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Commit 8cd87c72 authored by PETIT Manuel's avatar PETIT Manuel
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Merge remote-tracking branch 'origin/release/1.3.0'

parents b0ba7893 95fc7e13
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Pipeline #1095834 passed with warnings
Stage: build
    Stage: test
      Stage: deploy
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        .gitignore
        + 2
        − 0
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        ......@@ -108,3 +108,5 @@ doc/notebook.rst
        doc/README.rst
        doc/tutorials.rst
        *jitfailure-dolfin*/
        /doc/utils/
        /doc/_static/growth_scheme.png
        .gitlab-ci.yml
        + 12
        − 4
        View file @ 8cd87c72
        ......@@ -51,10 +51,16 @@ coverage:
        - python -m pip install -e .[test]
        # Test it with `pytest`:
        - pytest --version
        - pytest -v --cov=bvpy test/
        - pytest -v --cov=bvpy test/ --cov-report=term --cov-report=xml
        retry:
        max: 2
        when: runner_system_failure
        coverage: '/TOTAL.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
        artifacts:
        paths:
        - coverage.xml
        when: always
        expire_in: 7 days
        only:
        - develop
        - master
        ......@@ -94,8 +100,8 @@ pages:
        - large
        image: continuumio/miniconda3
        script:
        # Install required 'libgl1' system dependency:
        - apt-get update && apt-get install libgl1 wget -y
        # Install required 'libgl1' & 'pyvista xvfb' system dependency:
        - apt-get update && apt-get install libgl1 libgl1-mesa-glx xvfb wget -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
        ......@@ -116,13 +122,15 @@ pages:
        expire_in: 1 hour
        paths:
        - public
        exclude:
        - public/*.ipynb
        dependencies: []
        rules:
        - if: $CI_COMMIT_BRANCH =~ /^release/
        when: manual
        allow_failure: true
        - if: '$CI_COMMIT_BRANCH == "develop"'
        when: manual
        when: always
        allow_failure: true
        - if: '$CI_COMMIT_BRANCH == "master"'
        when: on_success
        ......
        .pkglts/clean.no deleted 100644 → 0
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        .pkglts/pkg_cfg.json deleted 100644 → 0
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        View file @ b0ba7893
        {
        "_pkglts": {
        "auto_install": true,
        "install_front_end": "stdout",
        "use_prompts": false,
        "version": 13
        },
        "base": {
        "authors": [
        [
        "Florian Gacon",
        "florian.gacon@inria.fr"
        ]
        ],
        "namespace": null,
        "pkgname": "bvpy",
        "url": null
        },
        "coverage": {},
        "doc": {
        "description": "A package implementing Boundary Value Problem.",
        "fmt": "rst",
        "keywords": []
        },
        "git": {},
        "license": {
        "name": "cecill-c",
        "organization": "INRIA",
        "project": "{{ base.pkgname }}",
        "year": 2020
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        "test": {
        "suite_name": "pytest"
        },
        "version": {
        "major": 1,
        "minor": 0,
        "post": 1
        }
        }
        .pkglts/pkg_hash.json deleted 100644 → 0
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        View file @ b0ba7893
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        \ No newline at end of file
        .pkglts/pkg_version.json deleted 100644 → 0
        + 0
        − 13
        View file @ b0ba7893
        {
        "base": "5.2.0",
        "coverage": "5.2.0",
        "doc": "5.2.0",
        "git": "5.2.0",
        "license": "5.2.0",
        "pysetup": "5.2.0",
        "reqs": "5.2.0",
        "sphinx": "5.2.0",
        "src": "5.2.0",
        "test": "5.2.0",
        "version": "5.2.0"
        }
        \ No newline at end of file
        .pkglts/regenerate.no deleted 100644 → 0
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        − 0
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        HISTORY.rst
        + 52
        − 0
        View file @ 8cd87c72
        ......@@ -6,3 +6,55 @@ creation (2020-08-26)
        ------------------------
        * First release on PyPI.
        version 1.3.0 (2025-01-11)
        --------------------------
        ### **Bug Fixes**
        - Fixed normal computation in the `boundary_normal` function for 3D cases.
        ---
        ### **New Features**
        1. **API Enhancements for Hyperelastic Models**
        - Introduced new classes for potential energy models:
        - `NeoHookeanPotential`
        - `StVenantKirchoffPotential`
        - `QuadraticGreenLagrangePotential`
        - Updated the API of `HyperElasticForm` to now require a potential energy as an argument. This change simplifies the implementation of new potential energy models.
        2. **Morphoelastic Problem Modeling**
        - Added `MorphoElasticForm` and `GBVP` classes to support modeling morphoelastic problems.
        3. **Domain and Mesh Handling**
        - Added `CustomDomainGmsh` class, which allows loading `.msh` files for working with complex domains.
        4. **Growth Laws and Heterogeneous Growth**
        - Added classes for different growth laws:
        - `ConstantGrowth`
        - `TimeDependentGrowth`
        - `StrainDependentGrowth`
        - Introduced the `HeterogeneousGrowth` class, enabling assignment of different growth laws to various subdomains.
        5. **Boundary Conditions Enhancement**
        - Improved boundary condition handling. Boundary conditions can now be scalar, vector, or tensor values with variables, increasing flexibility.
        ---
        ### **Documentation and Tutorials**
        - Added new tutorials:
        - **Visualization**: Demonstrations using `pyvista`.
        - **Domain Creation**: Tutorials on working with complex domains using `gmsh`.
        - **Morphoelastic Problems**: Examples of handling morphoelastic problems.
        README.rst
        + 6
        − 2
        View file @ 8cd87c72
        ......@@ -13,10 +13,14 @@ Despite this biological motivation, the **Bvpy** library has been implemented in
        .. sidebar:: **Bvpy**
        :Lead Development: Florian Gacon
        :Lead Development: Manuel Petit
        :Coordination: Olivier Ali
        :Main Contributors: Florian Gacon
        :Other Contributors: Guillaume Cerutti, Adrien Heymans, Jonathan Legrand
        :Active team: Inria project team `Mosaic <https://team.inria.fr/mosaic/>`_
        :Institutes: `Inria <http://www.inria.fr>`_
        ......@@ -61,7 +65,7 @@ You will need conda in order to install ``bvpy``, you can download it `here <ht
        git clone https://gitlab.inria.fr/mosaic/bvpy.git
        cd bvpy
        conda create -n bvpy-dev -c conda-forge "python=3.9" "fenics=2019.1.0"
        conda env create --file conda/env.yaml -n bvpy-dev
        conda activate bvpy-dev
        python -m pip install -e .
        ......
        conda/env.yaml
        + 2
        − 1
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        ......@@ -5,4 +5,5 @@ channels:
        dependencies:
        - python=3.9
        - python-gmsh=4.11.1
        - fenics=2019.1.0
        \ No newline at end of file
        - fenics=2019.1.0
        - h5py
        \ No newline at end of file
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        doc/_static/css/custom.css
        + 1
        − 1
        View file @ 8cd87c72
        ......@@ -5,5 +5,5 @@
        float: right;
        }
        .wy-nav-content {
        max-width: 1000px !important;
        max-width: 1200px !important;
        }
        doc/conf.py
        + 53
        − 34
        View file @ 8cd87c72
        ......@@ -15,43 +15,65 @@
        # serve to show the default.
        import os
        import re
        import sys
        import shutil
        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')
        # -------------------- Import Readme --------------------
        # -------------------- Copy images --------------------
        source_dir = '../tutorials/images'
        target_dir = './_static'
        os.system('cp ../README.rst .')
        print('import file: README.rst')
        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_domain.ipynb',
        'bvpy_tutorial_1_hello_world.ipynb',
        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']
        for i in notebooks:
        if '.' != i[0] and i in to_import:
        print('import file: '+i)
        os.system('cp ../tutorials/'+i+' '+i)
        with open("tutorials.rst","w+") as f:
        '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")
        ......@@ -100,17 +122,19 @@ extensions = [
        'sphinx.ext.todo',
        'sphinx.ext.viewcode',
        'nbsphinx',
        'recommonmark'
        'recommonmark',
        'pyvista.ext.plot_directive',
        'pyvista.ext.viewer_directive',
        'sphinx_design'
        ]
        # Enable plotly figure in the docs
        # Enable plotly figures and add custom CSS for hiding cells with `remove_cell` tags
        nbsphinx_prolog = r"""
        .. raw:: html
        <script src='http://cdnjs.cloudflare.com/ajax/libs/require.js/2.1.10/require.min.js'></script>
        <script>require=requirejs;</script>
        """
        nbsphinx_timeout = -1
        ......@@ -118,11 +142,11 @@ nbsphinx_timeout = -1
        # 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
        #try:
        # import matplotlib.sphinxext.plot_directive
        # extensions.append('matplotlib.sphinxext.plot_directive')
        #except ImportError:
        # pass
        ......@@ -158,9 +182,9 @@ copyright = u"2020, bvpy"
        #
        # The short X.Y version.
        version = "1.0.1"
        version = "1.3.0"
        # The full version, including alpha/beta/rc tags.
        release = "1.0.1"
        release = "1.3.0"
        # The language for content autogenerated by Sphinx. Refer to documentation
        ......@@ -290,14 +314,10 @@ htmlhelp_basename = "bvpydoc"
        # -- Options for LaTeX output ------------------------------------------
        latex_elements = {
        # The paper size ('letterpaper' or 'a4paper').
        # 'papersize': 'letterpaper',
        # The font size ('10pt', '11pt' or '12pt').
        # 'pointsize': '10pt',
        # Additional stuff for the LaTeX preamble.
        # 'preamble': '',
        'preamble': r'''
        \usepackage{amsmath} % For math expressions
        \usepackage{amssymb} % For symbols like \nabla
        ''',
        }
        # Grouping the document tree into LaTeX files. List of tuples
        ......@@ -370,7 +390,6 @@ texinfo_documents = [
        # If true, do not generate a @detailmenu in the "Top" node's menu.
        # texinfo_no_detailmenu = False
        # use apidoc to generate developer doc
        try:
        from sphinx.ext.apidoc import main
        ......
        doc/index.rst
        + 11
        − 11
        View file @ 8cd87c72
        .. image:: https://gitlab.inria.fr/mosaic/bvpy/badges/develop/coverage.svg
        :target: https://gitlab.inria.fr/mosaic/bvpy
        :target: https://gitlab.inria.fr/mosaic/bvpy/-/commits/develop
        .. image:: https://gitlab.inria.fr/mosaic/bvpy/badges/master/pipeline.svg
        :target: https://gitlab.inria.fr/mosaic/bvpy/pipelines
        .. image:: https://anaconda.org/mosaic/bvpy/badges/platforms.svg
        :target: https://anaconda.org/conda-forge/bvpy
        :target: https://anaconda.org/MOSAIC/bvpy
        .. image:: https://img.shields.io/conda/vn/conda-forge/bvpy.svg
        :target: https://anaconda.org/conda-forge/bvpy
        .. image:: https://anaconda.org/mosaic/bvpy/badges/version.svg
        :target: https://anaconda.org/MOSAIC/bvpy/files
        .. image:: https://anaconda.org/mosaic/bvpy/badges/license.svg
        :target: https://www.gnu.org/licenses/lgpl-3.0.txts
        .. image:: https://img.shields.io/badge/license-LGPL3-black
        :target: https://www.gnu.org/licenses/lgpl-3.0.html
        .. image:: https://anaconda.org/conda-forge/bvpy/badges/latest_release_date.svg
        :target: https://anaconda.org/conda-forge/bvpy
        .. image:: https://anaconda.org/mosaic/bvpy/badges/latest_release_date.svg
        :target: https://anaconda.org/MOSAIC/bvpy
        .. image:: https://anaconda.org/conda-forge/bvpy/badges/downloads.svg
        :target: https://anaconda.org/conda-forge/bvpy
        .. image:: https://anaconda.org/mosaic/bvpy/badges/downloads.svg
        :target: https://anaconda.org/MOSAIC/bvpy
        .. toctree::
        :caption: Table of contents
        ......@@ -31,4 +31,4 @@
        Sources <_dvlpt/modules>
        .. include:: README.rst
        .. include:: ../README.rst
        doc/utils/__init__.py 0 → 100644
        + 2
        − 0
        View file @ 8cd87c72
        #!/usr/bin/env python3
        # -*- coding: utf-8 -*-
        \ No newline at end of file
        doc/utils/convert_notebook.py 0 → 100644
        + 74
        − 0
        View file @ 8cd87c72
        import nbformat
        import re
        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.
        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)
        https://github.com/pyvista/pyvista/issues/5389 --> labelled scalar bar
        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
        dynamic_plot : bool, optional
        make the pyvista plot dynamic or static, by default False.
        """
        # 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:
        # 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"
        "# ---- end of online doc only ---- #"
        )
        )
        # Add metadata to hide the new cell in Sphinx-generated documentation
        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
        with open(output_path, 'w') as f:
        nbformat.write(nb, f)
        \ No newline at end of file
        pyproject.toml
        + 16
        − 4
        View file @ 8cd87c72
        [project]
        name = "bvpy"
        version = "1.1.0"
        version = "1.3.0"
        description = "A package implementing Boundary Value Problem."
        authors = [
        {name="Florian Gacon", email="florian.gacon@inria.fr"},
        ......@@ -12,14 +12,14 @@ maintainers= [
        readme = "README.rst"
        requires-python = ">=3.9, <4"
        dependencies = [
        "numpy<2",
        "numpy<1.25",
        "meshio",
        "importlib_metadata",
        "plotly",
        "pyvista[all]",
        "typing_extensions",
        "h5py",
        "nbformat>=4.2.0",
        "scipy"
        ]
        license = {file = "LICENSE"}
        ......@@ -38,7 +38,19 @@ doc = [
        "notebook",
        "chardet",
        "recommonmark",
        ]
        "pandoc",
        "pydata-sphinx-theme",
        "pypandoc",
        "pytest-sphinx",
        "sphinx-autobuild",
        "sphinx-copybutton",
        "sphinx-design",
        "sphinx-gallery",
        "sphinx-toolbox",
        "sphinxcontrib-asciinema",
        "sphinxcontrib-websupport",
        "typed-ast"
        ] # to visualize pyvista from notebooks
        test = [
        "pytest",
        "pytest-cov",
        ......
        src/bvpy/boundary_conditions/boundary.py
        + 1
        − 1
        View file @ 8cd87c72
        ......@@ -198,7 +198,7 @@ class Boundary(object):
        """
        if meshfunc is not None:
        self._domain.mark(meshfunc, valueTrue)
        self._domain.mark(meshfunc, valueTrue) # this mark the subdomain meshfunc using the condition
        else:
        meshfunc = fe.MeshFunction(type, mesh, dim_topology)
        meshfunc.set_all(valueFalse)
        ......
        src/bvpy/boundary_conditions/dirichlet.py
        + 19
        − 12
        View file @ 8cd87c72
        ......@@ -23,16 +23,10 @@ import fenics as fe
        from bvpy import logger
        import numpy as np
        from sympy import Symbol
        from sympy.parsing.sympy_parser import parse_expr
        from .boundary import Boundary
        from bvpy.domains.geometry import boundary_normal
        _XYZ = {'x': Symbol('x[0]'),
        'y': Symbol('x[1]'),
        'z': Symbol('x[2]')}
        from bvpy.utils.pre_processing import create_expression, _stringify_expression_from_string
        class ConstantDirichlet(object):
        """Defines a constant Dirichlet condition on a domain.
        ......@@ -121,10 +115,21 @@ class ConstantDirichlet(object):
        class VariableDirichlet(object):
        """Defines a variable Dirichlet condition on a domain.
        The `val` argument allows to pass a string expression that can be :
        val = "sin(x) + cos(y)" # scalar
        val = "(x, y * pow(x,2))" # vector
        Tensor expressions of rank 2 (matrices) may also be created:
        val = "((exp(x), sin(y)),
        (sin(x), tan(y))"
        See <cmath> for the available functions. https://cplusplus.com/reference/cmath/
        """
        def __init__(self, val, boundary="all",
        method='topological', subspace=None, degree=None):
        method='topological', subspace=None, degree=None, **kwargs):
        """Generator of the VariableDirichlet class.
        Parameters
        ......@@ -161,6 +166,7 @@ class VariableDirichlet(object):
        self._method = method
        self._subspace = subspace
        self._degree = degree
        self._extra_kwargs = kwargs
        def apply(self, functionSpace):
        """Applies the specified condition on the actual function space.
        ......@@ -177,12 +183,13 @@ class VariableDirichlet(object):
        The boundary condition in a fenics-readable format.
        """
        parse = parse_expr(self._val, local_dict=_XYZ, evaluate=False)
        # Pre-format the input value (if vector or tensor)
        val = _stringify_expression_from_string(self._val)
        if self._degree is None:
        expr = fe.Expression(str(parse),
        element=functionSpace.ufl_element())
        expr = create_expression(val, functionspace=functionSpace, **self._extra_kwargs)
        else:
        expr = fe.Expression(str(parse), degree=self._degree)
        expr = create_expression(val, degree=self._degree, **self._extra_kwargs)
        if self._subspace is None:
        dir = fe.DirichletBC(functionSpace, expr,
        ......
        src/bvpy/bvp.py
        + 8
        − 16
        View file @ 8cd87c72
        ......@@ -318,26 +318,18 @@ class BVP(object):
        Parameters
        ----------
        bnd_cond : :class:`ConstantDirichlet<femtk.boundary_conditions.
        dirichlet.ConstantDirichlet>`,
        :class:`VariableDirichlet<femtk.boundary_conditions.
        dirichlet.VariableDirichlet>`
        Class representing a boundary condition
        method : str
        Optional (default is 'topological'). Method to apply Dirichlet
        condition.
        subspace : int or None
        Optional (default is None). Index of the subspace
        to constrain for Dirichlet.
        degree : int or None
        Optional (default is None). Determines the degree for
        :class:`VariableDirichlet<femtk.boundary_conditions.
        dirichlet.VariableDirichlet>`
        bnd_cond : :class:`ConstantDirichlet <femtk.boundary_conditions.dirichlet.ConstantDirichlet>`, :class:`VariableDirichlet <femtk.boundary_conditions.dirichlet.VariableDirichlet>`
        Class representing a boundary condition.
        method : str, optional
        Method to apply Dirichlet condition (default is 'topological').
        subspace : int or None, optional
        Index of the subspace to constrain for Dirichlet (default is None).
        degree : int or None, optional
        Determines the degree for :class:`VariableDirichlet <femtk.boundary_conditions.dirichlet.VariableDirichlet>` (default is None).
        Returns
        -------
        None
        """
        if not isinstance(bnd_cond, (list, tuple)):
        bnd_cond = [bnd_cond]
        ......
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