test updates

bmorris3 · Jul 29, 2023 · 604bcce · 604bcce
1 parent 69125fb
commit 604bcce
Show file tree

Hide file tree

Showing 5 changed files with 94 additions and 141 deletions.
diff --git a/aesop/spectra.py b/aesop/spectra.py
@@ -316,7 +316,7 @@ def __init__(self, spectrum_list, header=None, name=None, fits_path=None,
         self.time = time
 
     @classmethod
-    def from_fits(cls, path):
+    def from_fits(cls, path, format=None):
         """
         Load an echelle spectrum from a FITS file.
 
@@ -326,7 +326,7 @@ def from_fits(cls, path):
             Path to the FITS file
         """
         spectrum_list = [Spectrum1D.from_specutils(s)
-                         for s in SpectrumCollection.read(path)]
+                         for s in SpectrumCollection.read(path, format=format)]
         header = fits.getheader(path)
 
         name = header.get('OBJNAME', None)
@@ -928,7 +928,7 @@ def _poly_model(p, x):
     Polynomial model for lstsq continuum normalization
     """
     x_mean = x.mean()
-    return np.polyval(p, (x - x_mean).value)
+    return np.polyval(p, x - x_mean)
 
 
 def _residuals(p, x, y):

diff --git a/aesop/tests/coveragerc b/aesop/tests/coveragerc
diff --git a/aesop/tests/test_spectrum1d.py b/aesop/tests/test_spectrum1d.py
@@ -4,7 +4,6 @@
 import astropy.units as u
 import pytest
 from astropy.units import UnitsError
-from astropy.tests.helper import remote_data
 from astropy.utils.data import download_file
 
 from ..spectra import Spectrum1D, EchelleSpectrum
@@ -25,20 +24,20 @@ def test_constructor():
                              flux=f)
 
 
-@remote_data
+@pytest.mark.remote_data
 def test_read_fits():
-    url = ('https://drive.google.com/uc?export=download&id='
-           '1vf8rNhAiUJ1NO9VkwZOhcK6avJICfETH')
+    url = ('https://stsci.box.com/shared/static/'
+           'mu4fa1fmq1lw8boem12e2umyi99skbdl.fits')
 
     path = download_file(url, show_progress=False)
 
-    echelle_spectrum = EchelleSpectrum.from_fits(path)
+    echelle_spectrum = EchelleSpectrum.from_fits(path, format='iraf')
 
     assert hasattr(echelle_spectrum, 'header')
     assert hasattr(echelle_spectrum, 'time')
     assert hasattr(echelle_spectrum, 'name')
     assert str(echelle_spectrum) == ('<EchelleSpectrum: 107 orders, '
-                                     '3506.8-10612.5 Angstrom>')
+                                     '3506.8-10612.4 Angstrom>')
 
     # There should be more flux in the 40th order (redder) than 0th (bluer)
     assert echelle_spectrum[40].flux.mean() > echelle_spectrum[0].flux.mean()

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -31,8 +31,8 @@ spectroscopic standard O star BD+28 4211. We also create an
 
     >>> from astropy.utils.data import download_file
 
-    >>> target_url = 'https://drive.google.com/uc?export=download&id=1lkZi4p6ZGeeyDf_Z0eexMy0GHnr92_dv'
-    >>> spectroscopic_standard_url = 'https://drive.google.com/uc?export=download&id=1YiY1DP5Ec4mumvzjWj4u5DmFiEyn9MgH'
+    >>> target_url = 'https://stsci.box.com/shared/static/mu4fa1fmq1lw8boem12e2umyi99skbdl.fits'
+    >>> spectroscopic_standard_url = 'https://stsci.box.com/shared/static/18fa008byy2500yrfhuooyxs5d6pwc6e.fits'
 
     >>> target_path = download_file(target_url, show_progress=False)
     >>> standard_path = download_file(spectroscopic_standard_url, show_progress=False)
@@ -65,8 +65,8 @@ make a quick plot of the 73rd order of the target's echelle spectrum:
 
     from astropy.utils.data import download_file
 
-    target_url = 'https://drive.google.com/uc?export=download&id=1lkZi4p6ZGeeyDf_Z0eexMy0GHnr92_dv'
-    spectroscopic_standard_url = 'https://drive.google.com/uc?export=download&id=1YiY1DP5Ec4mumvzjWj4u5DmFiEyn9MgH'
+    target_url = 'https://stsci.box.com/shared/static/mu4fa1fmq1lw8boem12e2umyi99skbdl.fits'
+    spectroscopic_standard_url = 'https://stsci.box.com/shared/static/18fa008byy2500yrfhuooyxs5d6pwc6e.fits'
 
     target_path = download_file(target_url)
     standard_path = download_file(spectroscopic_standard_url)
@@ -148,8 +148,8 @@ continuum normalization method,
 
     from astropy.utils.data import download_file
 
-    target_url = 'https://drive.google.com/uc?export=download&id=1lkZi4p6ZGeeyDf_Z0eexMy0GHnr92_dv'
-    spectroscopic_standard_url = 'https://drive.google.com/uc?export=download&id=1YiY1DP5Ec4mumvzjWj4u5DmFiEyn9MgH'
+    target_url = 'https://stsci.box.com/shared/static/mu4fa1fmq1lw8boem12e2umyi99skbdl.fits'
+    spectroscopic_standard_url = 'https://stsci.box.com/shared/static/18fa008byy2500yrfhuooyxs5d6pwc6e.fits'
 
     target_path = download_file(target_url)
     standard_path = download_file(spectroscopic_standard_url)
@@ -181,7 +181,7 @@ object:
 
     >>> spec1d = target_spectrum.to_Spectrum1D()
     >>> print(spec1d)
-    <Spectrum1D: 3561.9-10391.0 Angstrom>
+    <Spectrum1D: 3562.4-10380.9 Angstrom>
 
     >>> spec1d.plot() # doctest: +SKIP
 
@@ -194,8 +194,8 @@ telluric absorption. Here's what it looks like:
     import matplotlib.pyplot as plt
     from astropy.utils.data import download_file
 
-    target_url = 'https://drive.google.com/uc?export=download&id=1lkZi4p6ZGeeyDf_Z0eexMy0GHnr92_dv'
-    spectroscopic_standard_url = 'https://drive.google.com/uc?export=download&id=1YiY1DP5Ec4mumvzjWj4u5DmFiEyn9MgH'
+    target_url = 'https://stsci.box.com/shared/static/mu4fa1fmq1lw8boem12e2umyi99skbdl.fits'
+    spectroscopic_standard_url = 'https://stsci.box.com/shared/static/18fa008byy2500yrfhuooyxs5d6pwc6e.fits'
 
     target_path = download_file(target_url)
     standard_path = download_file(spectroscopic_standard_url)
@@ -217,95 +217,3 @@ telluric absorption. Here's what it looks like:
     plt.xlabel('Wavelength [Angstrom]')
     plt.ylabel('Flux')
     plt.show()
-
-.. _getting_started-alltogether:
-
-Putting it all together
------------------------
-
-Now let's do all of this analysis on a very different star -- this time a
-Wolf-Rayet star:
-
-.. code-block:: python
-
-    >>> # Download example spectra
-    >>> from astropy.utils.data import download_file
-
-    >>> target_url = 'http://staff.washington.edu/tzdw/wr_echelle/wr124.0001.wfrmcpc.fits'
-    >>> spectroscopic_standard_url = 'http://staff.washington.edu/tzdw/wr_echelle/HIP107864.0003.wfrmcpc.fits'
-
-    >>> target_path = download_file(target_url, show_progress=False) # doctest: +REMOTE_DATA
-    >>> standard_path = download_file(spectroscopic_standard_url, show_progress=False) # doctest: +REMOTE_DATA
-
-    >>> # Open those example spectra with aesop
-    >>> from aesop import EchelleSpectrum
-
-    >>> target_spectrum = EchelleSpectrum.from_fits(target_path)
-    >>> standard_spectrum = EchelleSpectrum.from_fits(standard_path)
-
-    >>> # Continuum normalize the spectra against a standard, and with lstsq
-    >>> target_spectrum.continuum_normalize_from_standard(standard_spectrum,
-    ...                                                   polynomial_order=8)
-    >>> target_spectrum.continuum_normalize_lstsq(polynomial_order=2)
-
-    >>> # Plot the concatenated 1D spectrum
-    >>> spec1d = target_spectrum.to_Spectrum1D()
-    >>> spec1d.plot() # doctest: +SKIP
-
-.. plot::
-
-    from astropy.utils.data import download_file
-
-    target_url = 'http://staff.washington.edu/tzdw/wr_echelle/wr124.0001.wfrmcpc.fits'
-    spectroscopic_standard_url = 'http://staff.washington.edu/tzdw/wr_echelle/HIP107864.0003.wfrmcpc.fits'
-
-    target_path = download_file(target_url, show_progress=False) # doctest: +REMOTE_DATA
-    standard_path = download_file(spectroscopic_standard_url, show_progress=False) # doctest: +REMOTE_DATA
-
-    from aesop import EchelleSpectrum
-
-    target_spectrum = EchelleSpectrum.from_fits(target_path)
-    standard_spectrum = EchelleSpectrum.from_fits(standard_path)
-
-    target_spectrum.continuum_normalize_from_standard(standard_spectrum,
-                                                      polynomial_order=8)
-    target_spectrum.continuum_normalize_lstsq(polynomial_order=2)
-
-    spec1d = target_spectrum.to_Spectrum1D()
-    spec1d.plot()
-    plt.ylim([0, 3])
-    plt.xlim([3500, 10000])
-    plt.xlabel('Wavelength [Angstrom]')
-    plt.ylabel('Flux')
-    plt.show()
-
-But note that these spectra have lots of emission, which our continuum
-normalization preserves:
-
-.. plot::
-
-    from astropy.utils.data import download_file
-
-    target_url = 'http://staff.washington.edu/tzdw/wr_echelle/wr124.0001.wfrmcpc.fits'
-    spectroscopic_standard_url = 'http://staff.washington.edu/tzdw/wr_echelle/HIP107864.0003.wfrmcpc.fits'
-
-    target_path = download_file(target_url, show_progress=False) # doctest: +REMOTE_DATA
-    standard_path = download_file(spectroscopic_standard_url, show_progress=False) # doctest: +REMOTE_DATA
-
-    from aesop import EchelleSpectrum
-
-    target_spectrum = EchelleSpectrum.from_fits(target_path)
-    standard_spectrum = EchelleSpectrum.from_fits(standard_path)
-
-    target_spectrum.continuum_normalize_from_standard(standard_spectrum,
-                                                      polynomial_order=8)
-    target_spectrum.continuum_normalize_lstsq(polynomial_order=2)
-
-    spec1d = target_spectrum.to_Spectrum1D()
-    spec1d.plot()
-    import matplotlib.pyplot as plt
-    plt.ylim([0, 6])
-    plt.xlim([6520, 6620])
-    plt.xlabel('Wavelength [Angstrom]')
-    plt.ylabel('Flux')
-    plt.show()
diff --git a/tox.ini b/tox.ini
@@ -0,0 +1,77 @@
+[tox]
+env_list =
+    check-style
+    test{-oldestdeps,-pyargs}
+    test-xdist
+    build-{dist,docs}
+isolated_build = true
+# This is included for testing of the template. You can remove it safely.
+skip_missing_interpreters = True
+
+[testenv:check-style]
+description = check code style with ruff
+change_dir = .
+skip_install = true
+deps =
+    ruff
+commands =
+    ruff .
+
+[testenv]
+# tox environments are constructed with so-called 'factors' (or terms)
+# separated by hyphens, e.g. test-devdeps-cov. Lines below starting with factor:
+# will only take effect if that factor is included in the environment name. To
+# see a list of example environments that can be run, along with a description,
+# run:
+#
+#     tox -l -v
+#
+description =
+    run tests
+    oldestdeps: with the oldest supported version of key dependencies
+    xdist: in parallel
+
+use_develop = true
+pass_env =
+    HOME
+    CI
+    TOXENV
+
+# Suppress display of matplotlib plots generated during docs build
+set_env =
+    MPLBACKEND=agg
+
+deps =
+    oldestdeps: minimum_dependencies
+    xdist: pytest-xdist
+
+# The following indicates which extras_require from setup.cfg will be installed
+extras =
+    test
+
+commands_pre =
+    oldestdeps: minimum_dependencies aesop --filename requirements-min.txt
+    oldestdeps: pip install -r requirements-min.txt
+    pip freeze
+
+commands =
+    pip freeze
+    test: pytest --pyargs aesop {toxinidir}/docs {posargs}
+
+[testenv:check-build]
+description = check PEP517 package build
+change_dir = .
+skip_install = true
+deps =
+    build
+    twine
+commands =
+    python -m build --sdist .
+    twine check dist/*
+
+[testenv:build-docs]
+description = invoke sphinx-build to build the HTML docs
+change_dir = docs
+extras = docs
+commands =
+    sphinx-build -W -b html . _build/html