Add pytests (#102)

* first pass at writing tests

* add test dependencies

* add test which uses cube_samples, and add MPI test

* Add tests to workflow (separate for with and without mpi)

* remember to install test dependencies

* minimal changes to pyproject.toml to get optional dependencies to work

* remove errant _mpi filename change from test

* revert changes to pyproject.toml and just put dependencies in CI

* use 3 mpi processes instead of 2 for "proper" mpi

* use --oversubscribe

Author: AdamOrmondroyd

.github/workflows/CI.yml

@@ -43,10 +43,45 @@ jobs:
       run: python run_pypolychord.py
 
     - name: Test pypolychord (MPI)
-      run: mpirun -np 2 python run_pypolychord.py
+      run: mpirun --oversubscribe -np 3 python run_pypolychord.py
 
     - name: Test pypolychord (anesthetic)
       if: ${{ ! contains( '3.6, 3.7', matrix.python-version ) }}
       run: |
         pip install -r requirements.txt
         python run_pypolychord.py
+
+
+  tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        include:
+          - os: ubuntu-20.04
+            python-version: '3.6'
+
+    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 (Linux)
+      run: sudo apt-get install gfortran libopenmpi-dev
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install mpi4py pytest pytest-mpi fortranformat
+
+    - name: Install pypolychord
+      run: pip install -v '.[test]'
+
+    - name: Test pypolychord (no MPI)
+      run: python -m pytest tests
+
+    - name: Test pypolychord (MPI)
+      run: mpirun --oversubscribe -np 3 python -m pytest tests --only-mpi 

tests/test_run_pypolychord.py

@@ -0,0 +1,92 @@
+import pytest
+import numpy as np
+import pypolychord
+from pypolychord.settings import PolyChordSettings
+from pypolychord.priors import UniformPrior
+
+
+def gaussian_likelihood(theta):
+    """ Simple Gaussian Likelihood"""
+
+    sigma = 0.1
+
+    nDims = len(theta)
+    r2 = sum(theta**2)
+    logL = -np.log(2*np.pi*sigma*sigma)*nDims/2.0
+    logL += -r2/2/sigma/sigma
+
+    return logL, [r2]
+
+
+default_settings = PolyChordSettings(4, 1)
+default_settings.file_root = 'settings'
+default_settings.nlive = 200
+default_settings.read_resume = False
+default_settings.feedback = 0
+
+cube_samples_settings = PolyChordSettings(4, 1)
+cube_samples_settings.file_root = 'cube_samples'
+cube_samples_settings.nlive = 200
+cube_samples_settings.read_resume = False
+cube_samples_settings.cube_samples = np.array([[0.1, 0.2, 0.3, 0.4],
+                                               [0.5, 0.6, 0.7, 0.8]])
+cube_samples_settings.feedback = 0
+
+
+@pytest.mark.parametrize("settings, likelihood, nDims, nDerived",
+                         [(default_settings, gaussian_likelihood, 4, 1),
+                          (cube_samples_settings, gaussian_likelihood, 4, 1)])
+def test_run(settings, likelihood, nDims, nDerived):
+    # Define a box uniform prior from -1 to 1
+    def prior(hypercube):
+        """ Uniform prior from [-1,1]^D. """
+        return UniformPrior(-1, 1)(hypercube)
+
+    # Optional dumper function giving run-time read access to
+    # the live points, dead points, weights and evidences
+
+    def dumper(live, dead, logweights, logZ, logZerr):
+        print("Last dead point:", dead[-1])
+
+    # Run PolyChord
+
+    print("Running PolyChord")
+    output = pypolychord.run_polychord(likelihood, nDims, nDerived, settings, prior, dumper)
+
+    # Create a paramnames file
+
+    paramnames = [('p%i' % i, r'\theta_%i' % i) for i in range(nDims)]
+    paramnames += [('r*', 'r')]
+    output.make_paramnames_files(paramnames)
+
+
+@pytest.mark.parametrize("settings, likelihood, nDims, nDerived",
+                         [(default_settings, gaussian_likelihood, 4, 1),
+                          (cube_samples_settings, gaussian_likelihood, 4, 1)])
+@pytest.mark.mpi
+def test_run_mpi(settings, likelihood, nDims, nDerived):
+    from mpi4py import MPI
+
+    settings.file_root += '_mpi'
+
+    # Define a box uniform prior from -1 to 1
+    def prior(hypercube):
+        """ Uniform prior from [-1,1]^D. """
+        return UniformPrior(-1, 1)(hypercube)
+
+    # Optional dumper function giving run-time read access to
+    # the live points, dead points, weights and evidences
+
+    def dumper(live, dead, logweights, logZ, logZerr):
+        print("Last dead point:", dead[-1])
+
+    # Run PolyChord
+
+    print("Running PolyChord")
+    output = pypolychord.run_polychord(likelihood, nDims, nDerived, settings, prior, dumper)
+
+    # Create a paramnames file
+
+    paramnames = [('p%i' % i, r'\theta_%i' % i) for i in range(nDims)]
+    paramnames += [('r*', 'r')]
+    output.make_paramnames_files(paramnames)