PPB: rtd added .ipynb

exoAtmospheres · Aug 6, 2024 · dc323e0 · dc323e0
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diff --git a/ForMoSA.egg-info/PKG-INFO b/ForMoSA.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ForMoSA
-Version: 1.1.2
+Version: 1.1.3
 Summary: ForMoSA: Forward Modeling Tool for Spectral Analysis
 Home-page: https://github.com/exoAtmospheres/ForMoSA
 Author: P. Palma-Bifani, S. Petrus, M. Ravet, A. Denis, M. Bonnefoy, G. Chauvin

diff --git a/ForMoSA/__init__.py b/ForMoSA/__init__.py
@@ -1,5 +1,5 @@
 import os
 
-__version__ = "1.1.2"
+__version__ = "1.1.3"
 
 __all__ = ['adapt', 'nested_sampling','plotting']
diff --git a/build/lib/ForMoSA/__init__.py b/build/lib/ForMoSA/__init__.py
@@ -1,5 +1,5 @@
 import os
 
-__version__ = "1.1.2"
+__version__ = "1.1.3"
 
 __all__ = ['adapt', 'nested_sampling','plotting']
diff --git a/build/lib/ForMoSA/adapt/adapt_grid.py b/build/lib/ForMoSA/adapt/adapt_grid.py
diff --git a/build/lib/ForMoSA/adapt/adapt_obs_mod.py b/build/lib/ForMoSA/adapt/adapt_obs_mod.py
@@ -4,6 +4,8 @@
 import xarray as xr
 from scipy.interpolate import interp1d
 
+sys.path.insert(0, os.path.abspath('../'))
+
 from adapt.extraction_functions import extract_observation
 from adapt.adapt_grid import adapt_grid
 from main_utilities import diag_mat

diff --git a/build/lib/ForMoSA/nested_sampling/nested_sampling.py b/build/lib/ForMoSA/nested_sampling/nested_sampling.py
@@ -1,11 +1,13 @@
 import numpy as np
-import os
+import os, sys
 import glob
 import nestle
 import time
 import xarray as xr
 import pickle
 
+sys.path.insert(0, os.path.abspath('../'))
+
 from nested_sampling.nested_modif_spec import modif_spec
 from nested_sampling.nested_prior_function import uniform_prior, gaussian_prior
 from nested_sampling.nested_logL_functions import *

diff --git a/build/lib/ForMoSA/plotting/plotting_class.py b/build/lib/ForMoSA/plotting/plotting_class.py
@@ -1,6 +1,6 @@
 
 from __future__ import print_function, division
-import os, glob
+import os, glob, sys
 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.backends.backend_pdf import PdfPages
@@ -10,6 +10,8 @@
 import pickle
 from tqdm import tqdm
 
+sys.path.insert(0, os.path.abspath('../'))
+
 # Import ForMoSA
 from main_utilities import GlobFile
 from nested_sampling.nested_modif_spec import modif_spec

diff --git a/dist/ForMoSA-1.1.2-py3-none-any.whl b/dist/ForMoSA-1.1.2-py3-none-any.whl
diff --git a/dist/ForMoSA-1.1.2.tar.gz b/dist/ForMoSA-1.1.2.tar.gz
diff --git a/dist/ForMoSA-1.1.3-py3-none-any.whl b/dist/ForMoSA-1.1.3-py3-none-any.whl
diff --git a/dist/ForMoSA-1.1.3.tar.gz b/dist/ForMoSA-1.1.3.tar.gz
diff --git a/docs/_build/doctrees/atm_grids.doctree b/docs/_build/doctrees/atm_grids.doctree
diff --git a/docs/_build/doctrees/demo.doctree b/docs/_build/doctrees/demo.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/tutorials/atmospheric_grid_info.ipynb → ...inx/tutorials/atmospheric_grid_info.ipynb b/docs/tutorials/atmospheric_grid_info.ipynb → ...inx/tutorials/atmospheric_grid_info.ipynb
@@ -81,7 +81,6 @@
    "pygments_lexer": "ipython3",
    "version": "3.7.13"
   },
-  "orig_nbformat": 4,
   "vscode": {
    "interpreter": {
     "hash": "9aec1e17db1a1c759b18bf85d14c335cdcfb4080f740d60b236f2747bc3cb68f"

diff --git a/docs/_build/doctrees/nbsphinx/tutorials/demoabpic.ipynb b/docs/_build/doctrees/nbsphinx/tutorials/demoabpic.ipynb
diff --git a/docs/_build/doctrees/nbsphinx/tutorials/exorem_info.ipynb b/docs/_build/doctrees/nbsphinx/tutorials/exorem_info.ipynb
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_demoabpic_11_1.png b/docs/_build/doctrees/nbsphinx/tutorials_demoabpic_11_1.png
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_demoabpic_13_2.png b/docs/_build/doctrees/nbsphinx/tutorials_demoabpic_13_2.png
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_demoabpic_15_1.png b/docs/_build/doctrees/nbsphinx/tutorials_demoabpic_15_1.png
diff --git a/docs/_build/doctrees/nbsphinx/tutorials_exorem_info_5_0.png b/docs/_build/doctrees/nbsphinx/tutorials_exorem_info_5_0.png
diff --git a/docs/_build/doctrees/tutorials/atmospheric_grid_info.doctree b/docs/_build/doctrees/tutorials/atmospheric_grid_info.doctree
diff --git a/docs/_build/doctrees/tutorials/demoabpic.doctree b/docs/_build/doctrees/tutorials/demoabpic.doctree
diff --git a/docs/_build/doctrees/tutorials/exorem_info.doctree b/docs/_build/doctrees/tutorials/exorem_info.doctree
diff --git a/docs/_build/html/_images/tutorials_demoabpic_11_1.png b/docs/_build/html/_images/tutorials_demoabpic_11_1.png
diff --git a/docs/_build/html/_images/tutorials_demoabpic_13_2.png b/docs/_build/html/_images/tutorials_demoabpic_13_2.png
diff --git a/docs/_build/html/_images/tutorials_demoabpic_15_1.png b/docs/_build/html/_images/tutorials_demoabpic_15_1.png
diff --git a/docs/_build/html/_images/tutorials_exorem_info_5_0.png b/docs/_build/html/_images/tutorials_exorem_info_5_0.png
diff --git a/docs/_build/html/_modules/ForMoSA/adapt/adapt_grid.html b/docs/_build/html/_modules/ForMoSA/adapt/adapt_grid.html
@@ -18,6 +18,7 @@
         <script src="../../../_static/documentation_options.js?v=51b770b3"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
@@ -42,10 +43,10 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">DEMO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../api.html">ForMoSA API</a></li>
 </ul>
 
@@ -78,7 +79,9 @@ <h1>Source code for ForMoSA.adapt.adapt_grid</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">xarray</span> <span class="k">as</span> <span class="nn">xr</span>
 <span class="kn">import</span> <span class="nn">time</span>
-<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
+
+<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;../&#39;</span><span class="p">))</span>
 
 <span class="kn">from</span> <span class="nn">adapt.extraction_functions</span> <span class="kn">import</span> <span class="n">adapt_model</span><span class="p">,</span> <span class="n">decoupe</span>
 

diff --git a/docs/_build/html/_modules/ForMoSA/adapt/adapt_obs_mod.html b/docs/_build/html/_modules/ForMoSA/adapt/adapt_obs_mod.html
@@ -18,6 +18,7 @@
         <script src="../../../_static/documentation_options.js?v=51b770b3"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
@@ -42,10 +43,10 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">DEMO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../api.html">ForMoSA API</a></li>
 </ul>
 
@@ -80,6 +81,8 @@ <h1>Source code for ForMoSA.adapt.adapt_obs_mod</h1><div class="highlight"><pre>
 <span class="kn">import</span> <span class="nn">xarray</span> <span class="k">as</span> <span class="nn">xr</span>
 <span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">interp1d</span>
 
+<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;../&#39;</span><span class="p">))</span>
+
 <span class="kn">from</span> <span class="nn">adapt.extraction_functions</span> <span class="kn">import</span> <span class="n">extract_observation</span>
 <span class="kn">from</span> <span class="nn">adapt.adapt_grid</span> <span class="kn">import</span> <span class="n">adapt_grid</span>
 <span class="kn">from</span> <span class="nn">main_utilities</span> <span class="kn">import</span> <span class="n">diag_mat</span>

diff --git a/docs/_build/html/_modules/ForMoSA/nested_sampling/nested_sampling.html b/docs/_build/html/_modules/ForMoSA/nested_sampling/nested_sampling.html
@@ -18,6 +18,7 @@
         <script src="../../../_static/documentation_options.js?v=51b770b3"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
@@ -42,10 +43,10 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">DEMO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../api.html">ForMoSA API</a></li>
 </ul>
 
@@ -75,13 +76,15 @@
 
   <h1>Source code for ForMoSA.nested_sampling.nested_sampling</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">glob</span>
 <span class="kn">import</span> <span class="nn">nestle</span>
 <span class="kn">import</span> <span class="nn">time</span>
 <span class="kn">import</span> <span class="nn">xarray</span> <span class="k">as</span> <span class="nn">xr</span>
 <span class="kn">import</span> <span class="nn">pickle</span>
 
+<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;../&#39;</span><span class="p">))</span>
+
 <span class="kn">from</span> <span class="nn">nested_sampling.nested_modif_spec</span> <span class="kn">import</span> <span class="n">modif_spec</span>
 <span class="kn">from</span> <span class="nn">nested_sampling.nested_prior_function</span> <span class="kn">import</span> <span class="n">uniform_prior</span><span class="p">,</span> <span class="n">gaussian_prior</span>
 <span class="kn">from</span> <span class="nn">nested_sampling.nested_logL_functions</span> <span class="kn">import</span> <span class="o">*</span>

diff --git a/docs/_build/html/_modules/ForMoSA/plotting/plotting_class.html b/docs/_build/html/_modules/ForMoSA/plotting/plotting_class.html
@@ -18,6 +18,7 @@
         <script src="../../../_static/documentation_options.js?v=51b770b3"></script>
         <script src="../../../_static/doctools.js?v=9a2dae69"></script>
         <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
@@ -42,10 +43,10 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">DEMO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../demo.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../api.html">ForMoSA API</a></li>
 </ul>
 
@@ -76,7 +77,7 @@
   <h1>Source code for ForMoSA.plotting.plotting_class</h1><div class="highlight"><pre>
 <span></span>
 <span class="kn">from</span> <span class="nn">__future__</span> <span class="kn">import</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">division</span>
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">glob</span>
+<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">glob</span><span class="o">,</span> <span class="nn">sys</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">from</span> <span class="nn">matplotlib.backends.backend_pdf</span> <span class="kn">import</span> <span class="n">PdfPages</span>
@@ -86,6 +87,8 @@ <h1>Source code for ForMoSA.plotting.plotting_class</h1><div class="highlight"><
 <span class="kn">import</span> <span class="nn">pickle</span>
 <span class="kn">from</span> <span class="nn">tqdm</span> <span class="kn">import</span> <span class="n">tqdm</span>
 
+<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;../&#39;</span><span class="p">))</span>
+
 <span class="c1"># Import ForMoSA</span>
 <span class="kn">from</span> <span class="nn">main_utilities</span> <span class="kn">import</span> <span class="n">GlobFile</span>
 <span class="kn">from</span> <span class="nn">nested_sampling.nested_modif_spec</span> <span class="kn">import</span> <span class="n">modif_spec</span>

diff --git a/docs/_build/html/_sources/atm_grids.rst.txt b/docs/_build/html/_sources/atm_grids.rst.txt
@@ -1,4 +1,9 @@
 .. _atm_grids:
 
 Atmospheric grids
-=================
+=================
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorials/exorem_info.ipynb
diff --git a/docs/_build/html/_sources/demo.rst.txt b/docs/_build/html/_sources/demo.rst.txt
@@ -39,12 +39,12 @@ Download the grid you want to use by clicking over it's name. Ideally, save it i
 * `ExoREM native <https://drive.google.com/file/d/1k9SQjHLnMCwmGOHtraRnhCgiZ1-4J3Wk/view?usp=share_link>`_ from `B. Charnay et al. 2018 <https://ui.adsabs.harvard.edu/abs/2018ApJ...854..172C/abstract>`_
 
 
-Learn more at:
+Learn more about:
 
 .. toctree::
    :maxdepth: 1
 
-   atm_grids
+   tutorials/exorem_info.ipynb
 
 
 

diff --git a/DEMO/inputs/atmospheric_grid_info.ipynb → ...tutorials/atmospheric_grid_info.ipynb.txt b/DEMO/inputs/atmospheric_grid_info.ipynb → ...tutorials/atmospheric_grid_info.ipynb.txt