Merge pull request #4 from LIBRA-project/pint

Pint support

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

.gitignore

@@ -210,3 +210,6 @@ __marimo__/
 *.yaml
 *.csv
 mwe.py
+*.json
+*.ipynb
+*.code-workspace

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
 ```

environment.yml

@@ -2,10 +2,12 @@ name: libra_sparging
 channels:
   - conda-forge
 dependencies:
+  - python>=3.12
   - fenics-dolfinx
   - matplotlib
   - pyvista
   - pyyaml
   - numpy
   - scipy
-  - pandas
+  - pandas
+  - pint

helpers.py

@@ -1,42 +1,38 @@
-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
 SHOW_ACTIVITY = True
-INPUT_PATH = os.path.join(os.getcwd(), sys.argv[1])
-OUTPUT_PATH = os.path.join(
-    os.getcwd(), sys.argv[1] + "_out" if len(sys.argv) < 3 else sys.argv[2]
+YAML_INPUT_PATH = os.path.join(os.getcwd(), sys.argv[1])
+OUTPUT_FOLDER = os.path.join(
+    os.getcwd(), sys.argv[1].split(".")[0].replace("_input", "")
 )
 
-
 if __name__ == "__main__":
-    params = get_input(INPUT_PATH + ".yaml")
-    properties = model.compute_properties(params)
+    params = get_input(YAML_INPUT_PATH)
+    sim_input = model.SimulationInput(params)
 
-    # breakpoint()
-    merged_dict = {}
-    merged_dict.update(params)
-    merged_dict.update(properties)
-
-    t_sparging_hr = [0, 1e20]  # time interval when sparger is ON
+    # TODO integrate to input file
+    t_sparging_hr = [24, 1e20]  # time interval when sparger is ON
     t_irr_hr = [0, 96]  # time interval when irradiation is ON
-    t_final = 10 * model.days_to_seconds
+    t_final = 6 * model.days_to_seconds
 
     results = model.solve(
-        merged_dict,
+        sim_input,
         t_final=t_final,
         t_irr=[t * model.hours_to_seconds for t in t_irr_hr],
         t_sparging=[t * model.hours_to_seconds for t in t_sparging_hr],
     )
-    # save_to_csv(c_T_volume)
 
-    results.to_yaml(OUTPUT_PATH + ".yaml", inputs=params, properties=properties)
-    results.to_json(OUTPUT_PATH + ".json", inputs=params, properties=properties)
-    results.profiles_to_csv(OUTPUT_PATH + "_profiles")
-    # breakpoint()
+    os.makedirs(OUTPUT_FOLDER, exist_ok=True)
+    results.to_yaml(os.path.join(OUTPUT_FOLDER, "restart.yaml"))
+    results.to_json(os.path.join(OUTPUT_FOLDER, "output.json"))
+    # results.profiles_to_csv(os.path.join(OUTPUT_FOLDER, "profiles"))
+
     if ANIMATE is True:
         # Create interactive animation
         try: