Fix all warnings

pyproject.toml

@@ -137,3 +137,14 @@ addopts = [
 ]
 log_cli_level = "info"
 xfail_strict = true
+filterwarnings = [
+    "error",
+    # Apparently bqplot is using deprecated traitlets APIs
+    'ignore:\s+Sentinel is not a public part of the traitlets API:DeprecationWarning',
+    # ginga is using something from asdf that has been deprecated
+    'ignore:AsdfInFits has been deprecated:DeprecationWarning',
+    # ipyautoui generates this warning...
+    'ignore:metadata \{.+\} was set from the constructor:DeprecationWarning',
+    # Generated from batman
+    'ignore:Conversion of an array with ndim > 0 to a scalar:DeprecationWarning',
+]

stellarphot/__init__.py

@@ -6,26 +6,4 @@
 from ._astropy_init import *   # noqa
 # ----------------------------------------------------------------------------
 
-# Enforce Python version check during package import.
-# This is the same check as the one at the top of setup.py
-import sys
-from distutils.version import LooseVersion
-
-__minimum_python_version__ = "3.10"
-
-__all__ = []
-
-
-class UnsupportedPythonError(Exception):
-    """
-    Wraps an exception to raise if a user tries to use stellarphot
-    with an unsupported version of Python.
-    """
-    pass
-
-
-if LooseVersion(sys.version) < LooseVersion(__minimum_python_version__):
-    raise UnsupportedPythonError("stellarphot does not support Python < {}"
-                                 .format(__minimum_python_version__))
-
 from .core import *

stellarphot/differential_photometry/tests/test_aij_rel_fluxes.py

@@ -108,9 +108,10 @@ def test_bad_comp_star(bad_thing):
 
     if bad_thing == 'RA':
         # "Jiggle" one of the stars by moving it by a few arcsec in one image.
-        coord_inp = SkyCoord(ra=last_one['ra'], dec=last_one['dec'],
+        coord_inp = SkyCoord(ra=last_one['ra'][0], dec=last_one['dec'][0],
                              unit=u.degree)
         coord_bad_ra = coord_inp.ra + 3 * u.arcsecond
+        print(len(last_one), coord_inp)
         input_table['ra'][-1] = coord_bad_ra.degree
     elif bad_thing == 'NaN':
         input_table['aperture_net_cnts'][-1] = np.nan

stellarphot/differential_photometry/tests/test_vsx_mags.py

@@ -30,7 +30,9 @@ def test_multi_vmag():
 
     vmag, error = calc_vmag(var_stars, star_data, comp_stars, band='Rc', star_data_mag_column='mag_inst_R')
     del var_stars['coords']
-    v_data = vstack([var_stars, var_stars])
+
+    # We really don't care about the metadata here, so silently accept one
+    v_data = vstack([var_stars, var_stars], metadata_conflicts='silent')
     v_data['coords'] = SkyCoord(ra=v_data['RAJ2000'],
                                 dec=v_data['DEJ2000'], unit='degree')
     v_table = calc_multi_vmag(v_data, star_data, comp_stars, band='Rc', star_data_mag_column='mag_inst_R')

stellarphot/io/tests/test_tess_submission.py

@@ -1,4 +1,5 @@
 import re
+import warnings
 
 import pytest
 
@@ -78,10 +79,27 @@ def test_target_file():
     # object
 
     tic_742648307 = SkyCoord(ra=104.733225, dec=49.968739, unit='degree')
+
     tess_target = TessTargetFile(tic_742648307, magnitude=12, depth=10)
 
     # Check that the first thing in the list is the tick object
-    check_coords = SkyCoord(ra=tess_target.table['RA'][0],
-                            dec=tess_target.table['Dec'][0],
-                            unit=('hour', 'degree'))
+    check_coords = SkyCoord(
+        ra=tess_target.table['RA'][0],
+        dec=tess_target.table['Dec'][0],
+        unit=('hour', 'degree')
+    )
     assert tic_742648307.separation(check_coords).arcsecond < 1
+
+    # On windows the temporary file cannot be deleted because if it is
+    # then the file immediately vanished. That means we get a warning
+    # about having an open file handle. We can ignore that warning
+    # because we don't care about it here.
+
+    # The warning doesn't get generated until the last reference to
+    # the object is deleted, so we need to do that here instead of
+    # letting it happen at the end of the test.
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore",
+                                message="unclosed file",
+                                category=ResourceWarning)
+        del tess_target

stellarphot/photometry/photometry.py

@@ -609,7 +609,7 @@ def multi_image_photometry(directory_with_images,
     reject_unmatched : bool, optional (Default: True)
         If ``True``, any sources that are not detected on all the images are
         rejected.  If you are interested in a source that can intermittently
-        fall below your detection limits, we suggest setting this to ``False`` 
+        fall below your detection limits, we suggest setting this to ``False``
         so that all sources detected on each image are reported.
 
     include_dig_noise : bool, optional (Default: True)
@@ -973,7 +973,7 @@ def calculate_noise(camera=None, counts=0.0, sky_per_pix=0.0,
 
         \\sigma = \\sqrt{G \\cdot N_C + A \\cdot \\left(1 + \\frac{A}{B}\\right)\\cdot \\left[ G\\cdot S + D \\cdot t + R^2 + (0.289 G)^2\\right]}
 
-    where :math:`\sigma` is the noise, :math:`G` is the gain,
+    where :math:`\\sigma` is the noise, :math:`G` is the gain,
     :math:`N_C` is the source counts (which is photon/electron counts divided by gain),
     :math:`A` is the aperture area in pixels,
     :math:`B` is the annulus area in pixels,
@@ -1053,4 +1053,3 @@ def calculate_noise(camera=None, counts=0.0, sky_per_pix=0.0,
         digitization = area_ratio * (gain * 0.289) ** 2
 
     return np.sqrt(poisson_source + sky + dark + rn_error + digitization)
-

stellarphot/photometry/tests/fake_image.py

@@ -18,8 +18,12 @@ class FakeImage:
 
     noise_dev : float, optional
         The standard deviation of the noise in the image.
+
+    seed : int, optional
+        The seed to use for the random number generator. If not specified,
+        the seed will be randomly generated.
     """
-    def __init__(self, noise_dev=1.0):
+    def __init__(self, noise_dev=1.0, seed=None):
         self.image_shape = [400, 500]
         data_file = get_pkg_data_filename('data/test_sources.csv')
         self._sources = Table.read(data_file)
@@ -29,7 +33,8 @@ def __init__(self, noise_dev=1.0):
                                                   self.sources)
         self._noise = make_noise_image(self._stars.shape,
                                        mean=self.mean_noise,
-                                       stddev=noise_dev)
+                                       stddev=noise_dev,
+                                       seed=seed)
         # Sky background per pixel should be the mean level of the noise.
         self._sources['sky_per_pix_avg'] = self.mean_noise
 
@@ -51,11 +56,16 @@ def image(self):
 class FakeCCDImage(CCDData):
     # Generates a fake CCDData object for testing purposes.
     def __init__(self, *args, **kwargs):
+        # Pull off the seed argument if it exists.
+        seed = kwargs.pop('seed', None)
+
         # If no arguments are passed, use the default FakeImage.
+        # This dodge is necessary because otherwise we can't copy the CCDData
+        # object apparently.
         if (len(args) == 0) and (len(kwargs) == 0):
-            base_data = FakeImage()
+            base_data = FakeImage(seed=seed)
             super().__init__(base_data.image.copy(), unit='adu')
-        
+
             # Append attributes from the base data object.
             self.sources = base_data.sources.copy()
             self.noise_dev = base_data.noise_dev
@@ -162,4 +172,4 @@ def shift_FakeCCDImage(ccd_data, x_shift, y_shift):
                                   stddev=shifted_ccd_data.noise_dev)
     shifted_ccd_data.data = srcs + background
 
-    return shifted_ccd_data
+    return shifted_ccd_data

stellarphot/photometry/tests/test_detection.py

@@ -1,17 +1,24 @@
+import warnings
+
 import numpy as np
 import pytest
 
 from astropy.table import QTable
 from astropy.stats import gaussian_sigma_to_fwhm
 from astropy import units as u
+from astropy.utils.exceptions import AstropyUserWarning
 
 from stellarphot.photometry import (source_detection, compute_fwhm)
 
 from fake_image import FakeImage
 
+# Make sure the tests are deterministic by using a random seed
+SEED = 5432985
+
+
 @pytest.mark.parametrize('units', [u.pixel, None])
 def test_compute_fwhm(units):
-    fake_image = FakeImage()
+    fake_image = FakeImage(seed=SEED)
     sources = fake_image.sources
     if units is not None:
         # It turns out having a unit on a column is not the same as
@@ -32,7 +39,7 @@ def test_compute_fwhm(units):
 def test_compute_fwhm_with_NaNs():
     # Regression test for https://github.com/feder-observatory/stellarphot/issues/161
     # We should be able to find FWHM for a source even with NaNs in the image.
-    fake_image = FakeImage()
+    fake_image = FakeImage(seed=SEED)
     sources = fake_image.sources
     x, y = sources['x_mean'].astype(int)[0], sources['y_mean'].astype(int)[0]
     image = fake_image.image.copy()
@@ -41,8 +48,13 @@ def test_compute_fwhm_with_NaNs():
     # usual row/column swap when going to x/y coordinates.
     image[y, x] = np.nan
 
-    fwhm_x, fwhm_y = compute_fwhm(image, sources,
-                                  x_column='x_mean', y_column='y_mean', fit=True)
+    # We expect a warning about NaNs in the image, so catch it
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore",
+                                message="Non-Finite input data has been removed",
+                                category=AstropyUserWarning)
+        fwhm_x, fwhm_y = compute_fwhm(image, sources,
+                                      x_column='x_mean', y_column='y_mean', fit=True)
 
     expected_fwhm = np.array(sources['x_stddev'] * gaussian_sigma_to_fwhm)
     assert np.allclose(fwhm_x, expected_fwhm, rtol=1e-2)
@@ -52,7 +64,7 @@ def test_detect_source_number_location():
     """
     Make sure we detect the sources in the input table....
     """
-    fake_image = FakeImage()
+    fake_image = FakeImage(seed=SEED)
     sources = QTable(fake_image.sources, units={'x_mean':u.pixel, 'y_mean':u.pixel,
                                                 'x_stddev':u.pixel, 'y_stddev':u.pixel})
     # print(sources)
@@ -85,7 +97,7 @@ def test_detect_source_with_padding():
     """
     Make sure we detect the sources in the input table....
     """
-    fake_image = FakeImage()
+    fake_image = FakeImage(seed=SEED)
     sources = QTable(fake_image.sources, units={'x_mean':u.pixel, 'y_mean':u.pixel,
                                                 'x_stddev':u.pixel, 'y_stddev':u.pixel})
     # Pass only one value for the sky background for source detection

stellarphot/photometry/tests/test_photometry.py

@@ -1,12 +1,15 @@
 import tempfile
 from pathlib import Path
+import warnings
 
 import numpy as np
 import pytest
 from astropy import units as u
 from astropy.coordinates import EarthLocation
 from astropy.io import ascii
 from astropy.utils.data import get_pkg_data_filename
+from astropy.utils.metadata.exceptions import MergeConflictWarning
+
 from fake_image import FakeCCDImage, shift_FakeCCDImage
 
 from stellarphot.core import Camera, SourceListData
@@ -16,6 +19,9 @@
 from stellarphot.settings import ApertureSettings
 
 GAINS = [1.0, 1.5, 2.0]
+# Make sure the tests are deterministic by using a random seed
+SEED = 5432985
+
 
 def test_calc_noise_defaults():
     # If we put in nothing we should get an error about is missing camera
@@ -224,7 +230,7 @@ def test_find_too_close():
 # The True case below is a regression test for #157
 @pytest.mark.parametrize('int_data', [True, False])
 def test_aperture_photometry_no_outlier_rejection(int_data):
-    fake_CCDimage = FakeCCDImage()
+    fake_CCDimage = FakeCCDImage(seed=SEED)
 
     sources = fake_CCDimage.sources
     aperture = sources['aperture'][0]
@@ -293,7 +299,7 @@ def test_aperture_photometry_with_outlier_rejection(reject):
     the photometry is correct when outliers are rejected and is
     incorrect when outliers are not rejected.
     """
-    fake_CCDimage = FakeCCDImage()
+    fake_CCDimage = FakeCCDImage(seed=SEED)
     sources = fake_CCDimage.sources
     aperture = sources['aperture'][0]
     inner_annulus = 2 * aperture
@@ -305,6 +311,8 @@ def test_aperture_photometry_with_outlier_rejection(reject):
 
     image = fake_CCDimage.data
 
+    print(f'{fake_CCDimage=}')
+    print(f"{sources['x_stddev'].mean()}")
     found_sources = source_detection(fake_CCDimage,
                                     fwhm=sources['x_stddev'].mean(),
                                     threshold=10)
@@ -363,7 +371,7 @@ def test_aperture_photometry_with_outlier_rejection(reject):
 
 def list_of_fakes(num_files):
     # Generate fake CCDData objects for use in photometry_on_directory tests
-    fake_images = [FakeCCDImage()]
+    fake_images = [FakeCCDImage(seed=SEED)]
 
     # Create additional images, each in a different position.
     for i in range(num_files-1):
@@ -397,6 +405,7 @@ def test_photometry_on_directory():
                             f"tempfile_{i:02d}.fit" for i in range(1, num_files + 1)]
         # Write the CCDData objects to files
         for i, image in enumerate(fake_images):
+            from time import sleep; sleep(1)
             image.write(temp_file_names[i])
 
         object_name = fake_images[0].header['OBJECT']
@@ -413,18 +422,22 @@ def test_photometry_on_directory():
                                         fwhm=fake_images[0].sources['x_stddev'].mean(),
                                         threshold=10)
 
-        phot_data = multi_image_photometry(temp_dir,
-                                object_name,
-                                found_sources,
-                                fake_camera,
-                                fake_obs,
-                                aperture_settings,
-                                shift_tolerance, max_adu, fwhm_estimate,
-                                include_dig_noise=True,
-                                reject_too_close=True,
-                                reject_background_outliers=True,
-                                passband_map=None,
-                                fwhm_by_fit=True)
+        with warnings.catch_warnings():
+            warnings.filterwarnings("ignore",
+                                    message="Cannot merge meta key",
+                                    category=MergeConflictWarning)
+            phot_data = multi_image_photometry(temp_dir,
+                                    object_name,
+                                    found_sources,
+                                    fake_camera,
+                                    fake_obs,
+                                    aperture_settings,
+                                    shift_tolerance, max_adu, fwhm_estimate,
+                                    include_dig_noise=True,
+                                    reject_too_close=True,
+                                    reject_background_outliers=True,
+                                    passband_map=None,
+                                    fwhm_by_fit=True)
 
     # For following assertion to be true, rad must be small enough that
     # no source lies within outer_annulus of the edge of an image.