Merge pull request #58 from ToFuProject/devel

Prepare 0.0.3

Author: Didou09

setup.py

@@ -175,9 +175,9 @@
     # of executable for the target platform.
     entry_points={
         'console_scripts': [
-            'spectrally-version=scripts.spectrallyversion:main',
-            'specrally-custom=scripts.spectrallycustom:main',
-            'spectrally=scripts.spectrally_bash:main',
+            'spectrally-version=spectrally.scripts.spectrallyversion:main',
+            'specrally-custom=spectrally.scripts.spectrallycustom:main',
+            'spectrally=spectrally.scripts.spectrally_bash:main',
         ],
     },
     # include_dirs=[np.get_include()],

spectrally/__init__.py

@@ -5,11 +5,13 @@
 import warnings
 
 
+from .version import __version__
 from ._class02_SpectralFit import SpectralFit as Collection
 from ._saveload import load
-from . import tests
 from ._class01_show import *
 from ._class01_display_models import *
+from . import tests
+from . import tutorials
 
 
 _PKG = 'spectrally'

spectrally/_class00_plot.py

@@ -267,7 +267,7 @@ def plot_axvlines(
     # if ne_scale is None:
         # ne_scale = 'log'
     # if Te_scale is None:
-        # Te_scale = 'linear'
+        # Te_scale = 'poly'
 
     # return
 
@@ -506,4 +506,4 @@ def plot_dominance_map(
         )
 
     return dax
-"""
+"""

spectrally/_class01_SpectralModel.py

@@ -61,15 +61,15 @@ def add_spectral_model(
                 'key': {'ref': k0, k1: [c0, c1], k2: [c0, c1]}
 
         Available function types for dmodel are:
-            - 'linear': typically a linear background
+            - 'poly': typically a polynomial background
             - 'exp': typically an exponential background
             - 'gauss': typically a doppler-broadened line
             - 'lorentz': ypically a natural-broadened line
             - 'pvoigt': typically a doppler-and-natural broadened line
 
         dconstraints holds a dict of constraints groups.
         Each group is a dict with a 'ref' variable
-        Other variables (keys) are compued as linear functions of 'ref'
+        Other variables (keys) are compued as poly functions of 'ref'
 
         Parameters
         ----------
@@ -202,6 +202,7 @@ def get_spectral_model_moments(
         key=None,
         key_data=None,
         lamb=None,
+        returnas=None,
     ):
         """
 
@@ -221,6 +222,10 @@ def get_spectral_model_moments(
             key to the data to be used as input for the model's free variables
         lamb:str or 1d np.ndarray, optional
             wavelenth vector to be used for computing limited integrals
+        returnas: str
+            Flag indicating whether to return dout as:
+                - 'dict_arrays': nested dict of {'ktype': {'kvar': array}}
+                - 'dict_varnames': dict of {'kfunc_var': values}
 
         Returns
         -------
@@ -234,6 +239,7 @@ def get_spectral_model_moments(
             key=key,
             key_data=key_data,
             lamb=lamb,
+            returnas=returnas,
         )
 
         return dout

spectrally/_class01_check_constraints.py

@@ -6,6 +6,7 @@
 """
 
 
+import copy
 import itertools as itt
 
 
@@ -148,6 +149,7 @@ def _check(
     # Format
     # ------------
 
+    dconstraints = copy.deepcopy(dconstraints)
     for k0, v0 in dconstraints.items():
         for k1, v1 in v0.items():
             if k1 != 'ref':

spectrally/_class01_check_model.py

@@ -101,11 +101,11 @@ def _dmodel_err(key, dmodel):
             pstr = ", ".join([f"'{tpar[0]}': {tpar[1]}" for tpar in lpar])
             stri = f"\t- 'f{ii}': " + "{" + f"'type': '{k0}', {pstr}" + "}"
 
-        if k0 == 'linear':
+        if k0 == 'poly':
             lstr.append("\t# background-oriented")
         elif k0 == 'gauss':
             lstr.append("\t# spectral lines-oriented")
-        elif k0 == 'pulse1':
+        elif k0 == 'pulse_exp':
             lstr.append("\t# pulse-oriented")
         lstr.append(stri)
 
@@ -183,7 +183,7 @@ def _check_dmodel(
         # check key
 
         if isinstance(k0, int):
-            if typ in ['linear', 'exp']:
+            if typ in ['poly', 'exp']:
                 k1 = f'bck{ibck}'
                 ibck += 1
             else:

spectrally/_class01_display_models.py

@@ -140,9 +140,9 @@ def _get_xx(xx, ftype):
     # set if None
     # -------------
 
-    lbck = ['linear', 'exp_lamb']
+    lbck = ['poly', 'exp_lamb']
     llines = ['gauss', 'lorentz', 'pvoigt', 'voigt']
-    lpulse = ['pulse1', 'pulse2', 'lognorm']
+    lpulse = ['pulse_exp', 'pulse_gauss', 'lognorm']
 
     if xx is None:
         if ftype in lbck + llines:
@@ -201,12 +201,13 @@ def _get_dpar_xfree(ftype, xx):
     # xfree
     # ---------------
 
-    if ftype == 'linear':
+    if ftype == 'poly':
 
-        a1 = -1/Dx
-        a0 = 2 - a1 * x0
+        a0 = 1
+        a1 = -0.2
+        a2 = -1
 
-        xfree = np.r_[a0, a1]
+        xfree = np.r_[a0, a1, a2]
 
     elif ftype == 'exp_lamb':
 
@@ -252,7 +253,7 @@ def _get_dpar_xfree(ftype, xx):
 
         xfree = np.r_[amp, vccos, sigma, gam]
 
-    elif ftype == 'pulse1':
+    elif ftype == 'pulse_exp':
 
         amp = 1
         t0 = 0.3
@@ -261,7 +262,7 @@ def _get_dpar_xfree(ftype, xx):
 
         xfree = np.r_[amp, t0, t_up, t_down]
 
-    elif ftype == 'pulse2':
+    elif ftype == 'pulse_gauss':
 
         amp = 1
         t0 = 0.3

spectrally/_class01_dparams.py

@@ -184,7 +184,7 @@ def _get_scale(
     # bck
     # ------------
 
-    if typ == 'linear':
+    if typ == 'poly':
 
         if var == 'c0':
             pass
@@ -614,4 +614,4 @@ def fit12d_dscales(dscales=None, dinput=None):
         indbs=dinput['valid']['indbs'],
     )
     return dscales
-"""
+"""