diff --git a/.gitignore b/.gitignore
index 0f2a07fa3e7d44347af04ff682a5e37827e5bfe1..7d30c4e33027e919e91ba0767556ba8790578c80 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,9 +3,6 @@
__pycache__/
*.py[cod]
-# pkglts files
-.pkglts/info.log*
-
# Packages
*.egg
*.egg-info
@@ -93,20 +90,15 @@ target/
# sphinx autogen file
doc/_dvlpt/
-
+doc/tutorials/
+doc/tutorials.rst
# #}
# user custom filters
*.DS_Store
report.txt
-doc/*.ipynb
*.h5
*.xdmf
-doc/notebook.rst
-doc/README.rst
-doc/tutorials.rst
*jitfailure-dolfin*/
-/doc/utils/
-/doc/_static/growth_scheme.png
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 67814915309c1ab25df76c07e703238e4962eee8..5676eda58b81c191abd244a546bb27b720c4465f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,11 @@ stages:
- build
- test
- deploy
+ - post-deploy
+ - release
+variables:
+ TUTORIALS_ZIP: "tutorials.zip"
conda_build:
stage: build
@@ -30,6 +34,9 @@ conda_build:
allow_failure: true
- if: '$CI_COMMIT_BRANCH == "master"'
when: on_success
+ - if: $CI_COMMIT_BRANCH =~ /^hotfix/
+ when: manual
+ allow_failure: true
coverage:
@@ -61,10 +68,18 @@ coverage:
- coverage.xml
when: always
expire_in: 7 days
- only:
- - develop
- - master
- - /^release/
+ rules:
+ - if: $CI_COMMIT_BRANCH =~ /^release/
+ when: manual
+ allow_failure: true
+ - if: '$CI_COMMIT_BRANCH == "develop"'
+ when: manual
+ allow_failure: true
+ - if: '$CI_COMMIT_BRANCH == "master"'
+ when: always
+ - if: $CI_COMMIT_BRANCH =~ /^hotfix/
+ when: manual
+ allow_failure: true
anaconda :
stage: deploy
@@ -101,7 +116,7 @@ pages:
image: continuumio/miniconda3
script:
# Install required 'libgl1' & 'pyvista xvfb' system dependency:
- - apt-get update && apt-get install libgl1 libgl1-mesa-glx xvfb wget -y
+ - apt-get update && apt-get install libgl1 libgl1-mesa-glx xvfb wget zip -y
# Download and install pandoc3.1.12.3 (version must be at least (2.14.2) but less than (4.0.0)):
- wget https://github.com/jgm/pandoc/releases/download/3.1.12.3/pandoc-3.1.12.3-1-amd64.deb
- dpkg -i pandoc-3.1.12.3-1-amd64.deb
@@ -115,6 +130,8 @@ pages:
- python -m pip install -e .[doc]
# Build the documentation with Sphinx:
- sphinx-build -b html doc/ public/
+ - echo "Zipping the tutorials folder..."
+ - zip -r public/tutorials.zip tutorials/
retry:
max: 2
when: runner_system_failure
@@ -123,7 +140,7 @@ pages:
paths:
- public
exclude:
- - public/*.ipynb
+ - public/**/*.ipynb
dependencies: []
rules:
- if: $CI_COMMIT_BRANCH =~ /^release/
@@ -134,6 +151,9 @@ pages:
allow_failure: true
- if: '$CI_COMMIT_BRANCH == "master"'
when: on_success
+ - if: $CI_COMMIT_BRANCH =~ /^hotfix/
+ when: manual
+ allow_failure: true
docker_build_deploy:
image: docker:latest
@@ -154,4 +174,4 @@ docker_build_deploy:
when: runner_system_failure
dependencies: []
only:
- - tags
+ - tags
\ No newline at end of file
diff --git a/AUTHORS.rst b/AUTHORS.rst
index 55cf4cab5901be7f642a44f09d8c3163f7eeab6f..454cdc1d09e369a3d951aa3bb6aeb745ec4eb0a4 100644
--- a/AUTHORS.rst
+++ b/AUTHORS.rst
@@ -5,17 +5,21 @@ Credits
Development Lead
----------------
-.. {# pkglts, doc.authors
+* Manuel Petit, <manuel.petit@inria.fr>
-* Florian Gacon, <florian.gacon@inria.fr>
-
-.. #}
-Contributors
+Main Contributors
------------
-.. {# pkglts, doc.contributors
-
* ALI Olivier <olivier.ali@inria.fr>
+* Florian Gacon, <florian.gacon@inria.fr>
+
+
+Other Contributors
+------------------
+
+* Jonathan Legrand
+* Guillaume Cerutti
+* Adrien Heymans
+* Gonzalo Revilla
-.. #}
diff --git a/HISTORY.rst b/HISTORY.rst
index 45e1ef0001ca24d4d830e9114bcdbea7ddd25a8d..8c2da189233ddbcc8de0db2b073879e387282708 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -7,6 +7,19 @@ creation (2020-08-26)
* First release on PyPI.
+version 1.1.0 (2024-03-25)
+--------------------------
+
+### **New Features**
+
+1. Added **PyVista** module `visu_pysta` for visualization.
+
+2. Improved handling of **3D geometry (tetra)** in `domains`.
+
+3. Improved access to solver parameters for better usability and flexibility:
+
+ - List all the parameters that can be access in `parameter.py`
+
version 1.3.0 (2025-01-11)
--------------------------
diff --git a/LICENSE b/LICENSE
index 650a3f2c7442de4804864065ca70f3d0b8951a2e..57e7a5350ad168208e8b3d6e5c6b9864fb115a95 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,4 +1,3 @@
-{# pkglts, license
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
@@ -153,6 +152,4 @@ Public License ever published by the Free Software Foundation.
If the Library as you received it specifies that a proxy can decide whether
future versions of the GNU Lesser General Public License shall apply, that
proxy's public statement of acceptance of any version is permanent
-authorization for you to choose that version for the Library.
-
-#}
+authorization for you to choose that version for the Library.
\ No newline at end of file
diff --git a/MANIFEST.in b/MANIFEST.in
index bfa8d262e4adabe18094820e1f5b511dc1eb9730..62ca18c91f5dab8cbafff464f7948ca025a39177 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,27 +1,19 @@
-# {# pkglts, pysetup
+# Include important documentation files
include AUTHORS.rst
include CONTRIBUTING.rst
include HISTORY.rst
include README.rst
-
include LICENSE
-include requirements.txt
-include requirements_minimal.txt
-
-
+# Include all test-related files for validating the library
recursive-include test *
-
-
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-
-
+# Include all documentation files (e.g., Sphinx files and additional docs)
recursive-include doc *.rst
include doc/conf.py
include doc/Makefile
include doc/make.bat
-
-# #}
+# Exclude unnecessary files and directories
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
diff --git a/README.rst b/README.rst
index 219c3e0868e98e91592897c94551a0064a6b25bd..cd32a0ddbf09ff911c6f33133eaa72ca54897da3 100644
--- a/README.rst
+++ b/README.rst
@@ -57,67 +57,60 @@ Requirements
Installation
------------
-You will need conda in order to install ``bvpy``, you can download it `here <https://docs.conda.io/en/latest/miniconda.html>`_.
+The full installation procedure is available `here <https://mosaic.gitlabpages.inria.fr/bvpy/>`_.
-- From sources:
+To install ``bvpy``, follow these steps:
-.. code-block:: bash
+1. **Using Anaconda** (recommended for most users):
- git clone https://gitlab.inria.fr/mosaic/bvpy.git
- cd bvpy
- conda env create --file conda/env.yaml -n bvpy-dev
- conda activate bvpy-dev
- python -m pip install -e .
+ - Install with a new environment:
-- From anaconda:
+ .. code-block:: bash
-.. code-block:: bash
+ conda create -n bvpy -c mosaic -c conda-forge bvpy
+ conda activate bvpy
- conda install -c mosaic bvpy
+ - Or install in an existing environment:
+ .. code-block:: bash
-**Important Note:** Bvpy is currently running on *FEniCS legacy* and not *FEniCSx*. If you are using an ARM-based computer (mac M1s, M2s), there is currently no ARM-Friendly conda package of *FEniCS legacy*. But you can still run x86-based packages. to do so type the following:
+ conda activate <your-environment-name>
+ conda install -c mosaic -c conda-forge bvpy
-.. code-block:: bash
-
- CONDA_SUBDIR=osx-64 conda create -n bvpy_x86
- conda activate bvpy_x86
- conda config --env --set subdir osx-64
+2. **Using Docker**:
-Once this is done, you can import manually all the required libraries, listed within the `conda/env_osx.yaml` configuration file.
+ - Pull the Docker image:
+ .. code-block:: bash
-- From docker
+ docker pull registry.gitlab.inria.fr/mosaic/bvpy:<TAG>
-.. code-block:: bash
+ - Run the container and launch Jupyter Notebook:
- docker pull registry.gitlab.inria.fr/mosaic/bvpy:<TAG>
+ .. code-block:: bash
-Where <TAG> is the version of bvpy you want. You can find all the available version on the `repository <https://gitlab.inria.fr/mosaic/bvpy/container_registry/>`_.
+ docker run -it -p 8888:8888 registry.gitlab.inria.fr/mosaic/bvpy:<TAG>
+ jupyter notebook --ip 0.0.0.0 --no-browser --allow-root --port 8888
-To run the docker container and launch jupyter use:
+3. **From Sources**:
-.. code-block:: bash
+ - Clone the repository:
- docker run -it -p 8888:8888 registry.gitlab.inria.fr/mosaic/bvpy:<TAG>
- jupyter notebook --ip 0.0.0.0 --no-browser --allow-root --port 8888
+ .. code-block:: bash
-And use the URL on the terminal to open the tutorials.
+ git clone https://gitlab.inria.fr/mosaic/bvpy.git
+ cd bvpy
+ conda env create --file conda/env.yaml -n bvpy-dev
+ conda activate bvpy-dev
+ python -m pip install -e .
-Test
-----
-
-If you install ``bvpy`` from sources install ``pytest`` and ``pytest-cov`` inside your environment:
-
-.. code-block:: bash
-
- python -m pip install -e ".[test]"
-
-And then run at the root of the project:
-
-.. code-block:: bash
-
- pytest -v --cov=bvpy test/
+.. The following content is commented out : no need
+ **Important Note:** Bvpy is currently running on *FEniCS legacy* and not *FEniCSx*. If you are using an ARM-based computer (mac M1s, M2s), there is currently no ARM-Friendly conda package of *FEniCS legacy*. But you can still run x86-based packages. to do so type the following:
+ .. code-block:: bash
+ CONDA_SUBDIR=osx-64 conda create -n bvpy_x86
+ conda activate bvpy_x86
+ conda config --env --set subdir osx-64
+ Once this is done, you can import manually all the required libraries, listed within the `conda/env_osx.yaml` configuration file.
Support
-------
diff --git a/conda/env_20240207.yaml b/conda/env_20240207.yaml
deleted file mode 100644
index 554b135747cd06666e6386da53bd0c805f16f288..0000000000000000000000000000000000000000
--- a/conda/env_20240207.yaml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: bvpy
-channels:
- - conda-forge
- - defaults
-dependencies:
- - python >=3.9,<4.0
- - ipython
- - numpy
- - pandas
- - matplotlib
- - python-gmsh=4.11
- - meshio
- - fenics=2019.1
- - importlib_metadata
- - notebook
- - vtk
- - plotly
- - pyvista
- - trame
- - ipywidgets
- - pytest
- - pytest-cov
- - sphinx
- - sphinx_rtd_theme
- - make
- - nbsphinx
- - recommonmark
- - typing_extensions
\ No newline at end of file
diff --git a/conda/meta.yaml b/conda/meta.yaml
index f9c5622a646f687a35748ea573a3a17d0d721f3b..709a8186ae35ca240e8df32376099ae909ce5c4a 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -1,6 +1,6 @@
{% set pyproject = load_file_data('../pyproject.toml', 'toml', from_recipe_dir=True) %}
{% set project = pyproject.get('project', {}) %}
-{% set deps = project.get('dependencies', {}) %}
+{% set deps = project.get('dependencies', []) %}
{% set urls = project.get('urls', {}) %}
# https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#loading-data-from-other-files
# Source code for Jinja context: https://github.com/conda/conda-build/blob/main/conda_build/jinja_context.py
@@ -25,6 +25,7 @@ requirements:
- python {{ python }}
- python-gmsh=4.11
- fenics=2019.1.0
+ - h5py
{% for dep in deps %}
- {{ dep }}
{% endfor %}
diff --git a/data/tutorial_results/tuto_6_result_4_paraview_snapshot.png b/data/tutorial_results/tuto_6_result_4_paraview_snapshot.png
deleted file mode 100644
index 1edb12898f9a16e45468f0cad925743c81187d7d..0000000000000000000000000000000000000000
Binary files a/data/tutorial_results/tuto_6_result_4_paraview_snapshot.png and /dev/null differ
diff --git a/doc/_static/nonempty.txt b/doc/_static/nonempty.txt
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/doc/conf.py b/doc/conf.py
index f4ae60995a112a302f8cae28a707bc84d13fce2f..eaa931499c0563a2707aa1ae4b580d6776e40ed1 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -1,4 +1,3 @@
-# {# pkglts, sphinx
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
@@ -17,98 +16,104 @@
import os
import sys
import shutil
+from sphinx.application import Sphinx
sys.path.insert(0, os.path.abspath('.')) # add doc/ to the path
-from utils.convert_notebook import modify_notebook_for_sphinx
-
-def setup(app):
- app.add_css_file('css/custom.css')
-
-# -------------------- Copy images --------------------
-
-source_dir = '../tutorials/images'
-target_dir = './_static'
-
-os.makedirs(target_dir, exist_ok=True)
-
-for filename in os.listdir(source_dir):
- if filename.endswith('.png'):
- source_file = os.path.join(source_dir, filename)
- target_file = os.path.join(target_dir, filename)
-
- # Remove the target file if it exists
- if os.path.exists(target_file):
- os.remove(target_file)
-
- # Copy the source file to the target location
- shutil.copyfile(source_file, target_file)
- print(f'Copied {source_file} to {target_file}')
-
-# -------------------- Import Notebooks --------------------
-
-for file in os.listdir('.'):
- if '.ipynb' in file:
- os.remove(file)
- if file == 'tutorials.rst':
- os.remove(file)
-
-notebooks = os.listdir('../tutorials')
-
-to_import = ['bvpy_tutorial_1_hello_world.ipynb',
- 'bvpy_tutorial_2_domains.ipynb',
- 'bvpy_tutorial_3_vforms.ipynb',
- 'bvpy_tutorial_4_bnd_cond.ipynb',
- 'bvpy_tutorial_5_reaction_diffusion.ipynb',
- 'bvpy_tutorial_6_linear_elasticity.ipynb',
- 'bvpy_tutorial_7_hyper_elasticity.ipynb',
- 'bvpy_tutorial_8_pyvista.ipynb',
- 'bvpy_tutorial_9_gmsh.ipynb',
- 'bvpy_tutorial_10_morphoelasticity.ipynb']
-
-# - Copy & update notebook if needed (pyvista is used ?)
-for file in notebooks:
- if file in to_import:
- print(f'Importing file: {file}')
- shutil.copy(f'../tutorials/{file}', file)
- modify_notebook_for_sphinx(file, inplace=True, dynamic_plot=False) # dynamic_plot should be set to True when
- # vtk.js have been updated
-
-with open("tutorials.rst", "w+") as f:
- f.write(".. _tutorials:\n\n")
- f.write("Tutorials\n")
- f.write("*********\n\n")
- f.write(".. toctree::\n")
- f.write("\t:titlesonly:\n")
- f.write("\t:maxdepth: 1\n\n")
- for i in to_import:
- f.write("\t"+i.replace(".ipynb", "")+"\n")
-
-
-# If extensions (or modules to document with autodoc) are in another
-# directory, add these directories to sys.path here. If the directory is
-# relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
-# sys.path.insert(0, os.path.abspath('.'))
-
-# Get the project root dir, which is the parent dir of this
-cwd = os.getcwd()
-project_root = os.path.dirname(cwd)
-src_dir = os.path.abspath(os.path.join(project_root, "src"))
-
-# Insert the project root dir as the first element in the PYTHONPATH.
-# This lets us ensure that the source package is imported, and that its
-# version is used.
-sys.path.insert(0, os.path.join(project_root, 'src'))
+#sys.path.insert(0, os.path.abspath('./tutorials')) # Add the `tutorials` directory
+
+from utils.convert_notebook import process_notebook, clean_and_reset_notebook
+
+# ---------------------- Process Tutorials ---------------------- #
+source_tutorials_dir = '../tutorials'
+tutorial_output_dir = './tutorials'
+tutorial_rst_path = "tutorials.rst"
+
+# List of tutorial notebooks to process
+notebooks = [
+ 'bvpy_tutorial_1_hello_world.ipynb',
+ 'bvpy_tutorial_2_domains.ipynb',
+ 'bvpy_tutorial_3_vforms.ipynb',
+ 'bvpy_tutorial_4_bnd_cond.ipynb',
+ 'bvpy_tutorial_5_reaction_diffusion.ipynb',
+ 'bvpy_tutorial_6_linear_elasticity.ipynb',
+ 'bvpy_tutorial_7_hyper_elasticity.ipynb',
+ 'bvpy_tutorial_8_pyvista.ipynb',
+ 'bvpy_tutorial_9_gmsh.ipynb',
+ 'bvpy_tutorial_10_morphoelasticity.ipynb',
+]
-# import bvpy as mypkg
+# Ensure the tutorials directory exists
+os.makedirs(tutorial_output_dir, exist_ok=True)
+
+# Copy supporting folders (images, tutorial_data)
+folders_to_copy = ['images', 'tutorial_data']
+for folder_name in folders_to_copy:
+ source_folder = os.path.join(source_tutorials_dir, folder_name)
+ target_folder = os.path.join(tutorial_output_dir, folder_name)
+ if os.path.exists(source_folder):
+ shutil.rmtree(target_folder, ignore_errors=True) # Clear old data
+ shutil.copytree(source_folder, target_folder)
+ print(f"Copied {source_folder} -> {target_folder}")
+ else:
+ print(f"Source folder {source_folder} not found. Skipping...")
+
+# Remove the old tutorials.rst file
+if os.path.exists(tutorial_rst_path):
+ print(f"Removing old {tutorial_rst_path}")
+ os.remove(tutorial_rst_path)
+
+# Generate tutorials.rst with a toctree
+tutorial_rst_lines = [
+ ".. _tutorials:\n\n",
+ "Tutorials\n*********\n\n",
+ "Download the tutorial notebooks and accompanying data as a ZIP file: "
+ "`tutorials.zip <https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip>`_\n\n\n",
+ ".. toctree::\n",
+ " :titlesonly:\n",
+ " :maxdepth: 1\n\n",
+]
-# -- General configuration ---------------------------------------------
+# Process each notebook
+for notebook in notebooks:
+ input_path = os.path.join(source_tutorials_dir, notebook)
+ output_path = os.path.join(tutorial_output_dir, notebook)
+ process_notebook(input_notebook_path=input_path, output_notebook_path=output_path, dynamic_plot=False)
+ tutorial_rst_lines.append(f" tutorials/{notebook.replace('.ipynb', '')}\n")
+
+# Write the tutorials.rst file
+with open(tutorial_rst_path, "w", encoding="utf-8") as f:
+ f.writelines(tutorial_rst_lines)
+print(f"Wrote {tutorial_rst_path}")
+
+# -------------------- Clean Tutorials After Build -------------------- #
+def clean_doc(app: Sphinx, exception):
+ """
+ Remove temporary folders created during the build process.
+ Cleans up the tutorials folder and the _dvlpt folder after the build is complete.
+ """
+ # clean the tutorials/ folder in order to zip its content in CI/CD
+ if os.path.exists(tutorial_output_dir):
+ print(f"Cleaning up notebooks in {tutorial_output_dir}")
+ for notebook in notebooks:
+ notebook_path = os.path.join(tutorial_output_dir, notebook)
+ clean_and_reset_notebook(input_notebook_path=notebook_path, output_notebook_path=notebook_path)
+
+ # Clean up the _dvlpt folder
+ dev_folder = os.path.abspath(os.path.join(project_root, "doc", "_dvlpt"))
+ if os.path.exists(dev_folder):
+ print(f"Cleaning up {dev_folder}")
+ shutil.rmtree(dev_folder, ignore_errors=True)
+
+# ---------------------- Sphinx Setup ---------------------- #
+def setup(app):
+ """Hook custom setup functionality into Sphinx."""
+ app.add_css_file('css/custom.css') # Add custom CSS
+ app.connect('build-finished', clean_doc)
-# If your documentation needs a minimal Sphinx version, state it here.
-# needs_sphinx = '1.0'
+# ------------------- General Configuration ------------------- #
+project_root = os.path.dirname(os.getcwd())
+sys.path.insert(0, os.path.join(project_root, 'src')) # Add src/ to the path
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
@@ -121,11 +126,12 @@ extensions = [
'sphinx.ext.napoleon',
'sphinx.ext.todo',
'sphinx.ext.viewcode',
+ 'sphinx_tabs.tabs',
'nbsphinx',
'recommonmark',
'pyvista.ext.plot_directive',
'pyvista.ext.viewer_directive',
- 'sphinx_design'
+ 'sphinx_design',
]
# Enable plotly figures and add custom CSS for hiding cells with `remove_cell` tags
@@ -134,263 +140,63 @@ nbsphinx_prolog = r"""
<script src='http://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js'></script>
<script>require=requirejs;</script>
-
"""
-nbsphinx_timeout = -1
-# try to add more extensions which are not default
-# but still useful
-# based on the fact that the extension is installed on the system
-
-#try:
-# import matplotlib.sphinxext.plot_directive
-# extensions.append('matplotlib.sphinxext.plot_directive')
-#except ImportError:
-# pass
-
-
-
-# default settings that can be redefined outside of the pkglts block
+nbsphinx_timeout = -1
todo_include_todos = True
autosummary_generate = True
-intersphinx_mapping = {'python': ('https://docs.python.org/3.4', None),
- # 'dolfin': ('https://fenicsproject.org/docs/dolfin/latest/python/', None),
- 'dolfin': ('https://fenicsproject.org/olddocs/dolfin/2019.1.0/python/', None),
- 'ufl': ('https://fenics.readthedocs.io/projects/ufl/en/latest/', None)}
-inheritance_node_attrs = dict(shape='ellipse', fontsize=12,
- color='orange', style='filled')
+intersphinx_mapping = {
+ 'python': ('https://docs.python.org/3.4', None),
+ 'dolfin': ('https://fenicsproject.org/olddocs/dolfin/2019.1.0/python/', None),
+ 'ufl': ('https://fenics.readthedocs.io/projects/ufl/en/latest/', None),
+}
+inheritance_node_attrs = dict(shape='ellipse', fontsize=12, color='orange', style='filled')
-# Add any paths that contain templates here, relative to this directory.
+# Templates, source files, and static paths
templates_path = ['_templates']
-
-# The suffix of source filenames.
source_suffix = '.rst'
-
-# The encoding of source files.
-# source_encoding = 'utf-8-sig'
-
-# The master toctree document.
master_doc = 'index'
+exclude_patterns = ['build', 'dist', '**.ipynb_checkpoints']
-# General information about the project.
-project = u"bvpy"
-copyright = u"2020, bvpy"
-
-# The version info for the project you're documenting, acts as replacement
-# for |version| and |release|, also used in various other places throughout
-# the built documents.
-#
-
-# The short X.Y version.
+# General information
+project = "bvpy"
+copyright = "2020, bvpy"
version = "1.3.0"
-# The full version, including alpha/beta/rc tags.
release = "1.3.0"
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-# language = None
-
-# There are two options for replacing |today|: either, you set today to
-# some non-false value, then it is used:
-# today = ''
-# Else, today_fmt is used as the format for a strftime call.
-# today_fmt = '%B %d, %Y'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns = ['build', 'dist', '**.ipynb_checkpoints']
-
-# The reST default role (used for this markup: `text`) to use for all
-# documents.
-# default_role = None
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-# add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-# add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-# show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
+# Syntax highlighting style
pygments_style = 'sphinx'
-# A list of ignored prefixes for module index sorting.
-# modindex_common_prefix = []
-
-# If true, keep warnings as "system message" paragraphs in the built
-# documents.
-# keep_warnings = False
-
-
-# -- Options for HTML output -------------------------------------------
-
-# The theme to use for HTML and HTML Help pages. See the documentation for
-# a list of builtin themes.
+# ------------------- HTML Output ------------------- #
html_theme = "sphinx_rtd_theme"
-
-# Theme options are theme-specific and customize the look and feel of a
-# theme further. For a list of options available for each theme, see the
-# documentation.
-# html_theme_options = {}
-
-# Add any paths that contain custom themes here, relative to this directory.
-# html_theme_path = []
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# "<project> v<release> documentation".
-# html_title = None
-
-# A shorter title for the navigation bar. Default is the same as
-# html_title.
-# html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the
-# top of the sidebar.
html_logo = "_static/logo_side.png"
-
-# The name of an image file (within the static path) to use as favicon
-# of the docs. This file should be a Windows icon file (.ico) being
-# 16x16 or 32x32 pixels large.
html_favicon = "_static/favicon.ico"
-
-# Add any paths that contain custom static files (such as style sheets)
-# here, relative to this directory. They are copied after the builtin
-# static files, so a file named "default.css" will overwrite the builtin
-# "default.css".
html_static_path = ['_static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page
-# bottom, using the given strftime format.
-# html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-# html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-# html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names
-# to template names.
-# html_additional_pages = {}
-
-# If false, no module index is generated.
-# html_domain_indices = True
-
-# If false, no index is generated.
-# html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-# html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-# html_show_sourcelink = True
-
-# If true, "Created using Sphinx" is shown in the HTML footer.
-# Default is True.
-# html_show_sphinx = True
-
-# If true, "(C) Copyright ..." is shown in the HTML footer.
-# Default is True.
-# html_show_copyright = True
-
-# If true, an OpenSearch description file will be output, and all pages
-# will contain a <link> tag referring to it. The value of this option
-# must be the base URL from which the finished HTML is served.
-# html_use_opensearch = ''
-
-# This is the file name suffix for HTML files (e.g. ".xhtml").
-# html_file_suffix = None
-
-# Output file base name for HTML help builder.
htmlhelp_basename = "bvpydoc"
-
-# -- Options for LaTeX output ------------------------------------------
-
+# ------------------- LaTeX Output ------------------- #
latex_elements = {
'preamble': r'''
- \usepackage{amsmath} % For math expressions
- \usepackage{amssymb} % For symbols like \nabla
+ \usepackage{amsmath}
+ \usepackage{amssymb}
''',
}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass
-# [howto/manual]).
-latex_documents = [
- (u"index", u"bvpy.tex",
- u"bvpy Documentation",
- u"moi", u"manual"),
-]
-
-# The name of an image file (relative to this directory) to place at
-# the top of the title page.
-# latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings
-# are parts, not chapters.
-# latex_use_parts = False
-
-# If true, show page references after internal links.
-# latex_show_pagerefs = False
-
-# If true, show URL addresses after external links.
-# latex_show_urls = False
-
-# Documents to append as an appendix to all manuals.
-# latex_appendices = []
-
-# If false, no module index is generated.
-# latex_domain_indices = True
-
-
-# -- Options for manual page output ------------------------------------
-
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
-man_pages = [
- (u"index", u"bvpy",
- u"bvpy Documentation",
- [u"moi"], 1)
+latex_documents = [
+ ('index', 'bvpy', 'bvpy Documentation', ['moi'], 1),
]
-# If true, show URL addresses after external links.
-# man_show_urls = False
-
-
-# -- Options for Texinfo output ----------------------------------------
-
+# ------------------- Texinfo Output ------------------- #
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
- (u"index", u"bvpy",
- u"bvpy Documentation",
- u"moi",
- u"bvpy",
- u"A package implementing Boundary Value Problem.",
- u"Miscellaneous"),
+ ('index', 'bvpy', 'bvpy Documentation', 'moi', 'bvpy', 'A package implementing Boundary Value Problem.',
+ 'Miscellaneous'),
]
-# Documents to append as an appendix to all manuals.
-# texinfo_appendices = []
-
-# If false, no module index is generated.
-# texinfo_domain_indices = True
-
-# How to display URL addresses: 'footnote', 'no', or 'inline'.
-# texinfo_show_urls = 'footnote'
-
-# If true, do not generate a @detailmenu in the "Top" node's menu.
-# texinfo_no_detailmenu = False
-
-# use apidoc to generate developer doc
+# ------------------- Apidoc generation ------------------- #
try:
from sphinx.ext.apidoc import main
except ImportError:
@@ -402,6 +208,5 @@ destdir = os.path.abspath(os.path.join(project_root, "doc", "_dvlpt"))
if not os.path.isdir(destdir):
os.makedirs(destdir)
+src_dir = os.path.abspath(os.path.join(project_root, "src"))
main(['-e', '-o', destdir, '-d', '4', '-s', source_suffix[1:], '--force', src_dir])
-
-# #}
diff --git a/doc/index.rst b/doc/index.rst
index cf290da8c46c8cb15672ce0c0d0bd74041352635..cbc505cef6520efb976976dac8b6662554645cb8 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -31,4 +31,213 @@
Sources <_dvlpt/modules>
-.. include:: ../README.rst
+Welcome
+-------
+
+.. image:: https://joss.theoj.org/papers/10.21105/joss.02831/status.svg
+ :target: https://doi.org/10.21105/joss.02831
+
+**Bvpy** is a python library, based on `FEniCS <https://fenicsproject.org/>`_ and `GMSH <http://gmsh.info/>`_, to easily implement and study numerically Boundary Value Problems (BVPs) as well as Initial Boundary Value Problems (IBVPs) through the Finite Element Method (FEM).
+
+Initially built up in the context of developmental biology and morphomechanics, **Bvpy** proposes an intuitive API as close as possible to the formal definition of BVPs. Its purpose is to enable users to quickly and efficiently estimate the behavior of a wide variety of fields (scalars, vectors, tensors) on biologically relevant structures (Riemannian and non-Rieamannian manifolds), inspired by biophysical and biochemical processes (morphogene patterning, active matter mechanics, diffusion-reaction processes, active transports...).
+
+Despite this biological motivation, the **Bvpy** library has been implemented in an *agnostic* manner that makes it suitable for many other scientific context.
+
+
+.. sidebar:: **Bvpy**
+
+ :Lead Development: Manuel Petit
+
+ :Coordination: Olivier Ali
+
+ :Main Contributors: Florian Gacon
+
+ :Other Contributors: Guillaume Cerutti, Adrien Heymans, Jonathan Legrand, Gonzalo Revilla
+
+ :Active team: Inria project team `Mosaic <https://team.inria.fr/mosaic/>`_
+
+ :Institutes: `Inria <http://www.inria.fr>`_
+
+ :Language: Python
+
+ :Supported OS: Linux, MacOS
+
+ :Licence: `LGPL`
+
+ :Funding: Inria ADT Gnomon (Christophe Godin)
+
+
+Documentation
+-------------
+
+A quick introduction to boundary-value problems and Initial-Boundary-value problems, as well as a the general philosophy behind the **Bvpy** library development can be found `here <https://mosaic.gitlabpages.inria.fr/bvpy/general_introduction.html>`_.
+
+A detailed description of the main classes and models of the library can be found `here <https://mosaic.gitlabpages.inria.fr/bvpy/library_description.html>`_.
+
+Some tutorials explaining basic manipulations are gathered `here <https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.html>`_.
+
+
+Requirements
+------------
+
+* Python 3.9
+* FEniCS 2019.1.0
+* GMSH 4.11
+
+
+Installation
+------------
+
+You will need conda in order to install ``bvpy``. If you don’t have conda installed, you can download it `here <https://docs.conda.io/en/latest/miniconda.html>`_.
+
+.. tabs::
+
+ .. tab:: Installing from Anaconda
+
+ ``bvpy`` can be installed directly from the `Anaconda` distribution using the **conda package manager**. You have the flexibility to either create a new environment or install it into an existing one.
+
+ 1. Open a terminal or Conda environment prompt.
+
+ 2. Choose one of the following installation methods:
+
+ - **Create a New Environment** (recommended):
+
+ .. code-block:: bash
+
+ conda create -n bvpy -c mosaic -c conda-forge bvpy
+ conda activate bvpy
+
+ - **Install into an Existing Environment**:
+
+ .. code-block:: bash
+
+ conda activate <your-environment-name>
+ conda install -c mosaic -c conda-forge bvpy
+
+ 3. Verify the ``bvpy`` installation:
+
+ .. code-block:: bash
+
+ python -c "from bvpy.utils.examples import cantilever_beam; cantilever_beam()"
+
+ This should produce a Pyvista Plotter showing the displacement field of the cantilever beam. If you see the correctly rendered visualization, the installation and dependencies of ``bvpy`` are working as expected.
+
+ **Note**: Replace `<your-environment-name>` with the name of your existing environment.
+
+ .. tab:: Installing from Docker
+
+ To install ``bvpy`` using Docker, follow these steps:
+
+ 1. Pull the Docker image:
+
+ .. code-block:: bash
+
+ docker pull registry.gitlab.inria.fr/mosaic/bvpy:<TAG>
+
+ Replace `<TAG>` with the desired version of ``bvpy``.
+ You can find all available versions on the `repository <https://gitlab.inria.fr/mosaic/bvpy/container_registry/>`_.
+
+ 2. Run the Docker container and launch Jupyter Notebook:
+
+ .. code-block:: bash
+
+ docker run -it -p 8888:8888 registry.gitlab.inria.fr/mosaic/bvpy:<TAG>
+ jupyter notebook --ip 0.0.0.0 --no-browser --allow-root --port 8888
+
+ Use the URL displayed in the terminal to open the Jupyter Notebook in your browser for running tutorials.
+
+ .. tab:: Installing from Sources
+
+ If you want to install ``bvpy`` from its source code (e.g., for development purposes or using the latest version), use the following steps:
+
+ 1. Clone the Repository:
+
+ .. code-block:: bash
+
+ git clone https://gitlab.inria.fr/mosaic/bvpy.git
+ cd bvpy
+
+ 2. Create a Development Environment:
+
+ Use the provided `conda` environment file to create a new development environment:
+
+ .. code-block:: bash
+
+ conda env create --file conda/env.yaml -n bvpy-dev
+
+ After the environment is created, activate it:
+
+ .. code-block:: bash
+
+ conda activate bvpy-dev
+
+ 3. Install ``bvpy`` in Editable Mode:
+
+ Install the repository in editable mode (using pip) to allow changes to the source code to take effect immediately:
+
+ .. code-block:: bash
+
+ python -m pip install -e .
+
+ 4. Verify the ``bvpy`` installation:
+
+ .. code-block:: bash
+
+ python -c "from bvpy.utils.examples import cantilever_beam; cantilever_beam()"
+
+ This should produce a Pyvista Plotter showing the displacement field of the cantilever beam. If you see
+ the correctly rendered visualization, the installation and dependencies of ``bvpy`` are working as expected.
+
+ **Optional: Run Tests**
+
+ If you installed ``bvpy`` from sources, install ``pytest`` and ``pytest-cov`` inside your environment:
+
+ .. code-block:: bash
+
+ python -m pip install -e ".[test]"
+
+ Then, run the tests from the root of the project directory to ensure that everything works correctly:
+
+ .. code-block:: bash
+
+ pytest -v --cov=bvpy test/
+
+
+.. The following content is commented out : no need
+ **Important Note:** Bvpy is currently running on *FEniCS legacy* and not *FEniCSx*. If you are using an ARM-based computer (mac M1s, M2s), there is currently no ARM-Friendly conda package of *FEniCS legacy*. But you can still run x86-based packages. to do so type the following:
+ .. code-block:: bash
+ CONDA_SUBDIR=osx-64 conda create -n bvpy_x86
+ conda activate bvpy_x86
+ conda config --env --set subdir osx-64
+ Once this is done, you can import manually all the required libraries, listed within the `conda/env_osx.yaml` configuration file.
+
+Support
+-------
+
+If you encounter an error or need help, please `raise an issue <https://gitlab.com/oali/bvpy/-/issues>`_.
+
+Contributing
+------------
+
+Bvpy is a is a collaborative project and contributions are welcome. If you want to contribute, please contact the `coordinator <mailto:olivier.ali@inria.fr>`_ prior to any `merge request <https://gitlab.com/oali/bvpy/-/merge_requests>`_ and
+check the `gitlab merge request guidelines <https://docs.gitlab.com/ee/development/contributing/merge_request_workflow.html>`_ if needed.
+
+Citation
+--------
+
+If you are using Bvpy in a published work, please use this bibtex entry as reference:
+
+.. code-block::
+
+ @article{Gacon2021,
+ doi = {10.21105/joss.02831},
+ url = {https://doi.org/10.21105/joss.02831},
+ year = {2021},
+ publisher = {The Open Journal},
+ volume = {6},
+ number = {59},
+ pages = {2831},
+ author = {Florian Gacon and Christophe Godin and Olivier Ali},
+ title = {BVPy: A FEniCS-based Python package to ease the expression and study of boundary value problems in Biology.},
+ journal = {Journal of Open Source Software}}
+
diff --git a/doc/utils/convert_notebook.py b/doc/utils/convert_notebook.py
index b9680bc70c6fd609e19805cf438071636edd01fa..bf256f226f5b216a005488aa16b7ed8f21092280 100644
--- a/doc/utils/convert_notebook.py
+++ b/doc/utils/convert_notebook.py
@@ -1,8 +1,142 @@
import nbformat
import re
+import os
+from nbconvert import HTMLExporter
+from nbconvert.preprocessors import ExecutePreprocessor, ClearOutputPreprocessor
-def modify_notebook_for_sphinx(input_path, output_path=None, inplace=True, dynamic_plot=False):
- """ Change the backend if pyvista is imported and update image paths.
+def process_notebook(input_notebook_path, output_notebook_path, dynamic_plot=False):
+ """ Process a Jupyter notebook: Clear outputs, modify for PyVista and write to another path.
+
+ This function orchestrates the following:
+ 1. Loads the notebook from the specified path.
+ 2. Clears all outputs.
+ 3. Modifies the notebook to support PyVista and Sphinx documentation.
+ 4. Write the notebook to the specified path
+
+ Parameters
+ ----------
+ input_notebook_path : str
+ Path to the input Jupyter notebook file (.ipynb).
+ output_notebook_path : str
+ Path to write the Jupyter notebook file (.ipynb).
+ dynamic_plot : bool, optional
+ Whether to enable PyVista dynamic plot mode, by default False.
+
+ Raises
+ ------
+ FileNotFoundError
+ If the notebook specified by `input_notebook_path` does not exist.
+ Exception
+ If any issues arise during the notebook clearing or modification
+
+ Notes
+ -----
+
+ - This function is part of a workflow for preparing Jupyter notebooks for HTML-based documentation.
+ - By enabling `dynamic_plot`, PyVista's interactive plot mode is incorporated into the notebook.
+ """
+ try:
+ # Step 1: Load the notebook from the specified path
+ if not os.path.exists(input_notebook_path):
+ raise FileNotFoundError(f"Notebook not found: {input_notebook_path}")
+
+ with open(input_notebook_path, 'r', encoding='utf-8') as f:
+ notebook_content = nbformat.read(f, as_version=4)
+ print(f"Loaded notebook: {input_notebook_path}")
+
+ # Step 2: Clear outputs
+ cleared_notebook = clear_notebook(notebook_content)
+
+ # Step 3: Modify notebook content for PyVista
+ modified_notebook = modify_notebook_for_pyvista(cleared_notebook,
+ dynamic_plot=dynamic_plot)
+
+ # Step 4: Write the modified notebook to the specified output path
+ with open(output_notebook_path, 'w', encoding='utf-8') as f:
+ nbformat.write(modified_notebook, f)
+ print(f"Modified notebook written to: {output_notebook_path}")
+
+ except Exception as e:
+ print(f"Unexpected error during notebook processing: {e}")
+ return None
+
+def clean_and_reset_notebook(input_notebook_path, output_notebook_path):
+ """
+ Clean and reset a Jupyter notebook.
+
+ Steps:
+ 1. Open the input notebook.
+ 2. Remove output cells using clear_notebook.
+ 3. Undo modifications made by modify_notebook_for_pyvista by removing specific cells.
+ 4. Save the cleaned and reset notebook to the specified output path.
+
+ Parameters
+ ----------
+ input_notebook_path : str
+ Path to the input Jupyter notebook file (.ipynb).
+ output_notebook_path : str
+ Path to save the cleaned and reset Jupyter notebook file (.ipynb).
+
+ """
+ try:
+ # Step 1: Load the notebook
+ if not os.path.exists(input_notebook_path):
+ raise FileNotFoundError(f"Notebook not found: {input_notebook_path}")
+
+ with open(input_notebook_path, 'r', encoding='utf-8') as f:
+ notebook_content = nbformat.read(f, as_version=4)
+ print(f"Loaded notebook: {input_notebook_path}")
+
+ # Step 2: Clear all notebook outputs
+ cleared_notebook = clear_notebook(notebook_content)
+
+ # Step 3: Undo modifications from `modify_notebook_for_pyvista`
+ cleaned_cells = []
+ for cell in cleared_notebook["cells"]:
+ # Only keep the cell if it doesn't match the pattern added by `modify_notebook_for_pyvista`
+ if cell["cell_type"] == "code" and re.search(r"# ---- for online doc only ---- #", cell["source"]):
+ print("Removing cell from notebook with PyVista modifications.")
+ continue # Skip this cell
+ # Add the cell to the cleaned list
+ cleaned_cells.append(cell)
+
+ # Update the notebook content with the cleaned cells
+ cleared_notebook["cells"] = cleaned_cells
+
+ # Step 4: Write the cleaned and reset notebook to output path
+ with open(output_notebook_path, 'w', encoding='utf-8') as f:
+ nbformat.write(cleared_notebook, f)
+ print(f"Cleaned and reset notebook written to: {output_notebook_path}")
+
+ except Exception as e:
+ print(f"Error during notebook cleaning and resetting: {e}")
+
+
+def clear_notebook(notebook_content):
+ """ Clear all outputs in a Jupyter notebook content.
+
+ This function removes all cell outputs and return the notebook content.
+
+ Parameters
+ ----------
+ notebook_content : dict, optional
+ The loaded notebook content (as a Python dictionary).
+ Returns
+ -------
+ dict
+ Cleared notebook content.
+ """
+ try:
+ # Clear outputs from the notebook
+ clear_preprocessor = ClearOutputPreprocessor()
+ cleared_notebook, _ = clear_preprocessor.preprocess(notebook_content, {})
+ print("Cleared notebook outputs.")
+ return cleared_notebook
+ except Exception as e:
+ print(f"Error while clearing notebook outputs: {e}")
+
+def modify_notebook_for_pyvista(notebook_content, dynamic_plot=False):
+ """ Modify notebook content for Sphinx documentation by changing pyvista backend configurations
TODO: follow issues to know when a full dynamic plot with `html` can be done
https://github.com/pyvista/pyvista/issues/6250 --> add_text (title)
@@ -10,65 +144,47 @@ def modify_notebook_for_sphinx(input_path, output_path=None, inplace=True, dynam
Parameters
----------
- input_path : str
- input path of the notebook
- output_path : str, optional
- output path of the notebook, by default None
- inplace : bool, optional
- update the notebook inplace, by default True
+ notebook_content : dict
+ The loaded notebook content (as a Python dictionary).
dynamic_plot : bool, optional
- make the pyvista plot dynamic or static, by default False.
+ Make the pyvista plot dynamic or static, by default False.
+
+ Returns
+ -------
+ dict
+ Modified notebook content.
"""
- # Load the notebook
- with open(input_path) as f:
- nb = nbformat.read(f, as_version=4)
-
- # List to store modified cells
- new_cells = []
-
- # Should be set to `html` as soon as vtk.js supports text & categorical labelling
- if dynamic_plot:
- pyvista_flag = 'html'
- else:
- pyvista_flag = 'static'
-
- for cell in nb.cells:
- # For markdown cells, update image references
- if cell.cell_type == "markdown":
- cell.source = re.sub(
- r'(<img\s+src=")images/([^"]+)(".*?>)',
- r'\1_static/\2\3',
- cell.source
- )
-
- # Append the original cell
- new_cells.append(cell)
-
- # Check if the cell is a code cell and contains 'import pyvista as pv'
- if cell.cell_type == "code":
- if 'import pyvista as pv' in cell.source:
+ try:
+ # List to store modified cells
+ new_cells = []
+
+ # Set the PyVista backend flag
+ pyvista_flag = 'html' if dynamic_plot else 'static'
+
+ for cell in notebook_content['cells']:
+ # Append the original (or modified) cell
+ new_cells.append(cell)
+
+ # Check if the cell is a code cell and contains 'import pyvista as pv'
+ if cell['cell_type'] == "code" and 'import pyvista as pv' in cell['source']:
# Create a new cell with PyVista backend configuration
new_cell = nbformat.v4.new_code_cell(
source=(
"# ---- for online doc only ---- #\n"
- f"pv.set_jupyter_backend('{pyvista_flag}')\n"
- "pv.start_xvfb()\n"
- "import time\n"
- "time.sleep(3) # Give time to xvfb to start \n"
+ f"pv.set_jupyter_backend('{pyvista_flag}')\n"
+ "pv.start_xvfb(3)\n"
"# ---- end of online doc only ---- #"
)
)
# Add metadata to hide the new cell in Sphinx-generated documentation
- new_cell.metadata["nbsphinx"] = "hidden"
+ new_cell['metadata']["nbsphinx"] = "hidden"
new_cells.append(new_cell)
- # Update notebook cells with modified cells
- nb.cells = new_cells
-
- # Save the modified notebook
- if inplace or (output_path is None):
- output_path = input_path
+ # Update notebook content
+ notebook_content['cells'] = new_cells
+ return notebook_content
- with open(output_path, 'w') as f:
- nbformat.write(nb, f)
\ No newline at end of file
+ except Exception as e:
+ print(f"Error while modifying notebook: {e}")
+ return None
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 394a172df01cb6e6cd40585cf1ae1c7f35a34237..1cbeddae54624fdb47d6e2e851988ea2fda51e83 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,13 +16,34 @@ dependencies = [
"meshio",
"importlib_metadata",
"plotly",
- "pyvista[all]",
+ "pyvista",
"typing_extensions",
"nbformat>=4.2.0",
- "scipy"
+ "scipy",
+ "trame",
+ "trame-vtk",
+ "trame-vuetify",
+ "ipywidgets"
]
license = {file = "LICENSE"}
+[roles]
+lead_development = [
+ {name = "Manuel Petit", email = "manuel.petit@inria.fr"}
+]
+coordination = [
+ {name = "Olivier Ali", email = "olivier.ali@inria.fr"}
+]
+main_contributors = [
+ {name = "Florian Gacon", email = "florian.gacon@inria.fr"}
+]
+other_contributors = [
+ {name = "Guillaume Cerutti"},
+ {name = "Adrien Heymans"},
+ {name = "Gonzalo Revilla"},
+ {name = "Jonathan Legrand"}
+]
+
[project.urls]
Homepage = "https://mosaic.gitlabpages.inria.fr/bvpy/"
Documentation = "https://mosaic.gitlabpages.inria.fr/bvpy/"
diff --git a/src/bvpy/utils/examples.py b/src/bvpy/utils/examples.py
new file mode 100644
index 0000000000000000000000000000000000000000..1bb1b3a9a5cc48eb8f5dbafdfefe00b1bd5a00d3
--- /dev/null
+++ b/src/bvpy/utils/examples.py
@@ -0,0 +1,109 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# bvpy.utils.examples
+#
+# File author(s):
+# Manuel Petit <manuel.petit@inria.fr>
+#
+# File contributor(s):
+# Manuel Petit <manuel.petit@inria.fr>
+#
+# File maintainer(s):
+# Manuel Petit <manuel.petit@inria.fr>
+#
+# Copyright © by Inria
+# Distributed under the LGPL License..
+# See accompanying file LICENSE.txt or copy at
+# https://www.gnu.org/licenses/lgpl-3.0.en.html
+#
+# -----------------------------------------------------------------------
+
+from bvpy.domains import Cylinder
+from bvpy.boundary_conditions import dirichlet
+from bvpy.vforms.elasticity import LinearElasticForm
+from bvpy.utils.visu import plot
+from bvpy.utils.visu_pyvista import visualize
+from bvpy.bvp import BVP
+
+def cantilever_beam(visualizer: str='pyvista'):
+ """ Example of a cantilever beam simulation.
+
+ This function models a cantilever beam as a cylindrical domain with clamped boundary conditions at one end and
+ a gravitational load applied along the negative Z-axis. The problem is solved using a variational formulation
+ for linear elasticity, and the solution is returned as a visualization of the displacement field.
+
+ Parameters
+ ----------
+ visualizer : str, optional
+ The type of visualizer to use for visualization purposes. Acceptable values are 'pyvista' (default) or
+ 'plotly'.
+
+ Returns
+ -------
+ None
+ This function visualizes the displacement field of the solved boundary value problem
+ either through a Pyvista Plotter or as a Plotly plot depending on the given `visualizer`
+ argument.
+
+ Notes
+ -----
+ The simulation steps include:
+ 1. Define the domain of the cantilever beam as a cylinder:
+ - Length of the cylinder: dx = 2 (unit length).
+ - Radius: r = 0.2.
+ - Meshing: tetrahedral cells with a size of 0.1.
+ - Algorithm: Frontal-Delaunay meshing.
+ - The domain is then discretized.
+
+ 2. Define boundary conditions:
+ - Dirichlet boundary conditions are applied to the end of the cylinder at x=0:
+ All translations (displacements) in X, Y, and Z are fixed.
+
+ 3. Define the variational formulation:
+ - Linear Elasticity Formulation.
+ - Material Parameters:
+ - Young's modulus = 1.
+ - Poisson's ratio = 0.3.
+ - Body force:
+ - Gravitational acceleration: g = 0.016.
+ - Density: Ï = 0.1.
+ - Source term: [0, 0, -Ï * g].
+
+ 4. Create and solve the boundary-value problem:
+ - Combine domain, boundary conditions, and variational form into a BVP instance.
+ - Solve the BVP for the cantilever beam.
+
+ 5. Visualize the displacement field at the mechanical equilibrium state
+
+ Examples
+ --------
+ >>> from bvpy.utils.examples import cantilever_beam
+ >>> cantilever_beam()
+ """
+ assert visualizer in ['pyvista', 'plotly'], "Acceptable values are 'pyvista' (default) or 'plotly'."
+
+ # - Create a cylinder and set up some parameters for the mesh construction
+ cylinder = Cylinder(x=0, dx=2, dz=0, r=0.2, cell_type='tetra',
+ cell_size=.1, algorithm='Frontal-Delaunay', clear=True)
+ cylinder.discretize() # discretize (from Gmsh -> FeniCS)
+
+ # - Create boundary conditions : clamp the beam at x=0
+ bc = [dirichlet(val=[0, 0, 0], boundary="near(x, 0, 1e-2)")]
+
+ # - Create the variational form
+ g = 0.016
+ rho = .1
+ vform = LinearElasticForm(young=1,
+ poisson=0.3,
+ source=[0, 0, -rho * g])
+
+ # - Create the boundary-value problem and solve it
+ bvp = BVP(domain=cylinder, vform=vform, bc=bc)
+ bvp.solve()
+
+ # - Visualize the resulting displacement field
+ if visualizer == 'pyvista':
+ visualize(bvp, 'solution')
+ elif visualizer == 'plotly':
+ visualize(bvp.solution)
diff --git a/src/bvpy/utils/io.py b/src/bvpy/utils/io.py
index 6a30e947cb37c28521c6996f676521387edc3a75..054adedca64c7fbdc1bd704f06377acd57d37b7c 100644
--- a/src/bvpy/utils/io.py
+++ b/src/bvpy/utils/io.py
@@ -166,21 +166,26 @@ def read_polygonal_data(path):
Values of these properties of each element
of the considered topolgocial degree.
+ Raises
+ ------
+ ValueError
+ If the file format is not supported.
+
"""
- try:
- assert path[-4:] in ['.txt', '.ply', '.obj']
- if path[-4:] == '.ply':
- return read_polygonal_ply(path)
+ if path[-4:] not in ['.txt', '.ply', '.obj']:
+ raise ValueError(
+ f"The format of the given file {path} is not supported. "
+ "Supported formats are: '.txt', '.ply', '.obj'."
+ )
- elif path[-4:] == '.obj':
- return read_polygonal_obj(path)
+ if path[-4:] == '.ply':
+ return read_polygonal_ply(path)
- elif path[-4:] == '.txt':
- return read_polygonal_txt(path)
+ elif path[-4:] == '.obj':
+ return read_polygonal_obj(path)
- except AssertionError:
- print('WARNING - utils.read():'
- + 'the format of the given file is not supported.')
+ elif path[-4:] == '.txt':
+ return read_polygonal_txt(path)
def read_polygonal_ply(path):
@@ -218,7 +223,7 @@ def read_polygonal_ply(path):
data = {0: None, 1: None, 2: None, 3: None}
property_infos = {0: [], 1: [], 2: [], 3: []}
- # -- Reading the data
+ # -- Reading the tutorial_data
with open(path, 'r') as file:
content = file.readlines()
header = content[:content.index('end_header\n')]
diff --git a/data/mesh.msh b/test/data/mesh_example.msh
similarity index 100%
rename from data/mesh.msh
rename to test/data/mesh_example.msh
diff --git a/data/simple_obj_example.obj b/test/data/obj_example.obj
similarity index 100%
rename from data/simple_obj_example.obj
rename to test/data/obj_example.obj
diff --git a/data/test_small.ply b/test/data/ply_example.ply
similarity index 100%
rename from data/test_small.ply
rename to test/data/ply_example.ply
diff --git a/data/tissue_example.txt b/test/data/tissue_example.txt
similarity index 100%
rename from data/tissue_example.txt
rename to test/data/tissue_example.txt
diff --git a/data/tissue_example_2.txt b/test/data/tissue_example_2.txt
similarity index 100%
rename from data/tissue_example_2.txt
rename to test/data/tissue_example_2.txt
diff --git a/test/test_io.py b/test/test_io.py
index 354f22461a020226cddde59386b49a686d5ceaea..d293ceb46f8ff8f9b9f858a3e728806b3beff636 100644
--- a/test/test_io.py
+++ b/test/test_io.py
@@ -1,5 +1,6 @@
import unittest
import tempfile
+from pathlib import Path
from fenics import UnitSquareMesh
from bvpy import BVP
@@ -19,45 +20,56 @@ class TestIO(unittest.TestCase):
"""
self.tmp = tempfile.TemporaryDirectory()
+ # Base directory where the `tutorial_data` folder resides
+ self.test_data_dir = Path(__file__).parent / "data"
+
def tearDown(self):
"""Concludes and closes the test.
"""
self.tmp.cleanup()
def test_read_gmsh_data(self):
- path = "data/mesh.msh"
+ path = str(self.test_data_dir / "mesh_example.msh")
dom = CustomDomainGmsh(path)
def test_read_polygonal_data_ply(self):
- path = "data/test_small.ply"
+ path = str(self.test_data_dir / "ply_example.ply")
points, cells, _ = read_polygonal_data(path)
self.assertEqual(len(points), 10)
self.assertEqual(len(cells), 1)
def test_read_polygonal_data_obj(self):
- path = "data/simple_obj_example.obj"
+ path = str(self.test_data_dir / "obj_example.obj")
points, cells, _ = read_polygonal_data(path)
self.assertEqual(len(points), 6)
self.assertEqual(len(cells), 2)
def test_read_polygonal_data_txt(self):
- path = "data/tissue_example.txt"
+ path = str(self.test_data_dir / "tissue_example.txt")
points, cells, _ = read_polygonal_data(path)
self.assertEqual(len(points), 220)
self.assertEqual(len(cells), 61)
def test_read_polygonal_data_txt_2(self):
- path = "data/tissue_example_2.txt"
+ path = str(self.test_data_dir / "tissue_example_2.txt")
points, cells, label = read_polygonal_data(path)
self.assertEqual(label[0], 0)
self.assertEqual(label[-1], 60)
self.assertEqual(len(label), 61)
def test_read_polygonal_data_wrong_type(self):
- path = "data/test_recording_mesh.xdmf"
- read_polygonal_data(path)
+ path = str(self.test_data_dir / "test_recording_mesh.xdmf")
+
+ with self.assertRaises(ValueError) as context:
+ read_polygonal_data(path)
+
+ # Check that the exception message is correct
+ self.assertIn(
+ f"The format of the given file {path} is not supported.",
+ str(context.exception)
+ )
def test_write_ply_mesh(self):
mesh = UnitSquareMesh(2, 2)
diff --git a/tutorials/bvpy_tutorial_10_morphoelasticity.ipynb b/tutorials/bvpy_tutorial_10_morphoelasticity.ipynb
index 2c3e00123e440386a9402afd573326c0e3f79480..e14c508fbdb2c1edb1bff26297c73eacc087a65a 100644
--- a/tutorials/bvpy_tutorial_10_morphoelasticity.ipynb
+++ b/tutorials/bvpy_tutorial_10_morphoelasticity.ipynb
@@ -10,6 +10,8 @@
"\n",
"To help understand the concepts and tools used in this notebook, we provide a brief theoretical background and context for the methods implemented here.\n",
"\n",
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip).\n",
+ "\n",
"## Overview of Functions and Methods\n",
"\n",
"This tutorial focuses on implementing and visualizing morphoelastic simulations using specialized classes and methods from `bvpy`. Here is an introduction to the main components utilized in this tutorial:\n",
diff --git a/tutorials/bvpy_tutorial_1_hello_world.ipynb b/tutorials/bvpy_tutorial_1_hello_world.ipynb
index 819f26bb05742b290d9d40e233a2a8d971e7c509..292058a77876c856b5700edd02b5c7eccfb75c89 100644
--- a/tutorials/bvpy_tutorial_1_hello_world.ipynb
+++ b/tutorials/bvpy_tutorial_1_hello_world.ipynb
@@ -14,9 +14,9 @@
"\n",
"- Basic classes: `Rectangle()` (domain), `PoissonForm()` (vform), `BVP()` and main methods/functions: `.solve()`, `.info()`, `save()`, `plot()`...\n",
"\n",
- "- Error analys.\n",
+ "- Error analysis.\n",
"\n",
- "Download the notebook: [bvpy_tutorial_1](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_1_hello_world.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
@@ -183,9 +183,11 @@
]
},
{
- "metadata": {},
"cell_type": "markdown",
- "source": "In its current state, **Bvpy** provides minimalist visualization and analysis tools. One may want to turn to other frameworks, such as **Paraview** for instance, to visualize and analyze simulation results. To do so, **Bvpy** enable the recording of simulation in the `.xdmf` format."
+ "metadata": {},
+ "source": [
+ "In its current state, **Bvpy** provides minimalist visualization and analysis tools. One may want to turn to other frameworks, such as **Paraview** for instance, to visualize and analyze simulation results. To do so, **Bvpy** enable the recording of simulation in the `.xdmf` format."
+ ]
},
{
"cell_type": "code",
@@ -194,7 +196,7 @@
"outputs": [],
"source": [
"from bvpy.utils.io import save\n",
- "save(prblm_1, '../data/tutorial_results/tuto_1_result_1.xdmf')"
+ "save(prblm_1, 'tutorial_data/tuto_1_result_1.xdmf')"
]
},
{
@@ -411,9 +413,7 @@
{
"cell_type": "markdown",
"metadata": {},
- "source": [
- "> **Note:** The `cdata` and `bdata` attributes are `MeshFunctionSizet`, *i.e.* **FEniCS** functions defined on a given mesh returning integer values. They can be useful for parametrization, as we will see in tutorial #6."
- ]
+ "source": "> **Note:** The `cdata` and `bdata` attributes are `MeshFunctionSizet`, *i.e.* **FEniCS** functions defined on a given mesh returning integer values. They can be useful for parametrization, as we will see in tutorial [Linear Elasticity](bvpy_tutorial_6_linear_elasticity.html)."
},
{
"cell_type": "markdown",
@@ -480,7 +480,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -494,7 +494,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.7.9"
+ "version": "3.9.20"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
diff --git a/tutorials/bvpy_tutorial_2_domains.ipynb b/tutorials/bvpy_tutorial_2_domains.ipynb
index 526f4776bfb4e46ee6882ca0f75b99e56bab2b95..3f070177fef36c5ef6776d2fceed01f8b0b24e0a 100644
--- a/tutorials/bvpy_tutorial_2_domains.ipynb
+++ b/tutorials/bvpy_tutorial_2_domains.ipynb
@@ -23,7 +23,7 @@
"- Generation of domains from existing files: `CustomDomain` and `CustomPolygonalDomain` classes.\n",
"\n",
"\n",
- "Download the notebook: [bvpy_tutorial_2](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_2_domains.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
@@ -392,7 +392,7 @@
"source": [
"from bvpy.domains import CustomDomain\n",
"\n",
- "path = '../data/example_meristem.ply'\n",
+ "path = 'tutorial_data/domains/example_meristem.ply'\n",
"\n",
"cd = CustomDomain.read(path)\n",
"\n",
@@ -419,7 +419,7 @@
"from bvpy.utils.visu import plot\n",
"from bvpy.domains import CustomPolygonalDomain\n",
"\n",
- "path ='../data/tissue_example_curved_big.txt'\n",
+ "path ='tutorial_data/domains/tissue_example_curved_big.txt'\n",
"\n",
"tissue = CustomPolygonalDomain.read(path)\n",
"\n",
diff --git a/tutorials/bvpy_tutorial_3_vforms.ipynb b/tutorials/bvpy_tutorial_3_vforms.ipynb
index 459e89c16fe6b788d35d016cc0367ff5dfa50488..17250c8c88c4b325cdfb4fd0376db283f79c808e 100644
--- a/tutorials/bvpy_tutorial_3_vforms.ipynb
+++ b/tutorials/bvpy_tutorial_3_vforms.ipynb
@@ -16,7 +16,7 @@
"\n",
"- Implementation of *de novo* `vform`: Definition of the variational formulation of a differential equation, instanciation of mandatory `@staticmethods`: `.construct_form()` and `.set_expression`.\n",
"\n",
- "Download the notebook: [bvpy_tutorial_3](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_3_vforms.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
@@ -321,7 +321,7 @@
"from bvpy.utils.io import save\n",
"\n",
"plot(prblm.solution)\n",
- "save(prblm.solution, '../data/tutorial_results/tuto_3_result_1.xdmf')"
+ "save(prblm.solution, 'tutorial_data/tuto_3_result_1.xdmf')"
]
}
],
diff --git a/tutorials/bvpy_tutorial_4_bnd_cond.ipynb b/tutorials/bvpy_tutorial_4_bnd_cond.ipynb
index 941388edef2808ab5f3a16125f8be6124dc884ff..c20c581cd4192354f5548a2a5595eeb145395cc4 100644
--- a/tutorials/bvpy_tutorial_4_bnd_cond.ipynb
+++ b/tutorials/bvpy_tutorial_4_bnd_cond.ipynb
@@ -23,7 +23,7 @@
"\n",
"- Example of visualization of boundary conditions when a bvp is defined.\n",
"\n",
- "Download the notebook: [bvpy_tutorial_4](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_4_bnd_cond.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
diff --git a/tutorials/bvpy_tutorial_5_reaction_diffusion.ipynb b/tutorials/bvpy_tutorial_5_reaction_diffusion.ipynb
index 864116f6a5237f55d022e961166618da92ca3564..21188ed3e4dd8b7a1ec68620ee109f350b9bcd99 100644
--- a/tutorials/bvpy_tutorial_5_reaction_diffusion.ipynb
+++ b/tutorials/bvpy_tutorial_5_reaction_diffusion.ipynb
@@ -25,7 +25,7 @@
"\n",
"\n",
"\n",
- "Download the notebook: [bvpy_tutorial_5](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_5_turing_system.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
@@ -152,16 +152,16 @@
]
},
{
- "cell_type": "code",
- "execution_count": null,
"metadata": {},
+ "cell_type": "code",
"outputs": [],
+ "execution_count": null,
"source": [
"t_min = 0\n",
"t_max = 29\n",
"dt = 0.1\n",
"\n",
- "wave_propagation.integrate(t_min, t_max, dt, '../data/tutorial_results/tuto_5_result_1.xdmf', store_steps=True)"
+ "wave_propagation.integrate(t_min, t_max, dt, 'tutorial_data/tuto_5_result_1.xdmf', store_steps=True)"
]
},
{
@@ -188,14 +188,14 @@
]
},
{
- "cell_type": "code",
- "execution_count": null,
"metadata": {},
+ "cell_type": "code",
"outputs": [],
+ "execution_count": null,
"source": [
"from IPython.display import Image\n",
"\n",
- "Image(filename='../data/tutorial_results/tuto_5_result_1_paraview_snapshot.gif.png')"
+ "Image(filename='tutorial_data/results/tuto_5_result_1_paraview_snapshot.gif.png')"
]
},
{
@@ -463,16 +463,16 @@
]
},
{
- "cell_type": "code",
- "execution_count": null,
"metadata": {},
+ "cell_type": "code",
"outputs": [],
+ "execution_count": null,
"source": [
"t_min = 0\n",
"t_max = 9\n",
"dt = 0.1\n",
"\n",
- "save_path = '../data/tutorial_results/tuto_5_result_2.xdmf'\n",
+ "save_path = 'tutorial_data/tuto_5_result_2.xdmf'\n",
"\n",
"turing_system.integrate(t_min, t_max, dt, save_path)"
]
@@ -522,16 +522,16 @@
]
},
{
- "cell_type": "code",
- "execution_count": null,
"metadata": {},
+ "cell_type": "code",
"outputs": [],
+ "execution_count": null,
"source": [
"from IPython.display import Image\n",
"\n",
- "Image(filename='../data/tutorial_results/tuto_5_result_2_paraview_snapshot.gif.png')\n",
+ "Image(filename='tutorial_data/results/tuto_5_result_2_paraview_snapshot.gif.png')\n",
"#from IPython.display import HTML\n",
- "#HTML('<img src=\"../data/tutorial_results/tuto_5_result_2_paraview_snapshot.gif\">')"
+ "#HTML('<img src=\"../tutorial_data/tutorial_results/tuto_5_result_2_paraview_snapshot.gif\">')"
]
}
],
diff --git a/tutorials/bvpy_tutorial_6_linear_elasticity.ipynb b/tutorials/bvpy_tutorial_6_linear_elasticity.ipynb
index bc3b1a80d432132175830978119d3cb0c207ec33..1625e8a77ec1e146978a37e5af8b4e4fee86bfc2 100644
--- a/tutorials/bvpy_tutorial_6_linear_elasticity.ipynb
+++ b/tutorials/bvpy_tutorial_6_linear_elasticity.ipynb
@@ -25,7 +25,7 @@
"\n",
"\n",
"\n",
- "Download the notebook: [bvpy_tutorial_6](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_6_linear_elasticity.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
@@ -273,7 +273,7 @@
"source": [
"from bvpy.utils.io import save\n",
"\n",
- "path = '../data/tutorial_results/tuto_6_result_1.xdmf'\n",
+ "path = 'tutorial_data/tuto_6_result_1.xdmf'\n",
"save(stretching, path)"
],
"outputs": [],
@@ -285,7 +285,7 @@
"source": [
"from IPython.display import Image\n",
"\n",
- "Image(filename='../data/tutorial_results/tuto_6_result_1_paraview_snapshot.png')"
+ "Image(filename='tutorial_data/results/tuto_6_result_1_paraview_snapshot.png')"
],
"outputs": [],
"execution_count": null
@@ -410,7 +410,7 @@
"source": [
"wound_displacement = wound_healing.solution\n",
"plot(wound_displacement, size=1)\n",
- "path = '../data/tutorial_results/tuto_6_result_2.xdmf'\n",
+ "path = 'tutorial_data/tuto_6_result_2.xdmf'\n",
"save(wound_healing, path)"
],
"outputs": [],
@@ -468,18 +468,14 @@
{
"cell_type": "code",
"metadata": {},
- "source": [
- "save(stress, '../data/tutorial_results/tuto_6_result_3.xdmf')"
- ],
+ "source": "save(stress, 'tutorial_data/tuto_6_result_3.xdmf')",
"outputs": [],
"execution_count": null
},
{
"cell_type": "code",
"metadata": {},
- "source": [
- "Image(filename=\"../data/tutorial_results/tuto_6_result_3_paraview_snapshot.png\")"
- ],
+ "source": "Image(filename=\"tutorial_data/results/tuto_6_result_3_paraview_snapshot.png\")",
"outputs": [],
"execution_count": null
},
@@ -508,7 +504,7 @@
"from bvpy.domains import CustomPolygonalDomain\n",
"from bvpy.utils.visu import plot\n",
"\n",
- "tissue = CustomPolygonalDomain.read(\"../data/example_domain_sepal_2D_slice.ply\",\n",
+ "tissue = CustomPolygonalDomain.read(\"tutorial_data/domains/example_domain_sepal_2D_slice.ply\",\n",
" cell_size=.5,\n",
" dim=2)\n",
"tissue.discretize()\n",
@@ -581,7 +577,7 @@
"displacement = prblm.solution\n",
"#plot(displacement, size=1, norm=True)\n",
"\n",
- "save(displacement, '../data/tutorial_results/tuto_6_result_4.xdmf')"
+ "save(displacement, 'tutorial_data/tuto_6_result_4.xdmf')"
],
"outputs": [],
"execution_count": null
@@ -610,8 +606,8 @@
"metadata": {},
"source": [
"stress = heterogeneous_elastic_response.get_stress(displacement)\n",
- "save(stress, \"../data/tutorial_results/tuto_6_result_5.xdmf\")\n",
- "Image(filename=\"../data/tutorial_results/tuto_6_result_5_paraview_snapshot.png\")"
+ "save(stress, \"tutorial_data/tuto_6_result_5.xdmf\")\n",
+ "Image(filename=\"tutorial_data/results/tuto_6_result_5_paraview_snapshot.png\")"
],
"outputs": [],
"execution_count": null
@@ -820,9 +816,9 @@
"cell_type": "code",
"metadata": {},
"source": [
- "fixed_center = [dirichlet(0, boundary='near(x, 0)', subspace=0),\n",
- " dirichlet(0, boundary='near(y, 0)', subspace=1),\n",
- " dirichlet(0, boundary='near(z, 0)', subspace=2)]"
+ "fixed_center = [dirichlet(0, boundary='near(x, 0)', subspace=0, method='pointwise'),\n",
+ " dirichlet(0, boundary='near(y, 0)', subspace=1, method='pointwise'),\n",
+ " dirichlet(0, boundary='near(z, 0)', subspace=2, method='pointwise')]"
],
"outputs": [],
"execution_count": null
@@ -851,7 +847,7 @@
"source": [
"displacement = pressurized_shell.solution\n",
"\n",
- "save(displacement, '../data/tutorial_results/tuto_6_result_6.xdmf')\n",
+ "save(displacement, 'tutorial_data/tuto_6_result_6.xdmf')\n",
"\n",
"plot(displacement, size=.25, norm=True)"
],
@@ -880,9 +876,7 @@
{
"cell_type": "code",
"metadata": {},
- "source": [
- "tissue = CustomPolygonalDomain.read('../data/example_domain_curved_cellularized_tissue.ply')"
- ],
+ "source": "tissue = CustomPolygonalDomain.read('tutorial_data/domains/example_domain_curved_cellularized_tissue.ply')",
"outputs": [],
"execution_count": null
},
@@ -958,7 +952,7 @@
"source": [
"displacement = prblm.solution\n",
"\n",
- "save(displacement, '../data/tutorial_results/tuto_6_result_7.xdmf')\n",
+ "save(displacement, 'tutorial_data/tuto_6_result_7.xdmf')\n",
"\n",
"plot(displacement, size=1000, norm=True)"
],
diff --git a/tutorials/bvpy_tutorial_7_hyper_elasticity.ipynb b/tutorials/bvpy_tutorial_7_hyper_elasticity.ipynb
index 820ce379d2b3fd275caa5567f34d8bcd063c678b..48b9fb1c98c5a6818378218dd6bea27144eac138 100644
--- a/tutorials/bvpy_tutorial_7_hyper_elasticity.ipynb
+++ b/tutorials/bvpy_tutorial_7_hyper_elasticity.ipynb
@@ -21,7 +21,7 @@
"\n",
"\n",
"\n",
- "Download the notebook: [bvpy_tutorial_7](https://gitlab.inria.fr/mosaic/publications/bvpy/-/raw/develop/tutorials/bvpy_tutorial_7_hyper_elasticity.ipynb?inline=false)."
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
@@ -684,7 +684,7 @@
" t_max = kwargs.get('t_max',2.5)\n",
" dt = kwargs.get('dt',.1)\n",
" \n",
- " save_path = kwargs.get('saving_path', '../data/tutorial_results/tuto_7_result_1.xdmf')\n",
+ " save_path = kwargs.get('saving_path', 'tutorial_data/tuto_7_result_1.xdmf')\n",
" \n",
" # -- Instancing Turing model\n",
" LE_model = CoupledTransportForm()\n",
@@ -770,7 +770,7 @@
" stress = compute_mecha_equi(concentrations)\n",
" concentrations = compute_turing_pattern(concentrations)\n",
"\n",
- " save(stress, f\"../data/tutorial_results/tuto_7_result_{1+step}.xdmf\")"
+ " save(stress, f\"tutorial_data/tuto_7_result_{1+step}.xdmf\")"
],
"outputs": [],
"execution_count": null
@@ -795,7 +795,7 @@
"source": [
"from IPython.display import Image\n",
"\n",
- "Image(filename=\"../data/tutorial_results/tuto_7_result_3_paraview_snapshot.gif.png\")"
+ "Image(filename=\"tutorial_data/results/tuto_7_result_3_paraview_snapshot.gif.png\")"
],
"outputs": [],
"execution_count": null
diff --git a/tutorials/bvpy_tutorial_8_pyvista.ipynb b/tutorials/bvpy_tutorial_8_pyvista.ipynb
index 553ecd8a7b4b15b63dae7a9134eac7f4aab10415..3e40b020ae43f3e893c96a4b1210b991f49ac57e 100644
--- a/tutorials/bvpy_tutorial_8_pyvista.ipynb
+++ b/tutorials/bvpy_tutorial_8_pyvista.ipynb
@@ -1,15 +1,17 @@
{
"cells": [
{
- "cell_type": "markdown",
- "id": "ce32e709",
"metadata": {},
+ "cell_type": "markdown",
"source": [
"\n",
"# Visualization with `PyVista`\n",
"\n",
- "This tutorial explores the use of `PyVista` for visualizing various objects within the `bvpy` library. While previous visualizations in `bvpy` primarily used `Plotly`, this tutorial demonstrates how `PyVista` can enhance the visualization experience. Users can still use `Plotly` if preferred; however, `PyVista` provides specific advantages in handling complex 3D meshes and volumetric data more efficiently.\n"
- ]
+ "This tutorial explores the use of `PyVista` for visualizing various objects within the `bvpy` library. While previous visualizations in `bvpy` primarily used `Plotly`, this tutorial demonstrates how `PyVista` can enhance the visualization experience. Users can still use `Plotly` if preferred; however, `PyVista` provides specific advantages in handling complex 3D meshes and volumetric data more efficiently.\n",
+ "\n",
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip).\n"
+ ],
+ "id": "c57d32315ff947c"
},
{
"metadata": {},
@@ -28,19 +30,19 @@
"\n",
"*Note: Visualization of tensor fields is currently not supported but will be introduced in a future release.*"
],
- "id": "1d939304979bb125"
+ "id": "a316fe34f491896a"
},
{
- "cell_type": "code",
- "id": "e8ec604b7f241a60",
"metadata": {},
+ "cell_type": "code",
+ "outputs": [],
+ "execution_count": null,
"source": [
"import pyvista as pv\n",
"import math\n",
"from bvpy.utils.visu_pyvista import visualize"
],
- "outputs": [],
- "execution_count": null
+ "id": "afbf7befc1a34a8b"
},
{
"cell_type": "markdown",
@@ -54,8 +56,10 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "6fd0fb4b-7f5d-4979-af33-ef96041d75cc",
"metadata": {},
+ "outputs": [],
"source": [
"from bvpy.domains.primitives import Cylinder\n",
"\n",
@@ -66,9 +70,7 @@
"cylinder = Cylinder(x=0, dx=L, dz=0, r=r, cell_type='triangle',\n",
" cell_size=.1, algorithm='Frontal-Delaunay', clear=True)\n",
"cylinder.discretize() # discretize (from Gmsh -> FeniCS)"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -80,29 +82,31 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "45c8981941e15904",
"metadata": {},
+ "outputs": [],
"source": [
"visualize(cylinder, visu_type='mesh')"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
"id": "9eb5b9c3fd496d6d",
"metadata": {},
- "source": "Notice that it is possible to give directly the `FeniCS` Mesh object"
+ "source": [
+ "Notice that it is possible to give directly the `FeniCS` Mesh object"
+ ]
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "b43a12b3-005d-4d2e-afc8-ce69eb00df43",
"metadata": {},
+ "outputs": [],
"source": [
"visualize(cylinder.mesh, visu_type='mesh', window_size=[600, 400]) # give the Mesh object and control the window size"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -117,12 +121,17 @@
{
"metadata": {},
"cell_type": "markdown",
- "source": "As an example, we will define a custom geometry called `CutCylinder`. This geometry represents a cylinder that is divided into two distinct subdomains. For detailed steps on generating this geometry, refer to the tutorial [Generate advanced geometries using Gmsh](bvpy_tutorial_9_gmsh).",
- "id": "497835f2c378930a"
+ "source": [
+ "\n",
+ "As an example, we will define a custom geometry called `CutCylinder`. This geometry represents a cylinder that is divided into two distinct subdomains. For detailed steps on generating this geometry, refer to the tutorial [Generate advanced geometries using Gmsh](bvpy_tutorial_9_gmsh.html)."
+ ],
+ "id": "dc47158816d1ea4d"
},
{
"metadata": {},
"cell_type": "code",
+ "outputs": [],
+ "execution_count": null,
"source": [
"from bvpy.domains.abstract import OccModel, AbstractDomain\n",
"\n",
@@ -156,19 +165,22 @@
" self.model.addPhysicalGroup(3, [right_surface], tag=2)\n",
" self.model.setPhysicalName(3, 2, \"Right_Subdomain\")"
],
- "id": "99e8589b7c70f8f9",
- "outputs": [],
- "execution_count": null
+ "id": "6547c0d4549458df"
},
{
- "metadata": {},
"cell_type": "markdown",
- "source": "We can now initialize and visualize an instance of the `CutCylinder` class, which represents the custom geometry defined above.",
- "id": "674698ebdbd01f11"
+ "id": "674698ebdbd01f11",
+ "metadata": {},
+ "source": [
+ "We can now initialize and visualize an instance of the `CutCylinder` class, which represents the custom geometry defined above."
+ ]
},
{
- "metadata": {},
"cell_type": "code",
+ "execution_count": null,
+ "id": "6b6950b42f835af5",
+ "metadata": {},
+ "outputs": [],
"source": [
"cut_cylinder = CutCylinder(length=L, radius=r,\n",
" cell_type='tetra', algorithm='Frontal-Delaunay',\n",
@@ -176,53 +188,60 @@
"cut_cylinder.discretize()\n",
"\n",
"print(f\"The available sub-domains are {cut_cylinder.sub_domain_names}\")"
- ],
- "id": "6b6950b42f835af5",
- "outputs": [],
- "execution_count": null
+ ]
},
{
- "metadata": {},
"cell_type": "code",
- "source": "visualize(cut_cylinder, visu_type='domain')",
+ "execution_count": null,
"id": "be0836fa9004f4fb",
+ "metadata": {},
"outputs": [],
- "execution_count": null
+ "source": [
+ "visualize(cut_cylinder, visu_type='domain')"
+ ]
},
{
- "metadata": {},
"cell_type": "markdown",
- "source": "Notice that it is possible to give directly the `FeniCS` MeshSizet object",
- "id": "66f4f0ee9e579385"
+ "id": "66f4f0ee9e579385",
+ "metadata": {},
+ "source": [
+ "Notice that it is possible to give directly the `FeniCS` MeshSizet object"
+ ]
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "a5be726f73bf8fa0",
"metadata": {},
- "source": "visualize(cut_cylinder.cdata, visu_type='domain', show_edges=False) # give the MeshSizet object and control the display of the edges",
"outputs": [],
- "execution_count": null
+ "source": [
+ "visualize(cut_cylinder.cdata, visu_type='domain', show_edges=False) # give the MeshSizet object and control the display of the edges"
+ ]
},
{
"cell_type": "markdown",
"id": "f5d23d182bc6da05",
"metadata": {},
- "source": "If you directly provide the `FeniCS` `MeshSizet` object, you can retrieve the sub-domain names by using the optional argument `dict_values`:"
+ "source": [
+ "If you directly provide the `FeniCS` `MeshSizet` object, you can retrieve the sub-domain names by using the optional argument `dict_values`:"
+ ]
},
{
- "metadata": {},
"cell_type": "code",
- "source": "visualize(cut_cylinder.cdata, visu_type='domain', dict_values=cut_cylinder.sub_domain_names)",
+ "execution_count": null,
"id": "8c9d36506e6a17ac",
+ "metadata": {},
"outputs": [],
- "execution_count": null
+ "source": [
+ "visualize(cut_cylinder.cdata, visu_type='domain', dict_values=cut_cylinder.sub_domain_names)"
+ ]
},
{
"cell_type": "markdown",
"id": "9bf14848-0641-4826-b4a2-d9f760344d79",
"metadata": {},
"source": [
- "### Diriclet boundary conditions\n",
+ "### Dirichlet boundary conditions\n",
"\n",
"In this section, we will visualize the Dirichlet boundary conditions to verify that they are correctly applied in the problem setup.\n",
"We will use a simple linear elastic problem where the previously defined cylinder is stretched at its ends."
@@ -230,8 +249,10 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "40f911dc-78ae-4b73-bd6d-65af44d5ed44",
"metadata": {},
+ "outputs": [],
"source": [
"from bvpy.boundary_conditions import dirichlet, Boundary\n",
"from bvpy.utils.pre_processing import HeterogeneousParameter\n",
@@ -252,9 +273,7 @@
"\n",
"### - Build the problem - ###\n",
"elastic_pb = BVP(cut_cylinder, elastic_model, bc1+bc2)"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -266,13 +285,13 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "def488a2833689cc",
"metadata": {},
+ "outputs": [],
"source": [
"visualize(elastic_pb, visu_type='dirichlet', scale=0.1, val_range=[0, 5])"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -286,36 +305,36 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "7793c8bac4680bf9",
"metadata": {},
+ "outputs": [],
"source": [
"# Available parameters from the weak form\n",
"print(f\"Available parameters from the weak form : {list(elastic_pb.vform._parameters.keys())}\")"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "467cf8b5-7433-4bac-a347-6f9f38f28360",
"metadata": {},
+ "outputs": [],
"source": [
"visualize(elastic_pb, visu_type='young')"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "ad63e001-dd9c-448b-93cc-6a6e379b753f",
"metadata": {},
+ "outputs": [],
"source": [
"# Do the same for the poisson parameter but change the camera view of the pyvista.Plotter\n",
"pl = visualize(elastic_pb, visu_type='poisson') # get the pyvisya.Plotter\n",
"pl.view_xz() # change the camera view"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -329,30 +348,30 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "d3d84515-748e-4f9b-8e12-c2a5d6e0f05c",
"metadata": {},
+ "outputs": [],
"source": [
"# - Solve the previous elastic problem\n",
"elastic_pb.solve()\n",
"\n",
"# - Visualize the resulting displacement field\n",
"visualize(elastic_pb, 'solution', scale=0.1)"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "b965cf59-d94e-4b74-b711-3e3468f37480",
"metadata": {},
+ "outputs": [],
"source": [
"print(type(elastic_pb.solution))\n",
"\n",
"# - You can also visualize any FeniCS Function\n",
"visualize(elastic_pb.solution, scale=0.1, show_mesh=False) # show directly the FeniCS Function & remove mesh"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -364,14 +383,14 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "7e77fab2-6171-4cbb-a093-348545cd9b0a",
"metadata": {},
+ "outputs": [],
"source": [
"pl = visualize(elastic_pb.solution, scale=0.1, show_mesh=False, show_plot=False) # show the FeniCS Function without the mesh\n",
"visualize(elastic_pb.domain.mesh, plotter=pl, actor_kwargs={'style':'wireframe', 'line_width': 2}) # add the mesh as a 'wireframe' & specify the edge size"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -397,8 +416,10 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "354f8ef0-2f33-44ac-a077-f451c9abe24b",
"metadata": {},
+ "outputs": [],
"source": [
"# - Some parameters\n",
"young = {1: 0.5, 2: 1.5}\n",
@@ -417,14 +438,14 @@
"\n",
"# - Compute the deformed mesh\n",
"deformed_cylinder = cut_cylinder.move(bvp.solution, return_cdata=False) # create a copy of the object & apply displacement field"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "60f96a29-b395-45d3-974c-bd74b5819cd2",
"metadata": {},
+ "outputs": [],
"source": [
"# - Define a pv.Plotter with 6 subplots (shape = (nrow, ncol))\n",
"pl = pv.Plotter(shape=(2, 3), window_size=[1000, 800])\n",
@@ -451,9 +472,7 @@
"\n",
"pl.link_views() # link the camera of the subplots\n",
"pl.show() # finally show the plot"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -467,7 +486,9 @@
"cell_type": "markdown",
"id": "1cd028f30cc62ca9",
"metadata": {},
- "source": "### Visualize sub-space of `FeniCS` object"
+ "source": [
+ "### Visualize sub-space of `FeniCS` object"
+ ]
},
{
"cell_type": "markdown",
@@ -479,15 +500,15 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "b8b0e47b3808d048",
"metadata": {},
+ "outputs": [],
"source": [
"stress = vform.get_stress(bvp.solution)\n",
"\n",
"print(f\"The stress field is a tensor field of shape {stress.ufl_shape}\")"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -499,17 +520,17 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "145fc3ce7d3ce05c",
"metadata": {},
+ "outputs": [],
"source": [
"SCALAR_BAR_ARGS = dict(title_font_size=12,\n",
" label_font_size=10,\n",
" n_labels=3,\n",
" italic=True,\n",
" fmt=\"%.1e\")"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
@@ -521,8 +542,10 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "c5619019b6d87755",
"metadata": {},
+ "outputs": [],
"source": [
"dict_sub = {'xx': 0, 'yy': 4, 'zz': 8} # FeniCS subspace index are organized in 1D --> xx, xy, xz, yx, yy, yz, zx, zy, zz\n",
"\n",
@@ -534,21 +557,23 @@
"\n",
"pl.link_views()\n",
"pl.show()"
- ],
- "outputs": [],
- "execution_count": null
+ ]
},
{
"cell_type": "markdown",
"id": "c7a5faacfdbc7609",
"metadata": {},
- "source": "### Use `Pyvista` widgets to enhance visualization options"
+ "source": [
+ "### Use `Pyvista` widgets to enhance visualization options"
+ ]
},
{
"cell_type": "markdown",
"id": "ce8999330d5618e4",
"metadata": {},
- "source": "Various `Pyvista` widgets can be used to help the visualization of `FeniCS` object. Feel free to consult the widgets from https://docs.pyvista.org/examples/03-widgets/index.html."
+ "source": [
+ "Various `Pyvista` widgets can be used to help the visualization of `FeniCS` object. Feel free to consult the widgets from https://docs.pyvista.org/examples/03-widgets/index.html."
+ ]
},
{
"cell_type": "markdown",
@@ -560,16 +585,16 @@
},
{
"cell_type": "code",
+ "execution_count": null,
"id": "ed38c8e729addf54",
"metadata": {},
+ "outputs": [],
"source": [
"pl = visualize(bvp.solution, show_plot=False, show_mesh=False, show_scalar_bar=False, actor_kwargs={'show_glyph': False}) # do not show mesh & glyph (arrows)\n",
"pl.add_mesh_clip_plane(pl.meshes[0], invert=True, assign_to_axis='y') # then retrieve the mesh and add a clip plane. Assign to one axis (can be deactivated)\n",
"pl.add_title('Displacement field\\n(with clip plane)', font_size=10)\n",
"pl.show()"
- ],
- "outputs": [],
- "execution_count": null
+ ]
}
],
"metadata": {
diff --git a/tutorials/bvpy_tutorial_9_gmsh.ipynb b/tutorials/bvpy_tutorial_9_gmsh.ipynb
index 83dcf7d6e80db3179c0532f37d9a11300d68b4dd..a663263dceef6c52ecf4df7cbce943f9f4bffeb4 100644
--- a/tutorials/bvpy_tutorial_9_gmsh.ipynb
+++ b/tutorials/bvpy_tutorial_9_gmsh.ipynb
@@ -21,7 +21,10 @@
"\n",
"> https://koehlerson.github.io/gmsh.jl/dev/examples/t1/\n",
"\n",
- "> https://gmsh.info/doc/texinfo/gmsh.html#Gmsh-tutorial"
+ "> https://gmsh.info/doc/texinfo/gmsh.html#Gmsh-tutorial\n",
+ "\n",
+ "\n",
+ "Download the tutorial notebooks and accompanying data as a ZIP file: [tutorials.zip](https://mosaic.gitlabpages.inria.fr/bvpy/tutorials.zip)."
]
},
{
diff --git a/data/example_domain_curved_cellularized_tissue.ply b/tutorials/tutorial_data/domains/example_domain_curved_cellularized_tissue.ply
similarity index 100%
rename from data/example_domain_curved_cellularized_tissue.ply
rename to tutorials/tutorial_data/domains/example_domain_curved_cellularized_tissue.ply
diff --git a/data/example_domain_sepal_2D_slice.ply b/tutorials/tutorial_data/domains/example_domain_sepal_2D_slice.ply
similarity index 100%
rename from data/example_domain_sepal_2D_slice.ply
rename to tutorials/tutorial_data/domains/example_domain_sepal_2D_slice.ply
diff --git a/data/example_meristem.ply b/tutorials/tutorial_data/domains/example_meristem.ply
similarity index 100%
rename from data/example_meristem.ply
rename to tutorials/tutorial_data/domains/example_meristem.ply
diff --git a/data/tissue_example_curved_big.txt b/tutorials/tutorial_data/domains/tissue_example_curved_big.txt
similarity index 100%
rename from data/tissue_example_curved_big.txt
rename to tutorials/tutorial_data/domains/tissue_example_curved_big.txt
diff --git a/data/tutorial_results/tuto_5_result_1_paraview_snapshot.gif.png b/tutorials/tutorial_data/results/tuto_5_result_1_paraview_snapshot.gif.png
similarity index 100%
rename from data/tutorial_results/tuto_5_result_1_paraview_snapshot.gif.png
rename to tutorials/tutorial_data/results/tuto_5_result_1_paraview_snapshot.gif.png
diff --git a/data/tutorial_results/tuto_5_result_2_paraview_snapshot.gif.png b/tutorials/tutorial_data/results/tuto_5_result_2_paraview_snapshot.gif.png
similarity index 100%
rename from data/tutorial_results/tuto_5_result_2_paraview_snapshot.gif.png
rename to tutorials/tutorial_data/results/tuto_5_result_2_paraview_snapshot.gif.png
diff --git a/data/tutorial_results/tuto_6_result_1_paraview_snapshot.png b/tutorials/tutorial_data/results/tuto_6_result_1_paraview_snapshot.png
similarity index 100%
rename from data/tutorial_results/tuto_6_result_1_paraview_snapshot.png
rename to tutorials/tutorial_data/results/tuto_6_result_1_paraview_snapshot.png
diff --git a/data/tutorial_results/tuto_6_result_3_paraview_snapshot.png b/tutorials/tutorial_data/results/tuto_6_result_3_paraview_snapshot.png
similarity index 100%
rename from data/tutorial_results/tuto_6_result_3_paraview_snapshot.png
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diff --git a/data/tutorial_results/tuto_6_result_5_paraview_snapshot.png b/tutorials/tutorial_data/results/tuto_6_result_5_paraview_snapshot.png
similarity index 100%
rename from data/tutorial_results/tuto_6_result_5_paraview_snapshot.png
rename to tutorials/tutorial_data/results/tuto_6_result_5_paraview_snapshot.png
diff --git a/data/tutorial_results/tuto_7_result_3_paraview_snapshot.gif.png b/tutorials/tutorial_data/results/tuto_7_result_3_paraview_snapshot.gif.png
similarity index 100%
rename from data/tutorial_results/tuto_7_result_3_paraview_snapshot.gif.png
rename to tutorials/tutorial_data/results/tuto_7_result_3_paraview_snapshot.gif.png