diff --git a/.CI-setup.sh b/.CI-setup.sh
new file mode 100644
index 0000000000000000000000000000000000000000..b14c0ced4c5e66ef22754ea248b85acbd4d49ba0
--- /dev/null
+++ b/.CI-setup.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+### Setup singularity ###
+# adapted from: https://sylabs.io/guides/3.0/user-guide/installation.html
+# install dependencies
+apt-get update
+apt-get install -y \
+ build-essential \
+ libssl-dev \
+ uuid-dev \
+ libgpgme11-dev \
+ squashfs-tools \
+ libseccomp-dev \
+ pkg-config \
+ wget
+# yum update -y && \
+# yum groupinstall -y 'Development Tools' && \
+# yum install -y \
+# openssl-devel \
+# libuuid-devel \
+# libseccomp-devel \
+# wget \
+# squashfs-tools
+
+
+
+# install go
+export GOVERSION=1.15.6 OS=linux ARCH=amd64
+wget https://dl.google.com/go/go$GOVERSION.$OS-$ARCH.tar.gz
+tar -C /usr/local -xzvf go$GOVERSION.$OS-$ARCH.tar.gz
+rm go$GOVERSION.$OS-$ARCH.tar.gz
+
+# install singularity
+export VERSION=3.9.1
+mkdir -p $GOPATH/src/github.com/sylabs
+cd $GOPATH/src/github.com/sylabs
+wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz
+tar -xzf singularity-ce-${VERSION}.tar.gz
+cd ./singularity
+./mconfig
+make -C ./builddir
+make -C ./builddir install
\ No newline at end of file
diff --git a/.Rbuildignore b/.Rbuildignore
index 509fef60bd8d852f15534cf4a3bb08b13f3ca015..ba2a974ee7d689362cc20de5de6e7a3fb0fc70b7 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,4 @@
^doc$
^Meta$
^data-raw$
+^ci$
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ac098d20b56cab50641ae82c2a6ad2f9eccb135a..731820c2747987e1de002035d443b4d5538d33ba 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,13 @@
-image: rocker/tidyverse
+# helpful Links:
+# https://docs.gitlab.com/ee/ci/variables/predefined_variables.html
+# https://www.youtube.com/watch?v=7I6tHw68DMQ
+
+stages:
+ - test
+ - test-benchmarks
test:
+ image: $CI_REGISTRY_IMAGE
stage: test
tags:
- envinf2
@@ -8,16 +15,13 @@ test:
R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib/"
RETICULATE_MINICONDA_PATH: "/root/.local/share/r-miniconda/" #default path
RETICULATE_PYTHON_ENV: "/root/.local/share/r-miniconda/envs/r-reticulate/"
- # RETICULATE_PYTHON: "$CI_PROJECT_DIR/ci/r-miniconda/envs/r-reticulate/bin/python3"
script:
- if [ ! -d "$R_LIBS_USER" ]; then mkdir -p "$R_LIBS_USER"; fi
- R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), devtools::install_deps(dependencies = T))'
# checks if the packages from the Imports, Suggests, LinkinTo field
# are already installed in the cache
- R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
- # python dependencies
- - if [ ! -d "$RETICULATE_MINICONDA_PATH" ]; then R -e 'reticulate::install_miniconda()'; fi
- - R -e 'if(tryCatch(reticulate::import("vtk"), error = function(e) return(TRUE))) reticulate::py_install("vtk")'
+ # Build and Check r2ogs6
- R CMD build . --no-build-vignettes --no-manual
- R CMD check $(ls -1t *.tar.gz | head -n 1) --no-build-vignettes --no-manual
cache:
@@ -25,8 +29,79 @@ test:
untracked: true
paths:
- "$R_LIBS_USER"
- - "$RETICULATE_MINICONDA_PATH"
- - "$RETICULATE_PYTHON_ENV"
- # script will only run then attempting to merge/push to master
- only:
- - merge_requests
\ No newline at end of file
+ rules:
+ - if: '$CI_PIPELINE_SOURCE == "merge_request_event" || $CI_PIPELINE_SOURCE == "web"'
+ - if: '$CI_COMMIT_BRANCH == "master"'
+benchmark:ref:
+ stage: test-benchmarks
+ tags:
+ - envinf1
+ image: "$CI_REGISTRY_IMAGE"
+ variables:
+ R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib/"
+ # change this as needed
+ OGS_VERSION: "6.4.1"
+ rules:
+ - if: '$CI_PIPELINE_SOURCE == "web"'
+ when: on_success
+ script:
+ - if [ ! -d "$R_LIBS_USER" ]; then mkdir -p "$R_LIBS_USER"; fi
+ - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), devtools::install_deps(dependencies = T))'
+ - R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
+ - Rscript ./ci/test_bm_script.R "$OGS_VERSION" "ref"
+ cache:
+ key: "$CI_COMMIT_REF_SLUG"
+ untracked: true
+ paths:
+ - "$R_LIBS_USER"
+ artifacts:
+ name: "$CI_JOB_NAME-$CI_COMMIT_REF_NAME"
+ expire_in: 4 hrs
+ paths:
+ - ref_exit.rda
+ - out_ref/logfiles/
+
+benchmark:r2ogs6:
+ stage: test-benchmarks
+ tags:
+ - envinf1
+ image: "$CI_REGISTRY_IMAGE"
+ variables:
+ R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib/"
+ # change this as needed
+ OGS_VERSION: "6.4.1"
+ rules:
+ - if: '$CI_PIPELINE_SOURCE == "web"'
+ when: on_success
+ script:
+ - if [ ! -d "$R_LIBS_USER" ]; then mkdir -p "$R_LIBS_USER"; fi
+ - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), devtools::install_deps(dependencies = T))'
+ - R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
+ - Rscript ./ci/test_bm_script.R "$OGS_VERSION" "r2ogs6"
+ cache:
+ key: "$CI_COMMIT_REF_SLUG"
+ untracked: true
+ paths:
+ - "$R_LIBS_USER"
+ artifacts:
+ name: "$CI_JOB_NAME-$CI_COMMIT_REF_NAME"
+ expire_in: 4 hrs
+ paths:
+ - test_exit.rda
+ - out_test/logfiles/
+
+compare-benchmarks:
+ needs: ["benchmark:ref", "benchmark:r2ogs6"]
+ stage: test-benchmarks
+ tags:
+ - envinf1
+ image: "$CI_REGISTRY_IMAGE"
+ rules:
+ - if: '$CI_PIPELINE_SOURCE == "web"'
+ when: on_success
+ dependencies:
+ - benchmark:ref
+ - benchmark:r2ogs6
+ script:
+ - Rscript ./ci/test_bm_script.R "$OGS_VERSION" "test"
+
diff --git a/R/analyse_xml.R b/R/analyse_xml.R
index 80b4eeaa9ecd82e42333e82296e947e4f857c361..333224923a1eeea8e8d246876b5f8dff57e3e3b4 100644
--- a/R/analyse_xml.R
+++ b/R/analyse_xml.R
@@ -271,11 +271,11 @@ get_required <- function(names, occurence_probabilities){
for(i in seq_len(length(names))) {
if(occurence_probabilities[[i]] < 1) {
- required[[names[[i]]]] <- FALSE
+ required[[paste0(names[[i]])]] <- FALSE
}else{
- required[[names[[i]]]] <- TRUE
+ required[[paste0(names[[i]])]] <- TRUE
}
}
- return(invisible(required))
+ return(required)
}
diff --git a/ci/test_bm_script.R b/ci/test_bm_script.R
new file mode 100644
index 0000000000000000000000000000000000000000..35a5df6678842c619d80377f4ae5c83e0563d5b0
--- /dev/null
+++ b/ci/test_bm_script.R
@@ -0,0 +1,146 @@
+
+# git clone --depth 1 --branch 6.4.1 https://gitlab.opengeosys.org/ogs/ogs
+# wget https://ogsstorage.blob.core.windows.net/binaries/ogs6/6.4.1/ogs-6.4.1-serial.sif
+
+# Setup -------------------------------------------------------------------
+if (commandArgs(trailingOnly=TRUE)[2] == "ref" |
+ commandArgs(trailingOnly=TRUE)[2 ]== "r2ogs6") {
+
+ ogs_version <- commandArgs(trailingOnly=TRUE)[1]
+
+ if (!dir.exists("/root/ogs")) {
+ system2(
+ command = c(
+ "git",
+ "clone",
+ "--depth",
+ "1",
+ "--branch",
+ ogs_version,
+ "https://gitlab.opengeosys.org/ogs/ogs.git/",
+ "/root/ogs"
+ )
+ )
+ }
+ if (!file.exists(paste0("/root/ogs-", ogs_version, "-serial.sif"))) {
+ system2(
+ command = c(
+ "wget",
+ "-nv", # no verbose
+ "-P",
+ "/root",
+ paste0("https://ogsstorage.blob.core.windows.net/binaries/ogs6/",
+ ogs_version, "/ogs-", ogs_version, "-serial.sif")
+ )
+ )
+ }
+ devtools::load_all(".")
+ library(dplyr)
+
+ ogs_repo <- "/root/ogs/"
+ prjs <- r2ogs6:::get_benchmark_paths(paste0(ogs_repo, "ProcessLib"))
+ # prjs <- prjs[c(6, 45, 46, 47, 249, 250, 251, 252)] # for testing
+
+ #### Exceptions #####
+ # exclude some prj files
+ prjs <- prjs[-grep("\\.xml$", prjs)]
+ prjs <- prjs[-grep("TH2M/THM/slab/THM_1d_dirichlet.prj", prjs)]
+ prjs <- prjs[-grep("InvalidProjectFiles/", prjs)]
+ #####################
+
+ ogs6_container <- paste0("/root/ogs-", ogs_version, "-serial.sif")
+
+ # include call with --app ogs flag for ogs < 6.4.1
+ if (as.numeric(gsub("[.]", "", ogs_version)) <= 640) {
+ ogs6_command_str <- c("singularity", "exec", "--app", "ogs",
+ ogs6_container, "ogs")
+ } else {
+ ogs6_command_str <- c("singularity", "exec", ogs6_container, "ogs")
+ }
+
+}
+
+# reference run -----------------------------------------------------------
+if (commandArgs(trailingOnly=TRUE)[2] == "ref") {
+
+ out_ref <- "-o /root/out_ref"
+ dir.create("/root/out_ref")
+ dir.create("/root/out_ref/logfiles/")
+
+ ref_exit <- tibble(benchmark = character(),
+ ref = numeric())
+
+ for (prj in prjs) {
+
+ print(paste0("Running benchmark ", prj))
+ prj_path <- paste0(ogs_repo, "Tests/Data/", prj)
+
+ log_ref <- paste0("> /root/out_ref/logfiles/",
+ sub(".prj",".txt", basename(prj)))
+
+ out <- system2(command = ogs6_command_str,
+ args = c(prj_path, out_ref, log_ref))
+
+ ref_exit <- add_row(ref_exit,
+ benchmark = prj,
+ ref = out)
+ }
+
+ save(ref_exit, file = "ref_exit.rda")
+ dir.create("out_ref")
+ file.copy("/root/out_ref/logfiles", to = "out_ref", recursive = TRUE)
+}
+
+# test run with r2ogs6 ----------------------------------------------------
+if (commandArgs(trailingOnly=TRUE)[2] == "r2ogs6") {
+
+ test_exit <- tibble(benchmark = character(),
+ test = numeric())
+ out_test <- "/root/out_test"
+ dir.create(out_test)
+ for (prj in prjs) {
+ print(paste0("Attempting to run benchmark ", prj))
+ prj_path <- paste0(ogs_repo, "Tests/Data/", prj)
+ out <- tryCatch({
+ r2ogs6:::run_benchmark(
+ prj_path = prj_path,
+ ogs6_bin_path = ogs6_container,
+ sim_path = out_test
+ )
+ },
+ error = function(e) {
+ message("\nrun_benchmark() failed!\nOriginal error message:")
+ message(e)
+ })
+
+ test_exit <- add_row(test_exit,
+ benchmark = prj,
+ test = out)
+ }
+ test_exit$test[which(is.na(test_exit$test))] <- 99
+ save(test_exit, file = "test_exit.rda")
+
+ dir.create("out_test")
+ file.copy("/root/out_test/logfiles", to = "out_test", recursive = TRUE)
+}
+
+if (commandArgs(trailingOnly=TRUE)[2] == "test") {
+
+ install.packages("dplyr")
+ load("ref_exit.rda")
+ load("test_exit.rda")
+ test_exit <- dplyr::full_join(ref_exit, test_exit, by = "benchmark")
+
+ print(test_exit, n = nrow(test_exit))
+
+ # benchmarks that passed with & without r2ogs6
+ r2ogs6_passed <- test_exit$test[which(test_exit$ref == 0)] == 0
+
+ if(!all(r2ogs6_passed)) {
+ cat(paste0(test_exit$benchmark[!r2ogs6_passed],
+ collapse = "\n"))
+ stop("Exit codes for r2ogs6 were nonzero for above benchmarks!")
+ }
+}
+
+