Merge branch 'fix-frontend-petsc' into 'master'

Fix frontend PETSc and relax notebook format requirements

See merge request ogs/ogs!4764

Tests/Data/Notebooks/testrunner.py

@@ -73,6 +73,66 @@ def save_to_website(exec_notebook_file, web_path):
  shutil.copytree(figures_path, symlink_figures_path)
 
 
+def check_and_modify_frontmatter():
+ # Check frontmatter has its own cell
+ first_cell = nb["cells"][0]
+ if (
+ first_cell.cell_type == "markdown"
+ and first_cell.source.startswith("+++")
+ and not first_cell.source.endswith("+++")
+ ):
+ print(
+ f"Error: {notebook_filename} notebook metadata is not a separate cell (in markdown: separate by two newlines)!"
+ )
+ success = False
+
+ # Modify metadata
+ first_cell = nb["cells"][0]
+ if first_cell.source.startswith("---"):
+ print(
+ f"Error: {notebook_filename} frontmatter is not in TOML format! Use +++ delimitiers!"
+ )
+ success = False
+ first_cell.source = first_cell.source.replace("+++\n", "+++\nnotebook = true\n", 1)
+
+ # Insert Jupyter header with notebook source and binderhub link in second cell
+ repo = "https://gitlab.opengeosys.org/ogs/ogs"
+ branch = "master"
+ 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"]
+ 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."""
+ 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,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" />
+</a>"""
+ text += f"""</p></div>\n\n"""
+
+ second_cell = nb["cells"][1]
+ if second_cell.cell_type == "markdown":
+ second_cell.source = text + second_cell.source
+ else:
+ # Insert a new markdown cell
+ nb["cells"].insert(1, nbformat.v4.new_markdown_cell(text))
+
+
 # Script arguments
 parser = argparse.ArgumentParser(description="Jupyter notebook testrunner.")
 parser.add_argument("notebooks", metavar="N", nargs="+", help="Notebooks to test.")
@@ -152,69 +212,8 @@ def save_to_website(exec_notebook_file, web_path):
 
  # Write new notebook
  with open(convert_notebook_file, "w", encoding="utf-8") as f:
- repo = "https://gitlab.opengeosys.org/ogs/ogs"
- branch = "master"
- 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"]
-
- # Check frontmatter has its own cell
- first_cell = nb["cells"][0]
- if (
- first_cell.cell_type == "markdown"
- and first_cell.source.startswith("+++")
- and not first_cell.source.endswith("+++")
- ):
- print(
- f"Error: {notebook_filename} notebook metadata is not a separate cell (in markdown: separate by two newlines)!"
- )
- success = False
-
- # Check second cell is markdown
- second_cell = nb["cells"][1]
- if second_cell.cell_type != "markdown":
- print(
- f"Error: {notebook_filename} first cell after the frontmatter needs to be a markdown cell! Move the first Python cell below."
- )
- success = False
-
- # Modify metadata
- first_cell = nb["cells"][0]
- if first_cell.source.startswith("---"):
- print(
- f"Error: {notebook_filename} frontmatter is not in TOML format! Use +++ delimitiers!"
- )
- success = False
- first_cell.source = first_cell.source.replace(
- "+++\n", "+++\nnotebook = true\n", 1
- )
-
- # 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."""
- 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,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" />
-</a>"""
- text += f"""</p></div>\n\n"""
- second_cell.source = text + second_cell.source
-
+ if args.hugo:
+ check_and_modify_frontmatter()
  nbformat.write(nb, f)
 
  status_string = ""

scripts/ci/extends/template-build-linux.yml

@@ -76,7 +76,7 @@
  ctest_arguments="${ctest_arguments} -LE large"
  fi
 
- if [[ "$CI_MERGE_REQUEST_LABELS" =~ [.*web\ only.*] ]]; then
+ if [[ "$CI_MERGE_REQUEST_LABELS" =~ .*web\ only.* ]]; then
  ctest_arguments="${ctest_arguments} -R nb-"
  fi
 

scripts/ci/jobs/web-preview.yml

@@ -26,6 +26,8 @@ preview web site:
  - scripts/ci/jobs/web.yml
  - scripts/ci/jobs/web-preview.yml
  - Tests/Data/**/*.ipynb
+ - Tests/Data/**/*.md
+ - Tests/Data/Notebooks/testrunner.py
  artifacts:
  paths:
  - web/public

scripts/cmake/DependenciesExternalProject.cmake

@@ -132,13 +132,14 @@ if(OGS_USE_PETSC)
  if(NOT "--download-fc" IN_LIST OGS_PETSC_CONFIG_OPTIONS)
  list(APPEND _configure_opts --with-fc=0)
  endif()
- if(DEFINED ENV{CC})
- list(APPEND _configure_opts --with-cc=$ENV{CC})
+ if(NOT "${HOSTNAME}" MATCHES "frontend.*")
+ if(DEFINED ENV{CC})
+ list(APPEND _configure_opts --with-cc=$ENV{CC})
+ endif()
+ if(DEFINED ENV{CXX})
+ list(APPEND _configure_opts --with-cxx=$ENV{CXX})
+ endif()
  endif()
- if(DEFINED ENV{CXX})
- list(APPEND _configure_opts --with-cxx=$ENV{CXX})
- endif()
- message(STATUS "config opts: ${_configure_opts}")
 
  unset(ENV{PETSC_DIR})
  BuildExternalProject(