Merge pull request #92 from pllim/doctest

TST: doctest and linkcheck
spacetelescope · Oct 10, 2019 · 9b0d584 · 9b0d584
2 parents cccbfc2 + 12224d4
commit 9b0d584
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diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -79,6 +79,24 @@ stages:
         codecov_token: $(CODECOV_TOKEN)
       displayName: 'Calculate coverage'
 
+  - job: 'LinkCheck'
+    pool:
+      vmImage: 'Ubuntu-16.04'
+    strategy:
+      maxParallel: 4
+
+    steps:
+    - task: UsePythonVersion@0
+
+    - script: |
+        python -m pip install --upgrade pip setuptools
+        pip install sphinx-astropy
+        python setup.py install
+    - bash: |
+        cd docs
+        make linkcheck
+      displayName: 'Run docs link check'
+
   - template: azure-templates.yml
     parameters:
       name: 'Older_Versions'

diff --git a/docs/conf.py b/docs/conf.py
@@ -148,3 +148,11 @@
 intersphinx_mapping.update({
     'astropy': ('https://docs.astropy.org/en/latest/', None),
     'synphot': ('https://synphot.readthedocs.io/en/latest/', None)})
+
+
+# -- Options for linkcheck output -------------------------------------------
+linkcheck_retry = 5
+linkcheck_ignore = ['https://hsthelp.stsci.edu',
+                    'https://www.as.arizona.edu/observing']
+linkcheck_timeout = 180
+linkcheck_anchors = False
diff --git a/docs/index.rst b/docs/index.rst
@@ -1,5 +1,3 @@
-.. doctest-skip-all
-
 .. _stsynphot_index:
 
 *********************************************
@@ -98,16 +96,22 @@ Below are the instructions to install:
    stsynphot/data_hst
    stsynphot/data_jwst
 
+.. testsetup::
+
+    >>> # This is not marked remote data because it is essential for VEGAMAG
+    >>> from stsynphot.spectrum import load_vega
+    >>> load_vega(vegafile='http://ssb.stsci.edu/cdbs/calspec/alpha_lyr_stis_009.fits', encoding='binary')  # doctest: +IGNORE_OUTPUT
+
 To ensure consistency for all data files used, **stsynphot silently overwrites
 synphot data file locations within the Python session**. For example::
 
     >>> from synphot.config import conf as syn_conf
-    >>> print(syn_conf.johnson_v_file)
+    >>> print(syn_conf.johnson_v_file)  # doctest: +IGNORE_OUTPUT
     http://ssb.stsci.edu/cdbs/comp/nonhst/johnson_v_004_syn.fits
     >>> from stsynphot.config import conf
-    >>> print(conf.rootdir)
+    >>> print(conf.rootdir)  # doctest: +IGNORE_OUTPUT
     /my/local/dir/cdbs/
-    >>> print(syn_conf.johnson_v_file)
+    >>> print(syn_conf.johnson_v_file)  # doctest: +IGNORE_OUTPUT
     /my/local/dir/cdbs//comp/nonhst/johnson_v_004_syn.fits
 
 You can also take advantage of
@@ -154,8 +158,8 @@ before proceeding.
 Display the current settings for graph and component tables, telescope area
 (in squared centimeter), and default wavelength set (in Angstrom)::
 
-    >>> import stsynphot as STS
-    >>> STS.showref()
+    >>> import stsynphot as stsyn
+    >>> stsyn.showref()  # doctest: +SKIP
     graphtable: /my/local/dir/cdbs/mtab/07r1502mm_tmg.fits
     comptable : /my/local/dir/cdbs/mtab/07r1502nm_tmc.fits
     thermtable: /my/local/dir/cdbs/mtab/tae17277m_tmt.fits
@@ -168,14 +172,16 @@ consistency, as stated in :ref:`stsynphot-installation-setup` (the double
 slash in path name does not affect software operation)::
 
     >>> import synphot
-    >>> synphot.conf.vega_file
-    '/my/local/dir/cdbs//calspec/alpha_lyr_stis_008.fits'
+    >>> synphot.conf.vega_file  # doctest: +IGNORE_OUTPUT
+    '/my/local/dir/cdbs//calspec/alpha_lyr_stis_009.fits'
 
 Plot the built-in Vega spectrum, which is used to compute VEGAMAG. This is
 pre-loaded at start-up for convenience::
 
     >>> from synphot import units
-    >>> STS.Vega.plot(right=20000, flux_unit=units.FLAM, title='Vega spectrum')
+    >>> stsyn.Vega.plot(
+    ...     right=20000, flux_unit=units.FLAM,
+    ...     title='Vega spectrum')  # doctest: +SKIP
 
 .. image:: stsynphot/images/vega_spec.png
     :width: 600px
@@ -184,8 +190,8 @@ pre-loaded at start-up for convenience::
 Construct a bandpass for HST/ACS camera using WFC1 detector and F555W filter;
 Then, show all the individual throughput files used in its construction::
 
-    >>> bp = STS.band('acs,wfc1,f555w')
-    >>> bp.showfiles()
+    >>> bp = stsyn.band('acs,wfc1,f555w')  # doctest: +SKIP
+    >>> bp.showfiles()  # doctest: +SKIP
     INFO: #Throughput table names:
     /my/local/dir/cdbs/comp/ota/hst_ota_007_syn.fits
     /my/local/dir/cdbs/comp/acs/acs_wfc_im123_004_syn.fits
@@ -198,14 +204,14 @@ star with blackbody temperature of 5770 Kelvin, at solar metallicity, and log
 surface gravity of 4.5, renormalized to 20 VEGAMAG in Johnson *V* filter,
 using IRAF SYNPHOT syntax::
 
-    >>> sp = STS.parse_spec(
-    ...     'rn(icat(k93models,5770,0.0,4.5),band(johnson,v),20,vegamag)')
+    >>> sp = stsyn.parse_spec(
+    ...     'rn(icat(k93models,5770,0.0,4.5),band(johnson,v),20,vegamag)')  # doctest: +SKIP
 
 Construct an extinction curve for Milky Way (diffuse) with :math:`E(B-V)` of
 0.7 mag. Then, apply the extinction to the source spectrum from before::
 
-    >>> ext = STS.ebmvx('mwavg', 0.7)
-    >>> sp_ext = sp * ext
+    >>> ext = stsyn.ebmvx('mwavg', 0.7)  # doctest: +REMOTE_DATA
+    >>> sp_ext = sp * ext  # doctest: +SKIP
 
 Construct an observation using the ACS bandpass and the extincted source
 spectrum. (For accurate detector binning, you can pass in the binned wavelength
@@ -214,8 +220,8 @@ observation mode is stored in ``bp.binset``.) Then, compute the count rate
 for HST collecting area::
 
     >>> from synphot import Observation
-    >>> obs = Observation(sp_ext, bp, binset=bp.binset)
-    >>> obs.countrate(area=STS.config.conf.area)
+    >>> obs = Observation(sp_ext, bp, binset=bp.binset)  # doctest: +SKIP
+    >>> obs.countrate(area=stsyn.config.conf.area)  # doctest: +SKIP
     <Quantity 23.839134880103543 ct / s>
 
 To find out exactly how ``bp.binset`` was computed, you can use the following
@@ -224,14 +230,15 @@ mode in use is stored in ``wavecats/acs.dat`` in the **stsynphot** software
 data directory (``synphot$``, which is named so for backward compatibility
 with ASTROLIB PYSYNPHOT)::
 
-    >>> STS.wavetable.WAVECAT['acs,wfc1,f555w']
+    >>> from stsynphot import wavetable
+    >>> wavetable.WAVECAT['acs,wfc1,f555w']
     'synphot$wavecats/acs.dat'
 
 Calculate thermal background for a HST/WFC3 bandpass for its IR detector using
 F110W filter::
 
-    >>> wfc3 = STS.band('wfc3,ir,f110w')
-    >>> wfc3.thermback()
+    >>> wfc3 = stsyn.band('wfc3,ir,f110w')  # doctest: +SKIP
+    >>> wfc3.thermback()  # doctest: +SKIP
     <Quantity 0.051636304994833425 ct / (pix s)>
 
 
@@ -332,7 +339,7 @@ Fukugita, M., Ichikawa, T., Gunn, J. E., Doi, M., Shimasaku, K., & Schneider, D.
 
 .. _stsynphot-ref-gunn2001:
 
-`Gunn, J. E., Hogg, D., Finkbeiner, D., & Schlegel, D. 2001, Photometry White Paper <http://www.sdss.org/dr3/algorithms/sdssphot.ps>`_
+`Gunn, J. E., Hogg, D., Finkbeiner, D., & Schlegel, D. 2001, Photometry White Paper <http://classic.sdss.org/dr3/algorithms/sdssphot.ps>`_
 
 .. _stsynphot-ref-gunn1983:
 
@@ -388,7 +395,7 @@ Lim, P. L., Diaz, R. I., & Laidler, V. 2015, PySynphot User's Guide (Baltimore,
 
 .. _stsynphot-ref-lim2016:
 
-Lim, P. L., et al. 2016, synphot User's Guide (Baltimore, MD: STScI), http://synphot.readthedocs.io/en/latest/
+Lim, P. L., et al. 2016, synphot User's Guide (Baltimore, MD: STScI), https://synphot.readthedocs.io/en/latest/
 
 .. _stsynphot-ref-lub1977:
 

diff --git a/docs/stsynphot/appendixa.rst b/docs/stsynphot/appendixa.rst
@@ -1,5 +1,3 @@
-.. doctest-skip-all
-
 .. _stsynphot-appendixa:
 
 Appendix A: Catalogs and Spectral Atlases
@@ -82,8 +80,8 @@ The example below generates a spectrum with metallicity ``[M/H] = +0.1``,
 temperature :math:`T_{\text{eff}} = 10000 \text{K}`, and gravity
 :math:`\log g = 3.0`::
 
-    >>> import stsynphot as STS
-    >>> sp = STS.grid_to_spec('ck04models', 10000, 0.1, 3.0)
+    >>> import stsynphot as stsyn
+    >>> sp = stsyn.grid_to_spec('ck04models', 10000, 0.1, 3.0)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-kurucz1993:
@@ -125,9 +123,9 @@ columns in the file are filled with zeroes::
     >>> from astropy.io import fits
     >>> filename = os.path.join(
     ...     os.environ['PYSYN_CDBS'], 'grid', 'k93models',
-    ...     'kp00', 'kp00_8000.fits')
-    >>> hdr = fits.getheader(filename)
-    >>> hdr
+    ...     'kp00', 'kp00_8000.fits')  # doctest: +SKIP
+    >>> hdr = fits.getheader(filename)  # doctest: +SKIP
+    >>> hdr  # doctest: +SKIP
     SIMPLE  =                    T / file does conform to FITS standard
     BITPIX  =                   16 / number of bits per data pixel
     NAXIS   =                    0 / number of data axes
@@ -166,16 +164,16 @@ means :math:`\log g = 3.0`::
 
     >>> filename = os.path.join(
     ...     os.environ['PYSYN_CDBS'], 'grid', 'k93models',
-    ...     'kp01', 'kp01_10000.fits')
-    >>> spec = fits.getdata(filename)
-    >>> wave = spec['WAVELENGTH']
-    >>> flux = spec['g30']
+    ...     'kp01', 'kp01_10000.fits')  # doctest: +SKIP
+    >>> spec = fits.getdata(filename)  # doctest: +SKIP
+    >>> wave = spec['WAVELENGTH']  # doctest: +SKIP
+    >>> flux = spec['g30']  # doctest: +SKIP
 
 The easier way is to use :func:`~stsynphot.catalog.grid_to_spec` (also see
 :ref:`stsynphot-spec-atlas`). Equivalent to the example above::
 
-    >>> import stsynphot as STS
-    >>> sp = STS.grid_to_spec('k93models', 10000, 0.1, 3.0)
+    >>> import stsynphot as stsyn
+    >>> sp = stsyn.grid_to_spec('k93models', 10000, 0.1, 3.0)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-phoenix:
@@ -205,8 +203,8 @@ The example below generates a spectrum with metallicity ``[M/H] = +0.1``,
 temperature :math:`T_{\text{eff}} = 10000 \text{K}`, and gravity
 :math:`\log g = 3.0`::
 
-    >>> import stsynphot as STS
-    >>> sp = STS.grid_to_spec('phoenix', 10000, 0.1, 3.0)
+    >>> import stsynphot as stsyn
+    >>> sp = stsyn.grid_to_spec('phoenix', 10000, 0.1, 3.0)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-calspec:
@@ -225,9 +223,9 @@ the header from G191B2B spectrum and then loads it into **stsynphot**::
     >>> from astropy.io import fits
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'calspec', 'g191b2b_mod_010.fits')
-    >>> hdr = fits.getheader(filename)
-    >>> hdr
+    ...     os.environ['PYSYN_CDBS'], 'calspec', 'g191b2b_mod_010.fits')  # doctest: +SKIP
+    >>> hdr = fits.getheader(filename)  # doctest: +SKIP
+    >>> hdr  # doctest: +SKIP
     SIMPLE  =                    T / Fits standard
     BITPIX  =                   16 / Bits per pixel
     NAXIS   =                    0 / Number of axes
@@ -259,7 +257,7 @@ the header from G191B2B spectrum and then loads it into **stsynphot**::
     HISTORY Vega Flux(5556A)=3.44e-9 (Bohlin 2014, AJ, 147, 127)
     HISTORY INPUT FILE: /internal/1/wd/dat/g191.rauch59000-nlte
     HISTORY Written by MAKE_MOD_CALSPEC.pro  23-Dec-2014 10:20:09.00
-    >>> sp = SourceSpectrum.from_file(filename)
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 Note that in some cases, the calibration spectrum is truncated in the blue or
 the red at wavelength longer or shorter, respectively, than the sensitivity
@@ -307,8 +305,8 @@ subset of the library::
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
     ...     os.environ['PYSYN_CDBS'], 'grid', 'pickles',
-    ...     'dat_uvk', 'pickles_uk_27.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     'dat_uvk', 'pickles_uk_27.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-bkmodels:
@@ -340,8 +338,8 @@ The example below loads Block S (models for the Sun and Vega) with
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'grid', 'bkmodels', 'bk_s0001.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'grid', 'bkmodels', 'bk_s0001.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-bz77:
@@ -361,8 +359,8 @@ The example below loads a source spectrum of spectral type G5V from the atlas::
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'grid', 'bz77', 'bz_27.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'grid', 'bz77', 'bz_27.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-gs:
@@ -385,8 +383,8 @@ The example below loads a source spectrum of spectral type G5V from the atlas::
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'grid', 'gunnstryker', 'gs_44.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'grid', 'gunnstryker', 'gs_44.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-bpgs:
@@ -419,8 +417,8 @@ The example below loads a source spectrum of spectral type G5V from the atlas::
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'grid', 'bpgs', 'bpgs_44.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'grid', 'bpgs', 'bpgs_44.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-jacobi:
@@ -444,8 +442,8 @@ The example below loads a source spectrum of spectral type G0V from the atlas::
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'grid', 'jacobi', 'jc_43.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'grid', 'jacobi', 'jc_43.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-bc95:
@@ -474,8 +472,8 @@ instantaneous burst::
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
     ...     os.environ['PYSYN_CDBS'], 'grid', 'bc95',
-    ...     'templates', 'bc95_c_50E5.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     'templates', 'bc95_c_50E5.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-kc96:
@@ -499,8 +497,8 @@ The example below loads a galaxy spectrum from the elliptical template::
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
     ...     os.environ['PYSYN_CDBS'], 'grid', 'kc96',
-    ...     'elliptical_template.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     'elliptical_template.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-agn:
@@ -523,8 +521,8 @@ The example below loads a Seyfert 2 spectrum::
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'grid', 'agn', 'seyfert2_template.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'grid', 'agn', 'seyfert2_template.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-galactic:
@@ -544,8 +542,8 @@ The example below loads the spectrum for Orion nebula::
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
     ...     os.environ['PYSYN_CDBS'], 'grid', 'galactic',
-    ...     'orion_template.fits')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     'orion_template.fits')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
 
 
 .. _stsynphot-appendixa-etcsource:
@@ -563,5 +561,5 @@ The example below loads a spectrum for Gliese 229B brown dwarf::
     >>> import os
     >>> from synphot import SourceSpectrum
     >>> filename = os.path.join(
-    ...     os.environ['PYSYN_CDBS'], 'etc', 'source', 'gl229b_001.dat')
-    >>> sp = SourceSpectrum.from_file(filename)
+    ...     os.environ['PYSYN_CDBS'], 'etc', 'source', 'gl229b_001.dat')  # doctest: +SKIP
+    >>> sp = SourceSpectrum.from_file(filename)  # doctest: +SKIP
diff --git a/docs/stsynphot/appendixb.rst b/docs/stsynphot/appendixb.rst
@@ -1,5 +1,3 @@
-.. doctest-skip-all
-
 .. include:: appb_ref.txt
 
 .. _stsynphot-appendixb: