From 15c4b53d9a8cda5435befaf8873287ade0195842 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Mon, 20 Oct 2025 18:29:55 -0700 Subject: [PATCH 1/6] enable codecov --- .github/workflows/ci.yml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a84b0112..3bdc8414 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,14 +34,14 @@ jobs: with: run-install: false - - name: Build package - run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build + # - name: Build package + # run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build - # - name: Run unit tests - # run: pixi run --environment ${{ matrix.environment }} devtools_test - # - # - name: Check unit test code coverage - # run: pixi run --environment ${{ matrix.environment }} codecov + - name: Run unit tests + run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test + + - name: Check unit test code coverage + run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov - name: Run R CMD CHECK run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck @@ -70,11 +70,11 @@ jobs: with: run-install: false - - name: Build package - run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build + # - name: Build package + # run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build - # - name: Run unit tests - # run: pixi run --environment ${{ matrix.environment }} devtools_test + - name: Run unit tests + run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test - name: Run R CMD CHECK run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck From 8c311cb4faad5c0f63d9f101fe6b3fe9945c4e13 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Mon, 20 Oct 2025 18:48:46 -0700 Subject: [PATCH 2/6] enable codecov --- .github/workflows/ci.yml | 20 +++++++++----------- tests/testthat.R | 1 + 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3bdc8414..c1a66d51 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,7 +17,7 @@ jobs: fail-fast: false matrix: environment: ["r43", "r44"] - + steps: - name: Checkout pull request branch uses: actions/checkout@v4 @@ -34,18 +34,17 @@ jobs: with: run-install: false - # - name: Build package - # run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build - - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test + - name: Run R CMD CHECK + run: + pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build + pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck + - name: Check unit test code coverage run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov - - name: Run R CMD CHECK - run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck - ci_osx-arm64: name: osx-arm64 CI runs-on: macos-14 @@ -70,11 +69,10 @@ jobs: with: run-install: false - # - name: Build package - # run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build - - name: Run unit tests run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test - name: Run R CMD CHECK - run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck + run: | + pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build + pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck diff --git a/tests/testthat.R b/tests/testthat.R index ebcc5c92..c6cafb2a 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,5 @@ library(testthat) +library(Rcpp) library(susieR) test_check("susieR") From c59cbbf526855e4fa3b997d4c76e7803c46e500e Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Tue, 21 Oct 2025 13:09:05 -0700 Subject: [PATCH 3/6] add mr.ash.alpha.mccreight --- pixi.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pixi.toml b/pixi.toml index 1a70954e..5658259c 100644 --- a/pixi.toml +++ b/pixi.toml @@ -36,6 +36,7 @@ r43 = {features = ["r44"]} "r-crayon" = "*" "r-ggplot2" = "*" "r-l0learn" = "*" +"r-mr.ash.alpha.mccreight" = "*" # Suggested dependencies (for testing and documentation) "r-curl" = "*" From 7da3704823ca9c2ed23988386d4c7d6450105ed9 Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Tue, 21 Oct 2025 13:12:18 -0700 Subject: [PATCH 4/6] add mr.ash.alpha.mccreight --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index 5658259c..a001ae23 100644 --- a/pixi.toml +++ b/pixi.toml @@ -36,7 +36,7 @@ r43 = {features = ["r44"]} "r-crayon" = "*" "r-ggplot2" = "*" "r-l0learn" = "*" -"r-mr.ash.alpha.mccreight" = "*" +"r-mr.ash.alpha_mccreight" = "*" # Suggested dependencies (for testing and documentation) "r-curl" = "*" From ac828be8d9f73f755698156ad9132cae12c25a4c Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Tue, 21 Oct 2025 13:21:14 -0700 Subject: [PATCH 5/6] fix typo --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c1a66d51..26fb0a81 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -38,7 +38,7 @@ jobs: run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test - name: Run R CMD CHECK - run: + run: | pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck From 8ff516b6f45abf19b4c289a8532091e89eeeb02c Mon Sep 17 00:00:00 2001 From: Daniel Nachun Date: Thu, 23 Oct 2025 12:12:03 -0700 Subject: [PATCH 6/6] only check coverage for newest version of R --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 26fb0a81..8235a542 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -43,6 +43,7 @@ jobs: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck - name: Check unit test code coverage + if: ${{ matrix.environment == 'r44' }} run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov ci_osx-arm64: