Update halos module with main compatability updates.

.github/workflows/codestyle.yaml

@@ -4,18 +4,22 @@ on:
     branches:
     - main
     - module/*
+    - 'v*x'
+    tags:
+    - 'v*'
   pull_request:
     branches:
     - main
     - module/*
+    - 'v*x'
 jobs:
   flake8:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Install Python 3.x
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
     - name: Install Dependencies

.github/workflows/compatibility.yaml

@@ -9,20 +9,20 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python: ['3.11']
-        toxenv: [py311-test, py311-test-dev]
+        python: ['3.13']
+        toxenv: [py313-test, py313-test-dev]
         release: [main, latest]
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - if: matrix.release != 'main'
       name: Checkout Release
       run: |
         git checkout tags/$(curl -s https://api.github.com/repos/skypyproject/skypy/releases/${{ matrix.release }} | python -c "import sys, json; print(json.load(sys.stdin)['tag_name'])")
     - name: Install Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
     - name: Install Dependencies

.github/workflows/tests.yaml

@@ -4,10 +4,14 @@ on:
     branches:
     - main
     - module/*
+    - 'v*x'
+    tags:
+    - 'v*'
   pull_request:
     branches:
     - main
     - module/*
+    - 'v*x'
 jobs:
   test:
     name: ${{ matrix.name }}
@@ -19,32 +23,32 @@ jobs:
 
           - name: latest supported versions
             os: ubuntu-latest
-            python: '3.11'
-            toxenv: py311-test-all-latest-cov
+            python: '3.13'
+            toxenv: py313-test-all-latest-cov
             toxposargs: --cov-report=xml:${GITHUB_WORKSPACE}/coverage.xml
 
           - name: oldest supported versions
             os: ubuntu-latest
-            python: 3.7
-            toxenv: py37-test-oldest
+            python: '3.9'
+            toxenv: py39-test-oldest
 
           - name: macOS latest supported
             os: macos-latest
-            python: '3.11'
-            toxenv: py311-test-latest
+            python: '3.13'
+            toxenv: py313-test-latest
 
           - name: Windows latest supported
             os: windows-latest
-            python: '3.11'
-            toxenv: py311-test-latest
+            python: '3.13'
+            toxenv: py313-test-latest
 
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Install Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
     - name: Install Dependencies
@@ -55,4 +59,4 @@ jobs:
         tox -e ${{ matrix.toxenv }} ${{ matrix.toxargs }} -- ${{ matrix.toxposargs }}
     - if: contains(matrix.toxenv, '-cov')
       name: Report Coverage
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3

.readthedocs.yml

@@ -1,13 +1,17 @@
 version: 2
 
 build:
-  image: latest
+  os: ubuntu-20.04
+  tools:
+    python: '3.13'
+  apt_packages:
+    - graphviz
 
 sphinx:
+  configuration: docs/conf.py
   fail_on_warning: true
 
 python:
-  version: 3.7
   install:
     - method: pip
       path: .

CONTRIBUTING.rst

@@ -168,7 +168,7 @@ Before your pull request can be merged into the codebase, it will be reviewed by
 General Guidelines
 ^^^^^^^^^^^^^^^^^^
 
-- SkyPy is compatible with Python>=3.7 (see `setup.cfg <https://github.com/skypyproject/skypy/blob/main/setup.cfg>`_). SkyPy *does not* support backwards compatibility with Python 2.x; `six`, `__future__` and `2to3` should not be used.
+- SkyPy is compatible with Python>=3.9 (see `setup.cfg <https://github.com/skypyproject/skypy/blob/main/setup.cfg>`_). SkyPy *does not* support backwards compatibility with Python 2.x; `six`, `__future__` and `2to3` should not be used.
 - All contributions should follow the `PEP8 Style Guide for Python Code <https://www.python.org/dev/peps/pep-0008/>`_. We recommend using `flake8 <https://flake8.pycqa.org/>`__ to check your code for PEP8 compliance.
 - Importing SkyPy should only depend on having `NumPy <https://www.numpy.org>`_, `SciPy <https://www.scipy.org/>`_ and `Astropy <https://www.astropy.org/>`__ installed.
 - Code is grouped into submodules based on broad science areas e.g. `galaxies <https://skypy.readthedocs.io/en/stable/galaxies.html>`_. There is also a `utils <https://skypy.readthedocs.io/en/stable/utils/index.html>`_ submodule for general utility functions.

docs/install.rst

@@ -40,7 +40,7 @@ can be installed directly from GitHub using a recent version of pip:
 Dependencies
 ------------
 
-SkyPy is compatble with Python versions 3.7 or later on Ubuntu, macOS and
+SkyPy is compatble with Python versions 3.9 or later on Ubuntu, macOS and
 Windows operating systems. It has the following core dependencies:
 
 - `astropy <https://www.astropy.org/>`__

examples/galaxies/plot_schechter.py

@@ -47,6 +47,7 @@
 from astropy.units import Quantity
 from matplotlib import pyplot as plt
 import numpy as np
+import scipy.integrate
 from skypy.galaxies import schechter_lf
 
 z_range = np.linspace(0.2, 1.0, 100)
@@ -81,7 +82,7 @@
     # SkyPy simulated galaxies
     z_mask = np.logical_and(redshift >= z_min, redshift < z_max)
     dV_dz = (cosmology.differential_comoving_volume(z) * sky_area).to_value('Mpc3')
-    dV = np.trapz(dV_dz, z)
+    dV = scipy.integrate.trapezoid(dV_dz, z)
     dM = (np.max(bins)-np.min(bins)) / (np.size(bins)-1)
     phi_skypy = np.histogram(magnitude[z_mask], bins=bins)[0] / dV / dM
 

setup.cfg

@@ -14,7 +14,7 @@ github_project = skypyproject/skypy
 [options]
 zip_safe = False
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.9
 setup_requires = setuptools_scm
 install_requires =
     astropy>=4

skypy/_astropy_init.py

@@ -1,52 +1,13 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
+import os
 
-__all__ = ['__version__']
-
-# this indicates whether or not we are in the package's setup.py
-try:
-    _ASTROPY_SETUP_
-except NameError:
-    import builtins
-    builtins._ASTROPY_SETUP_ = False
+__all__ = ['__version__', 'test']
 
 try:
     from .version import version as __version__
 except ImportError:
     __version__ = ''
 
-
-if not _ASTROPY_SETUP_:  # noqa
-    import os
-    from warnings import warn
-    from astropy.config.configuration import (
-        update_default_config,
-        ConfigurationDefaultMissingError,
-        ConfigurationDefaultMissingWarning)
-
-    # Create the test function for self test
-    from astropy.tests.runner import TestRunner
-    test = TestRunner.make_test_runner_in(os.path.dirname(__file__))
-    test.__test__ = False
-    __all__ += ['test']
-
-    # add these here so we only need to cleanup the namespace at the end
-    config_dir = None
-
-    if not os.environ.get('ASTROPY_SKIP_CONFIG_UPDATE', False):
-        config_dir = os.path.dirname(__file__)
-        config_template = os.path.join(config_dir, __package__ + ".cfg")
-        if os.path.isfile(config_template):
-            try:
-                update_default_config(
-                    __package__, config_dir, version=__version__)
-            except TypeError as orig_error:
-                try:
-                    update_default_config(__package__, config_dir)
-                except ConfigurationDefaultMissingError as e:
-                    wmsg = (e.args[0] +
-                            " Cannot install default profile. If you are "
-                            "importing from source, this is expected.")
-                    warn(ConfigurationDefaultMissingWarning(wmsg))
-                    del e
-                except Exception:
-                    raise orig_error
+# Create the test function for self test
+from astropy.tests.runner import TestRunner
+test = TestRunner.make_test_runner_in(os.path.dirname(__file__))

skypy/conftest.py

@@ -1,27 +1,29 @@
-# This file is used to configure the behavior of pytest when using the Astropy
-# test infrastructure. It needs to live inside the package in order for it to
-# get picked up when running the tests inside an interpreter using
-# packagename.test
+"""Configure Test Suite.
 
-import os
+This file is used to configure the behavior of pytest when using the Astropy
+test infrastructure. It needs to live inside the package in order for it to
+get picked up when running the tests inside an interpreter using
+`{{ cookiecutter.module_name }}.test()`.
+
+"""
 
-from astropy.version import version as astropy_version
+import os
 
-# For Astropy 3.0 and later, we can use the standalone pytest plugin
-if astropy_version < '3.0':
-    from astropy.tests.pytest_plugins import *  # noqa
-    del pytest_report_header
+try:
+    from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
     ASTROPY_HEADER = True
-else:
-    try:
-        from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
-        ASTROPY_HEADER = True
-    except ImportError:
-        ASTROPY_HEADER = False
+except ImportError:
+    ASTROPY_HEADER = False
 
 
 def pytest_configure(config):
+    """Configure Pytest with Astropy.
 
+    Parameters
+    ----------
+    config : pytest configuration
+
+    """
     if ASTROPY_HEADER:
 
         config.option.astropy_header = True
@@ -34,16 +36,3 @@ def pytest_configure(config):
         from . import __version__
         packagename = os.path.basename(os.path.dirname(__file__))
         TESTED_VERSIONS[packagename] = __version__
-
-# Uncomment the last two lines in this block to treat all DeprecationWarnings as
-# exceptions. For Astropy v2.0 or later, there are 2 additional keywords,
-# as follow (although default should work for most cases).
-# To ignore some packages that produce deprecation warnings on import
-# (in addition to 'compiler', 'scipy', 'pygments', 'ipykernel', and
-# 'setuptools'), add:
-#     modules_to_ignore_on_import=['module_1', 'module_2']
-# To ignore some specific deprecation warning messages for Python version
-# MAJOR.MINOR or later, add:
-#     warnings_to_ignore_by_pyver={(MAJOR, MINOR): ['Message to ignore']}
-# from astropy.tests.helper import enable_deprecations_as_exceptions  # noqa
-# enable_deprecations_as_exceptions()

skypy/galaxies/redshift.py

@@ -249,7 +249,7 @@ def redshifts_from_comoving_density(redshift, density, sky_area, cosmology, nois
     dN_dz *= density
 
     # integrate density to get expected number of galaxies
-    N = np.trapz(dN_dz, redshift)
+    N = scipy.integrate.trapezoid(dN_dz, redshift)
 
     # Poisson sample galaxy number if requested
     if noise:

skypy/galaxies/spectrum.py

@@ -4,8 +4,8 @@
 
 from astropy import units
 from astropy.io import fits
+from importlib import resources
 import numpy as np
-from pkg_resources import resource_filename
 from skypy.utils.photometry import SpectrumTemplates
 
 
@@ -107,7 +107,7 @@ class KCorrectTemplates(SpectrumTemplates):
     '''
 
     def __init__(self, hdu=1):
-        filename = resource_filename('skypy', 'data/kcorrect/k_nmf_derived.default.fits')
+        filename = resources.files('skypy') / 'data/kcorrect/k_nmf_derived.default.fits'
         with fits.open(filename) as hdul:
             self.templates = hdul[hdu].data * units.Unit('erg s-1 cm-2 angstrom-1')
             self.wavelength = hdul[11].data * units.Unit('angstrom')

skypy/galaxies/tests/test_redshift.py

@@ -1,5 +1,6 @@
 import numpy as np
 import pytest
+import scipy.integrate
 from scipy.stats import kstest
 
 
@@ -38,7 +39,7 @@ def test_schechter_lf_redshift():
     density *= (sky_area * cosmo.differential_comoving_volume(z)).to_value('Mpc3')
 
     # integrate total number
-    n_gal = np.trapz(density, z, axis=-1)
+    n_gal = scipy.integrate.trapezoid(density, z, axis=-1)
 
     # make sure noise-free sample has right size
     assert np.isclose(len(z_gal), n_gal, atol=1.0)
@@ -85,7 +86,7 @@ def test_schechter_smf_redshift():
     density *= (sky_area * cosmo.differential_comoving_volume(z)).to_value('Mpc3')
 
     # integrate total number
-    n_gal = np.trapz(density, z, axis=-1)
+    n_gal = scipy.integrate.trapezoid(density, z, axis=-1)
 
     # make sure noise-free sample has right size
     assert np.isclose(len(z_gal), n_gal, atol=1.0)

skypy/galaxies/tests/test_stellar_mass.py

@@ -68,7 +68,7 @@ def calc_cdf(m):
         mass_min = 10 ** 7
         mass_max = 10 ** 13
         pdf = calc_pdf(m, alpha, mass_star, mass_min, mass_max)
-        cdf = scipy.integrate.cumtrapz(pdf, m, initial=0)
+        cdf = scipy.integrate.cumulative_trapezoid(pdf, m, initial=0)
         cdf = cdf / cdf[-1]
         return cdf
 

skypy/galaxies/tests/test_velocity_dispersion.py

@@ -1,7 +1,7 @@
 import numpy as np
 from scipy.stats import kstest
 from scipy.special import gamma
-from scipy.integrate import cumtrapz
+from scipy.integrate import cumulative_trapezoid
 
 
 def test_schechter_vdf():
@@ -30,7 +30,7 @@ def calc_pdf(vd):
 
     def calc_cdf(m):
         pdf = calc_pdf(m)
-        cdf = cumtrapz(pdf, m, initial=0)
+        cdf = cumulative_trapezoid(pdf, m, initial=0)
         cdf /= cdf[-1]
         return cdf
 

skypy/utils/photometry.py

@@ -436,7 +436,7 @@ def logistic_completeness_function(magnitude, magnitude_95, magnitude_50):
         is array_like of shape (nb, ) it returns array_like of shape (nb, ).
 
     References
-    -----------
+    ----------
     .. [1] López-Sanjuan, C. et al., `2017A&A…599A..62L`_
     .. _2017A&A…599A..62L: https://ui.adsabs.harvard.edu/abs/2017A%26A...599A..62L