add unitest

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: "release"}
+          - {os: macOS-latest, r: "release"}
+          - {os: ubuntu-latest, r: "release"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "covr", "testthat"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
+

.github/workflows/test-coverage.yaml

@@ -0,0 +1,28 @@
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "covr"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
+

R/colocboost_utils.R

@@ -393,7 +393,7 @@ get_integrated_weight <- function(avWeight, weight_fudge_factor = 1.5){
 get_in_cos <- function(weights, coverage = 0.95){
 
   temp <- order(weights, decreasing=T)
-  csets <- temp[1:min(which(cumsum(weights[temp]) > coverage))] # 95%
+  csets <- temp[1:min(which(cumsum(weights[temp]) >= coverage))] # 95%
   return(list(csets))
 
 }

README.md

@@ -1,4 +1,5 @@
 # ColocBoost for multi-context colocalization in molecular QTL and GWAS studies
+[![Codecov test coverage](https://codecov.io/gh/StatFunGen/colocboost/branch/master/graph/badge.svg)](https://codecov.io/gh/StatFunGen/colocboost?branch=master)
 
 This R package implements ColocBoost --- motivated and designed for colocalization analysis ([first formulated here](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004383)) of multiple genetic association studies --- as a multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects, based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero effects on which subsets of response variables.
 

tests/README.md

@@ -0,0 +1,106 @@
+# colocboost unit-testing
+
+## Overview
+
+This repository contains a comprehensive testing framework for the [colocboost](https://github.com/StatFunGen/colocboost) R package. The framework is designed to ensure the reliability and correctness of the package's functionality through automated testing.
+
+## Quick Start
+
+1. Navigate to test folder:
+   ```bash
+   cd tests
+   ```
+
+2. **First time use**: run the setup script to install required packages and configure the testing environment:
+   ```r
+   # install.packages(c("devtools", "testthat", "covr", "roxygen2"))
+   source("setup_testthat.R")
+   ```
+
+3. Run all tests:
+   ```r
+   devtools::load_all()
+   devtools::test()
+   ```  
+   or,
+   ```bash
+   Rscript run_tests.R
+   ```
+   To test one file:
+   ```r
+   devtools::test_active_file("testthat/test_colocboost.R")
+   ```
+
+## Files and Structure
+
+- `setup_testthat.R`: Script to set up the testthat infrastructure
+- `run_tests.R`: Script to run all tests and generate test coverage reports
+- `testthat/`: Directory containing test files
+  - `test_package.R`: Tests for basic package functionality
+  - `test_colocboost.R`: Tests for the main colocalization functions
+  - `test_utils.R`: Tests for utility functions
+  - `test_model.R`: Tests for model fitting and prediction functions
+- `.github/workflows/`: GitHub Actions workflow configurations
+
+## How To Use
+
+### Running Tests Locally
+
+To run the tests locally, you can use:
+
+```r
+devtools::test()
+```
+
+Or run individual test files:
+
+```r
+devtools::test_file("testthat/test_colocboost.R")
+```
+
+### Adding New Tests
+
+When adding new functionality to the colocboost package, corresponding tests should be added to maintain test coverage. Follow these steps:
+
+1. Identify which test file should contain the new tests, or create a new test file if necessary
+2. Write test functions using the testthat package's expectations
+3. Run the tests to ensure they pass
+
+Example test:
+
+```r
+test_that("new_function produces expected output", {
+  # Arrange
+  input_data <- prepare_test_data()
+
+  # Act
+  result <- new_function(input_data)
+
+  # Assert
+  expect_equal(result$some_value, expected_value)
+  expect_true(is.data.frame(result$data))
+})
+```
+
+### Test Coverage
+
+The `covr` package is used to measure test coverage, which indicates what percentage of your code is being tested. Aim for at least 80% coverage for a reliable package.
+
+To generate a test coverage report:
+```r
+library(covr)
+coverage <- package_coverage()
+report(coverage)
+```
+
+## GitHub Actions Workflow
+
+This testing framework includes GitHub Actions workflows that automatically run the tests on every push and pull request. The workflows test the package on multiple operating systems (Windows, macOS, and Linux) to ensure cross-platform compatibility.
+
+The workflow is defined in `.github/workflows/R-CMD-check.yaml` and automatically runs:
+- R CMD check
+- Test coverage reporting
+
+Test results and coverage statistics are available on the GitHub Actions page after each push or pull request.
+
+For more information, check the [testthat documentation](https://testthat.r-lib.org/).

tests/run_tests.R

@@ -0,0 +1,39 @@
+#!/usr/bin/env Rscript
+
+# Script to install the package and run tests
+
+# Check for required packages
+required_packages <- c("devtools", "testthat", "covr")
+for (pkg in required_packages) {
+  if (!requireNamespace(pkg, quietly = TRUE)) {
+    stop(sprintf("Cannot find required package: %s\n", pkg))
+  }
+}
+
+# Path to working directory
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) > 0) {
+  work_dir <- args[1]
+} else {
+  work_dir <- getwd()
+}
+
+setwd(work_dir)
+cat(sprintf("Working directory: %s\n", work_dir))
+
+# Install the package
+# cat("Installing colocboost package...\n")
+# devtools::install(".", dependencies = FALSE, quiet = TRUE)
+
+# Run tests
+cat("Running tests...\n")
+devtools::load_all('../')
+testthat::test_dir("testthat/")
+
+# Calculate test coverage
+cat("Calculating test coverage...\n")
+coverage <- covr::package_coverage()
+print(coverage)
+covr::report(coverage)
+
+cat("Tests completed.\n")

tests/setup_testthat.R

@@ -0,0 +1,130 @@
+setwd("../")
+
+# Install necessary packages
+if (!requireNamespace("devtools", quietly = TRUE)) {
+  stop("devtools not found")
+}
+if (!requireNamespace("testthat", quietly = TRUE)) {
+  stop("testthat not found")
+}
+if (!requireNamespace("covr", quietly = TRUE)) {
+  stop("covr not found")
+}
+if (!requireNamespace("roxygen2", quietly = TRUE)) {
+  stop("roxygen2 not found")
+}
+
+# Set up testthat infrastructure
+if (!dir.exists("tests/testthat")) {
+  devtools::use_testthat()
+}
+
+# Create GitHub Actions workflow for continuous integration
+if (!dir.exists(".github/workflows")) {
+  dir.create(".github/workflows", recursive = TRUE, showWarnings = FALSE)
+}
+
+# Write GitHub Actions workflow file
+workflow_file <- ".github/workflows/R-CMD-check.yaml"
+writeLines(
+'
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: "release"}
+          - {os: macOS-latest, r: "release"}
+          - {os: ubuntu-latest, r: "release"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "covr", "testthat"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
+', workflow_file)
+
+# Create a test coverage workflow
+coverage_file <- ".github/workflows/test-coverage.yaml"
+writeLines(
+'
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes", "covr"))
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
+', coverage_file)
+
+# Add code coverage badge to README.md
+readme_file <- "README.md"
+if (file.exists(readme_file)) {
+  readme_content <- readLines(readme_file)
+  if (!any(grepl("codecov", readme_content))) {
+    badge <- "[![Codecov test coverage](https://codecov.io/gh/StatFunGen/colocboost/branch/master/graph/badge.svg)](https://codecov.io/gh/StatFunGen/colocboost?branch=master)"
+    # Add badge after the first line if it's a title
+    if (length(readme_content) > 0) {
+      readme_content <- c(readme_content[1], badge, readme_content[-1])
+    } else {
+      readme_content <- c("# colocboost", badge)
+    }
+    writeLines(readme_content, readme_file)
+  }
+}
+
+# Set up basic testthat structure
+message("testthat setup complete. Next, create test files for each R file in the package.")

tests/testthat.R

@@ -9,4 +9,4 @@
 library(testthat)
 library(colocboost)
 
-test_check("colocboost")
+test_check("colocboost")