Merge pull request #91 from desihub/scipy-integration-and-other-fixes

Scipy integration and other fixes

.github/workflows/python-package.yml

@@ -19,28 +19,28 @@ jobs:
       fail-fast: true
       matrix:
         os: [ubuntu-latest] # Add more os?
-        python-version: [3.8, 3.9]
+        python-version: ['3.8', '3.9']
         astropy-version: ['<5.0', '<5.1']
         numpy-version: ['<1.20', '<1.21', '<1.22']
         scipy-version: ['<1.6', '<1.7']
+        # matplotlib >= 3.3 brings in a dependency on Pillow, which requires numpy >= 1.21 unless it's pinned to Pillow<10.4.
         matplotlib-version: ['<3.4', '<3.5']
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools
-          python -m pip install pytest pytest-astropy pyyaml
-          # python -m pip install -r requirements.txt
+          python -m pip install pytest pytest-astropy pyyaml Pillow\<10.4
           python -m pip install 'scipy${{ matrix.scipy-version }}'
           python -m pip install 'matplotlib${{ matrix.matplotlib-version }}'
           python -m pip install 'astropy${{ matrix.astropy-version }}'
@@ -59,20 +59,20 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools
-          python -m pip install pytest pytest-astropy coveralls
-          python -m pip install pyyaml numpy\<1.21 scipy\<1.6 matplotlib\<3.3 astropy\<5.0
+          python -m pip install pytest pytest-astropy pyyaml coveralls
+          python -m pip install Pillow\<10.4 numpy\<1.21 scipy\<1.6 matplotlib\<3.4 astropy\<5.0
 
       - name: Run the test with coverage
         run: pytest --cov
@@ -90,24 +90,23 @@ jobs:
         fail-fast: false
         matrix:
             os: [ubuntu-latest]
-            python-version: [3.9]
+            python-version: ['3.8']
 
     steps:
         - name: Checkout code
-          uses: actions/checkout@v3
+          uses: actions/checkout@v4
           with:
             fetch-depth: 0
 
         - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v4
+          uses: actions/setup-python@v5
           with:
             python-version: ${{ matrix.python-version }}
 
         - name: Install Python dependencies
           run: |
-            python -m pip install --upgrade pip wheel setuptools docutils\<0.18 Sphinx
-            python -m pip install sphinx-astropy
-            python -m pip install speclite
+            python -m pip install --upgrade pip wheel setuptools Sphinx\<8
+            python -m pip install -e .[docs]
 
         - name: Test the documentation
           run: sphinx-build -W --keep-going -b html docs docs/_build/html
@@ -119,24 +118,24 @@ jobs:
       fail-fast: false
       matrix:
           os: [ubuntu-latest]
-          python-version: [3.9]
+          python-version: ['3.10']
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools flake8
 
-      - name: Test the style; failures are allowed
-        # This is equivalent to an allowed falure.
-        continue-on-error: true
+      - name: Test the style
+        # If allowed failures are needed, uncomment continue-on-error.
+        # continue-on-error: true
         run: flake8 speclite --count --max-line-length=100

conftest.py

@@ -0,0 +1,52 @@
+# this contains imports plugins that configure py.test for astropy tests.
+# by importing them here in conftest.py they are discoverable by py.test
+# no matter how it is invoked within the source tree.
+
+from astropy.version import version as astropy_version
+if astropy_version < '3.0':
+    # With older versions of Astropy, we actually need to import the pytest
+    # plugins themselves in order to make them discoverable by pytest.
+    from astropy.tests.pytest_plugins import *
+else:
+    # As of Astropy 3.0, the pytest plugins provided by Astropy are
+    # automatically made available when Astropy is installed. This means it's
+    # not necessary to import them here, but we still need to import global
+    # variables that are used for configuration.
+    from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
+
+from astropy.tests.helper import enable_deprecations_as_exceptions
+
+## Uncomment the following line to treat all DeprecationWarnings as
+## exceptions
+# enable_deprecations_as_exceptions()
+
+## Uncomment and customize the following lines to add/remove entries from
+## the list of packages for which version numbers are displayed when running
+## the tests. Making it pass for KeyError is essential in some cases when
+## the package uses other astropy affiliated packages.
+try:
+    PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
+    PYTEST_HEADER_MODULES['Pillow'] = 'PIL'
+    PYTEST_HEADER_MODULES['PyYAML'] = 'yaml'
+    del PYTEST_HEADER_MODULES['h5py']
+    del PYTEST_HEADER_MODULES['Pandas']
+except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
+    pass
+
+## Uncomment the following lines to display the version number of the
+## package rather than the version number of Astropy in the top line when
+## running the tests.
+# import os
+#
+## This is to figure out the affiliated package version, rather than
+## using Astropy's
+# try:
+#     from .version import version
+# except ImportError:
+#     version = 'dev'
+#
+# try:
+#     packagename = os.path.basename(os.path.dirname(__file__))
+#     TESTED_VERSIONS[packagename] = version
+# except NameError:   # Needed to support Astropy <= 1.0.0
+#     pass

docs/api.rst

@@ -20,7 +20,7 @@ Operations with Filters
 
 .. automodapi:: speclite.filters
     :no-inheritance-diagram:
-    :skip: get_path_of_data_file
+    :skip: get_path_of_data_file, trapz, simps
 
 Other Functions
 ===============

docs/conf.py

@@ -28,6 +28,7 @@
 import datetime
 import os
 import sys
+from importlib import import_module
 
 try:
     import astropy_helpers
@@ -84,7 +85,7 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-__import__(setup_cfg['package_name'])
+import_module(setup_cfg['package_name'])
 package = sys.modules[setup_cfg['package_name']]
 
 # The short X.Y version.

setup.cfg

@@ -25,7 +25,7 @@ license = BSD
 url = https://speclite.readthedocs.io/
 edit_on_github = True
 github_project = desihub/speclite
-install_requires = astropy scipy pyyaml pytest_astropy_header
+install_requires = astropy scipy pyyaml
 # version should be PEP440 compatible, e.g. 0.8 or 0.8.dev (http://www.python.org/dev/peps/pep-0440)
 version = 0.20.dev
 
@@ -36,6 +36,8 @@ version = 0.20.dev
 speclite_benchmark = speclite.benchmark:main
 
 [options.extras_require]
+test =
+    pytest-astropy
 docs =
     sphinx-astropy
 

speclite/conftest.py

@@ -24,12 +24,14 @@
 ## the list of packages for which version numbers are displayed when running
 ## the tests. Making it pass for KeyError is essential in some cases when
 ## the package uses other astropy affiliated packages.
-# try:
-#     PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
-#     PYTEST_HEADER_MODULES['scikit-image'] = 'skimage'
-#     del PYTEST_HEADER_MODULES['h5py']
-# except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
-#     pass
+try:
+    PYTEST_HEADER_MODULES['Astropy'] = 'astropy'
+    PYTEST_HEADER_MODULES['Pillow'] = 'PIL'
+    PYTEST_HEADER_MODULES['PyYAML'] = 'yaml'
+    del PYTEST_HEADER_MODULES['h5py']
+    del PYTEST_HEADER_MODULES['Pandas']
+except (NameError, KeyError):  # NameError is needed to support Astropy < 1.0
+    pass
 
 ## Uncomment the following lines to display the version number of the
 ## package rather than the version number of Astropy in the top line when

speclite/filters.py

@@ -237,7 +237,11 @@
 import numpy as np
 
 import scipy.interpolate
-import scipy.integrate
+
+try:
+    from scipy.integrate import trapezoid as trapz, simpson as simps
+except ImportError:
+    from scipy.integrate import trapz, simps
 
 import astropy.table
 import astropy.units
@@ -267,9 +271,7 @@
 _photon_weighted_unit = default_wavelength_unit**2 / _hc_constant.unit
 
 # Map names to integration methods allowed by the convolution methods below.
-_filter_integration_methods = dict(
-    trapz= scipy.integrate.trapz,
-    simps= scipy.integrate.simps)
+_filter_integration_methods = dict(trapz=trapz, simps=simps)
 
 # Group and band names must be valid python identifiers. Although a leading
 # underscore is probably not a good idea, it is simpler to stick with a
@@ -1806,7 +1808,7 @@ def load_filters(*names):
     """
     # Replace any group wildcards with the corresponding canonical names.
 
-    
+
     filters_path = get_path_of_data_file('filters/')
 
 
@@ -1945,7 +1947,7 @@ def load_filter(name, load_from_cache=True, verbose=False):
 
 def plot_filters(responses, wavelength_unit=None,
                  wavelength_limits=None, wavelength_scale='linear',
-                 legend_loc='upper right', legend_ncols=1, 
+                 legend_loc='upper right', legend_ncols=1,
                  response_limits=None, cmap='nipy_spectral'):
     """Plot one or more filter response curves.
 

speclite/resample.py

@@ -1,14 +1,12 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 """Resample spectra using interpolation.
 """
-from __future__ import print_function, division
-
 import numpy as np
 import numpy.ma as ma
 import scipy.interpolate
-import pkg_resources as pkgr
+from packaging import version
 
-if pkgr.parse_version(np.__version__)  >= pkgr.parse_version('1.16'):
+if version.parse(np.__version__)  >= version.parse('1.16'):
     import numpy.lib.recfunctions as rfn
 
 def resample(data_in, x_in, x_out, y, data_out=None, kind='linear'):
@@ -168,7 +166,7 @@ def resample(data_in, x_in, x_out, y, data_out=None, kind='linear'):
         for i,y in enumerate(y_names):
             y_in[:,i] = data_in[y].filled(np.nan)
     else:
-        if pkgr.parse_version(np.__version__)  >= pkgr.parse_version('1.16'):
+        if version.parse(np.__version__)  >= version.parse('1.16'):
             # The slicing does not work in numpy 1.16 and above
             # we use structured_to_unstructured to get the slice that we care about
             y_in = rfn.structured_to_unstructured(
@@ -178,7 +176,7 @@ def resample(data_in, x_in, x_out, y, data_out=None, kind='linear'):
             # View the structured 1D array as a 2D unstructured array (without
             # copying any memory).
             y_in = y_in.view(y_type).reshape(data_in.shape + y_shape)
-       
+
     # interp1d will only propagate NaNs correctly for certain values of `kind`.
     # With numpy = 1.6 or 1.7, only 'nearest' and 'linear' work.
     # With numpy = 1.8 or 1.9, 'slinear' and kind = 0 or 1 also work.

speclite/tests/test_accumulate.py

@@ -1,6 +1,4 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-from __future__ import print_function, division
-
 from astropy.tests.helper import pytest
 from ..accumulate import accumulate
 import numpy as np

speclite/tests/test_filters.py

@@ -1,6 +1,4 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-from __future__ import print_function, division
-
 from astropy.tests.helper import pytest
 from ..filters import *
 
@@ -261,7 +259,7 @@ def test_wavelength_property():
     wlen = [1, 2, 3] * u.Angstrom
     meta = dict(group_name='g', band_name='b')
     r = FilterResponse(wlen, [0,1,0], meta)
-    assert np.allclose(r.wavelength, r._wavelength) 
+    assert np.allclose(r.wavelength, r._wavelength)
     assert np.allclose(r.wavelength, validate_wavelength_array(wlen))
 
 def test_mag_flux_units():

speclite/tests/test_utils.py

@@ -0,0 +1,22 @@
+import os
+from ..utils import package_data
+
+
+def test_get_path_of_data_file():
+    data_file = package_data.get_path_of_data_file('filters/twomass-Ks.ecsv')
+    assert os.path.exists(data_file)
+
+
+def test_get_path_of_data_dir():
+    data_dir = package_data.get_path_of_data_dir()
+    assert os.path.isdir(data_dir)
+
+
+def test_get_path_of_data_dir_no_importlib(monkeypatch):
+    data_dir = package_data.get_path_of_data_dir()
+    def mock_resource(foo, bar):
+        return data_dir
+    monkeypatch.setattr(package_data, '_has_importlib', False)
+    monkeypatch.setattr(package_data, 'resource_filename', mock_resource)
+    data_dir2 = package_data.get_path_of_data_dir()
+    assert data_dir2 == data_dir

speclite/utils/package_data.py

@@ -1,21 +1,24 @@
 import os
 
-import pkg_resources
+_has_importlib = True
+try:
+    from importlib.resources import files
+    resource_filename = None
+except ImportError:
+    from pkg_resources import resource_filename
+    _has_importlib = False
 
 # TODO: should make these Path objects
 
-def get_path_of_data_file(data_file) -> str:
+def get_path_of_data_file(data_file):
     """convenience wrapper to return location of data file
     """
-    file_path = pkg_resources.resource_filename(
-        "speclite", os.path.join("data", f"{data_file}"))
+    return os.path.join(get_path_of_data_dir(), data_file)
 
-    return file_path
 
-
-def get_path_of_data_dir() -> str:
+def get_path_of_data_dir():
     """convenience wrapper to return location of data directory
     """
-    file_path = pkg_resources.resource_filename("speclite", "data")
-
-    return file_path
+    if _has_importlib:
+        return str(files('speclite') / 'data')
+    return resource_filename('speclite', 'data')