Merge branch 'fix-links' into 'master'

[web] Fix links.

See merge request ogs/ogs!4771

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/i_eigen.md

@@ -1,3 +1,3 @@
 Configuration for solvers from the Eigen library.
 
-For details see also the [documentation of the Eigen library](https://eigen.tuxfamily.org/dox/group__Sparse__Reference.html).
+For details see also the [documentation of the Eigen library](https://libeigen.gitlab.io/docs/group__Sparse__Reference.html).

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_angle.md

@@ -5,4 +5,4 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/>

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_l.md

@@ -4,4 +4,4 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/>

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_residual_update.md

@@ -5,4 +5,4 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/>

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_restart.md

@@ -5,4 +5,4 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/classEigen_1_1GMRES.html>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/classEigen_1_1GMRES.html>

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_s.md

@@ -4,4 +4,4 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/>

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_scaling.md

@@ -4,6 +4,6 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Note" in <https://eigen.tuxfamily.org/dox/classEigen_1_1SparseLU.html>
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/namespaceEigen.html>
+- "Note" in <https://libeigen.gitlab.io/docs/classEigen_1_1SparseLU.html>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/namespaceEigen.html>
 - References : D. Ruiz and B. Ucar, A Symmetry Preserving Algorithm for Matrix Scaling, INRIA Research report RR-7552

Documentation/ProjectFile/prj/linear_solvers/linear_solver/eigen/t_smoothing.md

@@ -4,4 +4,4 @@ through OGS_USE_EIGEN_UNSUPPORTED CMake option.
 
 See following links for detail description:
 
-- "Detailed Description" in <https://eigen.tuxfamily.org/dox/unsupported/>
+- "Detailed Description" in <https://libeigen.gitlab.io/docs/unsupported/>

MathLib/LinAlg/Eigen/EigenLinearSolver.cpp

@@ -259,7 +259,7 @@ class EigenIterativeLinearSolver final : public EigenLinearSolverBase
 
         // matrix must be copied, because Eigen's linear solver stores a
         // reference to it cf.
-        // https://eigen.tuxfamily.org/dox/classEigen_1_1IterativeSolverBase.html#a7dfa55c55e82d697bde227696a630914
+        // https://libeigen.gitlab.io/docs/classEigen_1_1IterativeSolverBase.html#a7dfa55c55e82d697bde227696a630914
         A_ = A;
 
         if (!A_.isCompressed())
@@ -339,7 +339,7 @@ std::unique_ptr<EigenLinearSolverBase> createIterativeSolver(
         case EigenOption::PreconType::ILUT:
             // TODO for this preconditioner further options can be passed.
             // see
-            // https://eigen.tuxfamily.org/dox/classEigen_1_1IncompleteLUT.html
+            // https://libeigen.gitlab.io/docs/classEigen_1_1IncompleteLUT.html
             return createIterativeSolver<Solver,
                                          Eigen::IncompleteLUT<double>>();
         default:

MathLib/ODE/ODESolverTypes.h

@@ -26,7 +26,7 @@ namespace ODE
  * \tparam N number of rows
  * \tparam M number of columns
  *
- * \see https://eigen.tuxfamily.org/dox/classEigen_1_1Map.html
+ * \see https://libeigen.gitlab.io/docs/classEigen_1_1Map.html
  */
 template <int N, int M>
 using MappedMatrix = Eigen::Map<Eigen::Matrix<double, N, M, Eigen::ColMajor>>;

Tests/Data/Notebooks/testrunner.py

@@ -16,6 +16,7 @@
 
 def save_to_website(exec_notebook_file, web_path):
     output_path_arg = ""
+    output_path = ""
     notebook = nbformat.read(exec_notebook_file, as_version=4)
     first_cell = notebook.cells[0]
     if "Tests/Data" in exec_notebook_file:
@@ -28,10 +29,9 @@ def save_to_website(exec_notebook_file, web_path):
             Path(build_dir)
             / Path("web/content/docs/benchmarks")
             / Path(parsed_frontmatter["web_subsection"])
+            / Path(exec_notebook_file).stem.lower()
         )
-        output_path_arg = (
-            f"--output-dir={Path(output_path) / Path(exec_notebook_file).stem}"
-        )
+        output_path_arg = f"--output-dir={Path(output_path)}"
 
     template = os.path.join(
         os.path.dirname(os.path.abspath(__file__)),
@@ -54,17 +54,19 @@ def save_to_website(exec_notebook_file, web_path):
     if not "Tests/Data" in exec_notebook_file:
         return
 
+    Path(output_path).mkdir(parents=True, exist_ok=True)
+
+    to_copy_path = Path(output_path) / "."
+
+    if is_jupytext:
+        shutil.copy(exec_notebook_file, to_copy_path)
+        print(f"Copying ${exec_notebook_file} to {to_copy_path}")
+
     for subfolder in ["figures", "images"]:
         figures_path = os.path.abspath(
             os.path.join(os.path.dirname(notebook_file_path), subfolder)
         )
-        symlink_figures_path = os.path.join(
-            web_path,
-            "content",
-            output_path,
-            os.path.splitext(os.path.basename(exec_notebook_file))[0].lower(),
-            subfolder,
-        )
+        symlink_figures_path = to_copy_path / subfolder
         if os.path.exists(figures_path) and not os.path.exists(symlink_figures_path):
             print(
                 f"{subfolder} folder detected, copying {figures_path} to "

scripts/ci/extends/test-artifacts.yml

@@ -10,6 +10,7 @@
       - build/*/*.tar.gz
       # Notebook testrunner:
       - build/**/*.ipynb.html
+      - build/**/*.ipynb
       - build/**/*out.txt
       - build/**/web/content
     expire_in: 1 week

scripts/ci/jobs/web-check.yml

@@ -4,7 +4,7 @@ check web links:
   tags: [docker]
   extends:
     - .rules-master-manual
-  needs: [ci_images, "build linux arch", "build mac petsc amd64"]
+  needs: [ci_images, "build linux arch", "build mac petsc arm64"]
   image: $WEB_IMAGE
   script:
     # Copy notebook pages

scripts/ci/jobs/web-preview.yml

@@ -10,12 +10,12 @@ preview web site:
   variables:
     HUGO_ENVIRONMENT: "staging"
   script:
-    # Copy notebook pages
-    - cp -rl build/*/web/content web/ || true
     - cd web
+    - python scripts/convert_notebooks.py
+    # Copy notebook pages
+    - cp -rl ../build/*/web/content ./ || true
     # Symlink for prj link checks (data-link shortcode)
     - ln -s ../Tests .
-    - python scripts/convert_notebooks.py
     - yarn
     - yarn build
   rules:

web/content/docs/devguide/advanced/configuration-options/index.md

@@ -46,7 +46,7 @@ CMake switches to enable / disable parts of OGS.
 - `OGS_CPU_ARCHITECTURE` - Optimizes for the given CPU architecture see [-march](https://gcc.gnu.org/onlinedocs/gcc-4.5.3/gcc/i386-and-x86_002d64-Options.html)-flag. Defaults to `native`. For redistributable binaries set to `generic` on Linux and `core2` on Mac OS. Can be disabled when set to `OFF`.
 - `CMAKE_LIBRARY_SEARCH_PATH` - Additional library installation path, e.g. `/opt/local` or `C:/libs`
 - `OGS_DEPENDENCY_VERSIONS` - Overwrite individual entries in `web/data/versions.json`. Should be quoted and `;`-separated, e.g.: `-DOGS_DEPENDENCY_VERSIONS="minimum_version.petsc=3.16.2;ctest.large_runtime=120"`.
-- `OGS_USE_MKL` - Enables MKL support. Requires MKL to be installed on the system.[^MKL] A CMake or environment variable `MKLROOT` or `MKL_DIR` has to point to the MKL installation directory. To enable 64-bit array indices in MKL add `-DMKL_USE_interface=ilp64` on the first CMake run (with a clean CMake cache) but this seems [not supported by Eigen](https://eigen.tuxfamily.org/dox/TopicUsingIntelMKL.html).
+- `OGS_USE_MKL` - Enables MKL support. Requires MKL to be installed on the system.[^MKL] A CMake or environment variable `MKLROOT` or `MKL_DIR` has to point to the MKL installation directory. To enable 64-bit array indices in MKL add `-DMKL_USE_interface=ilp64` on the first CMake run (with a clean CMake cache) but this seems [not supported by Eigen](https://libeigen.gitlab.io/docs/TopicUsingIntelMKL.html).
 - `OGS_USE_PETSC_MKL_EIGEN_OPENMP` - Also enables OpenMP multithreading when PETSc and MKL is used. This pulls in another OpenMP implementation besides the Intel MKL OpenMP. **Experimental feature!**
 
 [^MKL]: The `mkl_link_tool` (part of the MKL installation) is used for setting up necessary compiler flags. It is a 32-bit executable. On Arch Linux you need to enable the [multilib-repository](https://wiki.archlinux.org/title/official_repositories#Enabling_multilib) and then install the package `lib32-gcc-libs` (otherwise you may get this error when trying to run it: `mkl_link_tool: No such file or directory`) On other Linux distributions you have to install the package `lib32stdc++6` (Ubuntu / Debian) or `libstdc++.i686` (yum-based)! On Windows please also install the *Intel oneAPI Threading Building Blocks* during installation!