Merge pull request #254 from mhvk/remove-testrunner

Remove testrunner

.github/workflows/ci_workflows.yml

@@ -53,13 +53,13 @@ jobs:
           #   apt_packages: graphviz
 
           - name: Test oldest supported versions and coverage
-            python: "3.7"
-            toxenv: py37-test-oldestdeps-alldeps-cov
+            python: "3.10"
+            toxenv: py310-test-oldestdeps-alldeps-cov
             pip_packages: codecov
 
           - name: Developer version of baseband
-            python: "3.10"
-            toxenv: py310-test-basebanddev
+            python: "3.12"
+            toxenv: py312-test-basebanddev
 
     steps:
     - uses: actions/checkout@v2

.readthedocs.yml

@@ -1,4 +1,8 @@
 version: 2
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+  fail_on_warning: true
 
 build:
   os: "ubuntu-22.04"

CHANGES.rst

@@ -1,8 +1,13 @@
 0.4 (unreleased)
 ================
 
-- The minimum versions required by baseband-tasks are now python 3.7,
-  baseband 4.1, and its minimum dependencies (astropy 4.0 and numpy 1.17).
+- Numpy >= 2.0 is now supported.
+- The minimum versions required by baseband-tasks are now python 3.10 and
+  baseband 4.2.
+- Remove support for the deprecated ``astropy`` test runner. This means it is
+  no longer possible to test the installed baseband package with
+  ``baseband_tasks.test()`` inside python; instead, one should use
+  ``pytest --pyargs baseband_tasks`` from the command line.
 
 New Features
 ------------

baseband_tasks/__init__.py

@@ -1,13 +1,12 @@
 # Licensed under the GPLv3 - see LICENSE
 """Radio baseband data reduction."""
 
-# Packages may add whatever they like to this file, but
-# should keep this content at the top.
-# ----------------------------------------------------------------------------
-from ._astropy_init import *   # noqa
-# ----------------------------------------------------------------------------
+try:
+    from .version import version as __version__
+except ImportError:
+    __version__ = ''
 
 # Define minima for the documentation, but do not bother to explicitly check.
 __minimum_python_version__ = '3.7'
-__minimum_baseband_version__ = '4.1'
-__minimum_astropy_version__ = '4.0'
+__minimum_baseband_version__ = '4.2'
+__minimum_astropy_version__ = '5.1'

baseband_tasks/base.py

@@ -9,6 +9,10 @@
 from astropy import units as u
 from astropy.utils.metadata import MetaData
 
+try:
+    from astropy.utils.compat import COPY_IF_NEEDED
+except ImportError:
+    COPY_IF_NEEDED = False  # older astropy requires numpy < 2 anyway.
 
 __all__ = ['Base', 'BaseTaskBase', 'TaskBase', 'PaddedTaskBase',
            'SetAttribute', 'Task']
@@ -467,11 +471,11 @@ def __getitem__(self, item):
 
         return GetSlice(self, item)
 
-    def __array__(self, dtype=None):
+    def __array__(self, dtype=None, copy=COPY_IF_NEEDED):
         old_offset = self.tell()
         try:
             self.seek(0)
-            return np.array(self.read(), dtype=dtype, copy=False)
+            return np.array(self.read(), dtype=dtype, copy=copy)
         finally:
             self.seek(old_offset)
 

baseband_tasks/convolution.py

@@ -10,28 +10,17 @@
 __all__ = ['ConvolveSamples', 'Convolve']
 
 
-class ConvolveBase(PaddedTaskBase):
-    """Base class for convolutions.
+def adjust_response_dims(response, ih):
+    if response.ndim == 1 and ih.ndim > 1:
+        response = response.reshape(response.shape[:1]
+                                    + (1,) * (ih.ndim - 1))
+    else:
+        check_broadcast_to(response, response.shape[:1] + ih.sample_shape)
 
-    Parameters as for `~baseband_tasks.convolution.ConvolveSamples` and
-    `~baseband_tasks.convolution.Convolve` except allowing to pass through
-    arguments to `~baseband_tasks.base.PaddedTaskBase`.
-    """
-    def __init__(self, ih, response, *, offset=0, samples_per_frame=None,
-                 **kwargs):
-        if response.ndim == 1 and ih.ndim > 1:
-            response = response.reshape(response.shape[:1]
-                                        + (1,) * (ih.ndim - 1))
-        else:
-            check_broadcast_to(response, response.shape[:1] + ih.sample_shape)
-
-        pad = response.shape[0] - 1
-        super().__init__(ih, pad_start=pad-offset, pad_end=offset,
-                         samples_per_frame=samples_per_frame, **kwargs)
-        self._response = response
+    return response
 
 
-class ConvolveSamples(ConvolveBase):
+class ConvolveSamples(PaddedTaskBase):
     """Convolve a time stream with a response, in the time domain.
 
     Parameters
@@ -56,8 +45,9 @@ class ConvolveSamples(ConvolveBase):
     Convolve : convolution in the Fourier domain (usually faster)
     """
     def __init__(self, ih, response, *, offset=0, samples_per_frame=None):
-        # Just get rid of **kwargs in ConvolveBase.
-        super().__init__(ih, response, offset=offset,
+        self._response = adjust_response_dims(response, ih)
+        pad = self._response.shape[0] - 1
+        super().__init__(ih, pad_start=pad-offset, pad_end=offset,
                          samples_per_frame=samples_per_frame)
 
     def task(self, data):
@@ -72,7 +62,7 @@ def task(self, data):
         return result
 
 
-class Convolve(ConvolveBase):
+class Convolve(PaddedTaskBase):
     """Convolve a time stream with a response, in the Fourier domain.
 
     The convolution is done via multiplication in the Fourier domain, which
@@ -102,8 +92,10 @@ class Convolve(ConvolveBase):
     """
 
     def __init__(self, ih, response, *, offset=0, samples_per_frame=None):
+        self._response = adjust_response_dims(response, ih)
+        pad = self._response.shape[0] - 1
         FFT = fft_maker.get()
-        super().__init__(ih, response=response, offset=offset,
+        super().__init__(ih, pad_start=pad-offset, pad_end=offset,
                          samples_per_frame=samples_per_frame,
                          next_fast_len=FFT.next_fast_len)
         # Initialize FFTs for fine channelization and the inverse.

baseband_tasks/fourier/pyfftw.py

@@ -159,4 +159,11 @@ def __repr__(self):
         self._repr_kwargs.update(self._fftw_kwargs)
         return super().__repr__()
 
-    next_fast_len = staticmethod(pyfftw.next_fast_len)
+    @staticmethod
+    def next_fast_len(n):
+        """Smallest composite of primes between 2 and 13 which is >= n.
+
+        Defers to `pyfftw.next_fast_len`.  The primes 11 and 13 can
+        occur at most once.
+        """
+        return pyfftw.next_fast_len(n)

baseband_tasks/functions.py

@@ -1,6 +1,11 @@
 # Licensed under the GPLv3 - see LICENSE
 import numpy as np
 
+try:
+    from numpy._core import defchararray
+except ImportError:
+    from numpy.core import defchararray
+
 from .base import TaskBase, simplify_shape
 
 
@@ -43,7 +48,7 @@ def _default_polarization(self, ih):
         if not hasattr(ih, 'polarization'):
             return None
 
-        return np.core.defchararray.add(ih.polarization, ih.polarization)
+        return defchararray.add(ih.polarization, ih.polarization)
 
     def _repr_item(self, key, default, value=None):
         if key == 'polarization':
@@ -115,8 +120,8 @@ def _default_polarization(self, ih):
 
         # Given check_shape, ih.polarization is guaranteed to have 2 distinct
         # items, which are guaranteed to be along first axis.
-        return np.core.defchararray.add(ih.polarization[[0, 1, 0, 1]],
-                                        ih.polarization[[0, 1, 1, 0]])
+        return defchararray.add(ih.polarization[[0, 1, 0, 1]],
+                                ih.polarization[[0, 1, 1, 0]])
 
     def _repr_item(self, key, default, value=None):
         if (key == 'polarization' and hasattr(self.ih, 'polarization')

baseband_tasks/io/psrfits/hdu.py

@@ -10,6 +10,7 @@
 from astropy.utils import lazyproperty
 import numpy as np
 import operator
+
 from .psrfits_htm_parser import HDU_TEMPLATES
 
 
@@ -148,7 +149,7 @@ def frequency(self):
 
         freq = c_freq + (np.arange(1, n_chan + 1)
                          - ((n_chan + 1) // 2)) * chan_bw
-        return u.Quantity(freq, u.MHz, copy=False)
+        return freq << u.MHz
 
     @frequency.setter
     def frequency(self, freq):
@@ -159,7 +160,7 @@ def frequency(self, freq):
         # we assume the frequency resolution is the same across the band.
         freq_pad = np.insert(freq, 0, 2 * freq[0] - freq[1])
         c_chan = freq_pad[((n_chan + 1) // 2)]
-        bw = freq_pad.ptp()
+        bw = np.ptp(freq_pad)
         self.hdu.header['OBSNCHAN'] = n_chan
         self.hdu.header['OBSFREQ'] = c_chan
         self.hdu.header['OBSBW'] = bw
@@ -394,7 +395,7 @@ def polarization(self, value):
     @property
     def frequency(self):
         if 'DAT_FREQ' in self.data.names:
-            freqs = u.Quantity(self.data['DAT_FREQ'][0], u.MHz, copy=False)
+            freqs = self.data['DAT_FREQ'][0] << u.MHz
         else:
             freqs = super().frequency
 
@@ -501,8 +502,7 @@ def verify(self):
 
         # Check frequency
         if 'DAT_FREQ' in self.data.names:
-            freqs = u.Quantity(self.data['DAT_FREQ'],
-                               u.MHz, copy=False)
+            freqs = self.data['DAT_FREQ'] << u.MHz
             assert np.array_equiv(freqs[0], freqs), \
                 "Frequencies are not all the same for different rows."
 
@@ -532,7 +532,7 @@ def start_time(self):
         if "OFFS_SUB" in self.data.names:
             offset0 = (self.data['OFFS_SUB'][0]
                        - self.data['TSUBINT'][0] * self.samples_per_frame / 2)
-            start_time += u.Quantity(offset0, u.s, copy=False)
+            start_time += offset0 << u.s
 
         return start_time
 
@@ -562,7 +562,7 @@ def sample_rate(self):
         # NOTE we are assuming TSUBINT is uniform; tested in verify,
         # but as individual numbers seem to vary, take the mean.
         # TODO: check whether there really isn't a better way!.
-        sample_time = u.Quantity(self.data['TSUBINT'], u.s).mean()
+        sample_time = (self.data['TSUBINT'] << u.s).mean()
         return 1.0 / sample_time
 
     @sample_rate.setter

baseband_tasks/phases/phase.py

@@ -7,6 +7,7 @@
 from astropy.coordinates import Angle, Longitude
 from astropy.time.utils import day_frac
 
+from baseband_tasks.base import COPY_IF_NEEDED
 
 __all__ = ['Phase', 'FractionalPhase']
 
@@ -190,7 +191,7 @@ def __new__(cls, phase1, phase2=None, copy=True, subok=False):
                 phase1 = phase1.view(cls)
             return phase1.copy() if copy else phase1
 
-        phase1 = Angle(phase1, cls._unit, copy=False)
+        phase1 = Angle(phase1, cls._unit, copy=COPY_IF_NEEDED)
 
         if phase2 is not None:
             if isinstance(phase2, Phase):
@@ -199,7 +200,7 @@ def __new__(cls, phase1, phase2=None, copy=True, subok=False):
                     phase2 = phase2.view(cls)
                 return phase2
 
-            phase2 = Angle(phase2, cls._unit, copy=False)
+            phase2 = Angle(phase2, cls._unit, copy=COPY_IF_NEEDED)
 
         return cls.from_angles(phase1, phase2)
 
@@ -531,8 +532,11 @@ def max(self, axis=None, out=None, keepdims=False):
     def ptp(self, axis=None, out=None, keepdims=False):
         """Peak to peak (maximum - minimum) along a given axis.
 
-        This is similar to :meth:`~numpy.ndarray.ptp`, but adapted to ensure
+        This is similar to :func:`~numpy.ptp`, but adapted to ensure
         that the full precision is used.
+
+        .. note:: for numpy >= 2.0, ``np.ptp(phase)`` no longer defers
+                  to this method.
         """
         if out is not None:
             raise ValueError("An `out` argument is not yet supported.")
@@ -676,8 +680,7 @@ def __array_ufunc__(self, function, method, *inputs, **kwargs):
                or function is np.divide and i_self == 0)
               and basic_phase_out):
             try:
-                other = u.Quantity(inputs[1-i_self], u.dimensionless_unscaled,
-                                   copy=False).value
+                other = (inputs[1-i_self] << u.dimensionless_unscaled).value
                 if function is np.multiply:
                     return self.from_angles(self['int'], self['frac'],
                                             factor=other, out=phase_out)
@@ -732,8 +735,8 @@ def __array_ufunc__(self, function, method, *inputs, **kwargs):
         elif function in {np.absolute, np.fabs} and basic_phase_out:
             # Go via view to avoid having to deal with imaginary.
             v = self.view(np.ndarray)
-            return self.from_angles(u.Quantity(v['int'], u.cycle, copy=False),
-                                    u.Quantity(v['frac'], u.cycle, copy=False),
+            return self.from_angles(v['int'] << u.cycle,
+                                    v['frac'] << u.cycle,
                                     factor=np.sign(v['int'] + v['frac']),
                                     out=phase_out)