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Merged
Cristianetaniguti merged 3 commits into from
May 7, 2025
Merged

Development #28

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fe786c3
add back vcf example + fix testthat call
Cristianetaniguti May 7, 2025
1bc2403
add suggests packages for docs and checks
Cristianetaniguti May 7, 2025
393dd84
adapt actions wf
Cristianetaniguti May 7, 2025
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12 changes: 4 additions & 8 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -44,13 +44,9 @@ jobs:
any::rcmdcheck
any::covr
needs: check

- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true

- uses: codecov/codecov-action@v5
with:
token: ${{ secrets.CODECOV_TOKEN }}
slug: Breeding-Insight/BIGr

- name: Test coverage
run: |
covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
shell: Rscript {0}
7 changes: 7 additions & 0 deletions DESCRIPTION
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Expand Up @@ -57,5 +57,12 @@ Imports:
janitor,
quadprog,
tibble
Suggests:
covr,
spelling,
rmdformats,
knitr (>= 1.10),
rmarkdown,
testthat (>= 3.0.0)
Remotes:
RdMacros: Rdpack
Binary file removed inst/.DS_Store
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Binary file added inst/iris_DArT_VCF.vcf.gz
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4 changes: 4 additions & 0 deletions tests/testthat.R
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@@ -0,0 +1,4 @@
library(testthat)
library(BIGr)

test_check("BIGr")
4 changes: 2 additions & 2 deletions tests/testthat/test-check_ped.R
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Expand Up @@ -6,14 +6,14 @@ test_that("test imputation",{
ped_file <- system.file("check_ped_test.txt", package="BIGr")

#Calculations
output.list <- check_ped(ped_file, TRUE)
output.list <- check_ped(ped_file)

#Check
df_length <- length(output.list)
messy_parents <- output.list$messy_parents
missing_parents <- output.list$missing_parents

expect_true(df_length == 2)
expect_true(df_length == 4)
expect_true(all(messy_parents$id == c("grandfather2","grandfather3")))
expect_true(nrow(missing_parents) == 13)

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