Andres joss review

.github/workflows/conda.yml

@@ -55,4 +55,4 @@ jobs:
           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"
+          cd test && python3 -m pytest . || echo "Tests failed"

.github/workflows/ubuntu.yml

@@ -38,12 +38,15 @@ jobs:
         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 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"
-          conda activate fenicsx-env
-          cd test && pytest -v . || echo "Tests failed"
+          cd test && python3 -m pytest . || echo "Tests failed"

README.md

@@ -71,26 +71,15 @@ For a windows box:
 docker run --rm -ti -v "C:/...":/home/numerix" -w /home/numerix kumiori3\numerix:stable-amd64
 ```
 
-
-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
+git clone https://github.com/kumiori/irrevolutions.gt
 cd irrevolutions
 ```
 
 
-Finally, to install `irrevolutions` with poetry run
-```poetry install```
-
-Alternatively, `irrevolutions` can be installed using setuptools from the root directory
+Finally, `irrevolutions` can be installed using setuptools from the root directory
 ```python3 -m pip install .```
 
 

pyproject.toml

@@ -2,41 +2,40 @@
 requires = ["setuptools>=42", "wheel"]
 build-backend = "setuptools.build_meta"
 
-[tool.poetry]
+[project]
 name = "irrevolutions"
 version = "0.1.0"
 description = "A Python package for solving nonlinear and nonconvex evolutionary problems using a general energetic notion of stability and dolfinx."
-authors = ["Your Name <[email protected]>"]
-
-# Optional dependencies are specified in this section
-[tool.poetry.dependencies]
-python = "^3.9"
-pandas = "^1.2"
-sympy = "^1.8"
-pytest = "^6.0"
-matplotlib = "^3.4"
-gmsh = "^4.11.0"
-PyYAML = "^6.0.1"
-scipy = "^1.12.0"
-pyvista = "^0.43"
-numba = "^0.60.0"
-
-[tool.poetry.extras]
-dolfinx_support = []
+authors = [
+    {name = "Andrés A León Baldelli", email = "[email protected]"}
+]
+dependencies = [
+    "pandas>=1.2",
+    "sympy>=1.8",
+    "pytest>=6.0",
+    "matplotlib>=3.4",
+    "gmsh>=4.11.0",
+    "PyYAML>=6.0.1",
+    "scipy>=1.12.0",
+    "pyvista>=0.43",
+    "numpy<2",  # Pin NumPy to this version
+    "numba>=0.60.0"
+]
+readme = "README.md"
+requires-python = ">=3.9"
+license = {text = "GNU Lesser General Public License v3.0"}
 
-[tool.poetry.scripts]
-irrevolutions = 'irrevolutions:main'
+[project.urls]
+homepage = "https://github.com/kumiori3/irrevolutions"
+repository = "https://github.com/kumiori3/irrevolutions"
 
-# 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"]
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["irrevolutions*"]
 
-# Additional files to include (e.g., readme, licenses, configs)
-include = [
-    "README.md",
-    "LICENSE",
-    "src/irrevolutions/models/default_parameters.yml"
-]
+[project.scripts]
+irrevolutions = "irrevolutions:main"
 
-[tool.poetry.packages]
-irrevolutions = { from = "src/irrevolutions" }
+# Optional include files like configuration, license, etc.
+[tool.setuptools.package-data]
+irrevolutions = ["models/default_parameters.yml"]