From 4b226343a11a0440d4e8893b84f855c4ce2fb6b1 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 19:59:14 +0100 Subject: [PATCH 1/4] use bioc release to run GHA (#99) --- .github/workflows/rworkflows.yml | 17 +++++++++++------ DESCRIPTION | 2 +- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 93db5e8..b30549b 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -6,12 +6,16 @@ name: rworkflows - main - devel - RELEASE_** + - '*' + - '!gh-pages' pull_request: branches: - master - main - devel - RELEASE_** + - '*' + - '!gh-pages' jobs: rworkflows: permissions: write-all @@ -23,17 +27,17 @@ jobs: matrix: config: - os: ubuntu-latest - bioc: devel + bioc: release r: auto - cont: ghcr.io/bioconductor/bioconductor_docker:devel + cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_21 rspm: ~ - os: macOS-latest - bioc: devel - r: latest + bioc: release + r: auto cont: ~ rspm: ~ - os: windows-latest - bioc: devel + bioc: release r: auto cont: ~ rspm: ~ @@ -53,5 +57,6 @@ jobs: run_docker: ${{ false }} DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} runner_os: ${{ runner.os }} - cache_version: cache-v1 + cache_version: cache-v2 docker_registry: ghcr.io + force_install: ${{ true }} diff --git a/DESCRIPTION b/DESCRIPTION index 86fa707..c496851 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: miaSim Type: Package -Version: 1.9.2 +Version: 1.15.1 Authors@R: c(person(given = "Yagmur", family = "Simsek", role = c("cre", "aut"), email = "yagmur.simsek.98@gmail.com"), From 4671abb6e1367eb23facdd99954c1649a9984abb Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Tue, 1 Jul 2025 12:46:10 +0100 Subject: [PATCH 2/4] #96- plotSeries (#97) Signed-off-by: Daena Rys --- .github/workflows/rworkflows.yml | 3 ++- DESCRIPTION | 2 +- R/simulateHubbellRates.R | 3 ++- man/simulateHubbellRates.Rd | 3 ++- vignettes/miaSim.Rmd | 4 +++- 5 files changed, 10 insertions(+), 5 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index ebc5a11..0575dce 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -29,7 +29,7 @@ jobs: rspm: ~ - os: macOS-latest bioc: devel - r: auto + r: latest cont: ~ rspm: ~ - os: windows-latest @@ -55,3 +55,4 @@ jobs: runner_os: ${{ runner.os }} cache_version: cache-v1 docker_registry: ghcr.io + force_install: ${{ true }} diff --git a/DESCRIPTION b/DESCRIPTION index 744d11c..c496851 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: miaSim Type: Package -Version: 1.9.1 +Version: 1.15.1 Authors@R: c(person(given = "Yagmur", family = "Simsek", role = c("cre", "aut"), email = "yagmur.simsek.98@gmail.com"), diff --git a/R/simulateHubbellRates.R b/R/simulateHubbellRates.R index 42d26b1..7a87a03 100644 --- a/R/simulateHubbellRates.R +++ b/R/simulateHubbellRates.R @@ -22,7 +22,8 @@ #' set.seed(42) #' tse <- simulateHubbellRates(n_species = 5) #' -#' miaViz::plotSeries(tse, x = "time") +#' miaViz::plotSeries(tse, assay.type = "counts", +#' time.col = "time", colour.by = "rownames") #' #' # no migration, all stochastic birth and death #' set.seed(42) diff --git a/man/simulateHubbellRates.Rd b/man/simulateHubbellRates.Rd index 11d9d38..b617b49 100644 --- a/man/simulateHubbellRates.Rd +++ b/man/simulateHubbellRates.Rd @@ -80,7 +80,8 @@ time effect is considered to determine the next event. set.seed(42) tse <- simulateHubbellRates(n_species = 5) -miaViz::plotSeries(tse, x = "time") +miaViz::plotSeries(tse, assay.type = "counts", + time.col = "time", colour.by = "rownames") # no migration, all stochastic birth and death set.seed(42) diff --git a/vignettes/miaSim.Rmd b/vignettes/miaSim.Rmd index a539193..0a270b0 100644 --- a/vignettes/miaSim.Rmd +++ b/vignettes/miaSim.Rmd @@ -193,7 +193,9 @@ For instance, to plot population density we can use the `miaViz` package: ```{r eval=FALSE, include=FALSE} library(miaViz) p1 <- plotAbundanceDensity(tse_hubbell, assay.type = "counts") -p2 <- plotSeries(tse_hubbell, x = "time") +p2 <- plotSeries(tse_hubbell, assay.type = "counts", + time.col = "time", + colour.by = "rownames") print(p1+p2) ``` From 4a274ed269f20d35d32197a639484ec6b7bc78a6 Mon Sep 17 00:00:00 2001 From: YagmurSimsekk Date: Sun, 20 Jul 2025 16:37:39 +0200 Subject: [PATCH 3/4] changes the workflow check to devel --- .github/workflows/rworkflows.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 677f98b..bad80fa 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -33,7 +33,7 @@ jobs: cont: ~ rspm: ~ - os: windows-latest - bioc: release + bioc: devel r: auto cont: ~ rspm: ~ From 250f914b40779f2207df9ba30301f5a03633e7a7 Mon Sep 17 00:00:00 2001 From: YagmurSimsekk Date: Sun, 20 Jul 2025 17:10:39 +0200 Subject: [PATCH 4/4] changing target to devel --- .github/workflows/rworkflows.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 29739cd..3a998dd 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -25,7 +25,7 @@ jobs: - os: ubuntu-latest bioc: devel r: auto - cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_21 + cont: ghcr.io/bioconductor/bioconductor_docker:devel rspm: ~ - os: macOS-latest bioc: devel