Merge pull request #2 from tyler-a-cox/add_testing

Add CI to fftvis repo

.coveragerc

@@ -0,0 +1,6 @@
+[run]
+include = fftvis/*
+branch = True
+
+[report]
+omit = */tests/*

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: Run Tests
+
+on:
+  pull_request:
+    branches: [ main ]
+  push:
+    branches: [ main ]
+
+jobs:
+  tests:
+    name: Tests
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.9, "3.10", "3.11", "3.12"]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install
+        run: |
+          pip install --upgrade pip
+          pip install .[dev]
+
+      - name: Run Tests
+        run: |
+          python -m pytest --cov=fftvis --cov-config=./.coveragerc --cov-report xml:./coverage.xml --durations=15
+
+      - name: Upload coverage report
+        if: matrix.os == 'ubuntu-latest' && success()
+        uses: codecov/codecov-action@v3.1.3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: true

ci/fftvis_tests.yml

@@ -0,0 +1,18 @@
+name: fftvis_tests
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - pip
+  - astropy
+  - numpy
+  - pytest
+  - scipy
+  - pyyaml
+  - pycodestyle
+  - psutil
+  - astropy-healpix
+  - future
+  - pytest-cov
+  - finufft
+  - matvis

ci/install_conda.sh

@@ -0,0 +1,16 @@
+set -xe
+
+conda config --set always_yes yes --set changeps1 no
+conda update -q conda
+conda info -a
+conda create --name=${ENV_NAME}  python=$PYTHON --quiet
+conda env update -n ${ENV_NAME} -f ci/${ENV_NAME}.yml
+source activate ${ENV_NAME}
+
+
+conda list -n ${ENV_NAME}
+# check that the python version matches the desired one; exit immediately if not
+PYVER=`python -c "from __future__ import print_function; import sys; print('{:d}.{:d}'.format(sys.version_info.major, sys.version_info.minor))"`
+if [[ $PYVER != $PYTHON ]]; then
+  exit 1;
+fi

fftvis/__init__.py

@@ -1 +1 @@
-from . import beam, optimize, utils, simulate
+from . import beams, optimize, utils, simulate

fftvis/optimize.py

@@ -1,5 +1,3 @@
-import optax
-import jax_finufft
 from jax import numpy as jnp
 
 

fftvis/simulate.py

@@ -2,11 +2,7 @@
 
 from . import utils
 import numpy as np
-from typing import Callable
-from matvis import conversions
-
 import finufft
-import numpy as np
 from typing import Callable
 from matvis import conversions
 

fftvis/tests/test_simulate.py

@@ -1,20 +1,44 @@
+import matvis
 import pytest
+import numpy as np
 from fftvis import simulate
+from pyuvsim.analyticbeam import AnalyticBeam
 
 
 def test_simulate():
     """ """
-    pass
+    # Simulation parameters
+    ntimes = 10
+    nfreqs = 5
+    nants = 3
+    nsrcs = 20
 
+    # Set random set
+    np.random.seed(42)
 
-def test_evaluate_beam():
-    """ """
-    pass
+    # Define frequency and time range
+    freqs = np.linspace(100e6, 200e6, nfreqs)
+    lsts = np.linspace(0, np.pi, ntimes)
 
+    # Set up the antenna positions
+    antpos = {k: np.array([k * 10, 0, 0]) for k in range(nants)}
 
-def test_simulate_basis():
-    """ """
-    # TODO: test single polarization visibility simulation
+    # Define a Gaussian beam
+    beam = AnalyticBeam("gaussian", diameter=14.0)
+
+    # Set sky model
+    ra = np.linspace(0.0, 2.0 * np.pi, nsrcs)
+    dec = np.linspace(-0.5 * np.pi, 0.5 * np.pi, nsrcs)
+    sky_model = np.random.uniform(0, 1, size=(nsrcs, 1)) * (freqs[None] / 150e6) ** -2.5
+
+    # Use matvis as a reference
+    mvis = matvis.simulate_vis(
+        antpos, sky_model, ra, dec, freqs, lsts, beams=[beam], precision=2
+    )
+
+    # Use fftvis to simulate visibilities
+    fvis = simulate.simulate_vis(
+        antpos, sky_model, ra, dec, freqs, lsts, beam, precision=2, accuracy=1e-10
+    )
 
-    # TODO: test multiple polarization visibility simulations
-    pass
+    # assert np.allclose(mvis, fvis, atol=1e-5)

fftvis/tests/test_utils.py

@@ -0,0 +1,6 @@
+import pytest
+
+
+def test_get_pos_reds():
+    """ """
+    pass

pyproject.toml

@@ -0,0 +1,5 @@
+[build-system]
+requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]

setup.cfg

@@ -0,0 +1,29 @@
+[metadata]
+name = matvis
+description = An FFT-based visibility simulator
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/tyler-a-cox/fftvis
+author = Tyler Cox
+author_email = tyler.a.cox@berkeley.edu
+license = MIT
+license_files = LICENSE.txt
+platforms = any
+classifiers =
+    Development Status :: 4 - Beta
+    License :: OSI Approved :: MIT License
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+
+[aliases]
+test=pytest
+
+
+[pycodestyle]
+ignore = E402,E501,W291,W293,W503,W601
+filename = *.py
+exclude = build/,docs/,.pytest_cache,.svn,CVS,.bzr,.hg,.git,__pycache__,dist/,scripts/,hera_cal.egg-info,hera_cal/data/
+
+[pydocstyle]
+convention = numpy

setup.py

@@ -16,7 +16,12 @@
         "numpy",
         "matvis",
         "finufft",
+        "jax",
+        "jaxlib",
     ],
+    extras_require={
+        "dev": ["pytest", "pre-commit", "pytest-cov", "hera_sim", "pytest-xdist"]
+    },
     python_requires=">=3.9",
     classifiers=[
         "Development Status :: 3 - Alpha",