Merge pull request #922 from pllim/shhhhhh

Remove logging, handle test warnings, etc

CHANGES.rst

@@ -12,6 +12,9 @@ Bug Fixes
 Other Changes and Additions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+- Logger usage is removed. Warnings now issued using Python ``warnings`` module.
+  This enables more granular warning control for downstream packages. [#922]
+
 1.6.0 (2022-01-27)
 ------------------
 

docs/fitting.rst

@@ -61,12 +61,15 @@ uncertainty, we will produce an estimate of the uncertainty by calling the
 
 .. code-block:: python
 
+   >>> import warnings
    >>> from specutils.manipulation import noise_region_uncertainty
    >>> noise_region = SpectralRegion(0*u.um, 3*u.um)
    >>> spectrum = noise_region_uncertainty(spectrum, noise_region)
 
    >>> from specutils.fitting import find_lines_threshold
-   >>> lines = find_lines_threshold(spectrum, noise_factor=3)
+   >>> with warnings.catch_warnings():  # Ignore warnings
+   ...     warnings.simplefilter('ignore')
+   ...     lines = find_lines_threshold(spectrum, noise_factor=3)
 
    >>> lines[lines['line_type'] == 'emission']  # doctest:+FLOAT_CMP
    <QTable length=4>
@@ -95,8 +98,11 @@ An example using the `~specutils.fitting.find_lines_derivative`:
    >>> noise_region = SpectralRegion(0*u.um, 3*u.um)
 
    >>> # Derivative technique
+   >>> import warnings
    >>> from specutils.fitting import find_lines_derivative
-   >>> lines = find_lines_derivative(spectrum, flux_threshold=0.75)
+   >>> with warnings.catch_warnings():  # Ignore warnings
+   ...     warnings.simplefilter('ignore')
+   ...     lines = find_lines_derivative(spectrum, flux_threshold=0.75)
 
    >>> lines[lines['line_type'] == 'emission']  # doctest:+FLOAT_CMP
    <QTable length=2>
@@ -632,6 +638,7 @@ convenience functions to perform exactly this task.  An example is shown below.
     :align: center
     :context: close-figs
 
+    >>> import warnings
     >>> import numpy as np
     >>> import matplotlib.pyplot as plt
     >>> from astropy.modeling import models
@@ -649,7 +656,9 @@ convenience functions to perform exactly this task.  An example is shown below.
 
     >>> spectrum = Spectrum1D(flux=y*u.Jy, spectral_axis=x*u.um)
 
-    >>> g1_fit = fit_generic_continuum(spectrum)
+    >>> with warnings.catch_warnings():  # Ignore warnings
+    ...     warnings.simplefilter('ignore')
+    ...     g1_fit = fit_generic_continuum(spectrum)
 
     >>> y_continuum_fitted = g1_fit(x*u.um)
 
@@ -685,6 +694,7 @@ is specified by a sequence:
     :align: center
     :context: close-figs
 
+    >>> import warnings
     >>> import numpy as np
     >>> import matplotlib.pyplot as plt
     >>> import astropy.units as u
@@ -700,7 +710,9 @@ is specified by a sequence:
 
     >>> spectrum = Spectrum1D(flux=y * u.Jy, spectral_axis=x * u.um)
     >>> region = [(1 * u.um, 5 * u.um), (7 * u.um, 10 * u.um)]
-    >>> fitted_continuum = fit_continuum(spectrum, window=region)
+    >>> with warnings.catch_warnings():  # Ignore warnings
+    ...     warnings.simplefilter('ignore')
+    ...     fitted_continuum = fit_continuum(spectrum, window=region)
     >>> y_fit = fitted_continuum(x*u.um)
 
     >>> f, ax = plt.subplots()  # doctest: +IGNORE_OUTPUT

docs/index.rst

@@ -81,8 +81,11 @@ may have downloaded from some archive, or reduced from your own observations.
     Now maybe you want the equivalent width of a spectral line. That requires
     normalizing by a continuum estimate:
 
+    >>> import warnings
     >>> from specutils.fitting import fit_generic_continuum
-    >>> cont_norm_spec = spec / fit_generic_continuum(spec)(spec.spectral_axis) # doctest: +REMOTE_DATA
+    >>> with warnings.catch_warnings():  # Ignore warnings
+    ...     warnings.simplefilter('ignore')
+    ...     cont_norm_spec = spec / fit_generic_continuum(spec)(spec.spectral_axis) # doctest: +REMOTE_DATA
 
     >>> f, ax = plt.subplots()  # doctest: +IGNORE_OUTPUT
     >>> ax.step(cont_norm_spec.wavelength, cont_norm_spec.flux)  # doctest: +IGNORE_OUTPUT +REMOTE_DATA

docs/spectral_regions.rst

@@ -315,5 +315,4 @@ Reference/API
     :skip: test
     :skip: Spectrum1D
     :skip: SpectrumCollection
-    :skip: UnsupportedPythonError
     :skip: SpectralAxis

docs/spectrum1d.rst

@@ -297,4 +297,3 @@ Reference/API
     :skip: test
     :skip: SpectrumCollection
     :skip: SpectralRegion
-    :skip: UnsupportedPythonError

docs/spectrum_collection.rst

@@ -49,17 +49,19 @@ a list of :class:`~specutils.Spectrum1D`:
 
 .. code:: python
 
-    >>> from specutils import Spectrum1D, SpectrumCollection
-    >>> import astropy.units as u
+    >>> import warnings
     >>> import numpy as np
+    >>> from astropy import units as u
+    >>> from specutils import Spectrum1D, SpectrumCollection
     >>> spec = Spectrum1D(spectral_axis=np.linspace(0, 50, 50) * u.AA,
     ...                   flux=np.random.randn(50) * u.Jy,
     ...                   uncertainty=StdDevUncertainty(np.random.sample(50), unit='Jy'))
-    >>> spec1 = Spectrum1D(spectral_axis=np.linspace(20, 60, 50) * u.AA,
-    ...                    flux=np.random.randn(50) * u.Jy,
-    ...                    uncertainty=StdDevUncertainty(np.random.sample(50), unit='Jy'))
-
-    >>> spec_coll = SpectrumCollection.from_spectra([spec, spec1])
+    >>> with warnings.catch_warnings():  # Ignore warnings
+    ...     warnings.simplefilter('ignore')
+    ...     spec1 = Spectrum1D(spectral_axis=np.linspace(20, 60, 50) * u.AA,
+    ...                        flux=np.random.randn(50) * u.Jy,
+    ...                        uncertainty=StdDevUncertainty(np.random.sample(50), unit='Jy'))
+    ...     spec_coll = SpectrumCollection.from_spectra([spec, spec1])
 
     >>> spec_coll.shape
     (2,)
@@ -106,5 +108,4 @@ Reference/API
     :skip: test
     :skip: Spectrum1D
     :skip: SpectralRegion
-    :skip: UnsupportedPythonError
     :skip: SpectralAxis

setup.cfg

@@ -46,12 +46,24 @@ asdf_extensions =
 
 [tool:pytest]
 testpaths = "specutils" "docs"
+xfail_strict = true
 astropy_header = true
 doctest_plus = enabled
 text_file_format = rst
 addopts = --doctest-rst
 asdf_schema_root = specutils/io/asdf/schemas
 asdf_schema_tests_enabled = true
+filterwarnings =
+    error
+    ignore:distutils Version classes are deprecated:DeprecationWarning
+    ignore:unclosed file:ResourceWarning
+    ignore:numpy\.ndarray size changed:RuntimeWarning
+    ignore:invalid value encountered in .*divide:RuntimeWarning
+    ignore:.*contains multiple slashes:astropy.units.core.UnitsWarning
+    ignore::astropy.wcs.wcs.FITSFixedWarning
+    ignore:Input WCS indicates that the spectral axis is not last:UserWarning
+    ignore:No velocity defined on frame:astropy.coordinates.spectral_coordinate.NoVelocityWarning
+    ignore:No observer defined on WCS:astropy.utils.exceptions.AstropyUserWarning
 
 [coverage:run]
 omit =
@@ -86,6 +98,26 @@ exclude_lines =
     # Don't complain about IPython completion helper
     def _ipython_key_completions_
 
+# TODO: Un-ignore and fix these warnings.
+# E126 continuation line over-indented for hanging indent
+# E127 continuation line over-indented for visual indent
+# E128 continuation line under-indented for visual indent
+# E201 whitespace after '{'
+# E202 whitespace before ']'
+# E203 whitespace before ','
+# E221 multiple spaces before operator
+# E225 missing whitespace around operator
+# E226 missing whitespace around arithmetic operator
+# E227 missing whitespace around bitwise or shift operator
+# E231 missing whitespace after ','
+# E251 unexpected spaces around keyword / parameter equals
+# E501 line too long
+# E731 do not assign a lambda expression, use a def
+# E741 ambiguous variable name 'l'
+# W503 line break before binary operator
+# W504 line break after binary operator
+# W505 doc line too long
 [flake8]
 max-line-length = 100
 max-doc-length = 79
+ignore = E126,E127,E128,E201,E202,E203,E221,E225,E226,E227,E231,E251,E501,E731,E741,W503,W504,W505

specutils/__init__.py

@@ -10,25 +10,11 @@
 from astropy import config as _config
 # ----------------------------------------------------------------------------
 
-# Enforce Python version check during package import.
-# This is the same check as the one at the top of setup.py
-import sys
-
-__minimum_python_version__ = "3.5"
-
-
-class UnsupportedPythonError(Exception):
-    pass
-
-
-if sys.version_info < tuple((int(val) for val in __minimum_python_version__.split('.'))):
-    raise UnsupportedPythonError("packagename does not support Python < {}".format(__minimum_python_version__))
-
-if not _ASTROPY_SETUP_:
+if not _ASTROPY_SETUP_:  # noqa
     # For egg_info test builds to pass, put package imports here.
 
     # Allow loading spectrum object from top level module
-    from .spectra import *
+    from .spectra import *  # noqa
 
     # Load the IO functions
     from .io.default_loaders import *  # noqa
@@ -49,4 +35,5 @@ class Conf(_config.ConfigNamespace):
         'to zero. If it is not within ``threshold`` then a warning is raised.'
     )
 
+
 conf = Conf()

specutils/analysis/template_comparison.py

@@ -35,6 +35,7 @@ def _uncertainty_to_standard_deviation(uncertainty):
 
         return stddev
 
+
 def _normalize_for_template_matching(observed_spectrum, template_spectrum, stddev=None):
     """
     Calculate a scale factor to be applied to the template spectrum so the

specutils/analysis/width.py

@@ -5,11 +5,10 @@
 
 import numpy as np
 from astropy.stats.funcs import gaussian_sigma_to_fwhm
-from astropy.modeling.models import Gaussian1D
 from ..manipulation import extract_region
 from . import centroid
 from .utils import computation_wrapper
-from scipy.signal import chirp, find_peaks, peak_widths
+from scipy.signal import find_peaks, peak_widths
 
 
 __all__ = ['gaussian_sigma_width', 'gaussian_fwhm', 'fwhm', 'fwzi']