Merge remote-tracking branch 'upstream' into fenicsx

.github/workflows/ci.yml

@@ -0,0 +1,38 @@
+name: CI
+on: [pull_request, push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: myenv
+        # mamba-version: "*"
+        channels: conda-forge, defaults
+
+    - name: Create Conda environment
+      shell: bash -l {0}
+      run: |
+        # conda upgrade --strict-channel-priority -c conda-forge --all
+        conda install -c conda-forge fenics numpy=1.24
+
+    - name: Install dependencies
+      shell: bash -l {0}
+      run: |
+        pip install pytest pytest-cov
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        pytest test/ --cov festim --cov-report xml --cov-report term
+    
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/doctest.yml

@@ -0,0 +1,21 @@
+name: Documentation test
+
+on: [push, pull_request]
+
+jobs:
+  docbuild:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        activate-environment: festim-docs
+        environment-file: docs/environment.yml
+
+    - name: Doc Tests
+      shell: bash -l {0}
+      run: sphinx-build -b doctest docs/source docs/_build/doctest

.gitignore

@@ -64,7 +64,9 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+docs/*/_build/
+docs/*/_static/
+docs/*/_templates/
 
 # PyBuilder
 target/

CITATION.cff

@@ -3,33 +3,29 @@ title: FESTIM
 message: 'If you use this software, please cite it as below.'
 type: software
 authors:
-  - given-names: Rémi
-    family-names: Delaporte-Mathurin
-    email: [email protected]
-    orcid: 'https://orcid.org/0000-0003-1064-8882'
-  - given-names: James
-    family-names: Dark
+  - name: The FESTIM contributors
 
-repository-code: 'https://github.com/RemDelaporteMathurin/FESTIM'
-version: 0.8.1
+repository-code: 'https://github.com/festim-dev/FESTIM'
 preferred-citation:
   authors:
     - given-names: Rémi
       family-names: Delaporte-Mathurin
+    - given-names: James
+      family-names: Dark
+    - given-names: Gabriele
+      family-names: Ferrero
     - given-names: Etienne
       family-names: Hodille
-    - given-names: Jonathan
-      family-names: Mougenot
-    - given-names: Yann
-      family-names: Charles
-    - given-names: Christian
-      family-names: Grisolia
-  title: "Finite element analysis of hydrogen retention in ITER plasma facing components using FESTIM"
+    - given-names: Vladimir
+      family-names: Kulagin
+    - given-names: Samuele
+      family-names: Meschini
+  title: "FESTIM: An open-source code for hydrogen transport simulations"
   type: article
-  year: 2019
-  doi: 10.1016/j.nme.2019.100709
-  url: "http://www.sciencedirect.com/science/article/pii/S2352179119300547"
-  issn: 2352-1791
-  volume: 21
-  pages: 100709
-  journal: "Nuclear Materials and Energy"
+  year: 2024
+  doi: 10.1016/j.ijhydene.2024.03.184
+  url: "https://doi.org/10.1016/j.ijhydene.2024.03.184"
+  issn: 0360-3199
+  volume: 63
+  pages: 786-802
+  journal: "International Journal of Hydrogen Energy"

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behaviour that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behaviour and will take appropriate and fair corrective action in
+response to any behaviour that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behaviour may be
+reported to the community leaders responsible for enforcement at
+[email protected].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behaviour deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behaviour was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behaviour. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behaviour.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behaviour,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

README.md

@@ -1,27 +1,43 @@
 # FESTIM
+<<<<<<< HEAD
 [![Conda CI](https://github.com/RemDelaporteMathurin/FESTIM/actions/workflows/ci_conda.yml/badge.svg?branch=fenicsx)](https://github.com/RemDelaporteMathurin/FESTIM/actions/workflows/ci_conda.yml)
 [![Docker CI](https://github.com/RemDelaporteMathurin/FESTIM/actions/workflows/ci_docker.yml/badge.svg?branch=fenicsx)](https://github.com/RemDelaporteMathurin/FESTIM/actions/workflows/ci_docker.yml)
 [![codecov](https://codecov.io/gh/RemDelaporteMathurin/FESTIM/branch/master/graph/badge.svg?token=AK3A9CV2D3)](https://codecov.io/gh/RemDelaporteMathurin/FESTIM)
+=======
+[![NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org/)
+[![CI](https://github.com/festim-dev/FESTIM/actions/workflows/ci.yml/badge.svg)](https://github.com/festim-dev/FESTIM/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/festim-dev/FESTIM/branch/master/graph/badge.svg?token=AK3A9CV2D3)](https://codecov.io/gh/festim-dev/FESTIM)
+>>>>>>> upstream
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg?style=flat-square)](https://github.com/psf/black)
-![GitHub stars](https://img.shields.io/github/stars/RemDelaporteMathurin/FESTIM.svg?logo=github&label=Stars&logoColor=white)
-![GitHub forks](https://img.shields.io/github/forks/RemDelaporteMathurin/FESTIM.svg?logo=github&label=Forks&logoColor=white)
+![GitHub stars](https://img.shields.io/github/stars/festim-dev/FESTIM.svg?logo=github&label=Stars&logoColor=white)
+![GitHub forks](https://img.shields.io/github/forks/festim-dev/FESTIM.svg?logo=github&label=Forks&logoColor=white)
 
 FESTIM (Finite Elements Simulation of Tritium in Materials) is a tool for modeling hydrogen transport in materials. 
 It simulates the diffusion and trapping of hydrogen, coupled to heat transfer with [FEniCS](https://fenicsproject.org).
 
-:point_right: [Getting started](https://festim.readthedocs.io/en/latest/getting_started.html)
 
-:point_right: [Documentation](https://festim.readthedocs.io/)
+## Getting started
 
-:point_right: [Tutorials](https://github.com/RemDelaporteMathurin/FESTIM-workshop)
+The installation instructions are available [here](https://festim.readthedocs.io/en/latest/installation.html).
 
+## Documentation 
 
+Documentation can be viewed at https://festim.readthedocs.io/
 
-## References
-- R. Delaporte-Mathurin, _et al._, _Finite Element Analysis of Hydrogen Retention in ITER Plasma Facing Components using FESTIM_. Nuclear Materials and Energy, 21, (2019). https://doi.org/10.1016/j.nme.2019.100709.
+## Tutorials
 
-- R. Delaporte-Mathurin, _et al._, _Parametric Study of Hydrogenic Inventory in the ITER Divertor Based on Machine Learning_. Scientific Reports, 10, (2020). https://doi.org/10.1038/s41598-020-74844-w.
+Visit the FESTIM-workshop to view the available tutorials https://github.com/festim-dev/FESTIM-workshop
 
-- J. Dark, _et al._, _Influence of hydrogen trapping on WCLL breeding blanket performances_. Nuclear Fusion, 62, (2021). https://doi.org/10.1088/1741-4326/ac28b0.
+## Contact
 
-For full list of publications using FESTIM see the [publications](https://festim.readthedocs.io/en/latest/publications.html) section in the docs
+For questions on how to use FESTIM, visit our [Discourse page](https://festim.discourse.group/)
+or join our [Slack](https://join.slack.com/t/festimworkspace/shared_invite/zt-246hw8d6o-htWASLsbdosUo_2nRKCf9g) channel
+
+## Contributing
+
+The guidelines for contributions can be found in the documentation: https://festim.readthedocs.io/en/latest/devguide/index.html
+
+## Roadmap
+
+You can follow the public roadmap on the [FESTIM projects page](https://github.com/festim-dev/FESTIM/projects?query=is%3Aopen).
+Moreover, you can check out the development branch (with support of FEniCSx) on the [_fenicsx_](https://github.com/festim-dev/FESTIM/tree/fenicsx) branch.

docs/environment.yml

@@ -0,0 +1,19 @@
+name: festim-docs
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - fenics
+  - matplotlib==3.7.1
+  - pip>=20.1
+  - sphinx==7
+  - folium
+  - numpy==1.24
+  - pip:
+    - sympy
+    - sphinx_book_theme==1.1.2
+    - sphinx-design==0.5.0
+    - sphinxcontrib-bibtex
+    - sphinx-copybutton
+    - pillow
+    - sphinxcontrib-images

docs/source/_static/style.css

@@ -0,0 +1,49 @@
+@import url('https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;0,900;1,400;1,700;1,900&family=Open+Sans:ital,wght@0,400;0,600;1,400;1,600&display=swap');
+
+body {
+    font-family: 'Open Sans', sans-serif;
+}
+
+h1 {
+    font-family: "Lato", sans-serif;
+}
+
+pre,
+code {
+    font-size: 100%;
+    line-height: 155%;
+}
+
+/* Main page overview cards */
+
+.sd-card {
+    border-radius: 0;
+    padding: 30px 10px 20px 10px;
+    margin: 10px 0px;
+}
+
+.sd-card .sd-card-header {
+    text-align: center;
+}
+
+.sd-card .sd-card-title {
+    text-align: center;
+}
+
+.sd-card .sd-card-header .sd-card-text {
+    margin: 0px;
+}
+
+.sd-card .sd-card-img-top {
+    height: 52px;
+    width: 52px;
+    margin-left: auto;
+    margin-right: auto;
+}
+
+.sd-card .sd-card-header {
+    border: none;
+    font-size: var(--pst-font-size-h5);
+    font-weight: bold;
+    padding: 2.5rem 0rem 0.5rem 0rem;
+}