Support NumPy 2 (#61)

phasorpy · Apr 26, 2024 · b03f635 · b03f635
1 parent 08593fe
commit b03f635
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Showing 14 changed files with 119 additions and 57 deletions.
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -25,6 +25,7 @@ jobs:
           CIBW_ARCHS_LINUX: auto
           CIBW_ARCHS_MACOS: x86_64 arm64
           CIBW_ARCHS_WINDOWS: AMD64 ARM64
+          CIBW_BEFORE_BUILD: python -m pip install numpy>=2.0.0rc1
       - uses: actions/upload-artifact@v4
         with:
           path: ./wheelhouse/*.whl

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -76,7 +76,7 @@ jobs:
         make html
 
   build_wheels:
-    name: Test cibuildwheel
+    name: Test cibuildwheel and numpy 2
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -86,6 +86,8 @@ jobs:
       - uses: actions/checkout@v4
       - uses: pypa/cibuildwheel@v2.17.0
         env:
+          CIBW_BEFORE_TEST: python -m pip install numpy>=2.0.0rc1
+          CIBW_BEFORE_BUILD: python -m pip install numpy>=2.0.0rc1
           CIBW_BUILD: "cp311-manylinux_x86_64 cp312-win_amd64 cp312-macosx_x86_64"
           CIBW_SKIP:
       - uses: actions/upload-artifact@v4

diff --git a/pyproject.toml b/pyproject.toml
@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=68",
     "numpy",
-    "Cython",
+    "Cython>=3.0.10",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -81,6 +81,9 @@ version = { attr = "phasorpy.version.__version__" }
 [tool.setuptools.package-data]
 phasorpy = ["py.typed"]
 
+[tool.ruff.lint]
+select = ["NPY201"]
+
 [tool.pylint.format]
 max-line-length = 79
 max-module-lines = 2500
@@ -140,7 +143,7 @@ directory = "_htmlcov"
 minversion = "7"
 log_cli_level = "INFO"
 xfail_strict = true
-addopts = "-ra --strict-config --strict-markers --cov=phasorpy --cov-report html --doctest-modules --doctest-glob=*.py --doctest-glob=*.rst"
+addopts = "-rfEXs --strict-config --strict-markers --cov=phasorpy --cov-report html --doctest-modules --doctest-glob=*.py --doctest-glob=*.rst"
 doctest_optionflags = [
     "NORMALIZE_WHITESPACE",
     "ELLIPSIS",
@@ -156,7 +159,7 @@ norecursedirs = [
     ".pytest_cache",
     "adhoc",
     "build",
-    "docs",
+    "docs/_build",
     "fixture",
     "htmlcov",
     "_htmlcov",

diff --git a/src/phasorpy/cli.py b/src/phasorpy/cli.py
@@ -23,9 +23,16 @@ def main() -> int:
 
 
 @main.command(help='Show runtime versions.')
-def versions():
+@click.option(
+    '--verbose',
+    default=False,
+    is_flag=True,
+    type=click.BOOL,
+    help='Show module paths.',
+)
+def versions(verbose):
     """Versions command group."""
-    click.echo(version.versions())
+    click.echo(version.versions(verbose=verbose))
 
 
 @main.command(help='Fetch sample files from remote repositories.')

diff --git a/src/phasorpy/components.py b/src/phasorpy/components.py
@@ -107,8 +107,8 @@ def two_fractions_from_phasor(
         real, imag, real_components, imag_components
     )
     distances_to_first_component = numpy.hypot(
-        (numpy.array(projected_real) - first_component_phasor[0]),
-        (numpy.array(projected_imag) - first_component_phasor[1]),
+        numpy.asarray(projected_real) - first_component_phasor[0],
+        numpy.asarray(projected_imag) - first_component_phasor[1],
     )
     fraction_of_second_component = (
         distances_to_first_component / total_distance_between_components

diff --git a/src/phasorpy/conftest.py b/src/phasorpy/conftest.py
@@ -7,6 +7,10 @@
 
 from .datasets import fetch
 
+# numpy 2.0 changed the scalar type representation,
+# causing many doctests to fail.
+numpy.set_printoptions(legacy='1.21')
+
 
 @pytest.fixture(autouse=True)
 def add_doctest_namespace(doctest_namespace):

diff --git a/src/phasorpy/io.py b/src/phasorpy/io.py
@@ -536,7 +536,7 @@ def read_sdt(
 
     # TODO: get spatial coordinates from scanner settings?
     metadata = _metadata('QYXH'[-data.ndim :], data.shape, filename, H=times)
-    metadata['attrs']['frequency'] = 1e-6 / (times[-1] + times[1])
+    metadata['attrs']['frequency'] = 1e-6 / float(times[-1] + times[1])
     return DataArray(data, **metadata)
 
 

diff --git a/src/phasorpy/phasor.py b/src/phasorpy/phasor.py
@@ -218,15 +218,15 @@ def phasor_from_signal(
     (1.1, 0.0, 0.0)
 
     """
-    signal = numpy.array(signal, order='C', ndmin=1, copy=False)
-    samples = signal.shape[axis]  # this also verifies axis
+    signal = numpy.asarray(signal, order='C')
+    samples = numpy.size(signal, axis)  # this also verifies axis and ndim >= 1
 
     if sample_phase is not None:
         if harmonic is not None:
             raise ValueError('sample_phase cannot be used with harmonic')
         harmonics = [1]  # value not used
-        sample_phase = numpy.array(
-            sample_phase, dtype=numpy.float64, copy=False, ndmin=1
+        sample_phase = numpy.atleast_1d(
+            numpy.asarray(sample_phase, dtype=numpy.float64)
         )
         if sample_phase.ndim != 1 or sample_phase.size != samples:
             raise ValueError(f'{sample_phase.shape=} != ({samples},)')
@@ -237,7 +237,7 @@ def phasor_from_signal(
     elif isinstance(harmonic, int):
         harmonics = [harmonic]
     else:
-        a = numpy.array(harmonic, ndmin=1)
+        a = numpy.atleast_1d(numpy.asarray(harmonic))
         if a.dtype.kind not in 'iu' or a.ndim != 1:
             raise TypeError(f'invalid {harmonic=} type')
         harmonics = a.tolist()
@@ -358,7 +358,7 @@ def phasor_from_signal_fft(
     (1.1, array([0.5, 0.0]), array([0.5, -0]))
 
     """
-    signal = numpy.array(signal, copy=False, ndmin=1)
+    signal = numpy.asarray(signal)
     samples = numpy.size(signal, axis)
     if samples < 3:
         raise ValueError(f'not enough {samples=} along {axis=}')
@@ -372,7 +372,7 @@ def phasor_from_signal_fft(
                 f'harmonic={harmonic} out of range 1..{max_harmonic}'
             )
     else:
-        a = numpy.array(harmonic)
+        a = numpy.atleast_1d(numpy.asarray(harmonic))
         if a.dtype.kind not in 'iu' or a.ndim != 1:
             raise TypeError(f'invalid {harmonic=} type')
         if numpy.any(a < 1) or numpy.any(a > max_harmonic):
@@ -986,7 +986,7 @@ def phasor_to_apparent_lifetime(
     (array([inf, 0]), array([inf, 0]))
 
     """
-    omega = numpy.array(frequency, dtype=numpy.float64, copy=True)
+    omega = numpy.array(frequency, dtype=numpy.float64)  # makes copy
     omega *= math.pi * 2.0 * unit_conversion
     return _phasor_to_apparent_lifetime(real, imag, omega, **kwargs)
 
@@ -1068,7 +1068,7 @@ def phasor_from_apparent_lifetime(
     (array([1, 0.0]), array([0, 0.0]))
 
     """
-    omega = numpy.array(frequency, dtype=numpy.float64, copy=True)
+    omega = numpy.array(frequency, dtype=numpy.float64)  # makes copy
     omega *= math.pi * 2.0 * unit_conversion
     if modulation_lifetime is None:
         return _phasor_from_single_lifetime(phase_lifetime, omega, **kwargs)
@@ -1211,7 +1211,7 @@ def fraction_to_amplitude(
     array([0.2, 0.2])
 
     """
-    t = numpy.array(fraction, copy=True, dtype=numpy.float64)
+    t = numpy.array(fraction, dtype=numpy.float64)  # makes copy
     t /= numpy.sum(t, axis=axis, keepdims=True)
     numpy.true_divide(t, lifetime, out=t)
     return t
@@ -1419,10 +1419,10 @@ def phasor_from_lifetime(
     """
     if unit_conversion < 1e-16:
         raise ValueError(f'{unit_conversion=} < 1e-16')
-    frequency = numpy.array(frequency, dtype=numpy.float64, ndmin=1)
+    frequency = numpy.atleast_1d(numpy.asarray(frequency, dtype=numpy.float64))
     if frequency.ndim != 1:
         raise ValueError('frequency is not one-dimensional array')
-    lifetime = numpy.array(lifetime, dtype=numpy.float64, ndmin=1)
+    lifetime = numpy.atleast_1d(numpy.asarray(lifetime, dtype=numpy.float64))
     if lifetime.ndim > 2:
         raise ValueError('lifetime must be one- or two-dimensional array')
 
@@ -1435,7 +1435,9 @@ def phasor_from_lifetime(
         lifetime = lifetime.reshape(-1, 1)  # move components to last axis
         fraction = numpy.ones_like(lifetime)  # not really used
     else:
-        fraction = numpy.array(fraction, dtype=numpy.float64, ndmin=1)
+        fraction = numpy.atleast_1d(
+            numpy.asarray(fraction, dtype=numpy.float64)
+        )
         if fraction.ndim > 2:
             raise ValueError('fraction must be one- or two-dimensional array')
 
@@ -1541,7 +1543,7 @@ def polar_to_apparent_lifetime(
     (array([1.989, 1.989]), array([1.989, 2.411]))
 
     """
-    omega = numpy.array(frequency, dtype=numpy.float64, copy=True)
+    omega = numpy.array(frequency, dtype=numpy.float64)  # makes copy
     omega *= math.pi * 2.0 * unit_conversion
     return _polar_to_apparent_lifetime(phase, modulation, omega, **kwargs)
 
@@ -1611,7 +1613,7 @@ def polar_from_apparent_lifetime(
     (array([0.7854, 0.7854]), array([0.7071, 0.6364]))
 
     """
-    omega = numpy.array(frequency, dtype=numpy.float64, copy=True)
+    omega = numpy.array(frequency, dtype=numpy.float64)  # makes copy
     omega *= math.pi * 2.0 * unit_conversion
     if modulation_lifetime is None:
         return _polar_from_single_lifetime(phase_lifetime, omega, **kwargs)
@@ -1702,7 +1704,7 @@ def phasor_from_fret_donor(
     (array([0.1766, 0.2737, 0.1466]), array([0.3626, 0.4134, 0.2534]))
 
     """
-    omega = numpy.array(frequency, dtype=numpy.float64, copy=True)
+    omega = numpy.array(frequency, dtype=numpy.float64)  # makes copy
     omega *= math.pi * 2.0 * unit_conversion
     return _phasor_from_fret_donor(
         omega,
@@ -1820,7 +1822,7 @@ def phasor_from_fret_acceptor(
     (array([0.1996, 0.05772, 0.2867]), array([0.3225, 0.3103, 0.4292]))
 
     """
-    omega = numpy.array(frequency, dtype=numpy.float64, copy=True)
+    omega = numpy.array(frequency, dtype=numpy.float64)  # makes copy
     omega *= math.pi * 2.0 * unit_conversion
     return _phasor_from_fret_acceptor(
         omega,

diff --git a/src/phasorpy/plot.py b/src/phasorpy/plot.py
@@ -237,7 +237,10 @@ def plot(
             i,
             (re, im),
         ) in enumerate(
-            zip(numpy.array(real, ndmin=2), numpy.array(imag, ndmin=2))
+            zip(
+                numpy.atleast_2d(numpy.asarray(real)),
+                numpy.atleast_2d(numpy.asarray(imag)),
+            )
         ):
             lbl = None
             if label is not None:

diff --git a/src/phasorpy/version.py b/src/phasorpy/version.py
@@ -5,59 +5,67 @@
 __version__ = '0.1.dev'
 
 
-def versions(*, sep: str = '\n') -> str:
+def versions(
+    *, sep: str = '\n', dash: str = '-', verbose: bool = False
+) -> str:
     """Return versions of installed packages that phasorpy depends on.
 
     Parameters
     ----------
     sep : str, optional
         Separator between version items. The default is a newline character.
+    dash : str, optional
+        Separator between module name and version.
+    verbose : bool, optional
+        Include paths to Python interpreter and modules.
 
     Example
     -------
     >>> print(versions())
-    Python 3...
-    phasorpy 0...
-    numpy 1...
+    Python-3...
+    phasorpy-0...
+    numpy-...
     ...
 
     """
     import os
     import sys
 
-    try:
-        path = os.path.dirname(__file__)
-    except NameError:
-        path = ''
-
-    version_strings = [
-        f'Python {sys.version} ({sys.executable})',
-        f'phasorpy {__version__} ({path})',
-    ]
+    if verbose:
+        version_strings = [f'Python{dash}{sys.version}  ({sys.executable})']
+    else:
+        version_strings = [f'Python{dash}{sys.version.split()[0]}']
 
     for module in (
+        'phasorpy',
         'numpy',
-        'matplotlib',
-        'click',
-        'pooch',
-        'tqdm',
-        'xarray',
         'tifffile',
+        'imagecodecs',
         'lfdfiles',
         'sdtfile',
         'ptufile',
-        # 'scipy',
-        # 'skimage',
-        # 'sklearn',
-        # 'aicsimageio',
+        'matplotlib',
+        'scipy',
+        'skimage',
+        'sklearn',
+        'pandas',
+        'xarray',
+        'click',
+        'pooch',
     ):
         try:
             __import__(module)
         except ModuleNotFoundError:
-            version_strings.append(f'{module.lower()} N/A')
+            version_strings.append(f'{module.lower()}{dash}n/a')
             continue
         lib = sys.modules[module]
-        version_strings.append(
-            f"{module.lower()} {getattr(lib, '__version__', 'unknown')}"
-        )
+        ver = f"{module.lower()}{dash}{getattr(lib, '__version__', 'unknown')}"
+        if verbose:
+            try:
+                path = getattr(lib, '__file__')
+            except NameError:
+                pass
+            else:
+                ver += f'  ({os.path.dirname(path)})'
+        version_strings.append(ver)
     return sep.join(version_strings)
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -0,0 +1,21 @@
+"""Pytest configuration."""
+
+import os
+
+import phasorpy
+from phasorpy import versions
+from phasorpy.utils import number_threads
+
+
+def pytest_report_header(config, start_path, startdir):
+    """Return versions of relevant installed packages."""
+    return '\n'.join(
+        (
+            f'versions: {versions(sep=", ")}',
+            f'number_threads: {number_threads(0)}',
+            f'path: {os.path.dirname(phasorpy.__file__)}',
+        )
+    )
+
+
+collect_ignore = ['data']
diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -17,9 +17,9 @@ def test_version():
 def test_versions():
     """Test ``python -m phasorpy versions``."""
     runner = CliRunner()
-    result = runner.invoke(main, ['versions'])
+    result = runner.invoke(main, ['versions', '--verbose'])
     assert result.exit_code == 0
-    assert result.output.strip() == versions()
+    assert result.output.strip() == versions(verbose=True)
 
 
 def test_fetch():

diff --git a/tests/test_phasorpy.py b/tests/test_phasorpy.py
@@ -6,5 +6,9 @@
 def test_versions():
     """Test phasorpy.versions function."""
     ver = versions()
-    assert f'phasorpy {__version__}' in ver
-    assert 'numpy' in ver
+    assert 'Python-' in ver
+    assert f'phasorpy-{__version__}\nnumpy-' in ver
+    assert '(' not in ver
+
+    ver = versions(sep=', ', dash=' ', verbose=True)
+    assert f', phasorpy {__version__}  (' in ver