, 28 Jan 2025 15:52:19 -0700 Subject: [PATCH 17/18] removed rjags install --- .github/workflows/R-CMD-check.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 74acb995..c59e56fe 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -39,10 +39,6 @@ jobs: if: runner.os == 'macOS' run: brew install jags - - name: Install rjags on macOS - if: runner.os == 'macOS' - run: R -e "install.packages('rjags')" - - name: Download JAGS Windows if: runner.os == 'Windows' run: (New-Object System.Net.WebClient).DownloadFile('https://github.com/poissonconsulting/jags-win/raw/main/JAGS-4.3.1.exe', 'C:\JAGS-4.3.1.exe') From 3f880206dd551d2597ad2baa93bf5e645c47f909 Mon Sep 17 00:00:00 2001 From: Duncan Kennedy Date: Wed, 29 Jan 2025 10:06:03 -0700 Subject: [PATCH 18/18] install jags through `.pkg` instead of Homebrew --- .github/workflows/R-CMD-check.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c59e56fe..bb700233 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -37,7 +37,10 @@ jobs: - name: Install JAGS macOS if: runner.os == 'macOS' - run: brew install jags + run: | + curl -o wjags.pkg -L0 -k --url https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Mac%20OS%20X/JAGS-4.3.2.pkg + sudo installer -pkg wjags.pkg -target / + rm wjags.pkg - name: Download JAGS Windows if: runner.os == 'Windows'