Merge branch 'guix-deps' into 'master'

[guix] Include or package dependencies

See merge request ogs/ogs!4781

.gitmodules

@@ -7,6 +7,3 @@
 [submodule "ThirdParty/bilke/cmake-modules"]
 	path = ThirdParty/bilke/cmake-modules
 	url = https://github.com/bilke/cmake-modules.git
-[submodule "ThirdParty/collection"]
-	path = ThirdParty/collection
-	url = https://gitlab.opengeosys.org/ogs/libs/collection.git

.guix/modules/ogs-package.scm

@@ -19,6 +19,7 @@
   #:use-module (guix)
   #:use-module (guix packages)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
@@ -44,7 +45,7 @@
 (define vcs-file?
   ;; Return true if the given file is under version control.
   (or (git-predicate "../..") ; (current-source-directory)
-      (const #t)))            ;not in a Git checkout
+      (const #t)))            ; not in a Git checkout
 
 (define-public ogs
   (package
@@ -70,18 +71,22 @@
        #:cmake ,cmake)) ;for newer CMake version
     (inputs (list boost
                   eigen
-                  googletest
+                  exprtk
                   hdf5
+                  iphreeqc
                   json-modern-cxx
                   libxml2
                   metis
                   pybind11-2.10.4
                   python
                   range-v3
                   spdlog
+                  tclap
+                  tetgen
                   zlib
-                  vtk))
-    (native-inputs (list git ninja googletest nss-certs)) ; TODO: cpm
+                  vtk
+                  xmlpatch))
+    (native-inputs (list git ninja nss-certs)) ; TODO: cpm
     (synopsis "OpenGeoSys")
     (description
      "Simulation of thermo-hydro-mechanical-chemical (THMC) processes in porous and fractured media")
@@ -192,6 +197,113 @@
                   (sha256
                    (base32
                     "0rbcfvl7y472sykzdq3vrkw83kar0lpzhk3wq9yj9cdydl8cpfcz"))))))
+
+(define tetgen
+      (package
+        (name "tetgen")
+        (synopsis "A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator")
+        (license license:agpl3)
+        (description "TetGen is a program to generate tetrahedral meshes of any 3D polyhedral domains. TetGen generates exact constrained Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and Voronoi partitions.")
+        (home-page "http://www.tetgen.org/")
+        (version "1.5.1-1")
+        (source (origin
+                  (method git-fetch)
+                  (uri (git-reference
+                    (url "https://github.com/ufz/tetgen")
+                    (commit version)))
+                  (sha256
+                   (base32
+                    "1xp1qibm0q4z5qx0h178qpas3n7pqbladkxdalq9j4l98hdws46j"))))
+        (build-system cmake-build-system)
+        (arguments
+            `(#:tests? #f)
+        )))
+
+(define tclap
+      (package
+        (name "tclap")
+        (synopsis "Templatized Command Line Argument Parser")
+        (license license:expat)
+        (description "This is a simple C++ library that facilitates parsing command line arguments in a type independent manner.")
+        (home-page "https://sourceforge.net/p/tclap/discussion/")
+        (version "1.2.4-1")
+        (source (origin
+                  (method git-fetch)
+                  (uri (git-reference
+                    (url "https://github.com/ufz/tclap")
+                    (commit version)))
+                  (sha256
+                   (base32
+                    "0bijzfc9c8zny3m74y53i8m3f41kd8klcnmr9chy536syr9vdr5p"))))
+        (build-system cmake-build-system)
+        (arguments
+            `(#:tests? #f)
+        )))
+
+(define iphreeqc
+      (package
+        (name "iphreeqc")
+        (synopsis "Modules Based on the Geochemical Model PHREEQC for use in scripting and programming languages")
+        (license license:public-domain)
+        (description "")
+        (home-page "https://www.usgs.gov/software/phreeqc-version-3")
+        (version "3.5.0-1")
+        (source (origin
+                  (method git-fetch)
+                  (uri (git-reference
+                    (url "https://github.com/ufz/iphreeqc")
+                    (commit version)))
+                  (sha256
+                   (base32
+                    "1liwp6hkl2dbrl8bki9gzsw77s3prv12sdikmwz5h8ffxwdrnwli"))))
+        (build-system cmake-build-system)
+        (arguments
+            `(#:tests? #f)
+        )))
+
+(define xmlpatch
+      (package
+        (name "xmlpatch")
+        (synopsis "An XML Patch library")
+        (license license:lgpl2.1)
+        (description "")
+        (home-page "https://xmlpatch.sourceforge.net")
+        (version "0.4.3")
+        (source (origin
+                  (method git-fetch)
+                  (uri (git-reference
+                    (url "https://gitlab.opengeosys.org/ogs/libs/xmlpatch")
+                    (commit (string-append "v" version))))
+                  (sha256
+                   (base32
+                    "0872g9w1jd5r4c5a1s8ga4x1plg608b7rxyqjs6zv8ghjq9qlkvg"))))
+        (build-system cmake-build-system)
+        (inputs (list libxml2))
+        (arguments
+            `(#:tests? #f)
+        )))
+
+(define exprtk
+      (package
+        (name "exprtk")
+        (home-page "https://www.partow.net/programming/exprtk/index.html")
+        (synopsis "C++ Mathematical Expression Parsing And Evaluation Library")
+        (description "")
+        (license license:expat)
+        (version "0.0.2")
+        (source (origin
+                  (method git-fetch)
+                  (uri (git-reference
+                    (url "https://github.com/ArashPartow/exprtk.git")
+                    (commit version)))
+                  (sha256
+                   (base32
+                    "1w92qlfjpcan38d88fak3avq81lkcpai5mqpbvrsfv04mi5nfpk5"))))
+        (build-system copy-build-system)
+        (arguments
+         '(#:install-plan '(("exprtk.hpp" "include/")))
+        )))
+
 ;; return package
 ogs
 

.pre-commit-config.yaml

@@ -42,10 +42,10 @@ repos:
       - id: cmake-format
         additional_dependencies: ["cmakelang[YAML]"]
         args: [--config=.cmake-format.yaml]
-        exclude: "scripts/cmake/jedbrown/.*|PackagingMacros.cmake|conan.cmake|CPM.cmake|FindFilesystem.cmake|ConanSetup.cmake|Tests.cmake"
+        exclude: "scripts/cmake/jedbrown/.*|conan.cmake|CPM.cmake|FindFilesystem.cmake|FindMKL.cmake|JSONParser.cmake|ConanSetup.cmake|Tests.cmake"
       - id: cmake-lint
         additional_dependencies: ["cmakelang[YAML]"]
-        exclude: "scripts/cmake/jedbrown/.*|PackagingMacros.cmake|conan.cmake|CPM.cmake|FindFilesystem.cmake|ConanSetup.cmake|BuildExternalProject.cmake"
+        exclude: "scripts/cmake/jedbrown/.*|conan.cmake|CPM.cmake|FindFilesystem.cmake|FindMKL.cmake|JSONParser.cmake|ConanSetup.cmake|BuildExternalProject.cmake"
   - repo: https://github.com/igorshubovych/markdownlint-cli
     rev: v0.33.0
     hooks:

CMakeLists.txt

@@ -226,6 +226,8 @@ if(OGS_BUILD_CLI OR OGS_BUILD_UTILS OR OGS_BUILD_TESTING)
     add_subdirectory(ParameterLib)
     add_subdirectory(MaterialLib)
     add_subdirectory(ProcessLib)
+endif()
+if(TARGET OgsXdmf)
     add_subdirectory(Tests/xdmfdiff)
 endif()
 if(OGS_BUILD_TESTING AND PROJECT_IS_TOP_LEVEL)

ChemistryLib/CMakeLists.txt

@@ -9,7 +9,7 @@ append_source_files(SOURCES Common)
 ogs_add_library(ChemistryLib ${SOURCES})
 
 target_link_libraries(
-    ChemistryLib PUBLIC Eigen3::Eigen iphreeqc PRIVATE BaseLib MaterialLib
+    ChemistryLib PUBLIC Eigen3::Eigen IPhreeqc PRIVATE BaseLib MaterialLib
                                                        MathLib MeshLib NumLib
 )
 

scripts/cmake/CMakeSetup.cmake

@@ -16,27 +16,11 @@ if(WIN32 AND (NOT "${CMAKE_GENERATOR}" MATCHES "Visual Studio")
     message(FATAL_ERROR "Wheels only build in Visual Studio!")
 endif()
 
-set(_collection ${PROJECT_SOURCE_DIR}/ThirdParty/collection)
-# If submodules in ThirdParty/collection are initialized and this is a Guix
-# build use submodule as CPM sources.
-if(EXISTS ${_collection}/ufz/vtkdiff/CMakeLists.txt AND GUIX_BUILD)
-    include(${_collection}/Setup.cmake)
-endif()
-
-# Set additional CMake modules path To be replaced later. See
-# https://gitlab.kitware.com/cmake/cmake/-/issues/22831
-CPMAddPackage(
-    NAME findmkl_cmake
-    GITHUB_REPOSITORY bilke/findmkl_cmake
-    GIT_TAG ee49c4f973f66bb7bfd644658d14e43459f557fa
-    DOWNLOAD_ONLY YES
-)
+# Set additional CMake modules path
 set(CMAKE_MODULE_PATH
-    ${CMAKE_MODULE_PATH}
-    "${PROJECT_SOURCE_DIR}/scripts/cmake"
+    ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/scripts/cmake"
     "${PROJECT_SOURCE_DIR}/scripts/cmake/jedbrown"
     "${PROJECT_SOURCE_DIR}/scripts/cmake/vector-of-bool"
-    "${findmkl_cmake_SOURCE_DIR}/cmake"
 )
 
 list(