Fitter legacy (#137)

* Changed fittter_legacy module to fitting_legacy and added new fitting module

---------

Co-authored-by: Kristopher Cooper <[email protected]>
Co-authored-by: Shane Maloney <[email protected]>

changelog/137.breaking.rst

@@ -0,0 +1 @@
+Renamed `sunxspex_fitting` module to `fitting_legacy` and added a new `fitting` module.

docs/reference/index.rst

@@ -10,6 +10,6 @@ Software and API.
 .. automodapi:: sunkit_spex.io
 .. automodapi:: sunkit_spex.emission
 .. automodapi:: sunkit_spex.constants
-.. automodapi:: sunkit_spex.sunxspex_fitting
-.. automodapi:: sunkit_spex.sunxspex_fitting.io
+.. automodapi:: sunkit_spex.fitting_legacy
+.. automodapi:: sunkit_spex.fitting_legacy.io
 .. automodapi:: sunkit_spex.photon_power_law

sunkit_spex/__init__.py

@@ -4,4 +4,4 @@
 from .version import __version__
 
 __all__ = []
-from . import io, sunxspex_fitting, thermal
+from . import fitting_legacy, io, thermal

sunkit_spex/sunxspex_fitting/data_loader.py → sunkit_spex/fitting_legacy/data_loader.py

@@ -8,8 +8,8 @@
 
 from astropy.io import fits
 
-from sunkit_spex.sunxspex_fitting import instruments as inst  # sunkit_spex.sunxspex_fitting.instruments
-from sunkit_spex.sunxspex_fitting.parameter_handler import (  # sunkit_spex.sunxspex_fitting.parameter_handler
+from sunkit_spex.fitting_legacy import instruments as inst  # sunkit_spex.fitting_legacy.instruments
+from sunkit_spex.fitting_legacy.parameter_handler import (  # sunkit_spex.fitting_legacy.parameter_handler
     _make_into_list,
     isnumber,
 )
@@ -27,7 +27,7 @@ class LoadSpec:
     Parameters
     ----------
     *args : dict
-            Dictionaries for custom data to be passed to `sunkit_spex.sunxspex_fitting.instruments.CustomLoader`.
+            Dictionaries for custom data to be passed to `sunkit_spex.fitting_legacy.instruments.CustomLoader`.
             These will be added before any instrument file entries from `pha_file`.
 
     pha_file : string or list of strings
@@ -123,7 +123,7 @@ def __init__(self, *args, pha_file=None, arf_file=None, rmf_file=None, srm_file=
         self._construction_string = (f"LoadSpec(*{args}, pha_file={pha_file}, arf_file={arf_file}, rmf_file={rmf_file}, "
                                      f"srm_file={srm_file}, srm_custom={srm_custom}, custom_channel_bins={custom_channel_bins}, **{kwargs})")
 
-        # from sunkit_spex.sunxspex_fitting.instruments import * gives us the instrument specific loaders, keys should match up to the "TELESCOP" header entry in spec file
+        # from sunkit_spex.fitting_legacy.instruments import * gives us the instrument specific loaders, keys should match up to the "TELESCOP" header entry in spec file
         self.instrument_loaders = {"NuSTAR": inst.NustarLoader, "SOLO/STIX": inst.StixLoader, "RHESSI": inst.RhessiLoader}
 
         pha_file, arf_file, rmf_file, srm_file, srm_custom, custom_channel_bins, instruments = self._sort_files(pha_file=pha_file,

sunkit_spex/sunxspex_fitting/fitter.py → sunkit_spex/fitting_legacy/fitter.py

@@ -35,18 +35,18 @@
 
 from astropy.table import Table
 
-from sunkit_spex.logging import get_logger
-from sunkit_spex.sunxspex_fitting.data_loader import LoadSpec
-from sunkit_spex.sunxspex_fitting.instruments import rebin_any_array
-from sunkit_spex.sunxspex_fitting.likelihoods import LogLikelihoods
-from sunkit_spex.sunxspex_fitting.parameter_handler import Parameters, isnumber
-from sunkit_spex.sunxspex_fitting.photon_models_for_fitting import (  # noqa
+from sunkit_spex.fitting_legacy.data_loader import LoadSpec
+from sunkit_spex.fitting_legacy.instruments import rebin_any_array
+from sunkit_spex.fitting_legacy.likelihoods import LogLikelihoods
+from sunkit_spex.fitting_legacy.parameter_handler import Parameters, isnumber
+from sunkit_spex.fitting_legacy.photon_models_for_fitting import (  # noqa
     defined_photon_models,
     f_vth,
     thick_fn,
     thick_warm,
 )
-from sunkit_spex.sunxspex_fitting.rainbow_text import rainbow_text_lines
+from sunkit_spex.fitting_legacy.rainbow_text import rainbow_text_lines
+from sunkit_spex.logging import get_logger
 
 warnings.filterwarnings("ignore", category=RuntimeWarning)
 warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning)
@@ -66,7 +66,7 @@ class Fitter:
     Parameters
     ----------
     *args : dict
-            Dictionaries for custom data to be passed to `sunkit_spex.sunxspex_fitting.instruments.CustomLoader`.
+            Dictionaries for custom data to be passed to `sunkit_spex.fitting_legacy.instruments.CustomLoader`.
             These will be added before any instrument file entries from `pha_file`.
 
     pha_file : string or list of strings
@@ -270,7 +270,7 @@ class Fitter:
             Colour cycle to be used when plotting submodels.
             Default = plt.rcParams['axes.prop_cycle'].by_key()['color']
 
-    _construction_string_sunxspex : str
+    _construction_string_sunkit_spex : str
             String to be returned from __repr__() dunder method.
 
     _corresponding_submod_inputs : list of strings
@@ -401,8 +401,8 @@ def __init__(self, *args, pha_file=None, arf_file=None, rmf_file=None, srm_file=
         self.data = LoadSpec(*args, pha_file=pha_file, arf_file=arf_file, rmf_file=rmf_file, srm_file=srm_file, srm_custom=srm_custom,
                              custom_channel_bins=custom_channel_bins, custom_photon_bins=custom_photon_bins, **kwargs)
 
-        self._construction_string_sunxspex = (f"Fitter({args}, pha_file={pha_file}, arf_file={arf_file}, rmf_file={rmf_file}, srm_file={srm_file}, "
-                                              f"srm_custom={srm_custom}, custom_channel_bins={custom_channel_bins}, custom_photon_bins={custom_photon_bins}, **{kwargs})")
+        self._construction_string_sunkit_spex = (f"Fitter({args}, pha_file={pha_file}, arf_file={arf_file}, rmf_file={rmf_file}, srm_file={srm_file}, "
+                                                 f"srm_custom={srm_custom}, custom_channel_bins={custom_channel_bins}, custom_photon_bins={custom_photon_bins}, **{kwargs})")
 
         self.loglikelihood = "cstat"
 
@@ -778,7 +778,7 @@ def del_photon_model(self, function_name):
             logger.indo(f"Model {function_name} removed.")
         else:
             logger.warning(
-                "Default models imported from sunkit_spex.sunxspex_fitting.photon_models_for_fitting are protected.")
+                "Default models imported from sunkit_spex.fitting_legacy.photon_models_for_fitting are protected.")
 
     def add_var(self, overwrite=False, quiet=False, **user_kwarg):
         """ Add user variable to fitting namespace.
@@ -4685,7 +4685,7 @@ def __setstate__(self, d):
 
     def __repr__(self):
         """Provide a representation to construct the class from scratch."""
-        return self._construction_string_sunxspex
+        return self._construction_string_sunkit_spex
 
     def __str__(self):
         """Provide a printable, user friendly representation of what the class contains."""

sunkit_spex/sunxspex_fitting/tests/test_fitter.py → sunkit_spex/fitting_legacy/tests/test_fitter.py

@@ -4,8 +4,8 @@
 import pytest
 from numpy.testing import assert_allclose
 
-from sunkit_spex.sunxspex_fitting.fitter import Fitter
-from sunkit_spex.sunxspex_fitting.instruments import CustomLoader, InstrumentBlueprint
+from sunkit_spex.fitting_legacy.fitter import Fitter
+from sunkit_spex.fitting_legacy.instruments import CustomLoader, InstrumentBlueprint
 
 rng = np.random.default_rng(2022)
 

sunkit_spex/sunxspex_fitting/tests/test_io.py → sunkit_spex/fitting_legacy/tests/test_io.py

@@ -2,7 +2,7 @@
 
 import numpy as np
 
-from sunkit_spex.sunxspex_fitting.io import (
+from sunkit_spex.fitting_legacy.io import (
     _read_arf,
     _read_pha,
     _read_rhessi_spec_file,

sunkit_spex/sunxspex_fitting/tests/test_likelihoods.py → sunkit_spex/fitting_legacy/tests/test_likelihoods.py

@@ -1,7 +1,7 @@
 import numpy as np
 from numpy.testing import assert_allclose
 
-from sunkit_spex.sunxspex_fitting.likelihoods import LogLikelihoods
+from sunkit_spex.fitting_legacy.likelihoods import LogLikelihoods
 
 
 def test_cstat():