Merge pull request #92 from desihub/updates-for-kibo

Updates in preparation for next release

.github/workflows/python-package.yml

@@ -45,17 +45,23 @@ jobs:
           python -m pip install 'matplotlib${{ matrix.matplotlib-version }}'
           python -m pip install 'astropy${{ matrix.astropy-version }}'
           python -m pip install 'numpy${{ matrix.numpy-version }}'
+
       - name: Run the test
         run: pytest
 
+  #
+  # Temporarily use coverage to test more recent versions.
+  # Note that Astropy>=5.1 introduces an ordering change in unit display, which
+  # causes doctest failures.
+  #
   coverage:
     name: Test coverage
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ['3.10']
 
     steps:
       - name: Checkout code
@@ -72,7 +78,7 @@ jobs:
         run: |
           python -m pip install --upgrade pip wheel setuptools
           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
+          python -m pip install numpy\<1.23 scipy\<1.9 matplotlib\<3.9 astropy\<5.1
 
       - name: Run the test with coverage
         run: pytest --cov
@@ -87,38 +93,38 @@ jobs:
     name: Doc test
     runs-on: ${{ matrix.os }}
     strategy:
-        fail-fast: false
-        matrix:
-            os: [ubuntu-latest]
-            python-version: ['3.8']
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.10']
 
     steps:
-        - name: Checkout code
-          uses: actions/checkout@v4
-          with:
-            fetch-depth: 0
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-        - name: Set up Python ${{ matrix.python-version }}
-          uses: actions/setup-python@v5
-          with:
-            python-version: ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
 
-        - name: Install Python dependencies
-          run: |
-            python -m pip install --upgrade pip wheel setuptools Sphinx\<8
-            python -m pip install -e .[docs]
+      - name: Install Python dependencies
+        run: |
+          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
+      - name: Test the documentation
+        run: sphinx-build -W --keep-going -b html docs docs/_build/html
 
   style:
     name: Style test
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-          os: [ubuntu-latest]
-          python-version: ['3.10']
+        os: [ubuntu-latest]
+        python-version: ['3.10']
 
     steps:
       - name: Checkout code
@@ -139,3 +145,38 @@ jobs:
         # If allowed failures are needed, uncomment continue-on-error.
         # continue-on-error: true
         run: flake8 speclite --count --max-line-length=100
+
+  #
+  # Temporary test to make sure the package can at least be installed
+  # for more recent Python versions.
+  #
+  install:
+    name: Installation test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: true
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        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 numpy\<2.0 scipy matplotlib astropy pyyaml
+
+      - name: Test installing from the checkout
+        run: python -m pip install .
+
+      - name: Run a script that should have been installed
+        run: speclite_benchmark --all

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "astropy_helpers"]
 	path = astropy_helpers
-	url = https://github.com/astropy/astropy-helpers.git
+	url = https://github.com/bsipocz/astropy-helpers.git

docs/changes.rst

@@ -12,9 +12,13 @@ speclite Change Log
 -----------------
 
 - Fix ``scipy.integrate`` name changes; pin Pillow version so unit tests work (PR `#91`_).
-- *Planned*: fix several remaining issues.
+- Fix issues related to :meth:`~specutils.filters.FilterSequence.pad_spectrum` and
+  :meth:`~specutils.filters.FilterResponse.get_ab_maggies`; allow ``pip install``
+  on more recent Python versions;
+  replace deprecated ``matplotlib`` colormap function (PR `#92`_).
 
 .. _`#91`: https://github.com/desihub/speclite/pull/91
+.. _`#92`: https://github.com/desihub/speclite/pull/92
 
 0.19 (2024-04-30)
 -----------------

docs/conf.py

@@ -165,12 +165,12 @@
 if eval(setup_cfg.get('edit_on_github')):
     extensions += ['sphinx_astropy.ext.edit_on_github']
 
-    versionmod = __import__(setup_cfg['package_name'] + '.version')
+    versionmod = import_module(setup_cfg['package_name'] + '.version')
     edit_on_github_project = setup_cfg['github_project']
-    if versionmod.version.release:
-        edit_on_github_branch = "v" + versionmod.version.version
+    if versionmod.release:
+        edit_on_github_branch = "v" + versionmod.version
     else:
-        edit_on_github_branch = "master"
+        edit_on_github_branch = "main"
 
     edit_on_github_source_root = ""
     edit_on_github_doc_root = "docs"

speclite/benchmark.py

@@ -11,7 +11,7 @@
 import astropy.units as u
 import argparse
 
-import speclite
+import speclite.filters
 
 
 def magnitude_calculation(results, num_repeats):
@@ -85,18 +85,25 @@ def magnitude_calculation(results, num_repeats):
 
 
 def main(argv=None):
+    """Entry-point for :command:`speclite_benchmark`.
+
+    Returns
+    -------
+    :class:`int`
+        An integer suitable for passing to :func:`sys.exit`.
+    """
     # parse command-line arguments
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser.add_argument('-n', '--num-repeats', type=int, default=1000,
         help = 'number of times to repeat timing loops')
-    parser.add_argument('--all', action='store_true',
+    parser.add_argument('-a', '--all', action='store_true',
         help = 'run all benchmark suites')
-    parser.add_argument('--magnitude', action='store_true',
+    parser.add_argument('-m', '--magnitude', action='store_true',
         help = 'benchmark magnitude calculations')
-    parser.add_argument('--save', type=str, default=None,
+    parser.add_argument('-s', '--save', type=str, default=None,
         help='Name of file to save results to (or print if not set)')
-    parser.add_argument('--format', type=str,
+    parser.add_argument('-f', '--format', type=str,
         default='ascii.fixed_width_two_line',
         help='format to use for results')
     args = parser.parse_args(argv)
@@ -106,6 +113,9 @@ def main(argv=None):
         dtype=('S8', 'S40', float))
     if args.magnitude or args.all:
         results = magnitude_calculation(results, args.num_repeats)
+    else:
+        print('ERROR: No test suite specified (--magnitude or --all)!')
+        return 1
 
     results.write(args.save, format=args.format,
                   delimiter_pad=' ', position_char='=',

speclite/conftest.py

@@ -14,7 +14,7 @@
     # 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
+# from astropy.tests.helper import enable_deprecations_as_exceptions
 
 ## Uncomment the following line to treat all DeprecationWarnings as
 ## exceptions

speclite/filters.py

@@ -226,8 +226,6 @@
 default_flux_unit : :class:`astropy.units.Unit`
     The default units for spectral flux density per unit wavelength.
 """
-from __future__ import print_function, division # pragma: no cover
-
 import os
 import os.path
 import glob
@@ -1312,7 +1310,9 @@ def __init__(self, response, wavelength,
             self._response = load_filter(response)
         else:
             self._response = response
-        self._wavelength = validate_wavelength_array(wavelength, min_length=2)
+        # Work with a copy of the wavelength array,
+        # see https://github.com/desihub/speclite/issues/34
+        self._wavelength = validate_wavelength_array(wavelength, min_length=2).copy()
         self.num_wavelength = len(self._wavelength)
 
         # Check if extrapolation would be required.
@@ -1769,7 +1769,7 @@ def pad_spectrum(self, spectrum, wavelength, axis=-1, method='median'):
         padded_wavelength = np.asanyarray(wavelength)
         for response in sorted_responses:
             padded_spectrum, padded_wavelength = response.pad_spectrum(
-                padded_spectrum, padded_wavelength)
+                padded_spectrum, padded_wavelength, axis=axis, method=method)
         return padded_spectrum, padded_wavelength
 
 
@@ -1991,9 +1991,8 @@ def plot_filters(responses, wavelength_unit=None,
     min_wlen, max_wlen = min(effective_wavelengths), max(effective_wavelengths)
 
     import matplotlib.pyplot as plt
-    import matplotlib.cm as cm
 
-    cmap = cm.get_cmap(cmap)
+    cmap = plt.get_cmap(cmap)
     fig, ax = plt.subplots()
     plt.xscale(wavelength_scale)
     if wavelength_limits is not None:

speclite/resample.py

@@ -3,11 +3,9 @@
 """
 import numpy as np
 import numpy.ma as ma
+import numpy.lib.recfunctions as rfn
 import scipy.interpolate
-from packaging import version
 
-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'):
     """Resample the data of one spectrum using interpolation.
@@ -166,16 +164,9 @@ 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 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(
-                       data_in[y_names]).reshape(data_in.shape + y_shape)
-        else:
-            y_in = data_in[y_names]
-            # 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)
+        # 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(data_in[y_names]).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.