pyratbay 2.0.0b2__tar.gz → 2.0.0b3__tar.gz

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/CHANGELOG.txt

@@ -9514,3 +9514,119 @@ to allow renaming the post-process outputs.
 
 Updated version to 2.0.0b2
 
+
+*****  Di 22 Okt 2024 09:47:09 CEST  *****
+
+Corrected np.trapz() to np.trapezoid() to avoid deprecation warning.
+
+*****
+
+Removed numpy.core.numeric isscalar imports.
+
+*****
+
+Corrected np.in1d() to np.isin().
+
+
+*****  Di 05 Nov 2024 11:22:31 CET  *****
+
+Updated scipy requirement compatible with Numpy2.0.
+
+*****
+
+Updated docs theme, switched from read_the_docs to furo.
+
+Added docs/custom_style.py file.
+
+
+*****  Do 07 Nov 2024 11:47:50 CET  *****
+
+Added water isotopes for 228 and 227.
+
+*****
+
+Refactored tips() function to extend partition functions domain
+when some isotopes have higher temperature ranges.
+This is done with a cubic spline. Before the code was cutting off
+at the lowest maximum temperature.
+
+These are the affected molecules:
+H2O
+[5000 5000 5000 5000 5000 5000 6000 6000 6000]
+CO2 
+[5000 5000 3500 3500 3500 3500 5000 3500 5000 5000 3500 5000 5000]
+CH4
+[3500 3500 4500 3500]
+NO2
+[3500 1000]
+OH
+[9000 5000 5000]
+H2CO
+[3500 5000 5000]
+H2S
+[4000 5000 5000]
+
+****
+
+Refactored io.write_spectrum() to deal with the wavelength units
+always in microns. Removed wlunits argument.
+Added 'eclipse' type.
+
+Refactored io.read_spectrum() removing wlunits guessing.
+
+Refactored io.write_observations() to enable combining tophat
+and tabulated files as passband functions.
+
+*****
+
+Updated tests in test_io.py.
+test_read_write_spectrum
+test_read_write_spectrum_filter
+test_read_isotopes
+test_write_observations_mix_bandpass_tophats
+
+*****
+
+In spectrum.bin_spectrum() replaced ignore_gaps bool argument
+with gaps string argument.
+Allowed to keep the default behavior for gaps (raise Error),
+ignore them (keep nans), or patch with a linear interpolation.
+
+Updated docs and tests.
+
+*****
+
+Added wl variable to pyrat.spec, to return the wavelength array
+in microns.
+
+
+*****  Fr 22 Nov 2024 18:17:51 CET  *****
+
+Refactored PassBand() and Tophat() classes.
+Added counting_type argument and variable to specify whether the
+response function is per photon (default) or per energy.
+Re-named __call__() method to set_sampling().
+Added integrate() method to do the band_integration in-house.
+Now __call__() method points to intgrate().
+Added arguments to set the wn/wl sampling at initialization.
+Updated docstrings and tests.
+
+*****
+
+Added FILTERS constant, path pointing directly to the filters folder
+Added cheops and tess passbands filters.
+Renamed spitzer_irac?_sa.dat filters to spitzer_irac?.dat
+
+*****
+
+Updated tests on partition functions/isotopes according to latest
+changes.
+
+
+*****  Mo 25 Nov 2024 14:54:48 CET  *****
+
+Refactored PassBand() and Tophat() classes adding self.height
+and having self.response normalized to max(response)=1.
+Added passband docs to the cookbooks.
+Added kepler.dat passbands.
+

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyratbay
-Version: 2.0.0b2
+Version: 2.0.0b3
 Summary: Python Radiative Transfer in a Bayesian Framework
 Author-email: Patricio Cubillos <patricio.cubillos@oeaw.ac.at>
 License:                     GNU GENERAL PUBLIC LICENSE
@@ -348,7 +348,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: numpy>=1.23.5
-Requires-Dist: scipy>=1.5.4
+Requires-Dist: scipy>=1.13.0
 Requires-Dist: matplotlib>=3.3.4
 Requires-Dist: mc3>=3.2.0
 Requires-Dist: chemcat>=0.3.8

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/docs/atm_tutorial.rst

@@ -90,7 +90,7 @@ parameter (``tpars``): the temperature (:math:`T_0`) at all layers.
 Here is an example of an isothermal atmosphere configuration file:
 
 .. literalinclude:: ../examples/tutorial/pt_isothermal.cfg
-    :caption: pt_isothermal.cfg
+    :caption: File: pt_isothermal.cfg
 
 Guillot profile
 ^^^^^^^^^^^^^^^
@@ -126,6 +126,7 @@ Here is an example of a ``guillot`` atmosphere configuration file
 <https://github.com/pcubillos/pyratbay/blob/master/examples/tutorial/pt_guillot.cfg>`_):
 
 .. literalinclude:: ../examples/tutorial/pt_guillot.cfg
+    :caption: File: pt_guillot.cfg
 
 
 Madhu profile

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/docs/conf.py

@@ -22,7 +22,7 @@ import re
 from datetime import date
 
 # Do not add path to the package (following example from astropy).
-#sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('.'))
 import pyratbay as pb
 
 # -- General configuration ------------------------------------------------
@@ -58,7 +58,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'Pyrat Bay'
-copyright = u'2016-{:d}, Patricio Cubillos'.format(date.today().year)
+copyright = f'2016-{date.today().year:d}, Patricio Cubillos'
 author = u'Patricio Cubillos'
 
 # The version info for the project you're documenting, acts as replacement for
@@ -103,7 +103,8 @@ exclude_patterns = ['_build', '.DS_Store']
 #show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+#pygments_style = 'sphinx'
+pygments_style = 'custom_style.CustomStyle'
 
 # A list of ignored prefixes for module index sorting.
 #modindex_common_prefix = []
@@ -119,12 +120,17 @@ pygments_style = 'sphinx'
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'furo'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+html_theme_options = {
+    "sidebar_hide_name": False,
+    "light_css_variables": {
+        "color-background-border": "#d0d0d0",
+    },
+}
 
 # Add any paths that contain custom themes here, relative to this directory.
 #html_theme_path = []
@@ -149,6 +155,7 @@ html_favicon = 'figures/favicon.ico'
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+html_css_files = ["custom.css"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -164,7 +171,7 @@ html_static_path = ['_static']
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'*':['globaltoc.html', 'relations.html', 'searchbox.html']}
+#html_sidebars = {'*':['globaltoc.html', 'relations.html', 'searchbox.html']}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

pyratbay-2.0.0b3/docs/custom_style.py

@@ -0,0 +1,19 @@
+from pygments.style import Style
+from pygments.styles.friendly import FriendlyStyle
+from pygments.token import Token
+
+
+class CustomStyle(Style):
+    styles = FriendlyStyle.styles.copy()
+
+    background_color = "#f0f8ff"
+    background_color = "#f0f2f6"
+    styles[Token.Background] = background_color
+
+    comment = "italic #bb3322"
+    styles[Token.Comment] = comment
+    styles[Token.Comment] = comment
+    styles[Token.Comment.Multiline] = comment
+    styles[Token.Comment.Preproc] = comment
+    styles[Token.Comment.Single] = comment
+    styles[Token.Comment.Special] = comment

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/docs/docs_requirements.txt

@@ -1,4 +1,4 @@
-sphinx-rtd-theme>=2.0.0
+furo==2023.9.10
 nbsphinx
 sphinx_copybutton
 ipython>=8.17

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/docs/getstarted.rst

@@ -71,19 +71,8 @@ through the ``Pyrat Bay`` sub modules (see :ref:`API`).
 System Requirements
 -------------------
 
-Pyrat-Bay (version 1.0+) has been extensively tested to work on
-Unix/Linux and OS X machines, with the following software
-requirements:
-
-* Python >= 3.6
-* Numpy >= 1.8.1
-* Scipy >= 0.13.3
-* Matplotlib >= 1.3.1
-* Sympy >= 0.7.6
-* mc3 >= 3.0.7
-
-``Pyrat Bay`` may work with previous software versions; however, we do
-not guarantee nor provide support for that.
+Pyrat-Bay (version 2.0+) has been extensively tested to work on
+Unix/Linux and OS X machines and is available for Python 3.9+.
 
 .. _install:
 

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/pyproject.toml

@@ -21,7 +21,7 @@ authors = [
 
 dependencies = [
     'numpy>=1.23.5',
-    'scipy>=1.5.4',
+    'scipy>=1.13.0',
     'matplotlib>=3.3.4',
     'mc3>=3.2.0',
     'chemcat>=0.3.8',

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/pyratbay/atmosphere/tmodels/tmodels.py

@@ -13,7 +13,6 @@ import functools
 from collections.abc import Iterable
 
 import numpy as np
-from numpy.core.numeric import isscalar
 from scipy.ndimage import gaussian_filter1d
 
 from ... import constants as pc
@@ -151,7 +150,7 @@ class Guillot():
 
         if gravity is None:
             gravity = np.tile(1.0, len(pressure))
-        elif isscalar(gravity):
+        elif np.isscalar(gravity):
             gravity = np.tile(gravity, len(pressure))
         self.pressure = np.asarray(pressure, float)
         self.gravity = np.asarray(gravity, float)

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/pyratbay/constants/astrophysical_constants.py

@@ -54,7 +54,7 @@ __all__ = [
 import scipy.constants as sc
 
 """
-Constant values used in the pyrat project.
+Astrophysical constant values used in the pyrat project.
 
 Notes
 -----

{pyratbay-2.0.0b2 → pyratbay-2.0.0b3}/pyratbay/constants/code_constants.py

@@ -1,8 +1,9 @@
-# Copyright (c) 2021-2023 Patricio Cubillos
+# Copyright (c) 2021-2024 Patricio Cubillos
 # Pyrat Bay is open-source software under the GPL-2.0 license (see LICENSE)
 
 __all__ = [
     'ROOT',
+    'FILTERS',
     # Other constants
     'tlireclen',
     'dreclen',
@@ -30,11 +31,6 @@ import os
 
 """
 Constant values used in the pyrat project.
-
-Notes
------
-  Solar system constants come from:
-  http://nssdc.gsfc.nasa.gov/planetary/factsheet/
 """
 
 # TLI record lengths:
@@ -45,6 +41,7 @@ sreclen = 2  # Short byte length
 
 # Paths:
 ROOT = os.path.realpath(os.path.dirname(__file__) + '/../..') + '/'
+FILTERS = f'{ROOT}pyratbay/data/filters/'
 
 
 # Available line-transition databases:

pyratbay-2.0.0b3/pyratbay/data/filters/cheops.dat

@@ -0,0 +1,153 @@
+# wavelength response_function
+# um         electrons/photon 
+0.3501 0.0
+0.355  0.0027411990927
+0.360  0.00797897050977
+0.365  0.0195086216784
+0.370  0.0411218614515
+0.375  0.0752118221188
+0.380  0.123726031915
+0.385  0.182990904748
+0.390  0.235613083186
+0.395  0.27508727386
+0.400  0.310371291
+0.405  0.350973617968
+0.410  0.396183434394
+0.415  0.440679886285
+0.420  0.474983437512
+0.425  0.509118023539
+0.430  0.546594053869
+0.435  0.580665053284
+0.440  0.61231785024
+0.445  0.640825753382
+0.450  0.66638775439
+0.455  0.685952239434
+0.460  0.702357113621
+0.465  0.718952729781
+0.470  0.736597290741
+0.475  0.751432680246
+0.480  0.768113554576
+0.485  0.786228721503
+0.490  0.804713617615
+0.495  0.823763750283
+0.500  0.841738920542
+0.505  0.856601897198
+0.510  0.869511799782
+0.515  0.880924406794
+0.520  0.889500475679
+0.525  0.895731811957
+0.530  0.899624514302
+0.535  0.901117139234
+0.540  0.900657978882
+0.545  0.899288619291
+0.550  0.897535929378
+0.555  0.894691482043
+0.560  0.892322051731
+0.565  0.890306791982
+0.570  0.887238670023
+0.575  0.88472795775
+0.580  0.882811041004
+0.585  0.880514671386
+0.590  0.878080505701
+0.595  0.875861249406
+0.600  0.87402389494
+0.605  0.872220605615
+0.610  0.870136673945
+0.615  0.867120264899
+0.620  0.862993567457
+0.625  0.857295360164
+0.630  0.850586682705
+0.635  0.843122325548
+0.640  0.834538915009
+0.645  0.824113174223
+0.650  0.81331517441
+0.655  0.802664820696
+0.660  0.792245951224
+0.665  0.781135803582
+0.670  0.769618240135
+0.675  0.758664016809
+0.680  0.748350955321
+0.685  0.738277172433
+0.690  0.727460099003
+0.695  0.715028696896
+0.700  0.702650380513
+0.705  0.690612721557
+0.710  0.679047806526
+0.715  0.668514894715
+0.720  0.658375479632
+0.725  0.648619084352
+0.730  0.639158886067
+0.735  0.629901634372
+0.740  0.621610663174
+0.745  0.614327136495
+0.750  0.6069280875
+0.755  0.599500351801
+0.760  0.592278885904
+0.765  0.585623364451
+0.770  0.579097967609
+0.775  0.573161008124
+0.780  0.567412562313
+0.785  0.561770681617
+0.790  0.555686787498
+0.795  0.548937498336
+0.800  0.541756614175
+0.805  0.532442583575
+0.810  0.52226666243
+0.815  0.512886870883
+0.820  0.504241679007
+0.825  0.495630092675
+0.830  0.486907147865
+0.835  0.476977358928
+0.840  0.465827335946
+0.845  0.448459054657
+0.850  0.433570394249
+0.855  0.421349649078
+0.860  0.409483676347
+0.865  0.396452603181
+0.870  0.382589819691
+0.875  0.368465826954
+0.880  0.354744191751
+0.885  0.340886057712
+0.890  0.326423879478
+0.895  0.311525640326
+0.900  0.297007900727
+0.905  0.282786602612
+0.910  0.268656481576
+0.915  0.254611619835
+0.920  0.240431772782
+0.925  0.226229053501
+0.930  0.21246851051
+0.935  0.199976656786
+0.940  0.187456102885
+0.945  0.174880426118
+0.950  0.162404822193
+0.955  0.150013817103
+0.960  0.137594721948
+0.965  0.125102401373
+0.970  0.115122573749
+0.975  0.106121364121
+0.980  0.0971433084897
+0.985  0.0881597827042
+0.990  0.0795878492286
+0.995  0.072147468064
+1.000  0.0646671832343
+1.005  0.0571607837249
+1.010  0.0496324506148
+1.015  0.0429475053814
+1.020  0.0386065204087
+1.025  0.0342479284026
+1.030  0.0298839952236
+1.035  0.0267801891662
+1.040  0.0237630148355
+1.045  0.0207466360127
+1.050  0.0177228596147
+1.055  0.0146842542793
+1.060  0.012042030927
+1.065  0.0120386065349
+1.070  0.0120346454471
+1.075  0.012028071
+1.080  0.012017306142
+1.085  0.0120030919306
+1.090  0.0119867344622
+1.095  0.0119692066053
+1.100  0.0