sunpy · samaloney · Feb 26, 2026 · Feb 3, 2026 · Feb 3, 2026 · Feb 3, 2026
diff --git a/changelog/250.deprecation.rst b/changelog/250.deprecation.rst
@@ -0,0 +1 @@
+Deprecate the `sunkit-spex.legacy` module.
diff --git a/changelog/250.doc.rst b/changelog/250.doc.rst
@@ -0,0 +1 @@
+Split the gallery into `Examples` and `Legacy Examples` sections.
diff --git a/docs/conf.py b/docs/conf.py
@@ -5,7 +5,7 @@
 # http://www.sphinx-doc.org/en/master/config
 
 import datetime
-import pathlib
+from pathlib import Path
 
 from packaging.version import Version
 
@@ -76,10 +76,10 @@
 # Example configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3/", (None, "http://data.astropy.org/intersphinx/python3.inv")),
-    "numpy": ("https://docs.scipy.org/doc/numpy/", (None, "http://data.astropy.org/intersphinx/numpy.inv")),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", (None, "http://data.astropy.org/intersphinx/scipy.inv")),
-    "matplotlib": ("https://matplotlib.org/", (None, "http://data.astropy.org/intersphinx/matplotlib.inv")),
-    "astropy": ("http://docs.astropy.org/en/stable/", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy/", (None, "https://numpy.org/doc/stable/objects.inv")),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference/", (None, "https://docs.scipy.org/doc/scipy/objects.inv")),
+    "matplotlib": ("https://matplotlib.org/", (None, "https://matplotlib.org/stable/objects.inv")),
+    "astropy": ("http://docs.astropy.org/en/stable/", (None, "https://docs.astropy.org/en/stable/objects.inv")),
     "sunpy": ("https://docs.sunpy.org/en/stable/", None),
 }
 
@@ -117,18 +117,15 @@
 
 # -- Options for the Sphinx gallery -------------------------------------------
 
-path = pathlib.Path.cwd()
-example_dir = path.parent.joinpath("examples")
 sphinx_gallery_conf = {
-    "backreferences_dir": str(path.joinpath("generated", "modules")),
+    "backreferences_dir": str(Path("generated") / "modules"),
     "filename_pattern": "^((?!skip_).)*$",
-    "examples_dirs": example_dir,
-    "gallery_dirs": path.joinpath("generated", "gallery"),
+    "examples_dirs": str(Path("..") / "examples"),
+    "gallery_dirs": str(Path("generated") / "gallery"),
     "abort_on_example_error": False,
-    "plot_gallery": "True",
     "remove_config_comments": True,
     "only_warn_on_example_error": True,
-    'pypandoc': True
+    "parallel": True,
 }
 
 # -- Other options ----------------------------------------------------------
diff --git a/docs/how_to/index.rst b/docs/how_to/index.rst
@@ -11,3 +11,4 @@ you quickly accomplish common tasks.
    :maxdepth: 1
 
    ../generated/gallery/index
+   ../generated/gallery/legacy/index
diff --git a/docs/reference/legacy.rst b/docs/reference/legacy.rst
@@ -2,7 +2,7 @@ Legacy (`sunkit_spex.legacy`)
 *****************************
 
 .. warning::
-   The legacy module contains legacy code which will no longer be maintained and will be removed in the near future.
+   The legacy module has been deprecated since version 0.4 and will be removed in a future version.
 
 .. automodapi:: sunkit_spex.legacy
 .. automodapi:: sunkit_spex.legacy.thermal

diff --git a/examples/legacy/README.txt b/examples/legacy/README.txt
@@ -0,0 +1,5 @@
+Legacy Examples
+---------------
+
+.. warning::
+   The legacy module has been deprecated since version 0.4 and will be removed in a future version.
diff --git a/...ples/fitting_NuSTAR_spectra-duncan2021.py → ...gacy/fitting_NuSTAR_spectra-duncan2021.py b/...ples/fitting_NuSTAR_spectra-duncan2021.py → ...gacy/fitting_NuSTAR_spectra-duncan2021.py
@@ -57,15 +57,15 @@
 ]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./nustar/Duncan2021/")
+    dl.enqueue_file(base_url + fname, path="../../nustar/Duncan2021/")
 files = dl.download()
 
 
 #####################################################
 #
 # First, load in your data files, here we load in 2 spectra
 
-_dir = "./nustar/Duncan2021/"
+_dir = "../../nustar/Duncan2021/"
 spec = Fitter(pha_file=[_dir + "nu80410201001A06_1618_p_chu2_N_sr.pha", _dir + "nu80410201001B06_1618_p_chu2_N_sr.pha"])
 
 #####################################################

diff --git a/examples/fitting_NuSTAR_spectra-general.py → .../legacy/fitting_NuSTAR_spectra-general.py b/examples/fitting_NuSTAR_spectra-general.py → .../legacy/fitting_NuSTAR_spectra-general.py
@@ -47,7 +47,7 @@
 ]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./nustar/m3_time2628/")
+    dl.enqueue_file(base_url + fname, path="../../nustar/m3_time2628/")
 files = dl.download()
 
 #####################################################
@@ -56,7 +56,7 @@
 
 
 # First, load in your data files, here we load in 1 spectrum
-_dir = "./nustar/m3_time2628/"
+_dir = "../../nustar/m3_time2628/"
 spec = Fitter(pha_file=[_dir + "nu80414202001A06_chu23_S_cl_grade0_sr.pha"])
 
 #####################################################

diff --git a/...es/fitting_NuSTAR_spectra-glesener2020.py → ...cy/fitting_NuSTAR_spectra-glesener2020.py b/...es/fitting_NuSTAR_spectra-glesener2020.py → ...cy/fitting_NuSTAR_spectra-glesener2020.py
@@ -62,14 +62,14 @@
 ]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./nustar/Glesener2020/")
+    dl.enqueue_file(base_url + fname, path="../../nustar/Glesener2020/")
 files = dl.download()
 
 
 #####################################################
 #
 # First, load in your data files, here we load in 2 spectra
-_dir = "./nustar/Glesener2020/"
+_dir = "../../nustar/Glesener2020/"
 # 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...
 spec = Fitter(
     pha_file=_dir + "nu20312001001B06_cl_grade0_sr_grp.pha",
@@ -141,7 +141,7 @@
 # In the original Figure 3(c), a broken power law is used as the cold thick target does not exist ins XPSEC.
 #
 # First, load in your data files, here we load in 2 spectra
-_dir = "./nustar/Glesener2020/"
+_dir = "../../nustar/Glesener2020/"
 spec = Fitter(
     pha_file=[_dir + "nu20312001001A06_cl_grade0_sr_grp.pha", _dir + "nu20312001001B06_cl_grade0_sr_grp.pha"],
     arf_file=[_dir + "nu20312001001A06_cl_grade0_sr.arf", _dir + "nu20312001001B06_cl_grade0_sr.arf"],
@@ -227,7 +227,7 @@
 #
 # First, load in your data files, here we load in 1 spectrum
 
-_dir = "./nustar/Glesener2020/"
+_dir = "../../nustar/Glesener2020/"
 spec = Fitter(
     pha_file=_dir + "nu20312001001B06_cl_grade0_sr_grp.pha",
     arf_file=_dir + "nu20312001001B06_cl_grade0_sr.arf",
@@ -286,7 +286,7 @@
 #
 # First, load in your data files, here we load in 2 spectra
 
-_dir = "./nustar/Glesener2020/"
+_dir = "../../nustar/Glesener2020/"
 spec = Fitter(
     pha_file=[_dir + "nu20312001001A06_cl_grade0_sr_grp.pha", _dir + "nu20312001001B06_cl_grade0_sr_grp.pha"],
     arf_file=[_dir + "nu20312001001A06_cl_grade0_sr.arf", _dir + "nu20312001001B06_cl_grade0_sr.arf"],

diff --git a/.../fitting_NuSTAR_spectra-simultaneously.py → .../fitting_NuSTAR_spectra-simultaneously.py b/.../fitting_NuSTAR_spectra-simultaneously.py → .../fitting_NuSTAR_spectra-simultaneously.py
@@ -50,14 +50,14 @@
 ]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./nustar/m10_1616_1620/")
+    dl.enqueue_file(base_url + fname, path="../../nustar/m10_1616_1620/")
 files = dl.download()
 
 #####################################################
 #
 # Load in your data files, here we load in 2 spectra
 
-_dir = "./nustar/m10_1616_1620/"
+_dir = "../../nustar/m10_1616_1620/"
 spec = Fitter(
     pha_file=[_dir + "nu80415202001A06_chu13_N_cl_grade0_sr.pha", _dir + "nu80415202001B06_chu13_N_cl_grade0_sr.pha"]
 )

diff --git a/examples/fitting_RHESSI_spectra.py → examples/legacy/fitting_RHESSI_spectra.py b/examples/fitting_RHESSI_spectra.py → examples/legacy/fitting_RHESSI_spectra.py
@@ -43,7 +43,7 @@
 file_names = ["20021005_103800_spec.fits", "20021005_103800_srm.fits"]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./rhessi/")
+    dl.enqueue_file(base_url + fname, path="../../rhessi/")
 files = dl.download()
 
 #####################################################
@@ -61,7 +61,9 @@
 #
 # Load in the data...
 
-rhess_spec = RhessiLoader(spectrum_fn="./rhessi/20021005_103800_spec.fits", srm_fn="./rhessi/20021005_103800_srm.fits")
+rhess_spec = RhessiLoader(
+    spectrum_fn="../../rhessi/20021005_103800_spec.fits", srm_fn="../../rhessi/20021005_103800_srm.fits"
+)
 
 #####################################################
 #
@@ -358,7 +360,7 @@
 # ----------------
 #
 
-save_filename = "./sunxspexRhessiSpectralFitting.pickle"
+save_filename = "../sunxspexRhessiSpectralFitting.pickle"
 fitter.save(save_filename)
 
 #####################################################

diff --git a/examples/fitting_STIX_spectra.py → examples/legacy/fitting_STIX_spectra.py b/examples/fitting_STIX_spectra.py → examples/legacy/fitting_STIX_spectra.py
@@ -62,7 +62,7 @@
 ]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./stix/")
+    dl.enqueue_file(base_url + fname, path="../../stix/")
 files = dl.download()
 
 #####################################################
@@ -83,7 +83,7 @@
 # Load in the data...
 
 stix_spec = STIXLoader(
-    spectrum_file="./stix/stx_spectrum_2410019944_IM.fits", srm_file="./stix/stx_srm_2410019944_IM.fits"
+    spectrum_file="../../stix/stx_spectrum_2410019944_IM.fits", srm_file="../../stix/stx_srm_2410019944_IM.fits"
 )
 
 #####################################################
@@ -202,7 +202,7 @@
 # ----------------
 #
 
-save_filename = "./stix/sunkitspexSTIXpectralFitting.pickle"
+save_filename = "../../stix/sunkitspexSTIXpectralFitting.pickle"
 fitter.save(save_filename)
 
 #####################################################
@@ -266,8 +266,8 @@
 # ========================================================
 # Loading the data into the fitter loader
 #
-spec_bg, srm_bg = "./stix/stx_spectrum_2410019944_BKG.fits", "./stix/stx_srm_2410019944_BKG.fits"
-spec_im, srm_im = "./stix/stx_spectrum_2410019944_IM.fits", "./stix/stx_srm_2410019944_IM.fits"
+spec_bg, srm_bg = "../../stix/stx_spectrum_2410019944_BKG.fits", "../../stix/stx_srm_2410019944_BKG.fits"
+spec_im, srm_im = "../../stix/stx_spectrum_2410019944_IM.fits", "../../stix/stx_srm_2410019944_IM.fits"
 
 spec_joint = Fitter(pha_file=[spec_bg, spec_im], srm_file=[srm_bg, srm_im])
 

diff --git a/...ples/fitting_attenuated_RHESSI_spectra.py → ...gacy/fitting_attenuated_RHESSI_spectra.py b/...ples/fitting_attenuated_RHESSI_spectra.py → ...gacy/fitting_attenuated_RHESSI_spectra.py
@@ -33,7 +33,7 @@
 file_names = ["rhessi-2011-jul-stixbins-spec.fits", "rhessi-2011-jul-stixbins-srm.fits"]
 
 for fname in file_names:
-    dl.enqueue_file(base_url + fname, path="./rhessi/")
+    dl.enqueue_file(base_url + fname, path="../../rhessi/")
 files = dl.download()
 
 
@@ -42,7 +42,8 @@
 # Load in the spectrum and SRM, notice the warning about attenuator changes!
 
 rl = rhessi.RhessiLoader(
-    spectrum_fn="./rhessi/rhessi-2011-jul-stixbins-spec.fits", srm_fn="./rhessi/rhessi-2011-jul-stixbins-srm.fits"
+    spectrum_fn="../../rhessi/rhessi-2011-jul-stixbins-spec.fits",
+    srm_fn="../../rhessi/rhessi-2011-jul-stixbins-srm.fits",
 )
 
 #####################################################

diff --git a/examples/fitting_custom_spectra.py → examples/legacy/fitting_custom_spectra.py b/examples/fitting_custom_spectra.py → examples/legacy/fitting_custom_spectra.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -47,7 +47,7 @@ docs = [
   "packaging",
   "sphinx-changelog",
   "sphinx-gallery",
-  "pypandoc"
+  "joblib", # for sphinx-gallery parallel
 ]
 dev = [
     "sunkit-spex[docs,tests]",

diff --git a/pytest.ini b/pytest.ini
@@ -43,3 +43,4 @@ filterwarnings =
     ignore::pyparsing.warnings.PyparsingDeprecationWarning
     ignore::FutureWarning:arviz.*
     ignore:The isiterable function.*:astropy.utils.exceptions.AstropyDeprecationWarning
+    ignore:The legacy module.*:sunpy.util.exceptions.SunpyDeprecationWarning
diff --git a/sunkit_spex/legacy/__init__.py b/sunkit_spex/legacy/__init__.py
@@ -0,0 +1,9 @@
+import warnings
+
+from sunpy.util.exceptions import SunpyDeprecationWarning
+
+warnings.warn(
+    "The legacy module has been deprecated since version 0.4 and will be removed in a future version.",
+    SunpyDeprecationWarning,
+    stacklevel=2,
+)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Deprecate the `sunkit-spex.legacy` module.
samaloney marked this conversation as resolved. Outdated Show resolved Hide resolved
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Split the gallery into `Examples` and `Legacy Examples` sections.
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,3 +11,4 @@ you quickly accomplish common tasks.
		:maxdepth: 1

		../generated/gallery/index
		../generated/gallery/legacy/index
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