Refactor for new PEP standard and pyproject.toml

.github/worflows/CI.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.os == 'windows-latest' }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-latest, windows-latest]
+        python-version: [3.6, 3.7, 3.8, 3.9, '3.10']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install .
+    - name: Run Tests
+      run: |
+        python -m unittest --verbose

CHANGES.md

@@ -0,0 +1,5 @@
+# impala 0.1.9999
+* refactor to new PEP standards
+
+# impala 0.1
+* initial version of package

README.md

@@ -13,6 +13,10 @@ pip install git+https://github.com/lanl/impala.git
 
 ## References
 
+## Tests
+```console
+> python -m unittest
+```
 
 ************
 

impala/__init__.py

@@ -0,0 +1,3 @@
+from .physical_models_vec import *
+from .impala_noProbit_emu import *
+from .models_withLik import *

impala/superCal/models_withLik.py → impala/models_withLik.py

@@ -1,8 +1,7 @@
 import numpy as np
 import pyBASS as pb
 #import pyBayesPPR as pbppr
-#import physical_models_vec as pm_vec
-from impala import physics as pm_vec
+import impala.physical_models_vec as pm_vec
 from itertools import cycle
 from scipy.interpolate import interp1d
 from scipy.linalg import cho_factor, cho_solve, cholesky

pyproject.toml

@@ -0,0 +1,38 @@
+[project]
+name = "impala"
+version = "0.1.0"
+description = "Bayesian model calibration"
+authors = [
+    {name = "Devin Francom", email = "[email protected]"},
+    {name = "Arthur Lui", email = "[email protected]"},
+    {name = "Peter Trubey", email = "[email protected]"},
+	{name = "J. Derek Tucker", email = "[email protected]"}
+]
+license = {text = "BSD 3-Clause"}
+readme = "README.md"
+requires-python = ">=3.6"
+
+keywords = ["modelcalibration"]
+
+dependencies=[
+        "numpy",
+        "matplotlib",
+        "scipy",
+        "pyBASS",
+]
+
+classifiers = [
+    'License :: OSI Approved :: BSD License',
+    'Operating System :: OS Independent',
+    'Programming Language :: Python',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Mathematics',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.6',
+]
+
+[project.urls]
+repository = "http://www.github.com/lanl/impala"
+
+[tool.setuptools.packages.find]
+exclude = ["data*", "tests*"]

requirements.txt

@@ -0,0 +1,4 @@
+numpy
+pyBASS
+scipy
+matplotlib

tests/img/.gitignore

@@ -0,0 +1,2 @@
+*
+!.gitignore

tests/test_physics.py

@@ -0,0 +1,52 @@
+import unittest
+import numpy as np
+from impala import physical_models_vec as physics
+import matplotlib.pyplot as plt
+
+class TestPhysics(unittest.TestCase):
+    def test_physics(self):
+        consts = {
+            'alpha'  : 0.2,
+            'beta'   : 0.33,
+            'matomic': 45.9,
+            'Tmelt0' : 2110.,
+            'rho0'   : 4.419,
+            'Cv0'    : 0.525e-5,
+            'G0'     : 0.4,
+            'chi'    : 1.0,
+            'sgB'    : 6.44e-4
+        }
+
+        params = {
+            'theta' : np.array([0.1]),
+            'p'     : np.array([2.]),
+            's0'    : np.array([0.02]),
+            'sInf'  : np.array([0.01]),
+            'kappa' : np.array([0.3]),
+            'lgamma' : np.array([-12.]),
+            'y0'    : np.array([0.01]),
+            'yInf'  : np.array([0.003]),
+            'y1'    : np.array([0.09]),
+            'y2'    : np.array([0.7]),
+        }
+
+        ptw = physics.MaterialModel(
+            flow_stress_model=physics.PTW_Yield_Stress, shear_modulus_model=physics.Stein_Shear_Modulus,
+        )
+
+        edot = 2500 * 1e-6  # 2500/s
+        temp = 1000  # K
+        emax = 0.6
+        nhist = 100
+        sim_strain_histories = physics.generate_strain_history_new(emax=np.array([emax]), edot=np.array([edot]), nhist=nhist)
+        ptw.initialize(params, consts)
+        ptw.initialize_state(T = np.array([temp]), stress = np.zeros(1), strain = np.zeros(1))
+        sim_state_histories = ptw.compute_state_history(sim_strain_histories)
+        sim_strains = sim_state_histories[:,1].T  # 2d array: ntot, Nhist
+        sim_stresses = sim_state_histories[:,2].T  # 2d array: ntot, Nhist
+
+        img_path = "tests/img/sim-stresses.png"
+        plt.plot(sim_strains.T, sim_stresses.T)
+        plt.savefig(img_path)
+        plt.close()
+        print(f"Image saved to {img_path}")