Adding CI

.github/workflows/ci.yml

@@ -23,16 +23,15 @@ jobs:
           channels: conda-forge
           environment-file: environment.yml
 
-      - name: Run example
+      - name: install HISP
         shell: bash -l {0}
-        run: python simple_mb.py
+        run: python -m pip install .[test]
 
-      - name: Install dependencies 
+      - name: Run tests
         shell: bash -l {0}
         run: |
-          pip install pytest pytest-cov
+          pytest test/ --cov festim --cov-report xml --cov-report term
 
-      - name: Run tests
+      - name: Run example
         shell: bash -l {0}
-        run: |
-          pytest tests/ --cov festim --cov-report xml --cov-report term
+        run: python simple_mb.py

.gitignore

@@ -0,0 +1,112 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# version file
+**_version.py
+
+# Input/Output files
+*.bp
+*.xdmf
+*.h5

pyproject.toml

@@ -0,0 +1,38 @@
+[build-system]
+requires = ["setuptools >= 61", "wheel", "setuptools-scm[toml] >= 7.0.5"]
+build-backend = "setuptools.build_meta"
+
+[project]
+authors = [
+    { name = "Kaelyn Dunnell" },
+    { email = "kaelyn@mit.edu" },
+]
+dynamic = ["version"]
+name = "HISP"
+description = "Hydrogen Inventory Simulations of PFCs"
+readme = "README/md"
+requires-python = ">=3.9"
+license = { file = "LICENSE" }
+dependencies = ["h_transport_materials"]
+classifiers = [
+    "Natural Language :: English",
+    "Topic :: Scientific/Engineering",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "License :: OSI Approved :: MIT",
+    "Operating System :: OS Independent",
+]
+
+[project.optional-dependencies]
+test = ["pytest >= 5.4.3", "pytest-cov"]
+
+[project.urls]
+Homepage = "https://github.com/RemDelaporteMathurin/FESTIM"
+Issues = "https://github.com/RemDelaporteMathurin/FESTIM/issues"
+
+
+[tool.setuptools_scm]
+write_to = "src/hisp/_version.py"

simple_mb.py

@@ -10,8 +10,8 @@
 import dolfinx.fem as fem
 import dolfinx
 
-from helpers import PulsedSource, Scenario
-from new_h_transport_class import CustomProblem
+from hisp.helpers import PulsedSource, Scenario
+from hisp import CustomProblem
 
 # dolfinx.log.set_log_level(dolfinx.log.LogLevel.INFO)
 

src/hisp/__init__.py

@@ -0,0 +1,3 @@
+from .helpers import PulsedSource, Scenario
+
+from .h_transport_class import CustomProblem

test/test_scenario.py

@@ -0,0 +1,55 @@
+from hisp.helpers import Scenario
+import os
+import pytest
+import numpy as np
+import matplotlib.pyplot as plt
+
+current_dir = os.path.dirname(__file__)
+scenario_path = os.path.join(current_dir, "scenario_test.txt")
+
+
+def test_maximum_time():
+    # BUILD
+    my_scenario = Scenario(scenario_path)
+    expected_maximum_time = 2 * (455 + 455 + 650 + 1000) + 2 * (36 + 36 + 180 + 1000)
+
+    # RUN
+    computed_maximum_time = my_scenario.get_maximum_time()
+
+    # TEST
+    assert computed_maximum_time == expected_maximum_time
+
+
+@pytest.mark.parametrize("t, expected_row", [(0, 0), (6000, 1)])
+def test_get_pulse_row(t, expected_row):
+    my_scenario = Scenario(scenario_path)
+
+    pulse_row = my_scenario.get_row(t=t)
+
+    assert pulse_row == expected_row
+
+
+def test_reading_a_file():
+    my_scenario = Scenario(scenario_path)
+
+    times = np.linspace(0, my_scenario.get_maximum_time(), 1000)
+    pulse_types = []
+    for t in times:
+        pulse_type = my_scenario.get_pulse_type(t)
+        pulse_types.append(pulse_type)
+
+    # color the line based on the pulse type
+    color = {
+        "FP": "red",
+        "ICWC": "blue",
+        "RISP": "green",
+        "GDC": "orange",
+        "BAKE": "purple",
+    }
+
+    colors = [color[pulse_type] for pulse_type in pulse_types]
+
+    for i in range(len(times) - 1):
+        plt.plot(times[i : i + 2], np.ones_like(times[i : i + 2]), c=colors[i])
+    # plt.xscale("log")
+    # plt.show()