From b462c8ef0885a3f9829394d6e4cd0052451c6d6b Mon Sep 17 00:00:00 2001 From: Alex Chubaty Date: Thu, 6 Jun 2024 08:23:07 -0600 Subject: [PATCH 1/4] update all GHA workflows to use devel reproducible with 7d574693f9dac94fbebd4302cd4c17b115796f39 --- .github/workflows/R-CMD-check.yaml | 1 + .github/workflows/revdeps.yaml | 7 +++++++ .github/workflows/test-coverage.yaml | 1 + .github/workflows/update-citation-cff.yaml | 1 + 4 files changed, 10 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 30fa679f..1f4a7d95 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -63,6 +63,7 @@ jobs: - name: Install additional package dependencies run: | + pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} diff --git a/.github/workflows/revdeps.yaml b/.github/workflows/revdeps.yaml index 8943ba6e..620a3405 100644 --- a/.github/workflows/revdeps.yaml +++ b/.github/workflows/revdeps.yaml @@ -44,6 +44,13 @@ jobs: r-version: ${{ matrix.config.r }} use-public-rspm: false + - name: Install additional package dependencies + run: | + pak::pkg_install("PredictiveEcology/reproducible@development") + pak::pkg_install("ropensci/NLMR") + pak::pkg_install("s-u/fastshp") + shell: Rscript {0} + - uses: PredictiveEcology/actions/revdeps-check@v0.1 with: quiet: false diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 9ec299c0..a3c8a390 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -39,6 +39,7 @@ jobs: - name: Install additional package dependencies run: | + pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml index 5507c2ec..584490ae 100644 --- a/.github/workflows/update-citation-cff.yaml +++ b/.github/workflows/update-citation-cff.yaml @@ -44,6 +44,7 @@ jobs: - name: Install additional package dependencies run: | + pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} From 240158ff027914370f8910bc3649b6d36328585d Mon Sep 17 00:00:00 2001 From: Alex Chubaty Date: Thu, 6 Jun 2024 13:04:11 -0600 Subject: [PATCH 2/4] GHA: install devel reproducible sooner --- .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/pkgdown.yaml | 2 +- .github/workflows/test-coverage.yaml | 2 +- .github/workflows/update-citation-cff.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1f4a7d95..f31a8fa3 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,13 +57,13 @@ jobs: with: extra-packages: | any::rcmdcheck + PredictiveEcology/reproducible@development fastshp=?ignore NLMR=?ignore needs: check - name: Install additional package dependencies run: | - pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index fa6a0edf..e6bb5d3e 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -36,13 +36,13 @@ jobs: extra-packages: | any::pkgdown local::. + PredictiveEcology/reproducible@development fastshp=?ignore NLMR=?ignore needs: website - name: Install additional package dependencies run: | - pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index a3c8a390..7c57db16 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -34,12 +34,12 @@ jobs: with: extra-packages: | any::covr + PredictiveEcology/reproducible@development fastshp=?ignore NLMR=?ignore - name: Install additional package dependencies run: | - pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml index 584490ae..7676f1b4 100644 --- a/.github/workflows/update-citation-cff.yaml +++ b/.github/workflows/update-citation-cff.yaml @@ -39,12 +39,12 @@ jobs: extra-packages: | any::cffr any::V8 + PredictiveEcology/reproducible@development fastshp=?ignore NLMR=?ignore - name: Install additional package dependencies run: | - pak::pkg_install("PredictiveEcology/reproducible@development") pak::pkg_install("ropensci/NLMR") pak::pkg_install("s-u/fastshp") shell: Rscript {0} From 32fe05342bad5b7b4afc886e8f5c61c615b0c870 Mon Sep 17 00:00:00 2001 From: Alex Chubaty Date: Thu, 6 Jun 2024 13:51:31 -0600 Subject: [PATCH 3/4] use main (not master) in all GHA workflows --- .github/workflows/R-CMD-check.yaml | 4 ++-- .github/workflows/pkgdown.yaml | 4 ++-- .github/workflows/revdeps.yaml | 2 +- .github/workflows/test-coverage.yaml | 4 ++-- .github/workflows/update-citation-cff.yaml | 2 +- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index f31a8fa3..3afb0a28 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,11 +1,11 @@ on: push: branches: - - master + - main - development pull_request: branches: - - master + - main - development name: R-CMD-check diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index e6bb5d3e..a40187f9 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -2,9 +2,9 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: - branches: [main, master] + branches: main pull_request: - branches: [main, master] + branches: main release: types: [published] workflow_dispatch: diff --git a/.github/workflows/revdeps.yaml b/.github/workflows/revdeps.yaml index 620a3405..e522afcf 100644 --- a/.github/workflows/revdeps.yaml +++ b/.github/workflows/revdeps.yaml @@ -4,7 +4,7 @@ ## Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: pull_request: - branches: [main, master, development] + branches: [main, development] schedule: - cron: '23 23 * * 0 ' diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 7c57db16..aa1c9e78 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,11 +1,11 @@ on: push: branches: - - master + - main - development pull_request: branches: - - master + - main - development name: test-coverage diff --git a/.github/workflows/update-citation-cff.yaml b/.github/workflows/update-citation-cff.yaml index 7676f1b4..aa132fb7 100644 --- a/.github/workflows/update-citation-cff.yaml +++ b/.github/workflows/update-citation-cff.yaml @@ -8,7 +8,7 @@ on: release: types: [published] push: - branches: [master, main] + branches: main paths: - DESCRIPTION - inst/CITATION From 45bc4a9904434128a3236d62147c321860f19b84 Mon Sep 17 00:00:00 2001 From: Alex Chubaty Date: Thu, 6 Jun 2024 20:34:21 -0600 Subject: [PATCH 4/4] [v2.1.3] fix a failing test for windows - deal with windows short paths; - fix docs for `FilterRecursive`; - add `lme4` to Suggests for `loadSimList` test; --- DESCRIPTION | 3 ++- NEWS.md | 5 +++++ R/misc-methods.R | 2 +- man/FilterRecursive.Rd | 2 +- tests/testthat/test-load.R | 1 + tests/testthat/test-simList.R | 4 ++-- 6 files changed, 12 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 09c9e667..700377ad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,7 +15,7 @@ URL: https://spades-core.predictiveecology.org/, https://github.com/PredictiveEcology/SpaDES.core Date: 2024-06-06 -Version: 2.1.2 +Version: 2.1.3 Authors@R: c( person("Alex M", "Chubaty", , "achubaty@for-cast.ca", role = c("aut"), comment = c(ORCID = "0000-0001-7146-8135")), @@ -59,6 +59,7 @@ Suggests: httr, knitr, lattice, + lme4, logging, magrittr, NLMR (>= 1.1.1), diff --git a/NEWS.md b/NEWS.md index af31221d..8e66a390 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# SpaDES.core 2.1.3 + +* fix issue with Windows short paths in tests; +* improved documentation; + # SpaDES.core 2.1.2 * fixed bug in `restartSpades()`; diff --git a/R/misc-methods.R b/R/misc-methods.R index 8a721ad3..d791a076 100644 --- a/R/misc-methods.R +++ b/R/misc-methods.R @@ -414,7 +414,7 @@ moduleCodeFiles <- function(paths, modules) { } #' Recursively Filter a list -#' @inheritParams Filter +#' @inheritParams funprog #' @keywords internal FilterRecursive <- function(f, x) { Filter(f, x) |> diff --git a/man/FilterRecursive.Rd b/man/FilterRecursive.Rd index a77d530b..eb34e666 100644 --- a/man/FilterRecursive.Rd +++ b/man/FilterRecursive.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/helpers.R +% Please edit documentation in R/misc-methods.R \name{FilterRecursive} \alias{FilterRecursive} \title{Recursively Filter a list} diff --git a/tests/testthat/test-load.R b/tests/testthat/test-load.R index 6056ab83..136266e2 100644 --- a/tests/testthat/test-load.R +++ b/tests/testthat/test-load.R @@ -461,6 +461,7 @@ test_that("Filenames for simList", { test_that("loadSimList handles symlinked files sensibly", { skip_on_cran() skip_on_ci() + skip_if_not_installed("lme4") prjDir <- "~/GitHub/BC_HRV" diff --git a/tests/testthat/test-simList.R b/tests/testthat/test-simList.R index 7650afa6..c8cde333 100644 --- a/tests/testthat/test-simList.R +++ b/tests/testthat/test-simList.R @@ -40,8 +40,8 @@ test_that("simList object initializes correctly (1)", { rm(w) ## test path accessors - expect_identical(figurePath(mySim), normPath(file.path(outputPath(mySim), "figures"))) - expect_identical(logPath(mySim), normPath(file.path(outputPath(mySim), "log"))) + expect_identical(normPath(figurePath(mySim)), normPath(file.path(outputPath(mySim), "figures"))) + expect_identical(normPath(logPath(mySim)), normPath(file.path(outputPath(mySim), "log"))) ### SLOT .xData expect_is(envir(mySim), "environment")