added ci

.github/workflows/codecov.yml

@@ -0,0 +1,48 @@
+# This is a basic workflow to help you get started with Actions
+name: R Conda (with codecov)
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ master]
+  pull_request:
+    branches: [ master]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    strategy:
+      fail-fast: false      
+      matrix:
+        os: [ ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v3
+
+      - name: Create conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: mfassignr-dev
+          auto-update-conda: true
+          environment-file: conda/environment-dev.yaml
+          auto-activate-base: false
+      - run: |
+          conda init bash
+          conda env list
+
+      - name: Test coverage
+        run: |
+          conda activate mfassignr-dev
+          cd MFAssignR/
+          Rscript -e "covr::codecov(quiet = FALSE)"

MFAssignR/tests/testthat/test-IsoFiltR.R

@@ -1,5 +1,8 @@
 test_that("Isotope filtering works", {
-  load("../../data/Raw_Neg_ML.rda")
+  load(system.file("data", "Raw_Neg_ML.rda",
+    package = "MFAssignR",
+    mustWork = TRUE
+  ))
   expected <- readRDS("test-data/isotopes.rda")
 
   actual <- IsoFiltR(Raw_Neg_ML)

MFAssignR/tests/testthat/test-KMDNoise.R

@@ -1,5 +1,8 @@
 test_that("KMDNoise works", {
-  load("../../data/Raw_Neg_ML.rda")
+  load(system.file("data", "Raw_Neg_ML.rda",
+    package = "MFAssignR",
+    mustWork = TRUE
+  ))
   names(Raw_Neg_ML) <- c("mass", "intensity")
   actual <- KMDNoise(Raw_Neg_ML)
   expect_equal(actual$Noise, 346.0706, tolerance = 1e-4)

environment.yaml → conda/environment-dev.yaml

@@ -12,3 +12,4 @@ dependencies:
 - r-devtools
 - r-languageserver
 - radian
+- r-covr