def files, bash scipts for containers, testing yaml

.github/workflows/test-container-dl-calc.yaml

@@ -0,0 +1,67 @@
+name: CI tests for download and calculate with Apptainer
+
+on:
+  push:
+    branches:
+      - [main, dev]
+  pull_request:
+    branches:
+      - [main, dev]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Install Apptainer dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y \
+          libseccomp-dev \
+          squashfs-tools \
+          cryptsetup \
+          wget
+
+      - name: Install Apptainer
+        run: |
+          wget https://github.com/apptainer/apptainer/releases/download/v1.1.0/apptainer-1.1.0.tar.gz
+          tar -xvf apptainer-1.1.0.tar.gz
+          cd apptainer-1.1.0
+          ./mconfig && make -C builddir && sudo make -C builddir install
+
+      - name: Restore .sif file from cache
+        id: cache-sif
+        uses: actions/cache@v3
+        with:
+          path: beethoven_dl_calc.sif
+          key: sif-cache-${{ hashFiles('../../containers/beethoven_dl_calc.def') }}
+          restore-keys: sif-cache-
+
+      - name: Build the Apptainer container (if cache miss)
+        if: steps.cache-sif.outputs.cache-hit != 'true'
+        run: |
+          apptainer build my_container.sif path/to/Singularity.def
+
+      - name: Cache the .sif file
+        if: steps.cache-sif.outputs.cache-hit != 'true'
+        uses: actions/cache@v3
+        with:
+          path: beethoven_dl_calc.sif
+          key: sif-cache-${{ hashFiles('../../containers/beethoven_dl_calc.def') }}
+
+      - name: Create run_dl_calc_tests.R dynamically
+        run: |
+          echo 'testthat::test_file("/mnt/tests/testthat/test_download.R")' > tests/testthat/run_dl_calc_tests.R
+          echo 'testthat::test_file("/mnt/tests/testthat/test_calculate.R")' >> tests/testthat/run_dl_calc_tests.R
+
+
+      - name: Run tests inside the container
+        run: |
+          apptainer exec \
+            --bind $PWD/inst:/pipeline \
+            --bind $PWD/input:/input \
+            --bind $PWD/_targets:/opt/_targets \
+            --bind $PWD:/mnt \
+            Rscript mnt/tests/testhat/run_dl_calc_tests.R

container/beethoven_dl_calc.def

@@ -1,10 +1,6 @@
 BootStrap: docker
 From: rocker/geospatial:latest
 
-%files
-    /ddn/gs1/tools/set/R432/lib64/R/library /R_packages
-
-
 %post
     # Update package list
     apt-get update
@@ -27,7 +23,7 @@ From: rocker/geospatial:latest
     mkdir /input
     mkdir /opt/_targets
 
-    Rscript -e "install.packages(c('pak','targets','tarchetypes','crew','crew.cluster'))"
+    Rscript -e "install.packages(c('pak','targets','tarchetypes','crew','crew.cluster','testthat'))"
     Rscript -e "pak::pkg_install('NIEHS/amadeus')"
     Rscript -e "remotes::install_github('NIEHS/beethoven')"
 

container/build_dl_calc.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# usage: build_apptainer_image.sh [full file path]
+# where full file path ends with .sif, with full directory path to save the image
+# after the image is built, group write/execution privileges are given
+
+# Recommended to run this script interactively via `sh build_dl_calc.sh`
+apptainer build --fakeroot beethoven_dl_calc.sif beethoven_dl_calc.def

container/run_container_dl_calc.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=beethoven_001
+#SBATCH --partition=geo
+#SBATCH --mem=128G
+#SBATCH --cpus-per-task=4
+#SBATCH --ntasks=16
+#SBATCH --output=slurm_messages/slurm-%j.out
+#SBATCH --error=slurm_messages/slurm-%j.err
+#SBATCH --mail-user=kyle.messier@nih.gov
+#SBATCH --mail-type=ALL
+
+
+
+
+apptainer exec \
+  --bind $PWD/inst:/pipeline \
+  --bind $PWD/input:/input \
+  --bind $PWD/_targets:/opt/_targets \
+  --bind $PWD:/mnt \
+  beethoven_dl_calc.sif \
+  Rscript /mnt/run.R
+
+

container/run_dl_calc_local_tests.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=dl_calc_tests
+#SBATCH --partition=geo
+#SBATCH --mem=128G
+#SBATCH --cpus-per-task=4
+#SBATCH --ntasks=16
+#SBATCH --output=slurm_messages/slurm-%j.out
+#SBATCH --error=slurm_messages/slurm-%j.err
+#SBATCH --mail-user=kyle.messier@nih.gov
+#SBATCH --mail-type=ALL
+
+
+
+
+apptainer exec \
+  --bind $PWD/../inst:/pipeline \
+  --bind $PWD/../input:/input \
+  --bind $PWD/../_targets:/opt/_targets \
+  --bind $PWD/..:/mnt \
+  beethoven_dl_calc.sif \
+  Rscript /mnt/tests/testthat/test_download.R
+
+

tests/testthat/test_calculate.R

@@ -0,0 +1,13 @@
+################################################################################
+##### unit and integration tests for covariate calculations
+##### Currently arbitrary placeholders
+##### 
+
+################################################################################
+##### 
+testthat::test_that("calculate targets work", {
+
+ a <- 1
+ testthat::expect_equal(a, 1)
+
+})

tests/testthat/test_download.R

@@ -0,0 +1,13 @@
+################################################################################
+##### unit and integration tests for data download
+##### Currently arbitrary placeholders
+##### 
+
+################################################################################
+##### loadargs
+testthat::test_that("download targets work", {
+
+ a <- 1
+ testthat::expect_equal(a, 1)
+
+})