Merge branch 'release/1.0.1'

.gitignore

@@ -85,6 +85,9 @@ target/
 
 # svn
 .svn
+.cache/
+.pytest_cache/
+
 # coverage
 .coverage
 
@@ -102,4 +105,6 @@ doc/*.ipynb
 *.h5
 *.xdmf
 doc/notebook.rst
+doc/README.rst
+doc/tutorials.rst
 *jitfailure-dolfin*/

.gitlab-ci.yml

@@ -36,8 +36,7 @@ coverage:
   - conda env create -f conda/env.yaml
   - source activate bvpy
   - conda install conda-bld/linux-64/bvpy-*
-  - nosetests -v -x
-  - coverage report
+  - pytest --cov=bvpy -v -x
   retry:
     max: 2
     when: runner_system_failure
@@ -109,7 +108,6 @@ pages:
       - if: '$CI_COMMIT_BRANCH == "master"'
         when: on_success
 
-
 docker_build_deploy:
   image: docker:latest
   stage: deploy

.pkglts/pkg_cfg.json

@@ -47,11 +47,11 @@
     "namespace_method": "pkg_util"
   },
   "test": {
-    "suite_name": "nose"
+    "suite_name": "pytest"
   },
   "version": {
     "major": 1,
     "minor": 0,
-    "post": 0
+    "post": 1
   }
 }

.pkglts/pkg_hash.json

@@ -3,11 +3,11 @@
     "coverage": "Wdw0A46bthKCXu+bEDTYhUqOiC6oO1z6vr7BJzujMEDHrqYW6nwpebmtffbKEeQtJ+CllE6GyQ/S+E7WsGRN7g=="
   },
   ".gitignore": {
-    "git": "PQc3hvWK2Bkdaz48B41hV3wb8vasE0g/tt4SgjNxfsaUQQhe7V17qjwtDkE6q9ySjgQDSww10SmmibMnn8gT/A=="
+    "git": "77pwFZlnA/vkpAcyacCHkz6TTwwEUrNQspX9U4c8JSQ39A5NazBHfQFpmcWz/3L46HRH+X+RJ+4jFW9RXvs4MA=="
   },
   "AUTHORS.rst": {
     "doc.authors": "8m7WJgCsHuCrAK8j/orSy/0v36/TEHawg8zn8Fu98kw0G5doIGOSaOLizrkp3e/TCOaxTeCqFHaFmHMByRfgFA==",
-    "doc.contributors": "4ogNKmPWl19ent0JBpc2GefSpdxSyIp17Yq2XIzy5qF7fu6/rkRWPH+NvC1qURedbsgGOO10huCWl+opq16MfA=="
+    "doc.contributors": "pi2IMJvG9beHzzq+o4FlhAA4ncMolpvZrv9pDljrVTdaiwfXeiTySLkG7Rr1N57HcZAb5lJ9dRe1w5l+qOXtTg=="
   },
   "CONTRIBUTING.rst": {},
   "HISTORY.rst": {},
@@ -28,20 +28,20 @@
     "sphinx": "E9sFsnXAm9uPYBn7f0Qb6edct0UKizsXRIJyjZISRCjHbT2HldXK4GIj1yO69R/OVSfnmdAX5lzXQ4wONQNFgA=="
   },
   "requirements.txt": {
-    "reqs": "UY5N7ID42/r9fOX60LaDbFpZbuuklWjYPbn0oq7n3f2WOZ5MnrYZmCatYavLkr8alDbpcD5nN12JBNa52txGzA=="
+    "reqs": "T02TvsmYi9qrLOKFmlKzraUSIwfedls+Z0iG0JzFrz4SlI/wb3QrTsPofbdJV2KE2GA/Q3/j5YeZaVHnC5nN6g=="
   },
   "requirements_minimal.txt": {
     "reqs": "AWuoxM/eZa+Zy1+ouKN+Lrc/SBs640mRZm3y4E/rbAOGZuvR7CtvYjlndWAzxwLd5fQj99R6tu0YJ/9TeDcx9w=="
   },
   "setup.cfg": {
     "sphinx": "mYLeHXWNqXwTk9eWxY4wTrltnDTrAHQvl0l+kosuIfAgrbAuhWMgySq4WR2Y855Q5HDAtGZY7Pnt+BAU6niXIg==",
-    "test.nose": "8BEO3bAAzFeAdtXqubagljVsKlDTTlPhxqeM7FqH6eWNEjAPsfMimlW5LBo35uzE2WbJh7gL4SpkKuNlMU/LsA==",
-    "test.pytest": "vmiIOMqGhuXJBom/KrWFzvETfJmbSMcLkvZ6XDTcFWl7XRHJgu1tcb4eHn97TgcziEqpfD96M5qO0DV3z3S+CQ==",
+    "test.nose": "vmiIOMqGhuXJBom/KrWFzvETfJmbSMcLkvZ6XDTcFWl7XRHJgu1tcb4eHn97TgcziEqpfD96M5qO0DV3z3S+CQ==",
+    "test.pytest": "R5P5XMaQxSXsNQJ3hXYY45iLvnl8Mbec6XuIaFTum52gym+wTM2TfEbW/N2doHNaCkpdAWg07oblbYi15AwQkA==",
     "wheel": "vUJZkCvbK4LQuEURneKnX/SNIwhJ9/9EaT5T6Uw1K1fauKFFiHnq1DTDES7cgBD0OANelyvwCCZO/rV4Iok+ag=="
   },
   "setup.py": {
     "pysetup.call": "t30iIuCMd/sWxStR2XNYb8bCBgwanhKt8YYn2VKACyAqL5cKFRUWpVRIpAR+uxXUZ9PYYy2csMmECcONnRZE8w==",
-    "pysetup.kwds": "f4aACD9E05zMLYsGLGCmuXYWoJYRxvBWIPnYpSODKQihBS2+4TDmMjPDlKAUsZrUN88JKQhdIOxsqmZMdV0+OQ=="
+    "pysetup.kwds": "cAzFCKINVCtdrW5WhuidyviQrjIRX8YUv/rk3SF+rIsw8qmZw/sHOk10U61j0JP5yPh3jTQcLE3CRoC59uJl7A=="
   },
   "src/bvpy/__init__.py": {
     "src": "L2dZgUBRC5qv3o09+1CbMcgYfQtR1ZNSvP8KlP8REQazZiAQAktALjpCC2ijdxvKPv/tN9KsZrzNW+lZMszSfg==",

.pkglts/pkg_version.json

 {
-  "base": "5.1.9",
-  "coverage": "5.1.9",
-  "doc": "5.1.9",
-  "git": "5.1.9",
-  "license": "5.1.9",
-  "pysetup": "5.1.9",
-  "reqs": "5.1.9",
-  "sphinx": "5.1.9",
-  "src": "5.1.9",
-  "test": "5.1.9",
-  "version": "5.1.9"
+  "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

AUTHORS.rst

@@ -16,11 +16,6 @@ Contributors
 
 .. {# pkglts, doc.contributors
 
-* Florian <florian.gacon@inria.fr>
-* Olivier Ali <olivier.ali@inria.fr>
-* Florian <florian.gacon@gmail.com>
-* GACON Florian <florian.gacon@inria.fr>
-* Christophe Godin <christophe.godin@inria.fr>
 * ALI Olivier <olivier.ali@inria.fr>
 
 .. #}

README.rst

-========================
-``bvpy``
-========================
+Welcome
+-------
 
-.. {# pkglts, doc
+**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...).
 
-Package providing tools to solve BVP (Boundary Value Problem) and IBVP (Initial Boundary Value Problem).
+Despite this biological motivation, the **Bvpy** library has been implemented in an *agnostic* manner that makes it suitable for many other scientific context.
 
-It rely on FEniCS finite element library (https://fenicsproject.org/) and GMSH (http://gmsh.info/).
 
-The doc can be found  `here <https://mosaic.gitlabpages.inria.fr/bvpy>`_.
+.. sidebar:: **Bvpy**
 
-:Lead Development: Florian Gacon
+  :Lead Development: Florian Gacon
 
-:Coordination: Olivier Ali
+  :Coordination: Olivier Ali
 
-:Active team: Inria project team `Mosaic <https://team.inria.fr/mosaic/>`_
+  :Active team: Inria project team `Mosaic <https://team.inria.fr/mosaic/>`_
 
-:Institutes: `Inria <http://www.inria.fr>`_
+  :Institutes: `Inria <http://www.inria.fr>`_
 
-:Language: Python
+  :Language: Python
 
-:Supported OS: Linux, MacOS
+  :Supported OS: Linux, MacOS
 
-:Licence: `Cecill-C`
+  :Licence: `LGPL`
 
-:Funding: Inria ADT Gnomon (Christophe Godin)
+  :Funding: Inria ADT Gnomon (Christophe Godin)
+
+
+Documentation
+-------------
+
+The documentation can be found `here <https://mosaic.gitlabpages.inria.fr/bvpy/>`_.
+
+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 3.7+
+* FEniCS
+* GMSH
 
 
 Installation
@@ -49,7 +67,7 @@ You will need conda in order to install ``bvpy``, you can download it  `here <ht
 
 .. code-block:: bash
 
-	conda install -c mosaic -c conda-forge bvpy
+	conda install -c conda-forge bvpy
 
 
 - From docker
@@ -72,14 +90,46 @@ And use the URL on the terminal to open the tutorials.
 Test
 ----
 
-If you install ``bvpy`` from anaconda install ``nose`` and ``coverage`` inside your environment:
+If you install ``bvpy`` from anaconda install ``pytest`` and ``pytest-cov`` inside your environment:
 
 .. code-block:: bash
 
-	conda install -c conda-forge nose coverage
+	conda install -c conda-forge pytest pytest-cov
 
 And then run at the root of the project:
 
 .. code-block:: bash
 
-	nosetests -v
+	pytest -v
+
+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{gacon_2021,
+  doi = {xxx},
+  url = {xxx},
+  year = {2021},
+  publisher = {xxx},
+  volume = {x},
+  number = {xx},
+  pages = {xxxx},
+  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}
+  }

conda/env.yaml

@@ -7,8 +7,8 @@ dependencies:
   - ipython
   - numpy
   - python-gmsh=4.5.6
-  - nose
-  - coverage
+  - pytest
+  - pytest-cov
   - meshio
   - fenics
   - importlib_metadata
@@ -21,3 +21,4 @@ dependencies:
   - make
   - nbsphinx
   - recommonmark
+  - typing_extensions

conda/meta.yaml

@@ -20,7 +20,6 @@ requirements:
   - ipython
   - numpy
   - python-gmsh=4.5.6
-  - nose
   - meshio
   - fenics
   - importlib_metadata

doc/conf.py

@@ -22,6 +22,12 @@ import sys
 def setup(app):
     app.add_css_file('css/custom.css')
 
+# -------------------- Import Readme --------------------
+
+
+os.system('cp ../README.rst .')
+print('import file: README.rst')
+
 # -------------------- Import Notebooks --------------------
 
 for file in os.listdir('.'):
@@ -36,11 +42,12 @@ to_import = ['bvpy_tutorial_domain.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_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)
+        print('import file: '+i)
         os.system('cp ../tutorials/'+i+' '+i)
 
 
@@ -150,9 +157,9 @@ copyright = u"2020, bvpy"
 #
 
 # The short X.Y version.
-version = "1.0.0"
+version = "1.0.1"
 # The full version, including alpha/beta/rc tags.
-release = "1.0.0"
+release = "1.0.1"
 
 
 # The language for content autogenerated by Sphinx. Refer to documentation

doc/index.rst

-.. include:: substitutions.txt
+.. image:: https://gitlab.inria.fr/mosaic/bvpy/badges/develop/coverage.svg
+  :target: https://gitlab.inria.fr/mosaic/bvpy
 
-========================
-Bvpy
-========================
-
-.. image:: https://gitlab.inria.fr/mosaic/work-in-progress/bvpy/badges/develop/coverage.svg
-  :target: https://gitlab.inria.fr/mosaic/work-in-progress/bvpy
-
-.. image:: https://gitlab.inria.fr/mosaic/work-in-progress/bvpy/badges/develop/pipeline.svg
-  :target: https://gitlab.inria.fr/mosaic/work-in-progress/bvpy/pipelines
+.. 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/MOSAIC/bvpy
+  :target: https://anaconda.org/conda-forge/bvpy
 
-.. image:: https://anaconda.org/mosaic/bvpy/badges/version.svg
-  :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/license.svg
-  :target: https://cecill.info/licences/Licence_CeCILL-C_V1-en.txt
+  :target: https://www.gnu.org/licenses/lgpl-3.0.txts
 
-.. 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/latest_release_date.svg
+  :target: https://anaconda.org/conda-forge/bvpy
 
-.. image:: https://anaconda.org/mosaic/bvpy/badges/downloads.svg
-  :target: https://anaconda.org/MOSAIC/bvpy
+.. image:: https://anaconda.org/conda-forge/bvpy/badges/downloads.svg
+  :target: https://anaconda.org/conda-forge/bvpy
 
 .. toctree::
    :caption: Table of contents
@@ -37,86 +31,4 @@ Bvpy
    Sources <_dvlpt/modules>
 
 
-Welcome
--------
-
-**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 given in eq.$(\ref{eq:bvp})$. 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:: |name|
-
-  :Lead Development: Florian Gacon
-
-  :Coordination: Olivier Ali
-
-  :Active team: Inria project team `Mosaic <https://team.inria.fr/mosaic/>`_
-
-  :Institutes: `Inria <http://www.inria.fr>`_
-
-  :Language: Python
-
-  :Supported OS: Linux, MacOS
-
-  :Licence: `Cecill-C`
-
-  :Funding: Inria ADT Gnomon (Christophe Godin)
-
-
-Requirements
-------------
-
-* Python 3.6+
-* FEniCS
-* GMSH
-
-
-Installation
-------------
-
-In order to install ``bvpy`` you will need `conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/>`_.
-
-* From sources:
-
-.. code-block:: bash
-
-  git clone https://gitlab.inria.fr/mosaic/bvpy.git
-  cd bvpy
-  conda env create -f conda/env.yaml -n bvpy-dev
-  conda activate bvpy-dev
-  python setup.py develop --prefix=$CONDA_PREFIX
-
-
-* On `Anaconda Cloud <https://anaconda.org/mosaic/bvpy>`_:
-
-.. code-block:: bash
-
-	conda install -c mosaic -c conda-forge bvpy
-
-
-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 :ref:`here<general_introduction>`.
-
-A detailed description of the main classes and moduels of the library can be found :ref:`here<library_description>`.
-
-Some tutorials explaining basic manipulations are gathered :ref:`here<tutorials>`.
-
-.. Finally, the technical description (docblocks) of all the classes and modules can be found :ref:`here<_src>`.
-
-
-Contents
---------
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-
-Licence
--------
-
-You can distribute and/or modify **Bvpy** under the terms of the Inria licence. If **Bvpy** contributes to a project that leads to a scientific publication, please acknowledge this work by Citing the project.z
+.. include:: README.rst

doc/library_description.rst

 .. _library_description:
 
+.. math::
+  \newcommand{\euclid}[1]{\mathbb{R}^{#1}}
+  \newcommand{\pos}{\boldsymbol{x}}
+  \newcommand{\field}{u}
+  \newcommand{\source}{g}
+  \newcommand{\body}{\Omega}
+  \newcommand{\surf}{\partial\body}
+  \newcommand{\grad}[1]{\boldsymbol{\nabla}(#1)}
+  \newcommand{\tline}{[t_0, t_{\infty}]}
 
 Library description
 ###################
@@ -42,7 +51,7 @@ The purpose of the first four modules listed below is to provide the library wit
 
 Domains
 -------
-The ``bvpy.domains`` module contains the classes that can be used to implement the notion of integration domain, $\body$ in eq.($\ref{eq:bvp}$). It is built around the (abstract) mother class ``AbstractDomain``. All *domain classes* used as arguments for *BVPs*/*IBVPs* inherits from it. The  ``AbstractDomain`` encompasses two complementary description of the integration domain:
+The ``bvpy.domains`` module contains the classes that can be used to implement the notion of integration domain, :math:`\body` in :ref:`eq.(1)<eq_bvp>`. It is built around the (abstract) mother class ``AbstractDomain``. All *domain classes* used as arguments for *BVPs*/*IBVPs* inherits from it. The  ``AbstractDomain`` encompasses two complementary description of the integration domain:
 
 * A ``gmsh.model`` called the *geometry* of the domain and set by the ``geometry()`` abstract method.
 * A ``fenics.mesh`` called the *mesh* of the domain and produced by the ``discretize()`` method. Note that this method is not automatically called at instanciation but either by high-end functions such as ``plot()`` (from the ``bvpy.utils.visu`` module) or `bvp.solve()`.
@@ -119,7 +128,7 @@ The second class of sub-module  specifically tackles the problem differential sy
   \strain = \text{sym}\big(\grad{\mathbf{u}} \big)
   \end{cases}
 
-where $\mathbf{u}$ stands for the displacement field. The tensor $\stiffness$ accounts for the linear stiffness tensor of the considered material.
+where :math:`\mathbf{u}` stands for the displacement field. The tensor $\stiffness$ accounts for the linear stiffness tensor of the considered material.
 
 The latter encompasses hyper-elastic equations, *i.e.* valid beyond the linear deformation regime. They corresponds to the same general mathematical definition given above but with another strain definition:
 

doc/tutorials.rst

-.. _tutorials:
-
-Tutorials
-*********
-
-.. toctree::
-	:titlesonly:
-	:maxdepth: 1
-
-	bvpy_tutorial_domain
-	bvpy_tutorial_1_hello_world
-	bvpy_tutorial_2_domains
-	bvpy_tutorial_3_vforms
-	bvpy_tutorial_4_bnd_cond
-	bvpy_tutorial_5_reaction_diffusion
-	bvpy_tutorial_6_linear_elasticity