Address warnings (#292)

.github/workflows/ci.yml

@@ -41,11 +41,17 @@ jobs:
         with:
           fetch-depth: 1
 
+      - name: Create a .env file
+        run: |
+          touch .env
+          echo "NUMBA_NRT_STATS=1" >> .env
+          echo "NUMBA_CAPTURED_ERRORS='new_style'" >> .env
+
       - name: Install base codex-africanus
         run: pipenv install .[testing]
 
       - name: Run base test suite
-        run: pipenv run  NUMBA_NRT_STATS=1 py.test -s -vvv africanus/
+        run: pipenv run py.test -s -vvv africanus/
 
       - name: List the measures directory
         run: curl ftp://ftp.astron.nl/outgoing/Measures/ > measures_dir.txt
@@ -67,19 +73,16 @@ jobs:
           echo "measures.directory: ~/measures" > ~/.casarc
 
       - name: Install complete codex-africanus
-        # Need pyyaml for dask 2.17.0
-        # See https://github.com/dask/dask/issues/6221
         run: >
           pipenv install
           .[complete]
-          pyyaml
           git+https://gitlab.mpcdf.mpg.de/ift/nifty_gridder.git#egg=nifty-gridder
 
       - name: Log installed package versions
         run: pipenv graph
 
       - name: Run complete test suite
-        run: pipenv run NUMBA_NRT_STATS=1 py.test -s -vvv africanus/
+        run: pipenv run py.test -s -vvv africanus/
 
   deploy:
     needs: [test]
@@ -94,7 +97,7 @@ jobs:
       - name: Set up Python 3.10
         uses: actions/[email protected]
         with:
-          python-version: 3.10
+          python-version: '3.10'
 
       - name: Install latest setuptools, wheel, pip
         run: python3 -m pip install -U pip setuptools wheel

HISTORY.rst

@@ -4,6 +4,7 @@ History
 
 X.Y.Z (YYYY-MM-DD)
 ------------------
+* Address warnings (:pr:`292`)
 * Update github action versions (:pr:`291`)
 * Deprecate python 3.8 support (:pr:`290`)
 * Use pre-commit hooks for auto-linting (:pr:`290`)

africanus/averaging/tests/test_time_and_channel_averaging.py

@@ -55,25 +55,25 @@ def interval():
 @pytest.fixture
 def weight(time):
     shape = (time.shape[0], ncorr)
-    return np.arange(np.product(shape), dtype=np.float64).reshape(shape)
+    return np.arange(np.prod(shape), dtype=np.float64).reshape(shape)
 
 
 @pytest.fixture
 def sigma(time):
     shape = (time.shape[0], ncorr)
-    return np.arange(np.product(shape), dtype=np.float64).reshape(shape)
+    return np.arange(np.prod(shape), dtype=np.float64).reshape(shape)
 
 
 @pytest.fixture
 def weight_spectrum(time):
     shape = (time.shape[0], nchan, ncorr)
-    return np.arange(np.product(shape), dtype=np.float64).reshape(shape)
+    return np.arange(np.prod(shape), dtype=np.float64).reshape(shape)
 
 
 @pytest.fixture
 def sigma_spectrum(time):
     shape = (time.shape[0], nchan, ncorr)
-    return np.arange(np.product(shape), dtype=np.float64).reshape(shape)
+    return np.arange(np.prod(shape), dtype=np.float64).reshape(shape)
 
 
 @pytest.fixture

africanus/experimental/rime/fused/core.py

@@ -37,7 +37,7 @@ def rime(*args):
     def rime_impl(*args):
         raise NotImplementedError
 
-    @overload(rime_impl, jit_options=JIT_OPTIONS)
+    @overload(rime_impl, jit_options=JIT_OPTIONS, prefer_literal=True)
     def nb_rime(*args):
         if not len(args) > 0:
             raise TypeError(

africanus/gridding/perleypolyhedron/policies/baseline_transform_policies.py

@@ -83,7 +83,7 @@ def policy(uvw, ra0, dec0, ra, dec, policy_type):
     pass
 
 
-@overload(policy, inline="always")
+@overload(policy, inline="always", prefer_literal=True)
 def policy_impl(uvw, ra0, dec0, ra, dec, policy_type):
     if policy_type.literal_value == "None":
         return uvw_norotate

africanus/gridding/perleypolyhedron/policies/convolution_policies.py

@@ -349,7 +349,7 @@ def policy(
     pass
 
 
-@overload(policy, inline="always")
+@overload(policy, inline="always", prefer_literal=True)
 def policy_impl(
     scaled_u,
     scaled_v,

africanus/gridding/perleypolyhedron/policies/phase_transform_policies.py

@@ -38,7 +38,7 @@ def policy(vis, uvw, lambdas, ra0, dec0, ra, dec, policy_type, phasesign=1.0):
     pass
 
 
-@overload(policy, inline="always")
+@overload(policy, inline="always", prefer_literal=True)
 def policy_impl(vis, uvw, lambdas, ra0, dec0, ra, dec, policy_type, phasesign=1.0):
     if policy_type.literal_value == "None" or policy_type.literal_value is None:
         return phase_norotate

africanus/gridding/perleypolyhedron/policies/stokes_conversion_policies.py

@@ -5,7 +5,7 @@ def stokes2corr(vis_in, vis_out, policy_type):
     pass
 
 
-@overload(stokes2corr, inline="always")
+@overload(stokes2corr, inline="always", prefer_literal=True)
 def stokes2corrimpl(vis_in, vis_out, policy_type):
     if policy_type.literal_value == "XXYY_FROM_I":
 
@@ -143,7 +143,7 @@ def corr2stokes(vis_in, policy_type):
     pass
 
 
-@overload(corr2stokes, inline="always")
+@overload(corr2stokes, inline="always", prefer_literal=True)
 def corr2stokesimpl(vis_in, policy_type):
     if policy_type.literal_value == "I_FROM_XXYY":
         return lambda vis_in, policy_type: (vis_in[0] + vis_in[1]) * 0.5
@@ -183,7 +183,7 @@ def ncorr_out(policy_type):
     pass
 
 
-@overload(ncorr_out, inline="always")
+@overload(ncorr_out, inline="always", prefer_literal=True)
 def ncorr_outimpl(policy_type):
     if policy_type.literal_value == "XXYY_FROM_I":
         return lambda policy_type: 2

africanus/model/coherency/tests/test_convert.py

@@ -41,11 +41,11 @@ def visibility_factory(vis_shape, input_shape, in_type, backend="numpy", **kwarg
     shape = vis_shape + input_shape
 
     if backend == "numpy":
-        vis = np.arange(1.0, np.product(shape) + 1.0)
+        vis = np.arange(1.0, np.prod(shape) + 1.0)
         vis = vis.reshape(shape)
     elif backend == "dask":
         da = pytest.importorskip("dask.array")
-        vis = da.arange(1.0, np.product(shape) + 1.0, chunks=np.product(shape))
+        vis = da.arange(1.0, np.prod(shape) + 1.0, chunks=np.prod(shape))
         vis = vis.reshape(shape)
         vis = vis.rechunk(kwargs["vis_chunks"] + input_shape)
     else:

africanus/model/shape/shapelets.py

@@ -27,25 +27,21 @@ def factorial(n):
 
 
 @numba.jit(nogil=True, nopython=True, cache=True)
-def basis_function(n, xx, beta, fourier=False, delta_x=-1):
-    if fourier:
-        x = 2 * np.pi * xx
-        scale = 1.0 / beta
-    else:
-        x = xx
-        scale = beta
+def real_basis_function(n, xx, beta, delta_x=-1):
+    basis_component = 1.0 / np.sqrt(2.0**n * np.sqrt(np.pi) * factorial(n) * beta)
+    exponential_component = hermite(n, xx / beta) * np.exp(-(xx**2) / (2.0 * beta**2))
+    return basis_component * exponential_component
+
+
+@numba.jit(nogil=True, nopython=True, cache=True)
+def complex_basis_function(n, xx, beta, delta_x=-1):
+    x = 2 * np.pi * xx
+    scale = 1.0 / beta
     basis_component = 1.0 / np.sqrt(2.0**n * np.sqrt(np.pi) * factorial(n) * scale)
     exponential_component = hermite(n, x / scale) * np.exp(-(x**2) / (2.0 * scale**2))
-    if fourier:
-        return (
-            1.0j**n
-            * basis_component
-            * exponential_component
-            * np.sqrt(2 * np.pi)
-            / delta_x
-        )
-    else:
-        return basis_component * exponential_component
+    return (
+        1.0j**n * basis_component * exponential_component * np.sqrt(2 * np.pi) / delta_x
+    )
 
 
 @numba.jit(nogil=True, nopython=True, cache=True)
@@ -96,8 +92,8 @@ def shapelet(coords, frequency, coeffs, beta, delta_lm, dtype=np.complex128):
                             0
                             if coeffs[src][n1, n2] == 0
                             else coeffs[src][n1, n2]
-                            * basis_function(n1, fu, beta_u, True, delta_x=delta_l)
-                            * basis_function(n2, fv, beta_v, True, delta_x=delta_m)
+                            * complex_basis_function(n1, fu, beta_u, delta_x=delta_l)
+                            * complex_basis_function(n2, fv, beta_v, delta_x=delta_m)
                         )
                 out_shapelets[row, chan, src] = tmp_shapelet
     return out_shapelets
@@ -145,8 +141,8 @@ def shapelet_with_w_term(
                             0
                             if coeffs[src][n1, n2] == 0
                             else coeffs[src][n1, n2]
-                            * basis_function(n1, fu, beta_u, True, delta_x=delta_l)
-                            * basis_function(n2, fv, beta_v, True, delta_x=delta_m)
+                            * complex_basis_function(n1, fu, beta_u, delta_x=delta_l)
+                            * complex_basis_function(n2, fv, beta_v, delta_x=delta_m)
                         )
                 w_term = phase_steer_and_w_correct((u, v, w), (l, m), frequency[chan])
                 out_shapelets[row, chan, src] = tmp_shapelet * w_term
@@ -183,17 +179,16 @@ def shapelet_1d(u, coeffs, fourier, delta_x=1, beta=1.0):
         if delta_x is None:
             raise ValueError("You have to pass in a value for delta_x in Fourier mode")
         out = np.zeros(nrow, dtype=np.complex128)
+        for row, ui in enumerate(u):
+            for n, c in enumerate(coeffs):
+                out[row] += c * complex_basis_function(n, ui, beta, delta_x=delta_x)
     else:
         out = np.zeros(nrow, dtype=np.float64)
-    for row, ui in enumerate(u):
-        for n, c in enumerate(coeffs):
-            out[row] += c * basis_function(
-                n, ui, beta, fourier=fourier, delta_x=delta_x
-            )
-    return out
+        for row, ui in enumerate(u):
+            for n, c in enumerate(coeffs):
+                out[row] += c * real_basis_function(n, ui, beta, delta_x=delta_x)
 
-
-# @numba.jit(nogil=True, nopython=True, cache=True)
+    return out
 
 
 def shapelet_2d(u, v, coeffs_l, fourier, delta_x=None, delta_y=None, beta=1.0):

africanus/rime/zernike.py

@@ -123,7 +123,7 @@ def zernike_dde(
     npoly = coeffs.shape[-1]
 
     # Flatten correlation dimensions for numba function
-    fcorrs = np.product(corr_shape)
+    fcorrs = np.prod(corr_shape)
     ddes = np.empty((sources, times, ants, chans, fcorrs), coeffs.dtype)
 
     coeffs = coeffs.reshape((ants, chans, fcorrs, npoly))

africanus/util/nvcc.py

@@ -3,6 +3,7 @@
 
 import ast
 import contextlib
+import importlib.resources
 import logging
 import os
 import re
@@ -12,7 +13,6 @@
 import tempfile
 
 from os.path import join as pjoin
-from pkg_resources import resource_filename
 
 import distutils
 from distutils import errors
@@ -486,8 +486,8 @@ def compile_using_nvcc(source, options=None, arch=None, filename="kern.cu"):
 
     options += ["-cubin"]
 
-    cupy_path = resource_filename("cupy", pjoin("core", "include"))
-    settings["include_dirs"].append(cupy_path)
+    cupy_path = importlib.resources.files("cupy") / "core" / "include"
+    settings["include_dirs"].append(str(cupy_path))
 
     with _tempdir() as tmpdir:
         tmpfile = pjoin(tmpdir, filename)

setup.cfg

@@ -19,7 +19,7 @@ exclude = docs
 test = pytest
 
 [tool:pytest]
-collect_ignore = ['setup.py']
+addopts = --ignore=setup.py
 
 [pycodestyle]
 ignore = E121,E123,E126,E133,E226,E241,E242,E704,W503,W504,E741