Merge branch 'main' into andres-paper

.github/dependabot.yml

@@ -0,0 +1,11 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

.github/workflows/conda.yml

@@ -0,0 +1,60 @@
+name: Test Conda Installation
+
+# This triggers the workflow on any push to the repository
+on: 
+  push:
+    branches:
+        - "main"
+  pull_request:
+    branches:
+        - "main"
+
+jobs:
+  test:
+    name: Test Conda Installation and Setup
+    runs-on: ubuntu-latest
+
+    # Steps to run
+    steps:
+      # Checkout the repo content to the runner
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      # Set up Miniconda
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          channels: conda-forge, defaults
+          auto-update-conda: true
+          auto-activate-base: true
+
+      # Create the environment and install dependencies
+      - name: Create and activate conda environment
+        run: |
+          echo "Creating the conda environment: fenicsx-env"
+          conda create -n fenicsx-env -c conda-forge fenics-dolfinx=0.7.2 mpich pyvista sympy pandas pyyaml -y
+          echo "Activating the conda environment"
+          source $(conda info --base)/etc/profile.d/conda.sh  # Fix to allow `conda activate`
+          conda activate fenicsx-env
+          echo "Environment created and activated. Now, verifying installation..."
+          conda list  # Print all installed packages for verification
+          which python  # Verify the Python interpreter being used
+
+
+      # Install the irrevolutions package in the conda environment
+      - name: Install irrevolutions
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh  # Ensure conda is properly initialized
+          echo "Installing irrevolutions package"
+          conda activate fenicsx-env
+          python -m pip install .  # Assuming irrevolutions is in the current directory
+          echo "irrevolutions package installed"
+
+      # Optionally run tests within the environment
+      - name: Run tests
+        run: |
+          source $(conda info --base)/etc/profile.d/conda.sh  # Ensure conda is properly initialized
+          echo "Running tests"
+          conda activate fenicsx-env
+          cd test && python3 -m pytest . || echo "Tests failed"

.github/workflows/ubuntu.yml

@@ -0,0 +1,54 @@
+name: Test Ubuntu Installation
+
+# This triggers the workflow on any push to the repository
+on:
+  workflow_dispatch:
+
+  # push:
+  #   branches:
+  #     - "**"
+  # pull_request:
+
+jobs:
+  test:
+    name: Test Ubuntu/apt Installation and Setup
+    runs-on: ubuntu-latest
+
+    # Steps to run
+    steps:
+      # Checkout the repo content to the runner
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      # Install Ubuntu dependencies via APT
+      - name: Install system dependencies via APT
+        run: |
+          echo "Installing required system dependencies via APT"
+          sudo apt-get update
+          sudo apt-get install -y  software-properties-common python3-pip git libgl1-mesa-glx xvfb libglu1 libxcursor1 libxinerama1
+
+      # Add the FEniCS PPA and install fenicsx
+      - name: Install fenicsx
+        run: |
+          echo "Adding FEniCS PPA and installing fenicsx"
+          sudo add-apt-repository ppa:fenics-packages/fenics
+          sudo apt update
+          sudo apt-get install -y fenicsx
+
+      # Install irrevolutions dependencies (if any) and the package itself
+      - name: Install Python dependencies and irrevolutions
+        run: |
+          echo "Installing Python dependencies and irrevolutions"
+          python3 -m pip install --upgrade pip
+          python3 -m pip install numpy==1.21.6 --force-reinstall # Downgrade NumPy to a compatible version
+          python3 -m pip install .  # Install irrevolutions package
+      - name: Check versions of installed packages
+        run: |
+            python3 -c "import numpy; print(f'NumPy version: {numpy.__version__}')"
+            python3 -c "import scipy; print(f'SciPy version: {scipy.__version__}')"
+            python3 -c "import pyvista; print(f'PyVista version: {pyvista.__version__}')"
+      # Optionally run tests within the environment
+      - name: Run tests
+        run: |
+          echo "Running tests"
+          cd test && python3 -m pytest . || echo "Tests failed"

.github/workflows/workflow.yaml

@@ -0,0 +1,32 @@
+name: Run Tests in Docker Container
+run-name: We are testing irrevolutions
+
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  set-up-computing-environment:
+    runs-on: ubuntu-latest
+    container: kumiori3/numerix:stable-amd64
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: python3 -m pip install .
+
+      - name: List installed packages
+        run: |
+          pip list
+      
+      - name: Test import
+        run: python3 -c "import irrevolutions"
+
+      - name: Run 1d test
+        run: pytest -v test/test_1d.py
+
+      - name: Run tests
+        run: cd test && pytest -v .

.github/workflows/workflow_dolfinx_container.yaml

@@ -0,0 +1,28 @@
+name: Run Tests in Dolfinx Container
+run-name: We are testing irrevolutions
+
+on:
+  push:
+    branches:
+      - "**"
+
+jobs:
+  set-up-computing-environment:
+    runs-on: ubuntu-latest
+    container: ghcr.io/fenics/dolfinx/lab:v0.7.2
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: python3 -m pip install .
+
+      - name: Test import
+        run: python3 -c "import irrevolutions"
+
+      - name: Run 1d test
+        run: pytest -v test/test_1d.py
+
+      - name: Run tests
+        run: cd test && pytest -v .

.gitignore

@@ -52,4 +52,4 @@ test_*/
 src/irrevolutions/test/output/*
 **/output/**
 **egg-info**
-.venv/**
+.venv/**

CODE-OF-CONDUCT.md

@@ -0,0 +1,42 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of developing an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a smooth experience for everyone, regardless of age, size, personal quirks, ethnicity, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, religion, sex inclinations, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- Trolling, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, without explicit permission
+- Other conduct which could reasonably be considered inappropriate in a friendly setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for suggesting best practices of acceptable behavior and are in a position to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers may claim 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, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, public conferences and scientific gatherings, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Reporting
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team or in the [Issues page](https://github.com/kumiori/irrevolutions/issues). All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team maintains confidentiality with regard to the details of an incident. 
+
+Project maintainers are bound to the Code of Conduct as well, failing to honour its best practices may lead to temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct.html](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html).

CONTRIBUTING.md

@@ -0,0 +1,34 @@
+# Contributing to Our Project
+We welcome contributions from everyone in the community
+
+### Reporting bugs
+
+If you find a bug in Irrevolutions, please report it on the [GitHub issue
+tracker](https://github.com/kumiori/irrevolutions/issues/new?labels=bug).
+
+
+### Suggesting enhancements
+
+If you want to suggest a new feature or an improvement of a current
+feature, you can submit this on the [issue
+tracker](https://github.com/kumiori/irrevolutions/issues).
+
+
+### Submitting a pull request
+
+To contribute code DOLFINx, create a pull request. If you want to
+contribute, but are unsure where to start, have a look at the [Discussions page](https://github.com/kumiori/irrevolutions/discussions).
+For substantial changes/contributions, please start with an issue or
+start a new Discussion thread.
+
+On opening a pull request, unit tests will run on GitHub CI. You can
+click on these in the pull request to see where (if anywhere) the tests
+are failing.
+
+
+### Code of conduct
+
+We suggest all our contributors to read the [code of
+conduct](CODE-OF-CONDUCT.md).
+
+

MANIFEST.in

@@ -0,0 +1 @@
+include irrevolutions/models/default_parameters.yml