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devel branch to work for GHAs #52

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devel branch to work for GHAs #52

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dd7add3
devel branch to work for GHAs
federicomarini Mar 27, 2024
c2e69b8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 27, 2024
8bcc0a5
Roxygenize
pre-commit-ci[bot] Mar 27, 2024
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8 changes: 4 additions & 4 deletions .github/workflows/pkgdown.yml
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Expand Up @@ -7,9 +7,9 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
branches: [devel]
pull_request:
branches: [main, master]
branches: [devel]
workflow_dispatch:

name: pkgdown
Expand Down Expand Up @@ -41,7 +41,7 @@ jobs:
shell: Rscript {0}

- name: Deploy to GitHub pages 🚀
if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/devel'
uses: JamesIves/[email protected]
with:
clean: false
Expand All @@ -50,7 +50,7 @@ jobs:

- name: Deploy to Netlify
uses: nwtgck/[email protected]
if: github.ref != 'refs/heads/main' && github.ref != 'refs/heads/master'
if: github.ref != 'refs/heads/main' && github.ref != 'refs/heads/devel'
with:
publish-dir: "./docs"
github-token: ${{ secrets.GITHUB_TOKEN }}
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4 changes: 2 additions & 2 deletions .github/workflows/test-coverage.yml
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Expand Up @@ -5,9 +5,9 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
branches: [devel]
pull_request:
branches: [main, master]
branches: [devel]

name: test-coverage

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4 changes: 2 additions & 2 deletions .github/workflows/test.yml
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Expand Up @@ -4,9 +4,9 @@
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
pull_request:
branches: [main, master, dev]
branches: [devel]
push:
branches: [main, master, dev]
branches: [devel]

name: R-CMD-check

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -14,7 +14,7 @@ Description: SimBu can be used to simulate bulk RNA-seq datasets with known cell
License: GPL-3 + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
Imports:
basilisk,
BiocParallel,
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3 changes: 1 addition & 2 deletions R/simulator.R
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Expand Up @@ -74,7 +74,7 @@ simulate_sample <- function(data,
if (n == 0) {
n <- 1
}
if(!is.na(seed)){
if (!is.na(seed)) {
# fix seed for random selection of cells
set.seed(seed)
}
Expand Down Expand Up @@ -437,7 +437,6 @@ simulate_bulk <- function(data,

# sample cells and generate pseudo-bulk profiles
all_samples <- BiocParallel::bplapply(seq_along(simulation_vector_list), function(i) {

simulation_vector <- simulation_vector_list[[i]]
sample <- simulate_sample(
data = data,
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13 changes: 13 additions & 0 deletions man/SimBu.Rd
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15 changes: 7 additions & 8 deletions tests/testthat/test_simulator.R
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Expand Up @@ -48,15 +48,14 @@ test_that("test RNG", {
seed <- 123
sim1 <- SimBu::simulate_bulk(data = dataset, scenario = "even", scaling_factor = "NONE", balance_even_mirror_scenario = 0, nsamples = 10, ncells = 100, run_parallel = FALSE, seed = seed)
sim2 <- SimBu::simulate_bulk(data = dataset, scenario = "even", scaling_factor = "NONE", balance_even_mirror_scenario = 0, nsamples = 10, ncells = 100, run_parallel = FALSE, seed = seed)
x1 <- Matrix::rowSums(assays(sim1$bulk)[['bulk_counts']])
x2 <- Matrix::rowSums(assays(sim2$bulk)[['bulk_counts']])
testthat::expect_equal(x1,x2)

# test that samples inside one simulation still are different
sample1 <- sim1$bulk[,1]
sample2 <- sim1$bulk[,2]
testthat::expect_false(all(assays(sample1)[['bulk_counts']] == assays(sample2)[['bulk_counts']]))
x1 <- Matrix::rowSums(assays(sim1$bulk)[["bulk_counts"]])
x2 <- Matrix::rowSums(assays(sim2$bulk)[["bulk_counts"]])
testthat::expect_equal(x1, x2)

# test that samples inside one simulation still are different
sample1 <- sim1$bulk[, 1]
sample2 <- sim1$bulk[, 2]
testthat::expect_false(all(assays(sample1)[["bulk_counts"]] == assays(sample2)[["bulk_counts"]]))
})

test_that("test different scaling factor calculations + mRNA bias removal from counts", {
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