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Deprecate legacy and separate example galleries (#250)
* Deprecate legacy and separate example galleries * Add changelogs * Fix doc build * Apply suggestions from code review
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‎changelog/250.deprecation.rst‎

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Deprecate the `sunkit_spex.legacy` module.

‎changelog/250.doc.rst‎

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Split the gallery into `Examples` and `Legacy Examples` sections.

‎docs/conf.py‎

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# http://www.sphinx-doc.org/en/master/config
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import datetime
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import pathlib
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from pathlib import Path
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from packaging.version import Version
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3/", (None, "http://data.astropy.org/intersphinx/python3.inv")),
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"numpy": ("https://docs.scipy.org/doc/numpy/", (None, "http://data.astropy.org/intersphinx/numpy.inv")),
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"scipy": ("https://docs.scipy.org/doc/scipy/reference/", (None, "http://data.astropy.org/intersphinx/scipy.inv")),
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"matplotlib": ("https://matplotlib.org/", (None, "http://data.astropy.org/intersphinx/matplotlib.inv")),
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"astropy": ("http://docs.astropy.org/en/stable/", None),
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"numpy": ("https://docs.scipy.org/doc/numpy/", (None, "https://numpy.org/doc/stable/objects.inv")),
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"scipy": ("https://docs.scipy.org/doc/scipy/reference/", (None, "https://docs.scipy.org/doc/scipy/objects.inv")),
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"matplotlib": ("https://matplotlib.org/", (None, "https://matplotlib.org/stable/objects.inv")),
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"astropy": ("http://docs.astropy.org/en/stable/", (None, "https://docs.astropy.org/en/stable/objects.inv")),
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"sunpy": ("https://docs.sunpy.org/en/stable/", None),
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}
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# -- Options for the Sphinx gallery -------------------------------------------
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path = pathlib.Path.cwd()
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example_dir = path.parent.joinpath("examples")
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sphinx_gallery_conf = {
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"backreferences_dir": str(path.joinpath("generated", "modules")),
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"backreferences_dir": str(Path("generated") / "modules"),
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"filename_pattern": "^((?!skip_).)*$",
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"examples_dirs": example_dir,
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"gallery_dirs": path.joinpath("generated", "gallery"),
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"examples_dirs": str(Path("..") / "examples"),
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"gallery_dirs": str(Path("generated") / "gallery"),
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"abort_on_example_error": False,
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"plot_gallery": "True",
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"remove_config_comments": True,
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"only_warn_on_example_error": True,
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'pypandoc': True
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"parallel": True,
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}
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# -- Other options ----------------------------------------------------------

‎docs/how_to/index.rst‎

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:maxdepth: 1
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../generated/gallery/index
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.. toctree::
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:maxdepth: 1
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:hidden:
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../generated/gallery/legacy/index

‎docs/reference/legacy.rst‎

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*****************************
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.. warning::
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The legacy module contains legacy code which will no longer be maintained and will be removed in the near future.
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The legacy module has been deprecated since version 0.4 and will be removed in a future version.
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.. automodapi:: sunkit_spex.legacy
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.. automodapi:: sunkit_spex.legacy.thermal

‎examples/legacy/README.txt‎

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Legacy Examples
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---------------
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.. warning::
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The legacy module has been deprecated since version 0.4 and will be removed in a future version.

examples/fitting_NuSTAR_spectra-duncan2021.py renamed to examples/legacy/fitting_NuSTAR_spectra-duncan2021.py

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]
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for fname in file_names:
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dl.enqueue_file(base_url + fname, path="./nustar/Duncan2021/")
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dl.enqueue_file(base_url + fname, path="../../nustar/Duncan2021/")
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files = dl.download()
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#####################################################
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#
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# First, load in your data files, here we load in 2 spectra
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_dir = "./nustar/Duncan2021/"
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_dir = "../../nustar/Duncan2021/"
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spec = Fitter(pha_file=[_dir + "nu80410201001A06_1618_p_chu2_N_sr.pha", _dir + "nu80410201001B06_1618_p_chu2_N_sr.pha"])
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#####################################################

examples/fitting_NuSTAR_spectra-general.py renamed to examples/legacy/fitting_NuSTAR_spectra-general.py

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]
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for fname in file_names:
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dl.enqueue_file(base_url + fname, path="./nustar/m3_time2628/")
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dl.enqueue_file(base_url + fname, path="../../nustar/m3_time2628/")
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files = dl.download()
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#####################################################
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# First, load in your data files, here we load in 1 spectrum
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_dir = "./nustar/m3_time2628/"
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_dir = "../../nustar/m3_time2628/"
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spec = Fitter(pha_file=[_dir + "nu80414202001A06_chu23_S_cl_grade0_sr.pha"])
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#####################################################

examples/fitting_NuSTAR_spectra-glesener2020.py renamed to examples/legacy/fitting_NuSTAR_spectra-glesener2020.py

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]
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for fname in file_names:
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dl.enqueue_file(base_url + fname, path="./nustar/Glesener2020/")
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dl.enqueue_file(base_url + fname, path="../../nustar/Glesener2020/")
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files = dl.download()
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#####################################################
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#
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# First, load in your data files, here we load in 2 spectra
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_dir = "./nustar/Glesener2020/"
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_dir = "../../nustar/Glesener2020/"
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# In the files here, the ARF and RMF file have different names to the PHA files so cannot use the PHA file name to help find the others so...
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spec = Fitter(
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pha_file=_dir + "nu20312001001B06_cl_grade0_sr_grp.pha",
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# In the original Figure 3(c), a broken power law is used as the cold thick target does not exist ins XPSEC.
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#
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# First, load in your data files, here we load in 2 spectra
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_dir = "./nustar/Glesener2020/"
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_dir = "../../nustar/Glesener2020/"
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spec = Fitter(
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pha_file=[_dir + "nu20312001001A06_cl_grade0_sr_grp.pha", _dir + "nu20312001001B06_cl_grade0_sr_grp.pha"],
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arf_file=[_dir + "nu20312001001A06_cl_grade0_sr.arf", _dir + "nu20312001001B06_cl_grade0_sr.arf"],
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#
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# First, load in your data files, here we load in 1 spectrum
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_dir = "./nustar/Glesener2020/"
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_dir = "../../nustar/Glesener2020/"
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spec = Fitter(
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pha_file=_dir + "nu20312001001B06_cl_grade0_sr_grp.pha",
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arf_file=_dir + "nu20312001001B06_cl_grade0_sr.arf",
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#
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# First, load in your data files, here we load in 2 spectra
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_dir = "./nustar/Glesener2020/"
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_dir = "../../nustar/Glesener2020/"
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spec = Fitter(
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pha_file=[_dir + "nu20312001001A06_cl_grade0_sr_grp.pha", _dir + "nu20312001001B06_cl_grade0_sr_grp.pha"],
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arf_file=[_dir + "nu20312001001A06_cl_grade0_sr.arf", _dir + "nu20312001001B06_cl_grade0_sr.arf"],

examples/fitting_NuSTAR_spectra-simultaneously.py renamed to examples/legacy/fitting_NuSTAR_spectra-simultaneously.py

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]
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for fname in file_names:
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dl.enqueue_file(base_url + fname, path="./nustar/m10_1616_1620/")
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dl.enqueue_file(base_url + fname, path="../../nustar/m10_1616_1620/")
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files = dl.download()
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#####################################################
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#
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# Load in your data files, here we load in 2 spectra
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_dir = "./nustar/m10_1616_1620/"
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_dir = "../../nustar/m10_1616_1620/"
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spec = Fitter(
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pha_file=[_dir + "nu80415202001A06_chu13_N_cl_grade0_sr.pha", _dir + "nu80415202001B06_chu13_N_cl_grade0_sr.pha"]
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)

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