Merge pull request #5 from LIBRA-project/ci

CI

Author: RemDelaporteMathurin

.github/workflows/ci.yml

@@ -0,0 +1,36 @@
+name: CI
+on: [pull_request, push]
+
+jobs:
+  run-tests:
+    name: run-tests
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v5
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: libra_sparging
+        environment-file: environment.yml
+        miniforge-version: latest
+        use-mamba: false
+        channels: conda-forge
+
+    - name: Install package
+      shell: bash -l {0}
+      run: |
+        python -m pip install -e .[dev]
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        python -m pytest test
+    
+    # - name: Upload to codecov
+    #   uses: codecov/codecov-action@v4
+    #   with:
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+    #     files: ./coverage.xml

README.md

@@ -15,7 +15,12 @@ conda env create -f environment.yml
 conda activate libra_sparging
 ```
 
+```
+python -m pip install -e .[dev]
+```
+
+## How to run tests
 
 ```
-python model.py
+python -m pytest test
 ```

main.py

@@ -1,8 +1,8 @@
-import model
+import src.sparging.model as model
 import sys
 import os
-from animation import create_animation
-from helpers import get_input
+from sparging.animation import create_animation
+from sparging.helpers import get_input
 
 
 ANIMATE = True

pyproject.toml

@@ -0,0 +1,55 @@
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "libra_sparging"
+version = "0.1.0"
+description = "A finite element model for sparging processes"
+readme = "README.md"
+requires-python = ">=3.10"
+license = {text = "LICENSE"}
+authors = [
+    {name = "Author Name", email = "author@example.com"},
+]
+keywords = ["FEM", "sparging", "dolfinx"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 3 - Alpha",
+]
+
+dependencies = [
+    "fenics-dolfinx",
+    "matplotlib",
+    "pyvista",
+    "pyyaml",
+    "numpy",
+    "scipy",
+    "pandas",
+    "pint",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest>=7.0",
+    "pytest-cov",
+]
+
+[project.urls]
+Repository = "https://github.com/libra_project/libra_sparging"
+
+[tool.setuptools]
+packages = ["sparging"]
+package-dir = {"" = "src"}
+
+[tool.pytest.ini_options]
+testpaths = ["test"]
+python_files = "test_*.py"
+addopts = "-v"
+
+[tool.setuptools.package-data]
+sparging = ["*.yaml", "*.yml"]

src/sparging/__init__.py

@@ -0,0 +1,19 @@
+"""
+libra_sparging: A finite element model for sparging processes using FEniCSx/DOLFINX.
+"""
+
+from .config import ureg, const_R, const_g, VERBOSE
+from .model import SimulationResults
+from .animation import ConcentrationAnimator
+from .helpers import *
+from .correlations import *
+
+__all__ = [
+    "SimulationInput",
+    "SimulationResults",
+    "ConcentrationAnimator",
+    "ureg",
+    "const_R",
+    "const_g",
+    "VERBOSE",
+]

animation.py src/sparging/animation.pyanimation.py renamed to src/sparging/animation.py

@@ -2,7 +2,7 @@
 import matplotlib.pyplot as plt
 from matplotlib import gridspec
 from matplotlib.widgets import Slider, Button
-from model import SimulationResults
+from sparging.model import SimulationResults
 
 molar_mass_T2 = 3.016 * 2  # g/mol T2
 specific_activity_tritium = 3.57e14  # Bq/g

config.py src/sparging/config.pyconfig.py renamed to src/sparging/config.py

@@ -1,5 +1,9 @@
 from __future__ import annotations
-from config import *
+from sparging.config import ureg, const_R, const_g, VERBOSE
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from sparging.model import SimulationInput
 import numpy as np
 import scipy.constants as const
 import warnings
@@ -77,7 +81,7 @@ def get_d_b(flow_g_vol: float, nozzle_diameter: float, nb_nozzle: int) -> float:
     )
 
 
-def get_Re(input: SimulationInput) -> float:
+def get_Re(input: "SimulationInput") -> float:
     try:
         u = input.u_g0
         Re_old = input.Re
@@ -97,7 +101,7 @@ def get_Re(input: SimulationInput) -> float:
     return Re.to("dimensionless")
 
 
-def get_u_g0(input: SimulationInput) -> float:  # TODO move inside class ?
+def get_u_g0(input: "SimulationInput") -> float:  # TODO move inside class ?
     """
     bubble initial velocity [m/s], correlation for terminal velocity from Clift 1978
     """
@@ -121,7 +125,7 @@ def get_u_g0(input: SimulationInput) -> float:  # TODO move inside class ?
     return u_g0
 
 
-def get_eps_g(input: SimulationInput) -> float:
+def get_eps_g(input: "SimulationInput") -> float:
     """computes gas void fraction from ideal gas law and Young-Laplace pressure in the bubbles (neglecting hydrostatic pressure variation)"""
     eps_g = (
         const_R
@@ -142,7 +146,7 @@ def get_eps_g(input: SimulationInput) -> float:
 def get_h_higbie(D_l: float, u_g: float, d_b: float) -> float:
     """mass transfer coefficient [m/s] for tritium in liquid FLiBe using Higbie penetration model"""
     h_l = (
-        (D_l * u_g) / (ufl.pi * d_b)
+        (D_l * u_g) / (const.pi * d_b)
     ) ** 0.5  # mass transport coefficient Higbie penetration model
     return h_l
 

correlations.py src/sparging/correlations.pycorrelations.py renamed to src/sparging/correlations.py

@@ -1,11 +1,11 @@
 import yaml
 import numpy as np
-from config import *
+from sparging.config import *
 
 
 # TODO this could be a dataclass?
 # see issue #3
-def get_input(yaml_input_path):
+def get_input(yaml_input_path) -> dict:
     with open(yaml_input_path, "r") as file:
         params = yaml.safe_load(file)
         if "input" in params: