Remove doctest submodule and update gitmodules

.devcontainer/Dockerfile

@@ -3,10 +3,18 @@ FROM mcr.microsoft.com/vscode/devcontainers/base:debian
 RUN sudo apt-get update && export DEBIAN_FRONTEND=noninteractive \
     && sudo apt-get install -y \
         cmake-curses-gui \
-        clangd \
         git \
         libeigen3-dev \
         libopenmpi-dev \
         r-cran-rcpp \
-        r-cran-rinside 
+        r-cran-rinside \
+        gdb
 
+RUN git clone https://github.com/doctest/doctest.git /doctest \
+    && cd /doctest \
+    && mkdir build \
+    && cd build \
+    && cmake .. \
+    && make install \
+    && cd / \
+    && rm -rf /doctest

.gitlab-ci.yml

@@ -24,7 +24,7 @@ stages:          # List of stages for jobs, and their order of execution
   - test
 
 variables:
-  GIT_SUBMODULE_STRATEGY: recursive
+#  GIT_SUBMODULE_STRATEGY: recursive
   SOURCE_ARCHIVE_NAME: 'poet_${CI_COMMIT_TAG}_sources.tar.gz'
   CHANGELOG_FILE: 'commit_changelog.md'
 

.gitmodules

@@ -2,12 +2,6 @@
 	path = ext/tug
 	url = ../tug.git
 
-[submodule "ext/doctest"]
-	path = ext/doctest
-	url = https://github.com/doctest/doctest.git
-[submodule "ext/phreeqc"]
-	path = ext/phreeqc
-	url = git@git.gfz-potsdam.de:naaice/phreeqcpoet.git
 [submodule "ext/iphreeqc"]
 	path = ext/iphreeqc
-	url = git@git.gfz-potsdam.de:naaice/iphreeqc.git
+	url = ../iphreeqc.git

CMakeLists.txt

@@ -37,7 +37,6 @@ add_subdirectory(ext/iphreeqc EXCLUDE_FROM_ALL)
 option(POET_ENABLE_TESTING "Build test suite for POET" OFF)
 
 if (POET_ENABLE_TESTING)
-  add_subdirectory(ext/doctest EXCLUDE_FROM_ALL)
   add_subdirectory(test)
 endif()
 

ext/doctest

@@ -1 +0,0 @@
-Subproject commit ae7a13539fb71f270b87eb2e874fbac80bc8dda2

ext/tug

@@ -1 +1 @@
-Subproject commit 3ffa0ef6242d467a269be83751c857cb24ae532e
+Subproject commit b104fdcf5238a8a2948b4e835b2d99b64758bb2a

test/CMakeLists.txt

@@ -2,8 +2,10 @@ file(GLOB test_SRC
   CONFIGURE_DEPENDS
   "*.cpp" "*.c")
 
+find_package(doctest REQUIRED)
+
 add_executable(testPOET ${test_SRC})
-target_link_libraries(testPOET doctest POETLib)
+target_link_libraries(testPOET doctest::doctest POETLib)
 target_include_directories(testPOET PRIVATE "${PROJECT_SOURCE_DIR}/src")
 
 get_filename_component(TEST_RInsideSourceFile "RInsidePOET_funcs.R" REALPATH)

util/ci.Dockerfile

@@ -1,11 +0,0 @@
-FROM debian
-
-RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
-    && apt-get install -y \
-        cmake \
-        git \
-        libeigen3-dev \
-        libopenmpi-dev \
-        r-cran-rcpp \
-        r-cran-rinside \
-        libssl-dev