Merge pull request #283 from sblunt/hip-otherinputs

Hip otherinputs
sblunt · Oct 13, 2021 · fb7a912 · fb7a912
2 parents bb9752b + 2570dbf
commit fb7a912
Show file tree

Hide file tree

Showing 61 changed files with 4,769 additions and 2,457 deletions.
diff --git a/docs/api.rst b/docs/api.rst
@@ -6,9 +6,14 @@ Detailed API Documentation
 .. toctree::
    :titlesonly:
 
+   basis
    driver
+   gaia
+   hipparcos
    kepler
    lnlike
+   nbody
+   plot
    priors
    read_input
    results

diff --git a/docs/conf.py b/docs/conf.py
@@ -121,7 +121,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # 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_static_path = []
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.

diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -0,0 +1,11 @@
+Contributing to the Code
+========================
+
+``orbitize`` is under active development, and we've still got a lot to do! To get involved,
+check out our `contributor guidelines <https://github.com/sblunt/orbitize/blob/master/contributor_guidelines.md>`_,
+look over our `issues list <https://github.com/sblunt/orbitize/issues>`_, and/or reach out to 
+`Sarah <https://sites.google.com/g.harvard.edu/sarah/contact?authuser=0>`_. We'd love to have
+you on our team!
+
+Members of our team have collectively drafted `this community agreement <https://docs.google.com/document/d/1ZzjkoB20vVTlg2wbNpS7sRjmcSrECdh8kQ11-waZQhw/edit>`_ stating both our values and ground rules. 
+In joining our team, we ask that you read and (optionally) suggest changes to this document. 
diff --git a/docs/conversions.rst b/docs/conversions.rst
diff --git a/docs/gaia.rst b/docs/gaia.rst
@@ -0,0 +1,8 @@
+.. _gaia:
+
+Gaia API Module
+===============
+.. module:: orbitize
+
+.. automodule:: orbitize.gaia
+	:members:
diff --git a/docs/index.rst b/docs/index.rst
@@ -35,7 +35,8 @@ Attribution:
 * If you use the OFTI algorithm, please also cite `Blunt et al (2017) <https://ui.adsabs.harvard.edu/#abs/2017AJ....153..229B/abstract>`_. 
 * If you use the Affine-invariant MCMC algorithm from ``emcee``, please also cite `Foreman-Mackey et al (2013) <https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F/abstract>`_. 
 * If you use the parallel-tempered Affine-invariant MCMC algorithm from ``ptemcee``, please also cite `Vousden et al (2016) <https://ui.adsabs.harvard.edu/abs/2016MNRAS.455.1919V/abstract>`_. 
-* If you use the Hipparcos intermediate astrometric data (IAD) fitting capability, please also cite `Nielsen et al (2020) <https://ui.adsabs.harvard.edu/abs/2020AJ....159...71N/abstract>`_.
+* If you use the Hipparcos intermediate astrometric data (IAD) fitting capability, please also cite `Nielsen et al (2020) <https://ui.adsabs.harvard.edu/abs/2020AJ....159...71N/abstract>`_ and `van Leeuwen et al (2007)  <https://ui.adsabs.harvard.edu/abs/2007A%26A...474..653V/abstract>`_.
+* If you use Gaia data, please also cite `Gaia Collaboration et al (2018; for DR2) <https://ui.adsabs.harvard.edu/abs/2018A%26A...616A...1G/abstract>`_, or `Gaia Collaboration et al (2021; for eDR3) <https://ui.adsabs.harvard.edu/abs/2021A%26A...649A...1G/abstract>`_.
 
 
 User Guide:
@@ -47,26 +48,9 @@ User Guide:
    installation
    tutorials
    faq
+   contributing
    api
 
-Contributing:
-+++++++++++++
-
-``orbitize`` is under active development, and we've still got a lot to do! To get involved,
-check out our `contributor guidelines <https://github.com/sblunt/orbitize/blob/master/contributor_guidelines.md>`_,
-look over our `issues list <https://github.com/sblunt/orbitize/issues>`_, and/or reach out to 
-`Sarah <https://sites.google.com/g.harvard.edu/sarah/contact?authuser=0>`_. We'd love to have
-you on our team!
-
-Members of our team have collectively drafted `this community agreement <https://docs.google.com/document/d/1ZzjkoB20vVTlg2wbNpS7sRjmcSrECdh8kQ11-waZQhw/edit>`_ stating both our values and ground rules. 
-In joining our team, we ask that you read and (optionally) suggest changes to this document. 
-
-
-**Some major planned updates:**
-
-* fit Gaia astrometry
-* marginalize over instrumental uncertainties
-
 Changelog:
 ++++++++++
 
@@ -75,6 +59,7 @@ Changelog:
 This is the beta release of orbitize! version 2.
 
 Big changes:
+
 - N-body Kepler solver backend! (@sofiacovarrubias)
 - Fitting in XYZ orbital basis! (@rferrerc)
 - API for fitting in arbitrary new orbital bases! (@TirthDS)
@@ -84,6 +69,7 @@ Big changes:
 - KDE prior added (inspiration=training on RV fits) (@jorgellop)
 
 Small changes:
+
 - HD 4747 rv data file fix for the RV tutorial (@lhirsch238)
 - Add check_prior_support to sampler.MCMC (@adj-smith)
 - Update example generation code in MCMC v OFTI tutorial (@semaphoreP)

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -35,7 +35,16 @@ to learn more about ``conda`` virtual environments.
 For Windows Users
 +++++++++++++++++
 
-There is a bug with the ``ptemcee`` installation that, as far as we know, only affects Windows users. 
+Many of the packages that we use in ``orbitize`` were originally written for Linux or macOS.
+For that reason, we highly recommend installing the 
+`Windows Subsystem for Linux (WSL) <https://docs.microsoft.com/en-us/windows/wsl/about>`_
+which is an entire Linux development environment within Windows. See `here <https://github.com/semaphoreP/codeastro/blob/main/Day0/INSTALL_WINDOWS.md#windows-subsystem-for-linux-wsl>`_ 
+for a handy getting started guide.
+
+If you don't want to use WSL, there are a few extra steps you'll need to follow
+to get ``orbitize`` running:
+
+1. There is a bug with the ``ptemcee`` installation that, as far as we know, only affects Windows users. 
 To work around this, download ``ptemcee`` from `its pypi page <https://pypi.org/project/ptemcee/>`_. 
 Navigate to the root ``ptemcee`` folder, remove the ``README.md`` file, then install:
 
@@ -45,6 +54,29 @@ Navigate to the root ``ptemcee`` folder, remove the ``README.md`` file, then ins
 	$ rm README.md
 	$ pip install . --upgrade
 
+2. Some users have reported issues with installing ``curses``. If this happens to you, you can install 
+``windows-curses`` which should work as a replacement.
+
+.. code-block:: bash
+
+	$ pip install windows-curses
+
+3. Finally, ``rebound`` is not compatible with windows, so you'll need to git clone
+orbitize, remove rebound from orbitize/requirements.txt, then install from
+the command line. 
+
+.. code-block:: bash
+
+    $ git clone https://github.com/sblunt/orbitize.git
+    $ cd orbitize
+
+Open up orbitize/requirements.txt, remove ``rebound``, and save.
+
+.. code-block:: bash
+
+    $ pip install . --upgrade
+
+
 For Developers
 ++++++++++++++
 

diff --git a/docs/nbody.rst b/docs/nbody.rst
@@ -0,0 +1,8 @@
+.. _nbody:
+
+N-body Backend
+===============
+.. module:: orbitize
+
+.. automodule:: orbitize.nbody
+	:members:
diff --git a/docs/plot.rst b/docs/plot.rst
@@ -0,0 +1,8 @@
+.. _plot:
+
+Plotting Methods
+================
+.. module:: orbitize
+
+.. automodule:: orbitize.plot
+	:members:
diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -11,8 +11,11 @@ For an advanced plotting demo, see "Advanced Plotting," and to learn
 about the differences between OFTI and MCMC algorithms,
 we suggest "MCMC vs OFTI Comparison."
 
+We also have a bunch of tutorials designed to introduce you to specific features
+of our code, listed below.
+
 Many of these tutorials are also available as jupyter notebooks 
-`here <https://github.com/sblunt/orbitize/tree/master/docs>`_.
+`here <https://github.com/sblunt/orbitize/tree/main/docs/tutorials>`_.
 
 If you find a bug, or if something is unclear, please create an issue
 on GitHub! We'd love any feedback on how to make ``orbitize`` more
@@ -25,27 +28,33 @@ style of using and explaining the code. If you are confused by part of
 one tutorial, we suggest looking at some of the others (and then contacting
 us if you are still confused).
 
-**Basic Tutorials:**
-
 .. toctree::
    :maxdepth: 1
+   :caption: Basic Tutorials
 
    tutorials/Quick-Start.ipynb
    formatting_inputs
    tutorials/OFTI_tutorial.ipynb
    tutorials/MCMC_tutorial.ipynb
 
-**Advanced Tutorials:**
-
 .. toctree::
    :maxdepth: 1
+   :caption: Advanced Tutorials
 
-   tutorials/RV_MCMC_Tutorial.ipynb
-   tutorials/Multiplanet_Tutorial.ipynb
    tutorials/Modifying_Priors.ipynb
-   tutorials/Using_nonOrbitize_Posteriors_as_Priors.ipynb
    tutorials/Plotting_tutorial.ipynb
    tutorials/MCMC_vs_OFTI.ipynb
    tutorials/Modifying_MCMC_initial_positions.ipynb
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Feature Tutorials
+
+   tutorials/RV_MCMC_Tutorial.ipynb
+   tutorials/Multiplanet_Tutorial.ipynb
+   tutorials/Using_nonOrbitize_Posteriors_as_Priors.ipynb
+   tutorials/Changing_bases_tutorial.ipynb
+   tutorials/Hipparcos_IAD.ipynb
+
+