Andres joss review

.github/workflows/conda.yml

@@ -0,0 +1,58 @@
+name: Test Conda Installation
+
+# This triggers the workflow on any push to the repository
+on: 
+  push:
+    branches:
+      - "**"
+  pull_request:
+
+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 && pytest -v . || echo "Tests failed"

.github/workflows/ubuntu.yml

@@ -0,0 +1,49 @@
+name: Test Ubuntu Installation
+
+# This triggers the workflow on any push to the repository
+on: 
+  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 -r requirements.txt  # Adjust this if you're using a different file for dependencies
+          python3 -m pip install .  # Install irrevolutions package
+
+      # Optionally run tests within the environment
+      - name: Run tests
+        run: |
+          echo "Running tests"
+          conda activate fenicsx-env
+          cd test && pytest -v . || echo "Tests failed"

.github/workflows/workflow.yaml

@@ -17,7 +17,11 @@ jobs:
 
       - name: Install dependencies
         run: python3 -m pip install .
-
+
+      - name: List installed packages
+        run: |
+          pip list
+
       - name: Test import
         run: python3 -c "import irrevolutions"
 

README.md

@@ -27,22 +27,30 @@ https://docs.godotengine.org/en/3.1/community/contributing/pr_workflow.html
 
 ### Installation
 
-Before installing `irrevolutions`, ensure you have `dolfinx` and other dependencies installed. You can install `dolfinx` using one of the following methods:
+Before installing `irrevolutions`, ensure you have `dolfinx` and other dependencies installed.
+
+DOLFINx (and some other libraries like MPI and PyVista) have complex dependencies, it may be best to install them using conda from the conda-forge channel. Conda handles the environment setup and dependency conflicts well for these low-level libraries. Otherwise, you install from source using Spack or us a pre-built docker image.
+
+Then, install your Python package dependencies with Poetry. After installing system-level dependencies with Conda (or another method), you can use Poetry to manage the Python-specific packages and virtual environment for your project. Poetry will not attempt to reinstall DOLFINx or other system-level packages.
+
+More specifically, you can install `dolfinx` using one of the following methods:
 
 - Using conda
 ```
-conda create -n fenicsx-env -c conda-forge fenics-dolfinx=0.7.2 mpich pyvista
+conda create -n fenicsx-env -c conda-forge fenics-dolfinx=0.7.2 mpich pyvista sympy pandas pyyaml
 conda activate fenicsx-env
 ```
 
 - Using Spack
 see https://github.com/FEniCS/dolfinx/blob/main/README.md#spack
 
-- Using Apt (ubuntu)
+- Using Apt (ubuntu 23.04 build)
 ```
+apt-get install -y  software-properties-common python3-pip git libgl1-mesa-glx xvfb libglu1 libxcursor1 libxinerama1
+
 add-apt-repository ppa:fenics-packages/fenics
 apt update
-apt install fenicsx=1:0.7.3-3~ppa1~lunar1
+apt-install fenicsx
 ```
 
 For detailed instructions, see https://github.com/FEniCS/dolfinx/blob/main/README.md#installation
@@ -63,8 +71,26 @@ For a windows box:
 docker run --rm -ti -v "C:/...":/home/numerix" -w /home/numerix kumiori3\numerix:stable-amd64
 ```
 
-Finally, to install `irrevolutions` head to the package root directory and run
 
+We recommend using Poetry to manage Python dependencies and the virtual environment for the project. Follow the instructions below to install Poetry and set up the environment.
+
+```
+curl -sSL https://install.python-poetry.org | python3 -
+export PATH="$HOME/.local/bin:$PATH"
+```
+
+Clone this repository:
+
+```
+git clone https://github.com/kumiori/irrevolutions.git
+cd irrevolutions
+```
+
+
+Finally, to install `irrevolutions` with poetry run
+```poetry install```
+
+Alternatively, `irrevolutions` can be installed using setuptools from the root directory
 ```python3 -m pip install .```
 
 
@@ -77,7 +103,6 @@ This code was initially conceived as a support for the teaching course MEC647,
 
 ### Acknowledgements
 
-
 To all the students for their effort, participation, and motivation.
 
 This project contains code from the DOLFINy project (https://github.com/fenics-dolfiny/dolfiny), which is licensed under the LGPLv3 license. We acknowledge and thank the DOLFINy contributors for their work.

pyproject.toml

@@ -10,7 +10,7 @@ authors = ["Your Name <[email protected]>"]
 
 # Optional dependencies are specified in this section
 [tool.poetry.dependencies]
-python = "^3.8"
+python = "^3.9"
 pandas = "^1.2"
 sympy = "^1.8"
 pytest = "^6.0"
@@ -26,3 +26,17 @@ dolfinx_support = []
 
 [tool.poetry.scripts]
 irrevolutions = 'irrevolutions:main'
+
+# Ensure that non-code files (e.g., default_parameters.yml) are included in the package
+[tool.poetry.include]
+irrevolutions = ["src/irrevolutions/models/default_parameters.yml"]
+
+# Additional files to include (e.g., readme, licenses, configs)
+include = [
+    "README.md",
+    "LICENSE",
+    "src/irrevolutions/models/default_parameters.yml"
+]
+
+[tool.poetry.packages]
+irrevolutions = { from = "src/irrevolutions" }

setup.py

@@ -6,7 +6,14 @@
     package_dir={"": "src"},  # The root package is under the 'src' directory
     packages=find_packages("src"),  # Find packages under the 'src' directory
     include_package_data=True,
+    description="A Python package for solving nonlinear and nonconvex evolutionary problems using a general energetic notion of stability and dolfinx.",
+    author="Andrés A León Baldelli",
+    author_email="[email protected]",
+    url="https://github.com/kumiori3/irrevolutions",  # Replace with your repo
+
     package_data={
         "irrevolutions.models": ["default_parameters.yml"],
     },
+    python_requires=">=3.9",
+
 )

src/irrevolutions/solvers/slepcblockproblem.py

@@ -8,6 +8,30 @@
 
 from .function import vec_to_functions
 
+# -----------------------------------------------------------------------------
+#  License
+#  The code is based on dolfiny, by Michal Habera and Andreas Zilian.
+#  dolfiny is free software: you can redistribute it and/or modify it under the terms of
+#  the GNU Lesser General Public License as published by the Free Software Foundation, 
+#  either version 3 of the License, or (at your option) any later version.
+#
+#  dolfiny is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
+#  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+#  See the GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License along with 
+#  dolfiny. If not, see http://www.gnu.org/licenses/.
+#
+#  The original code can be found at:
+#  https://github.com/fenics-dolfiny/dolfiny
+#
+#  Original Authors:
+#    Michal Habera, Rafinex, Luxembourg.
+#    Andreas Zilian, University of Luxembourg, Luxembourg.
+#
+#  Modifications and contributions:
+#    Andrés A León Baldelli, CNRS.
+# -----------------------------------------------------------------------------
 
 class SLEPcBlockProblem:
     def __init__(

src/irrevolutions/solvers/snesblockproblem.py

@@ -10,6 +10,30 @@
 
 from .function import functions_to_vec, vec_to_functions
 
+# -----------------------------------------------------------------------------
+#  License
+#  The code is based on dolfiny, by Michal Habera and Andreas Zilian.
+#  dolfiny is free software: you can redistribute it and/or modify it under the terms of
+#  the GNU Lesser General Public License as published by the Free Software Foundation, 
+#  either version 3 of the License, or (at your option) any later version.
+#
+#  dolfiny is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
+#  without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
+#  See the GNU Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public License along with 
+#  dolfiny. If not, see http://www.gnu.org/licenses/.
+#
+#  The original code can be found at:
+#  https://github.com/fenics-dolfiny/dolfiny
+#
+#  Original Authors:
+#    Michal Habera, Rafinex, Luxembourg.
+#    Andreas Zilian, University of Luxembourg, Luxembourg.
+#
+#  Modifications and contributions:
+#    Andrés A León Baldelli, CNRS.
+# -----------------------------------------------------------------------------
 
 class SNESBlockProblem:
     def __init__(