Merge branch 'BHE_Meshing_Doc' into 'master'

[Web] Tutorial of creating mesh with BHEs and enhanced notebook to web conversion See merge request ogs/ogs!4704
ufz · Oct 11, 2023 · abb8a73 · abb8a73
2 parents 97dbae5 + 71343c1
commit abb8a73
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -38,7 +38,7 @@ repos:
     rev: v2.2.2
     hooks:
       - id: codespell
-        exclude: 'ThirdParty/.*|Tests/Data/.*|.*\.ya?ml|.*\.bib|^web/content/imprint.md|^GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd|^Applications/FileIO/Legacy/OGSIOVer4.cpp|^scripts/cmake/CPM.cmake|Documentation/.vale/.*'
+        exclude: 'ThirdParty/.*|Tests/Data/.*|.*\.ya?ml|.*\.bib|^web/content/imprint.md|^GeoLib/IO/XmlIO/OpenGeoSysSTN.xsd|^Applications/FileIO/Legacy/OGSIOVer4.cpp|^scripts/cmake/CPM.cmake|Documentation/.vale/.*|.*\.ipynb|.*\.svg'
   - repo: https://github.com/cheshirekow/cmake-format-precommit
     rev: v0.6.13
     hooks:
@@ -73,11 +73,15 @@ repos:
         language: system
         pass_filenames: false
         files: \.(h|cpp)$
+  - repo: https://github.com/errata-ai/vale
+    rev: v2.24.4
+    hooks:
       - id: vale
-        name: Check spelling with vale
-        entry: bash -c 'if command -v vale &> /dev/null; then vale sync; VALE_MIN_ALERT_LEVEL=error scripts/ci/helper/run-vale; else exit 0; fi'
+        name: vale sync
         pass_filenames: false
-        language: system
+        args: [sync]
+      - id: vale
+        args: [--output=line, --minAlertLevel=error]
   - repo: https://github.com/charliermarsh/ruff-pre-commit
     rev: "v0.0.262"
     hooks:

diff --git a/Applications/Utils/Tests.cmake b/Applications/Utils/Tests.cmake
@@ -1403,3 +1403,9 @@ AddTest(
     square_1x1_geometry_bottom.vtu square_1x1_geometry_bottom.vtu 1e-16
     square_1x1_geometry_top.vtu    square_1x1_geometry_top.vtu 1e-16
 )
+
+if(NOT OGS_USE_PETSC)
+    NotebookTest(NOTEBOOKFILE ../../web/content/docs/tutorials/bhe_meshing/notebook-bhe_meshing.md
+                 PYTHON_PACKAGES openpyxl
+                 RUNTIME 10)
+endif()
diff --git a/Documentation/.vale/Vocab/ogs/accept.txt b/Documentation/.vale/Vocab/ogs/accept.txt
@@ -40,7 +40,7 @@ fmt
 Forchheimer
 Fortran
 Francesco
-frontmatter
+[Ff]rontmatter
 Galerkin
 Genuchten
 Geoenergy

diff --git a/ProcessLib/LiquidFlow/Tests.cmake b/ProcessLib/LiquidFlow/Tests.cmake
@@ -611,7 +611,7 @@ if(NOT OGS_USE_MPI)
     OgsTest(PROJECTFILE Parabolic/LiquidFlow/SimpleSynthetics/PrimaryVariableConstraintDirichletBC/cuboid_1x1x1_hex_1000_Dirichlet_Dirichlet_3.prj)
     OgsTest(PROJECTFILE Parabolic/LiquidFlow/SimpleSynthetics/FunctionParameterTest.prj)
     OgsTest(PROJECTFILE Parabolic/LiquidFlow/BlockingConductingFracture/block_conduct_frac.prj)
-    NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/BlockingConductingFracture/LiquidFlow.ipynb RUNTIME 6)
+    NotebookTest(NOTEBOOKFILE Parabolic/LiquidFlow/BlockingConductingFracture/BlockingConductingFracture.ipynb RUNTIME 6)
 endif()
 
 # inclined mesh

diff --git a/Tests/Data/Elliptic/cube_1x1x1_SteadyStateDiffusion/ssd-cube.ipynb b/Tests/Data/Elliptic/cube_1x1x1_SteadyStateDiffusion/ssd-cube.ipynb
@@ -10,14 +10,24 @@
     "author = \"Lars Bilke\"\n",
     "web_subsection = \"elliptic\"\n",
     "draft = true\n",
-    "<!--eofm-->"
+    "<!--eofm-->\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "35326dbe",
+   "metadata": {},
+   "source": [
+    "This notebook is just for testing and does not show up on the web page because `draft = true` in the metadata."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 5,
    "id": "59877add-6b0e-4ee4-9bca-301ea5c23f6d",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "import os\n",
@@ -41,7 +51,9 @@
    "cell_type": "code",
    "execution_count": 14,
    "id": "6c5503b0-ba41-4273-b19a-0fafdb717bb0",
-   "metadata": {},
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
    "outputs": [],
    "source": [
     "resolution = \"2e4\"\n",
@@ -78,14 +90,6 @@
     "plotter.add_mesh(mesh, scalars=\"v\")  # pressure\n",
     "plotter.show()"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "651a2d8c-52d8-448c-ab63-30f95ad70f3d",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

diff --git a/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md b/Tests/Data/Mechanics/Linear/DiscWithHole/Linear_Disc_with_hole.md
@@ -1,26 +1,12 @@
----
-jupyter:
-  jupytext:
-    text_representation:
-      extension: .md
-      format_name: markdown
-      format_version: '1.3'
-      jupytext_version: 1.14.5
-  kernelspec:
-    display_name: Python 3 (ipykernel)
-    language: python
-    name: python3
----
-
-<!-- #raw -->
++++
 title = "Linear elasticity: disc with hole"
 date = "2022-04-27"
 author = "Linda Günther, Sophia Einspänner, Robert Habel, Christoph Lehmann and Thomas Nagel"
 web_subsection = "small-deformations"
-<!--eofm-->
-<!-- #endraw -->
++++
 
-|<div style="width:330px"><img src="https://www.ufz.de/static/custom/weblayout/DefaultInternetLayout/img/logos/ufz_transparent_de_blue.png" width="300"/></div>|<div style="width:330px"><img src="https://discourse.opengeosys.org/uploads/default/original/1X/a288c27cc8f73e6830ad98b8729637a260ce3490.png" width="300"/></div>|<div style="width:330px"><img src="https://tubaf.org/_nuxt/img/logo_de.c04ca6f.svg" width="300"/></div>|
+
+|<div style="width:330px"><img src="https://www.ufz.de/static/custom/weblayout/DefaultInternetLayout/img/logos/ufz_transparent_de_blue.png" width="300"/></div>|<div style="width:330px"><img src="https://discourse.opengeosys.org/uploads/default/original/1X/a288c27cc8f73e6830ad98b8729637a260ce3490.png" width="300"/></div>|<div style="width:330px"><img src="https://upload.wikimedia.org/wikipedia/commons/e/e8/TUBAF_Logo.svg" width="300"/></div>|
 |---|---|--:|
 
 In this benchmark example we consider a linear elastic small deformation problem. More specifically, a plate with a central hole that is put under tension on its top boundary is simulated. By exploiting symmetries, below we evaluate this problem just for the top right quarter of this disc.
@@ -119,7 +105,7 @@ def kirsch_sig_rt(sig, r, theta, a):
 
 ### Stress distribution along the $x$-axis ($\theta= -90°$, orthogonal to the load)
 
-At larger distances from the hole the stresses are approximately distibuted as if the plate had no hole ($\sigma_{rr} \equiv \sigma_{xx} \approx 0$, $\sigma_{r\theta} \equiv \sigma_{xy} = 0$, $\sigma_{\theta\theta} \equiv \sigma_{yy} = 10\,\text{kPa}$).
+At larger distances from the hole the stresses are approximately distributed as if the plate had no hole ($\sigma_{rr} \equiv \sigma_{xx} \approx 0$, $\sigma_{r\theta} \equiv \sigma_{xy} = 0$, $\sigma_{\theta\theta} \equiv \sigma_{yy} = 10\,\text{kPa}$).
 As the hole is approached, the tangential stress increases until it reaches its maximum value directly at the contour.
 Interestingly, that value is three times as high as the applied traction. It can be concluded that the hole leads to a **threefold stress concentration**.
 
@@ -244,7 +230,7 @@ $$
 
 For the simulation of the numerical model, some assumptions have to be made:
 
-* The analytical solution is stricty correct only for an infinitely extended plate.
+* The analytical solution is strictly correct only for an infinitely extended plate.
     This requirement can only be approximated in the numerical method. The dimensions of the considered plate must be much larger than the hole. With a hole diameter of $4\, \text{cm}$ and a size of $20\times20\, \text{cm}$ the plate can be considered as infinitely extended. Indeed, a general rule implied that the range of borders should be about five times the size of the cavity.
 * For numerical simulations, it is necessary to specify the mesh resolution with which the model is calculated. A finer mesh provides more detailed gradients but takes more time for calculation, whereas a coarser mesh yields less accurate values, but in a shorter time.
 * Another assumption that enables us to work with a two-dimensional plate model is the plain strain condition. That means that deformations only occur in one plane.

diff --git a/Tests/Data/Notebooks/testrunner.py b/Tests/Data/Notebooks/testrunner.py
@@ -19,7 +19,22 @@ def save_to_website(exec_notebook_file, web_path):
     output_path = "docs/benchmarks"
     notebook = nbformat.read(exec_notebook_file, as_version=4)
     first_cell = notebook.cells[0]
-    if first_cell.cell_type == "raw":
+    if is_jupytext:
+        if "Tests/Data" not in exec_notebook_file:
+            output_path = str(Path(exec_notebook_file).parent.parent)
+        else:
+            lines = first_cell.source.splitlines()
+            toml_begin = lines.index("+++")
+            toml_end = max(loc for loc, val in enumerate(lines) if val == "+++")
+            toml_lines = lines[toml_begin + 1 : toml_end]
+            parsed_frontmatter = toml.loads("\n".join(toml_lines))
+            output_path = (
+                Path(build_dir)
+                / Path("web/content")
+                / Path(output_path)
+                / Path(parsed_frontmatter["web_subsection"])
+            )
+    elif first_cell.cell_type == "raw":
         lines = first_cell.source.splitlines()
         last_line = lines[-1]
         if "<!--eofm-->" not in last_line:
@@ -34,6 +49,7 @@ def save_to_website(exec_notebook_file, web_path):
                 "'web_subsection'!"
             )
         output_path = os.path.join(output_path, parsed_frontmatter["web_subsection"])
+        output_path = Path(build_dir) / (Path("web/content") / Path(output_path))
     else:
         print(
             f"Warning: {exec_notebook_file} does not contain a RAW cell as its first "
@@ -85,11 +101,14 @@ def save_to_website(exec_notebook_file, web_path):
 if "OGS_DATA_DIR" not in os.environ:
     os.environ["OGS_DATA_DIR"] = os.path.join(ogs_source_path, "Tests/Data")
 os.makedirs(args.out, exist_ok=True)
+build_dir = Path(args.out).parent.parent
 success = True
 
 for notebook_file_path in args.notebooks:
     notebook_success = True
-    convert_notebook_file = notebook_file_path
+    is_jupytext = False
+    if Path(notebook_file_path).suffix in [".md", ".py"]:
+        is_jupytext = True
     notebook_file_path_relative = (
         Path(notebook_file_path).absolute().relative_to(ogs_source_path)
     )
@@ -105,13 +124,17 @@ def save_to_website(exec_notebook_file, web_path):
         os.makedirs(notebook_output_path, exist_ok=True)
         os.environ["OGS_TESTRUNNER_OUT_DIR"] = notebook_output_path
         notebook_filename = os.path.basename(notebook_file_path)
-        convert_notebook_file = os.path.join(
-            notebook_output_path, Path(notebook_filename).stem
-        )
+        convert_notebook_file = notebook_output_path
+        if not is_jupytext:
+            convert_notebook_file = os.path.join(
+                convert_notebook_file, Path(notebook_filename).stem
+            )
         convert_notebook_file += ".ipynb"
 
-        if Path(notebook_file_path).suffix == ".md":
+        if is_jupytext:
             nb = jupytext.read(notebook_file_path)
+            convert_notebook_file = convert_notebook_file.replace("notebook-", "")
+            jupytext.write(nb, convert_notebook_file)
         else:
             with open(notebook_file_path, mode="r", encoding="utf-8") as f:
                 nb = nbformat.read(f, as_version=4)
@@ -154,27 +177,63 @@ def save_to_website(exec_notebook_file, web_path):
             if "CI_MERGE_REQUEST_SOURCE_PROJECT_URL" in os.environ:
                 repo = os.environ["CI_MERGE_REQUEST_SOURCE_PROJECT_URL"]
                 branch = os.environ["CI_MERGE_REQUEST_SOURCE_BRANCH_NAME"]
+
+            # Modify metadata
+            meta_cell = nb["cells"][0]
+            if is_jupytext:
+                if meta_cell.source.startswith("---"):
+                    print(
+                        f"Error: {notebook_filename} frontmatter is not in TOML format! Use +++ delimitiers!"
+                    )
+                    success = False
+                meta_cell.source = meta_cell.source.replace(
+                    "+++\n", "+++\nnotebook = true\n", 1
+                )
+            else:
+                meta_cell.source = f"notebook = true\n{meta_cell.source}"
+
             # Insert Jupyter header with notebook source and binderhub link
             binder_link = f"https://mybinder.org/v2/gh/bilke/binder-ogs-requirements/master?urlpath=git-pull%3Frepo={repo}%26urlpath=lab/tree/ogs/{notebook_file_path_relative}%26branch={branch}"
             text = f"""
 <div class="note">
     <p style="margin-top: 0; margin-bottom: 0;">
         <img style="margin-top: 0; margin-bottom: 0; height: 2em;" class="inline-block mr-2 no-fancybox"
             src="https://upload.wikimedia.org/wikipedia/commons/3/38/Jupyter_logo.svg" alt="">
-        This page is based on a Jupyter notebook.
-        <a href="{repo}/-/blob/{branch}/{notebook_file_path_relative}"><img src="https://img.shields.io/static/v1?label=Source:&message={notebook_filename}&color=brightgreen" class="no-fancybox"
-                style="display: inline; margin-top: 0; margin-bottom: 0; margin-left: 1em;" /></a>
-        <a href="{binder_link}">
-            <img class="no-fancybox" style="display: inline; margin-top: 0; margin-bottom: 0; margin-left: 1em;"
-                src="https://img.shields.io/static/v1?label=&message=Launch notebook&color=5c5c5c&logo=data:image/png;base64,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" />
-        </a>
-    </p>
-</div>
-            """
-            meta_cell = nb["cells"][0]
-            if meta_cell.cell_type == "raw":
-                meta_cell.source = f"notebook = true\n{meta_cell.source}"
-            nb["cells"].insert(1, nbformat.v4.new_markdown_cell(text))
+        This page is based on a Jupyter notebook."""
+            if is_jupytext:
+                download_file_name = (
+                    Path(convert_notebook_file)
+                    .rename(Path(convert_notebook_file).with_suffix(".ipynb"))
+                    .name
+                )
+                text += f"""
+<a href="./{download_file_name}" download="{download_file_name}"><img class="no-fancybox" style="display: inline; margin-top: 0; margin-bottom: 0; margin-left: 1em;" src="https://img.shields.io/static/v1?label=Download:&message={download_file_name}&color=blue" /></a>"""
+            text += f"""
+<a href="{repo}/-/blob/{branch}/{notebook_file_path_relative}"><img src="https://img.shields.io/static/v1?label=Source:&message={notebook_filename}&color=brightgreen" class="no-fancybox"
+        style="display: inline; margin-top: 0; margin-bottom: 0; margin-left: 1em;" /></a>
+<a href="{binder_link}">
+    <img class="no-fancybox" style="display: inline; margin-top: 0; margin-bottom: 0; margin-left: 1em;"
+        src="https://img.shields.io/static/v1?label=&message=Launch notebook&color=5c5c5c&logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABwAAAAcCAYAAAByDd+UAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAABmJLR0QA/wD/AP+gvaeTAAAACXBIWXMAAC4jAAAuIwF4pT92AAAAB3RJTUUH4gsEADkvyr8GjAAABQZJREFUSMeVlnlsVFUUh7/7ZukwpQxdoK2yGGgqYFKMQkyDUVBZJECQEERZVLQEa4iKiggiFjfqbkADhVSgEVkETVSiJBATsEIRja1RoCwuU5gC7Qww03Zm3rzrH/dOfJSZUm4y6Xt9957vnnN/55wruI7RVjMNQAA3AiX6bxw4BTQAQQDvnF1pbYjrAAEUAmXADGAQ0AOQwCWgHqgGdgCRdNBrAm2wW4A1wN2ACZwG/gbcQBFwg/Z2I/AS0JoKanQzmoXAamA0cBx4EhgDTAYmAvcArwNhYD6wHHDbNts9D20LlgMrgWPAXKAO/j8rPc8A5uiNAUwH9tjnddfDAn1mFkJWyoRR58hsv8KIfraAz/QvC3golf2UwEBZBYGyCoJfj/LFz/ceDxRJ09Hccbz/6dDu0ozg7lICZRVXrNFQEyWaDmAkkNslMAnSE59x9IrsMVt8awBP4rI3P9acs83hC3+BkFMAd2eoHn8BrdpG77RA2+IiYDPwHnAbEAOkMGQMcAKTdNheBXqmgDoBhw6xda2Q9tGHPhE4hRTlrrxQGRB29IqE3IUtTyDFu9rQC8AiwAiUVdgFNhTIA85oT68G2nb5ODABJf25niL/emfexX1AA0IWeIr8xWbY+yKwBJVzC4FSm71MlFIdwH505UnnYT5KWRawCvgp0eYBCKEqSBwpFuVMqp2a5Q1WO6TcakiZ55DWwyVVKxDC8gLPA1OAJh32q8qcHTgEKEbl2ncAua99lPy2FdgskH2FlFXNI8IVewcO8P+WUyjr8vqPfmvt+plhmVltIJeilLoK+CWVopy250LAgyrELcl/9nB/ixkbF3GKyOJ/rJs8hxNDZx1KDFvsz+9jJvINAQz1EKvxR7OddzrroyXGiRV5zvp1WPlSzN7bJVCmEtKDF38khguQeR5iBRYGFoaZaUUv9YsEc+KGYfq9vssN1qDsP2MDHRZiYBRXpoEMwa1XAe3Gm4A2YDDQ1z7JTbyvG3O1hXEvcNI0xFPzTh5ZueB4HeXH6hoGR1onC2SlhQgD5RnEl7kwXTOqfu4SeBT4Q5/jVIBtL29KfnsUGAecsISY++W+mpohwQujXJYlPAnzh2HBc7Uxw1iGSpU2VAu7C6Az1A68gEr4ZI6NXT78Pkxh9JEwU4JlGsYbO3a+c7g50/esFGIqcBb4fEzgNBlWwgI2AVsAH13V0oL1K5LvNcBOYACwsfb7qiX3n2mcmGXGirPjHf8uPHqw/Xy/IeuAV/TG3gaOAGyfPwJUbm4HosAdpKilzk7vIVT1iAPTTWG8Of5MY/vIFn8Pt2UVZkfbqi0hvFrFlcBaQNo2DKoxt6CqjQ84nzKktkV+YIE+hz1OaUVyou0iKx41BAR02KYB7wMdnWBJm4aOgOz8MWUDTpa6/NazGdUlo8c2ZuVukdBWfOnCtHlffXAwdPsEK2o47Ju0i2MysAt1xxkLtOpwpwzpFd4+sOHXKHDAIa16YNTJrJzS3x9ZVdvoy+WbecNTLfUCs7Xd/aQr3umGy0rgshIhQ8pNhpSmIeVzTZm9pnjNuLDLXT97gKdRKXUWXUvt3qUNqX1oYz2Bj1H3mXPABh22JlRnuBl4DHWPAVgKfAjIzkDntYB6hIHFKPXO0gbLUQp0oO49Xv1eCXySCtYtDzt56kU159moQulDqfEccAD4FDgEJFLBrgtog4I6r36oG0IC1d0DqNZEOhjAfzgw6LulUF3CAAAAJXRFWHRkYXRlOmNyZWF0ZQAyMDE4LTExLTA0VDAwOjU3OjQ3LTA0OjAwLtN9UwAAACV0RVh0ZGF0ZTptb2RpZnkAMjAxOC0xMS0wNFQwMDo1Nzo0Ny0wNDowMF+Oxe8AAAAASUVORK5CYII=" />
+</a>"""
+            text += f"""</p></div>\n\n"""
+
+            for cell in nb["cells"]:
+                # Check frontmatter has its own cell
+                if (
+                    cell.cell_type == "markdown"
+                    and cell.source.startswith("+++")
+                    and not cell.source.endswith("+++")
+                ):
+                    print(
+                        f"Error: {notebook_filename} notebook metadata is not a separate cell (in markdown: separate by two newlines)!"
+                    )
+                    success = False
+                # Get first regular markdown cell
+                if cell.cell_type == "markdown" and not cell.source.startswith("+++"):
+                    first_markdown_cell = cell
+                    break
+
+            first_markdown_cell.source = text + first_markdown_cell.source
             nbformat.write(nb, f)
 
         # 5. Symlink images or figures subfolder

diff --git a/...ockingConductingFracture/LiquidFlow.ipynb → ...Fracture/BlockingConductingFracture.ipynb b/...ockingConductingFracture/LiquidFlow.ipynb → ...Fracture/BlockingConductingFracture.ipynb
diff --git a/scripts/ci/helper/run-vale b/scripts/ci/helper/run-vale