MNT: Doc and CI updates

.github/workflows/tox-tests.yml

@@ -35,20 +35,20 @@ jobs:
           linux: py310-test-oldestdeps
           toxargs: -v
 
-        - name: Python 3.10 on Windows with minimal dependencies
-          windows: py310-test
+        - name: Python 3.11 on Windows with minimal dependencies
+          windows: py311-test
           toxargs: -v
 
-        - name: Python 3.10 on OSX with minimal dependencies
-          macos: py310-test
+        - name: Python 3.11 on OSX with minimal dependencies
+          macos: py311-test
           toxargs: -v
 
-        - name: Python 3.11 on Linux with all dependencies, remote data, and coverage
-          linux: py311-test-alldeps-cov
+        - name: Python 3.12 on Linux with all dependencies, remote data, and coverage
+          linux: py312-test-alldeps-cov
           coverage: codecov
           toxargs: -v
           posargs: --remote-data=any
 
-        - name: (Allowed Failure) Python 3.12 on Linux with dev dependencies
-          linux: py312-test-devdeps
+        - name: (Allowed Failure) Python 3.13 on Linux with dev dependencies
+          linux: py313-test-devdeps
           toxargs: -v

.readthedocs.yaml

@@ -5,7 +5,7 @@ build:
   apt_packages:
     - graphviz
   tools:
-    python: "3.11"
+    python: "3.13"
 
 sphinx:
   builder: html

conftest.py

@@ -1,4 +1,12 @@
-"""Need to repeat the astropy header config here for tox."""
+# This file is used to configure the behavior of pytest
+
+import numpy as np
+import pytest
+from astropy import units as u
+from astropy.io import fits
+from astropy.nddata import CCDData, NDData, VarianceUncertainty
+from astropy.utils.data import get_pkg_data_filename
+from specutils import Spectrum1D, SpectralAxis
 
 try:
     from pytest_astropy_header.display import PYTEST_HEADER_MODULES, TESTED_VERSIONS
@@ -7,6 +15,103 @@
     ASTROPY_HEADER = False
 
 
+# Test image is comprised of 30 rows with 10 columns each. Row content
+# is row index itself. This makes it easy to predict what should be the
+# value extracted from a region centered at any arbitrary Y position.
+def _mk_test_data(imgtype, nrows=30, ncols=10):
+    image_ones = np.ones(shape=(nrows, ncols))
+    image = image_ones.copy()
+    for j in range(nrows):
+        image[j, ::] *= j
+    if imgtype == "raw":
+        pass  # no extra processing
+    elif imgtype == "ccddata":
+        image = CCDData(image, unit=u.Jy)
+    else:  # spectrum
+        flux = image * u.DN
+        uncert = VarianceUncertainty(image_ones)
+        if imgtype == "spec_no_axis":
+            image = Spectrum1D(flux, uncertainty=uncert)
+        else:  # "spec"
+            image = Spectrum1D(flux, spectral_axis=np.arange(ncols) * u.um, uncertainty=uncert)
+    return image
+
+
+@pytest.fixture
+def mk_test_img_raw():
+    return _mk_test_data("raw")
+
+
+@pytest.fixture
+def mk_test_img():
+    return _mk_test_data("ccddata")
+
+
+@pytest.fixture
+def mk_test_spec_no_spectral_axis():
+    return _mk_test_data("spec_no_axis")
+
+
+@pytest.fixture
+def mk_test_spec_with_spectral_axis():
+    return _mk_test_data("spec")
+
+
+# Test data file already transposed like this:
+# fn = download_file('https://stsci.box.com/shared/static/exnkul627fcuhy5akf2gswytud5tazmw.fits', cache=True)  # noqa: E501
+# img = fits.getdata(fn).T
+@pytest.fixture
+def all_images():
+    np.random.seed(7)
+
+    filename = get_pkg_data_filename(
+        "data/transposed_det_image_seq5_MIRIMAGE_P750Lexp1_s2d.fits", package="specreduce.tests")
+    img = fits.getdata(filename)
+    flux = img * (u.MJy / u.sr)
+    sax = SpectralAxis(np.linspace(14.377, 3.677, flux.shape[-1]) * u.um)
+    unc = VarianceUncertainty(np.random.rand(*flux.shape))
+
+    all_images = {}
+    all_images['arr'] = img
+    all_images['s1d'] = Spectrum1D(flux, spectral_axis=sax, uncertainty=unc)
+    all_images['s1d_pix'] = Spectrum1D(flux, uncertainty=unc)
+    all_images['ccd'] = CCDData(img, uncertainty=unc, unit=flux.unit)
+    all_images['ndd'] = NDData(img, uncertainty=unc, unit=flux.unit)
+    all_images['qnt'] = img * flux.unit
+    return all_images
+
+
+@pytest.fixture
+def spec1d():
+    np.random.seed(7)
+    flux = np.random.random(50)*u.Jy
+    sa = np.arange(0, 50)*u.pix
+    spec = Spectrum1D(flux, spectral_axis=sa)
+    return spec
+
+
+@pytest.fixture
+def spec1d_with_emission_line():
+    np.random.seed(7)
+    sa = np.arange(0, 200)*u.pix
+    flux = (np.random.randn(200) +
+            10*np.exp(-0.01*((sa.value-130)**2)) +
+            sa.value/100) * u.Jy
+    spec = Spectrum1D(flux, spectral_axis=sa)
+    return spec
+
+
+@pytest.fixture
+def spec1d_with_absorption_line():
+    np.random.seed(7)
+    sa = np.arange(0, 200)*u.pix
+    flux = (np.random.randn(200) -
+            10*np.exp(-0.01*((sa.value-130)**2)) +
+            sa.value/100) * u.Jy
+    spec = Spectrum1D(flux, spectral_axis=sa)
+    return spec
+
+
 def pytest_configure(config):
 
     if ASTROPY_HEADER:

docs/conf.py

@@ -28,6 +28,8 @@
 import sys
 import datetime
 
+import sphinx
+
 from specreduce import __version__
 
 try:
@@ -36,6 +38,14 @@
     print('ERROR: the documentation requires the sphinx-astropy package to be installed')
     sys.exit(1)
 
+# xref: https://github.com/sphinx-doc/sphinx/issues/13232#issuecomment-2608708175
+if sys.version_info[:2] >= (3, 13) and sphinx.version_info[:2] < (8, 2):
+    import pathlib
+
+    from sphinx.util.typing import _INVALID_BUILTIN_CLASSES
+
+    _INVALID_BUILTIN_CLASSES[pathlib.Path] = "pathlib.Path"
+
 # -- General configuration ----------------------------------------------------
 
 # By default, highlight as Python 3.

pyproject.toml

@@ -76,21 +76,19 @@ filterwarnings = [
     "ignore:numpy\\.ufunc size changed:RuntimeWarning",
     "ignore:numpy\\.ndarray size changed:RuntimeWarning",
     "ignore:Can\\'t import specreduce_data package",
+    "ignore:.*unclosed <ssl.SSLSocket",
     # Python 3.12 warning from dateutil imported by matplotlib
     "ignore:.*utcfromtimestamp:DeprecationWarning",
-    "ignore:.*unclosed <ssl.SSLSocket",
+    # DeprecationWarning from gwcs 0.18.3 in oldestdeps
+    "ignore:.*pkg_resources.*:DeprecationWarning",
 ]
 
 [tool.coverage]
 
     [tool.coverage.run]
         omit = [
-            "specreduce/_astropy_init*",
-            "specreduce/conftest.py",
             "specreduce/tests/*",
             "specreduce/version*",
-            "*/specreduce/_astropy_init*",
-            "*/specreduce/conftest.py",
             "*/specreduce/tests/*",
             "*/specreduce/version*",
         ]

specreduce/calibration_data.py

@@ -303,33 +303,38 @@ class AtmosphericExtinction(Spectrum1D):
 
     Parameters
     ----------
-    model : Name of atmospheric extinction model provided by ``specreduce_data``. Valid
+    model : str
+        Name of atmospheric extinction model provided by ``specreduce_data``. Valid
         options are:
 
-        kpno - Kitt Peak National Observatory (default)
-        ctio - Cerro Tololo International Observatory
-        apo - Apache Point Observatory
-        lapalma - Roque de los Muchachos Observatory, La Palma, Canary Islands
-        mko - Mauna Kea Observatories
-        mtham - Lick Observatory, Mt. Hamilton station
-        paranal - European Southern Observatory, Cerro Paranal station
+        * kpno - Kitt Peak National Observatory (default)
+        * ctio - Cerro Tololo International Observatory
+        * apo - Apache Point Observatory
+        * lapalma - Roque de los Muchachos Observatory, La Palma, Canary Islands
+        * mko - Mauna Kea Observatories
+        * mtham - Lick Observatory, Mt. Hamilton station
+        * paranal - European Southern Observatory, Cerro Paranal station
 
-    extinction : Optionally provided extinction data for this spectrum. Used along with
+    extinction : float, `~astropy.units.Quantity`, or `None`, optional
+        Provides extinction data for this spectrum. Used along with
         spectral_axis to build custom atmospheric extinction model. If no units are provided,
         assumed to be given in magnitudes.
 
-    spectral_axis : Optional Dispersion information with the same shape as the last (or only)
+    spectral_axis : `~astropy.coordinates.SpectralCoord`, `~astropy.units.Quantity`, or `None`, optional
+        Dispersion information with the same shape as the last (or only)
         dimension of flux, or one greater than the last dimension of flux
         if specifying bin edges. Used along with flux to build custom atmospheric
         extinction model.
 
-    Properties
+    Attributes
     ----------
-    extinction_mag : Extinction expressed in dimensionless magnitudes
+    extinction_mag : `~astropy.units.Quantity`
+        Extinction expressed in dimensionless magnitudes
 
-    transmission : Extinction expressed as fractional transmission
+    transmission : `~astropy.units.Quantity`
+        Extinction expressed as fractional transmission
 
-    """
+    """  # noqa: E501
     def __init__(
         self,
         model: str = "kpno",