simple cleanup

.github/workflows/ci.yml

@@ -1,7 +1,7 @@
 name: Continuous Integration
 
 on:
-  pull_request_target:
+  pull_request:
     paths-ignore:
       - .github/*
       - .gitignore
@@ -46,39 +46,6 @@ jobs:
       - name: Check unit test code coverage
         run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov
 
-  ci_osx-64:
-    name: osx-64 CI
-    runs-on: macos-13
-    strategy:
-      fail-fast: false
-      matrix:
-        environment: ["r43", "r44"]
-
-    steps:
-      - name: Checkout pull request branch
-        uses: actions/checkout@v5
-        with:
-          fetch-depth: 0
-
-      - name: Create TOML from recipe
-        run: |
-          .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE}
-          mkdir /tmp/pixi
-          mv ${GITHUB_WORKSPACE}/pixi.toml /tmp/pixi
-
-      - name: Setup pixi
-        uses: prefix-dev/setup-pixi@v0.9.2
-        with:
-          manifest-path: /tmp/pixi/pixi.toml
-
-      - 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
-
   ci_osx-arm64:
     name: osx-arm64 CI
     runs-on: macos-14

vignettes/ColocBoost_Wrapper_Pipeline.Rmd

@@ -63,7 +63,7 @@ outputs:
 
 The following example demonstrates how to set up input data with 3 phenotypes and 2 cohorts. The first cohort has 2 phenotypes and the second cohort has 1 phenotype. The first phenotype has 2 genes and the second phenotype has 1 gene.
 
-```{r, data-loader-individual}
+```{r, data-loader-individual, eval = FALSE}
 # Example of loading individual-level data
 region = "chr1:1000000-2000000"
 genotype_list = c("plink_cohort1.1", "plink_cohort1.2")
@@ -127,7 +127,7 @@ outputs:
 
 The following example demonstrates how to set up input data with 2 summary statistics and one LD reference.
 
-```{r, data-loader-sumstat}
+```{r, data-loader-sumstat, eval = FALSE}
 # Example of loading summary statistics
 sumstat_path_list = c("sumstat1.tsv.gz", "sumstat2.tsv.gz")
 column_file_path_list = c("column_mapping_sumstat1.yml", "column_mapping_sumstat2.yml")
@@ -222,7 +222,7 @@ Example: for sQTL, `list(type_pattern = ".*clu_(\\d+_[+-?]).*", valid_pattern =
 outputs:
 - **`colocboost_results`**: List of colocboost objects (with `xqtl_coloc`, `joint_gwas`, `separate_gwas`); Output of the `colocboost_analysis_pipeline` function. If the mode is not run, the corresponding element will be `NULL`.
 
-```{r, colocboost-analysis}
+```{r, colocboost-analysis, eval = FALSE}
 # load in individual-level and sumstat data
 region_data_combined <- load_multitask_regional_data(
     region = region,
@@ -277,4 +277,4 @@ colocboost_plot(colocboost_results$joint_gwas)
 for (i in 1:length(colocboost_results$separate_gwas)) {
     colocboost_plot(colocboost_results$separate_gwas[[i]])
 }
-```
+```