PPB: pip install path issue

ForMoSA/adapt/adapt_grid.py

@@ -2,7 +2,9 @@
 import numpy as np
 import xarray as xr
 import time
-import os
+import os, sys
+
+sys.path.insert(0, os.path.abspath('../'))
 
 from adapt.extraction_functions import adapt_model, decoupe
 

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

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 *

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

docs/_build/doctrees/nbsphinx/demoabpic.ipynb

@@ -0,0 +1,56 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# AB Pic demo"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    ".. toctree::\n",
+    "   :maxdepth: 2\n",
+    "   :titlesonly:\n",
+    "\n",
+    "   demo_basic.rst\n",
+    "\n",
+    "   tutorials/demo_basic.ipynb\n",
+    "\n",
+    "   :doc:`tutorials/demo_basic.ipynb`"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "exo_formosa_multi3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/_build/doctrees/nbsphinx/tutorials/demoabpic.ipynb

@@ -0,0 +1,60 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# demo AB Pic b\n",
+    "\n",
+    "\n",
+    "This tutorial is intended as a quick start. \n",
+    "You will use medium resolution VLT/SINFONI K-band data, published in `P. Palma-Bifani et al (2023) <https://www.aanda.org/articles/aa/pdf/2023/02/aa44294-22.pdf>`_.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    ".. toctree::\n",
+    "   :maxdepth: 2\n",
+    "   :titlesonly:\n",
+    "\n",
+    "   demo_basic.rst\n",
+    "\n",
+    "   tutorials/demo_basic.ipynb\n",
+    "\n",
+    "   :doc:`tutorials/demo_basic.ipynb`"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "exo_formosa_multi3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: e37828ad0a669d84937aa2fd2f827506
+config: 3d69bd81622fe4392ef94600d12c6fdb
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_modules/index.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" /> 

docs/_build/html/_sources/demo.rst.txt

@@ -28,7 +28,7 @@ Atmospheric grids
 
 This is the list of the publically available atmospheric grids which we have formated for ForMoSA. 
 
-You need to download the grid you want to use by clicking over the name and save it inside the ``atm_grids/`` subfolder.
+Download the grid you want to use by clicking over it's name. Ideally, save it inside the ``atm_grids/`` subdirectory.
 
 * `ATMO native <https://drive.google.com/file/d/1S1dcBD7UiuUCZIcNBNnJi6LMymrnkagM/view?usp=share_link>`_ from `M.W. Phillips et al. 2020 <https://ui.adsabs.harvard.edu/abs/2020A%26A...637A..38P/abstract>`_
 
@@ -39,7 +39,13 @@ You need to download the grid you want to use by clicking over the name and save
 * `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 here: :doc:`atm_grids`
+Learn more at:
+
+.. toctree::
+   :maxdepth: 1
+
+   atm_grids
+
 
 
 
@@ -49,9 +55,8 @@ List of tutorials:
 
 .. toctree::
    :maxdepth: 1
-   :caption: Demo AB Pic b
 
-   demoabpic.ipynb
+   tutorials/demoabpic
 ..
    demo_mosaic.rst
    demo_pymultinest.rst

docs/_build/html/_sources/demo_basic.rst.txt

@@ -4,4 +4,10 @@ demo AB Pic b
 =============
 
 This tutorial is intended as a quick start. 
-You will use medium resolution VLT/SINFONI K-band data, published in `P. Palma-Bifani et al (2023) <https://www.aanda.org/articles/aa/pdf/2023/02/aa44294-22.pdf>`_.
+You will use medium resolution VLT/SINFONI K-band data, published in `P. Palma-Bifani et al (2023) <https://www.aanda.org/articles/aa/pdf/2023/02/aa44294-22.pdf>`_.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   demoabpic

docs/_build/html/_sources/demoabpic.ipynb.txt

@@ -0,0 +1,56 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# AB Pic demo"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    ".. toctree::\n",
+    "   :maxdepth: 2\n",
+    "   :titlesonly:\n",
+    "\n",
+    "   demo_basic.rst\n",
+    "\n",
+    "   tutorials/demo_basic.ipynb\n",
+    "\n",
+    "   :doc:`tutorials/demo_basic.ipynb`"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "exo_formosa_multi3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/_build/html/_sources/tutorials/demoabpic.ipynb.txt

@@ -0,0 +1,60 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# demo AB Pic b\n",
+    "\n",
+    "\n",
+    "This tutorial is intended as a quick start. \n",
+    "You will use medium resolution VLT/SINFONI K-band data, published in `P. Palma-Bifani et al (2023) <https://www.aanda.org/articles/aa/pdf/2023/02/aa44294-22.pdf>`_.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    ".. toctree::\n",
+    "   :maxdepth: 2\n",
+    "   :titlesonly:\n",
+    "\n",
+    "   demo_basic.rst\n",
+    "\n",
+    "   tutorials/demo_basic.ipynb\n",
+    "\n",
+    "   :doc:`tutorials/demo_basic.ipynb`"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "exo_formosa_multi3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}