installation instructions and non-code files handling

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

@@ -26,3 +26,18 @@ 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.package]
+# Map the source code to the correct directory structure
+package = { "irrevolutions": "src/irrevolutions" }