Documentation fix

docs/docsfordocs.rst

@@ -0,0 +1,69 @@
+1) index.rst : main file / Home page of readthedocs.
+    Must cointain all the other .rst files in the toctrees!!!
+    eg. : .. toctree::
+             :hidden:
+             :maxdepth: 6
+             :caption: tutorials based on gui
+   
+             gui (file)
+             rvs (file)
+             transit (file)
+             rvtran (file)
+             otbfpu (file)
+             stability (file)
+
+ Each toctree is a new section on the Sphinx Template.
+
+2) All the .rst files contained in a toctree must start with
+   eg. for gui.rst file 
+       .. _gui:
+       (.. _filename:)
+   in order to be linked with the toctree!!!
+
+3) The headline of a document must be underlined with ... !!!
+   eg. in gui.rst file
+       GUI Layout
+       ..........
+
+    and each sub-header must be underlined with --- or === !!
+    eg. in gui.rst file
+        Data area
+        ---------
+
+4) Insert a picture/gif file
+   eg. in gui.rst file
+       .. figure:: /images/homepage.png
+
+          (comments)
+
+5) Bold words with the symbol **
+   eg. **Exostriker** 
+
+6) Emphasis words with the symbol *
+   eg. *Exostriker*
+
+7) Superscripts
+   eg. χ\ :sup:`2`: chi-squared
+
+8) Subscripts
+   eg. a\ :sub:`pl`\ /(divided) R\ :sub:`*`\ : planet semimajor axis in units of stellar radius.
+
+9) Add extra lines to seperate paragraphs with the symbol --- 
+   eg. in gui.rst file
+       ----------------------------------------------------------------------------------------------------------
+
+10) Add hyperlinks 
+    eg. in gui.rst file
+        For more information visit `pyqtgraph documentation`_.
+
+        .. _pyqtgraph documentation : https://pyqtgraph.readthedocs.io/en/latest/index.html
+
+11) Bullet point with the symbol *
+    eg. in gui.rst file
+       * Stdout/Stderr
+
+
+For more info check links : 1) https://docutils.sourceforge.io/docs/ref/rst/roles.html#customization
+2) https://docutils.sourceforge.io/docs/ref/doctree.html#element-hierarchy
+3) https://docutils.sourceforge.io/docs/ref/rst/directives.html#admonitions
+4) https://docutils.sourceforge.io/docs/ref/rst/restructuredtext.html#indentation

docs/source/credits.rst

@@ -20,55 +20,64 @@ If you made the use of The Exo-Striker for your paper, I would appreciate it if
 
 * The AMD stability check function was donated by **Stefan Dreizler** (IAG, Germany). 
 
-The Exo-Striker relies on many open-source packages, which if you had made the use of (some of) them while working with the tool, you should acknowledge too. (It is your responsibility to find the correct references in the literature):
+The Exo-Striker relies on many open-source packages, which if you had made the use of 
+(some of) them while working with the tool, you should acknowledge too. (It is your responsibility
+to find the correct references in the literature):
 
+* The interactive plotting is done with a custom version of the "`pyqtgraph`_".
 
+.. _pyqtgraph: http://www.pyqtgraph.org/
 
+* "GLS" and "MLP" periodograms are taken from `Mathias Zechmeister's`_ repo. 
 
-* The interactive plotting is done with a custom version of the "pyqtgraph": 
+.. _Mathias Zechmeister's:  https://github.com/mzechmeister/python
 
-http://www.pyqtgraph.org/
+* Transit least squares is taken from "`TLS`_" 
 
-* "GLS" and "MLP" periodograms are taken from **Mathias Zechmeister's** repo: 
+.. _TLS: https://github.com/hippke/tls
 
-https://github.com/mzechmeister/python
-
-* "TLS" is taken from: 
-
-https://github.com/hippke/tls
-
-* The transit modeling is done with "batman":
+* The transit modeling is done with "`batman`_".
 
-https://github.com/lkreidberg/batman
+.. _batman: https://github.com/lkreidberg/batman
 
-* MCMC sampling is done with "emcee": 
+* MCMC sampling is done with "`emcee`_".
 
-https://github.com/dfm/emcee
+.. _emcee: https://github.com/dfm/emcee
 
-* Nested Sampling is done with "dynesty": 
+* Nested Sampling is done with "`dynesty`_".
 
-https://github.com/joshspeagle/dynesty
+.. _dynesty: https://github.com/joshspeagle/dynesty
 
-* TTV models are adopted from "TTVfast-python":
+* TTV models are adopted from "`TTVfast-python`_".
 
-https://github.com/mindriot101/ttvfast-python
+.. _TTVfast-python: https://github.com/mindriot101/ttvfast-python
 
-* The "Text editor" used in the tool is a hack between "Megasolid Idiom" 
-  and "PyEdit2":
+* The "Text editor" used in the tool is a hack between "`Megasolid Idiom`_" 
+  and "`PyEdit2`_".
 
-https://github.com/mfitzp/15-minute-apps/tree/master/wordprocessor
+.. _Megasolid Idiom: https://github.com/mfitzp/15-minute-apps/tree/master/wordprocessor
 
-https://github.com/Axel-Erfurt/PyEdit2'
+.. _PyEdit2: https://github.com/Axel-Erfurt/PyEdit2'
 
-* N-body tests are performed using a custom version of the "Swift" N-body library,
+* N-body tests are performed using a custom version of the "`Swift`_" N-body library,
   modified by **Man Hoi Lee** (HKU) and **Trifon Trifonov** (MPIA).
 
-https://www.boulder.swri.edu/~hal/swift.html
+.. _Swift: https://www.boulder.swri.edu/~hal/swift.html
 
 
 * Additionally, the Exo-Striker uses many "standard" Python libraries like 
   "PyQt5", "matplotlib", "numpy", "scipy", "dill", "Jupyter", "qtconsole",
   and more.
 
+* The Exo-Striker project was inspired by the "`Systemic project`_".
+
+.. _Systemic project: http://www.stefanom.org/systemic/
+
+Scientific papers which one way or another made the use of the Exo-Striker (to my knowledge):
+
+`Check in ADS`_
+
+.. _Check in ADS : https://ui.adsabs.harvard.edu/abs/2019ascl.soft06004T/citations
+
 
 

docs/source/gui.rst

@@ -5,7 +5,7 @@ GUI Layout
 
 Before starting the tutorials, it is kind to familiarize yourself with the
 basic parameters that exostriker uses to determine the goodness of a fit but also
-the ones that describe the planet orbits. All of these parameters can be seen on the 
+the ones that describe the planets orbits. All of these parameters can be seen on the 
 homepage of exostriker.
 
 .. figure:: /images/homepage.png
@@ -55,6 +55,166 @@ homepage of exostriker.
 * **m** [**M**\ :sub:`jup`\ ] : planets mass. 
 * **t**\ :sub:`ω`\ [**d**]: ? 
 
-Now, depending on the type of data that you are trying to fit, you have to choose
-between Radial Velocities (RV data), Transits (Transit data) and TTVs (Transit timing variations) on the 
-**Data area** and then add the data files.
+----------------------------------------------------------------------------------------------------------
+
+Data area
+---------
+
+Depending on the type of data that you are trying to fit, you can choose
+between Radial Velocities (RV data), Transits (Transit data) and TTVs (Transit timing variations).
+
+* RV data
+   Load RVs, include Offset/Jitter parameters, choose a RV trend, bin data.
+
+* Transit data
+   Load Transits, include Offset/Jitter parameters, add Limb-darkening parameters to the model,
+   detrend the data.
+
+* TTVs (Transit-Timing Variations)
+   ?
+
+* Activity
+   ?
+
+* Limits and Priors
+   Set limits to the parameters range.
+
+Help widgets area
+-----------------
+
+* Shells 
+   *Exostriker* offers 3 command-line interpreters.
+
+   **Jupyter**: A Qt-based console for working with Jupyter kernels. It provides a number of enhancements 
+   only possible in a GUI, such as inline figures, proper multi-line editing with syntax highlighting, graphical
+   calltips, and much more. For more information visit `qtconsole documentation`_.
+
+   .. _qtconsole documentation : https://qtconsole.readthedocs.io/en/stable/
+
+   **Bash shell**: Work in progress.
+
+   **pqg shell**: PyQtGraph is a graphics and user interface library for Python. For more information visit `pyqtgraph documentation`_.
+
+   .. _pyqtgraph documentation : https://pyqtgraph.readthedocs.io/en/latest/index.html
+
+* Extra plots 
+   In this section plots of the most prominent peaks of the RV data are displayed phase folded (phase diagrams).
+   Additionally, periodograms of the RV data are included.   
+
+* Data inspector
+   Inspect the data on your local machine through the options *This computer* or *RVBank* and load them to exostriker. 
+
+* Text editor
+   Through the *text editor* you can inspect and edit the data files. (Works for .dat, .tran, .vels extensions)
+
+* **Calculator**
+
+* Stdout/Stderr
+   This section provides information about the version of the GUI you are using. Also
+   informs about the progress of all processes.
+
+   .. WARNING::
+      Before starting any project make sure that you run the latest version of *exostriker*. You can
+      be updated about the latest version of *exostriker* on exostriker's `github page`_ .
+
+      .. _github page: https://github.com/3fon3fonov/exostriker
+
+Plotting widgets area
+---------------------
+
+* RV
+   **RVs**: Radial velocity graph.
+
+   **RVs o-c**: Radial velocity residuals graph.
+
+   **GLS**: Generalized Lomb-Scargle periodogram of the initial signal. Options including Cross hair & jitter to graph.
+
+   **GLS o-c**: Generalized Lomb-Scargle periodogram of the residual signal. Adopt best parameter option ??
+
+   **MLP**: Maximum Likelihood Periodogram. 
+
+   **Window (DFT)**: ?
+
+
+* Transit
+   **Tran.**: Transit graph.
+
+   **Tran. o-c**: Transit residuals graph.
+
+   **TLS**: Transit Least Squares of the initial signal.
+
+   **TLS o-c**: Transit Least Squares of the residual signal.
+
+* TTV
+   **TTVs**: TTVs graph.
+
+   **TTVs o-c**: TTVs residuals graph.
+
+* Activity
+   **Time series**: ?
+
+   **GLS**: ?
+
+   **Correlations**: ?
+
+* Sample corr.
+   ?
+
+* Orb. Evol.
+   Orbital parameters evolution graphs.
+
+Input/Output parameters area
+----------------------------
+
+* Planet param.
+   Planetary parameters. The values change whenever a model is fitted. The values can also be fixed.
+
+* GP param.
+   Gaussian processes parameters. ?
+
+* Stellar param.
+   Edit stellar parameters depending on your system.
+
+* **Models param.**
+
+
+   .. image:: images/modelsparam.gif
+
+
+   Edit RV model parameters.
+
+   Choose between different minimizers in SciPy param. section.
+
+   Configure the GLS/MLP/TLS options and MCMC/NS simulation parameters.
+
+   Set the maximum number of planets Auto fit to look for. 
+
+* Limits and Priors
+   Set bounds to planetary parameters before the simulations.
+
+* N-body
+   Perform long-term stability check of multi-planet systems by setting the maximum time 
+   of evolution. 
+
+   Evolution of arbitrary planetary values can also be performed. 
+
+* **Plot opt.**
+
+
+   .. image:: images/plotopt.gif
+
+
+   Customize the RV/Transit/TTVs graph (Change the size of the data points, their transparency (Alpha).
+
+   Enable cross hair.
+
+   Shift the planets phase signal.
+
+   Configure the model.
+
+   Configure GLS/MLP/TLS/DFT graphs (Select the number of peaks that 
+   will be visible in the graphs).
+
+   Show aliases in cross hair.
+
+   Customize MCMC/NS sampling cornerplots and generate them.

docs/source/index.rst

@@ -2,7 +2,6 @@
 Welcome to the complete beginner's guide to Exostriker!
 =======================================================
 
-
 Review
 ......
 
@@ -53,7 +52,6 @@ What works
 What is to be implemented
 .........................
 
-
 * Larger arsenal of N-body/dynamical simulation/analysis tools (+ "REBOUND" is planned to be included).
 * Internal TTV and photo-dynamical modeling (i.e. the external "TTVFast" will become a secondary option).
 * Swap "celerite" with "celerite2" (the dSHO kernel from "celerite2" is available).
@@ -65,18 +63,6 @@ Developer
 * **Trifon Trifonov**, MPIA Heidelberg.
 * with contributions by **Mathias Zechmeister**, **Jakub Morawski**, **Man Hoi Lee**, **Stefan Dreizler**, **Grigorii Smirnov-Pinchukov**, **Stephan Stock** and **Jonas Kemmer**.
 
-
-
-
-
-
-
-
-
-
-
-
-
 .. toctree::
    :hidden:
    :maxdepth: 5
@@ -86,13 +72,15 @@ Developer
 
 .. toctree::
    :hidden:
-   :maxdepth: 5
+   :maxdepth: 6
    :caption: tutorials based on gui
 
    gui
    rvs
    transit
    rvtran
+   otbfpu
+   stability
 
 .. toctree::
    :hidden:
@@ -101,7 +89,6 @@ Developer
 
    tutorials2
 
-
 .. toctree::
    :hidden:
    :maxdepth: 1