deploy github page

docs/build/html/.buildinfo

@@ -0,0 +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: e3a31627e343aa0fef40c32d2f1595b2
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_sources/api.rst.txt

@@ -0,0 +1,45 @@
+API
+===
+
+Here are the some of the functions that are available in the NEMESISPY package.
+
+common
+------
+
+.. autofunction:: nemesispy.calc_hydrostat
+
+.. autofunction:: nemesispy.disc_weights
+
+.. autofunction:: nemesispy.gauss_lobatto_weights
+
+.. autofunction:: nemesispy.get_gas_name
+
+.. autofunction:: nemesispy.get_gas_id
+
+.. autofunction:: nemesispy.interp_gcm_X
+
+models
+------
+
+.. autofunction:: nemesispy.TP_Guillot
+
+.. autofunction:: nemesispy.TP_Guillot14
+
+.. autofunction:: nemesispy.Model4
+
+radtran
+-------
+
+.. autofunction:: nemesispy.calc_layer
+
+.. autofunction:: nemesispy.calc_mmw
+
+.. autofunction:: nemesispy.calc_planck
+
+.. autofunction:: nemesispy.calc_radiance
+
+.. autofunction:: nemesispy.read_kta
+
+.. autofunction:: nemesispy.read_kls
+
+.. autofunction:: nemesispy.read_cia

docs/build/html/_sources/index.rst.txt

@@ -0,0 +1,94 @@
+.. NEMESISPY documentation master file, created by
+   sphinx-quickstart on Sun Mar 10 22:23:59 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to NEMESISPY's documentation!
+=====================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Table of Contents:
+
+Table of Contents
+-----------------
+
+.. toctree::
+
+   usage
+   tutorial
+   api
+   publications
+
+Introduction
+------------
+
+**NEMESISPY** is a Python package developed for atmospheric retrievals,
+which is the inference of atmospheric properties such as chemical abundances
+from observed spectra of planetary atmospheres. The workflow of atmospheric
+retrievals can be devided into two steps: **forward modelling** and **model fitting**:
+
+* The **forward modelling** step requires an atmospheric model for the observed
+  planet and a radiative transfer pipeline that can calculate model spectra given an atmospheric model.
+
+* The **model fitting** step requires a parameter estimation code that can
+  constrain the free parameters of the forward model by fitting the observed spectra.
+
+**NEMESISPY** can perform both parametric atmospheric modelling
+and radiative transfer calculation for the retrievals of planetary spectra.
+It is a recent development of the well-established Fortran `NEMESIS library <https://github.com/nemesiscode>`_,
+which has been applied to the atmospheric retrievals of both solar system planets
+and exoplanets.
+**NEMESISPY** can be easily interfaced with Bayesian inference algorithms
+such as nested sampling to retrieve atmospheric properties from spectroscopic observations.
+The radiative transfer calculations in **NEMESISPY** are done with the
+fast correlated-k method, and are accelerated with the
+``Numba`` just-in-time compiler to match the speed of
+compiled languages such as Fortran. The radiative transfer
+routines are based on the well-tested `NEMESIS library <https://github.com/nemesiscode>`_
+developed by Patrick Irwin (University of Oxford) and collaborators.
+
+**NEMESISPY** comes ready with some spectral data and General Circulation
+Model (GCM) data so you can start simulating spectra immediately.
+There are a few demonstration routines in the ``nemesispy/examples`` folder;
+in particular, ``demo_fit_eclipse.py`` contains an interactive plot routine
+which allows you to fit a hot Jupiter eclipse spectrum by hand by varying
+its chemical abundance and temperature profile.
+The current release of **NEMESISPY** is focused on the calculation of
+thermal emission spectra of exoplanets. It is capale of calculating emission spectra
+at multiple orbital phases from an arbitray atmospheric model.
+Future releases will include more features such
+as multiple scattering and transmission geometry.
+
+**NEMESISPY** has the following nice features:
+
+* Written fully in Python (not a wrapper!): highly portable and customisable
+  compared to packages written in compiled languages and
+  can be easily installed on computer clusters.
+* Fast calculation speed: the most time consuming routines are accelerated with
+  just-in-time (JIT) compilation, which compiles Python code to machine
+  code at run time.
+* Radiative transfer routines are benchmarked against
+  the extensively used `NEMESIS library <https://github.com/nemesiscode>`_.
+* Contains routines to simulate spectra from General
+  Circulation Models (GCMs).
+* Contains unit tests to check if
+  the code is working correctly after modifications.
+
+To install the package and keep it editable, clone the repository and type
+the following in the terminal:
+
+.. code-block:: console
+
+    $ pip install --editable .
+
+To run all unit tests, change directory to the software folder and type the
+following in the terminal:
+
+.. code-block:: console
+
+    $ python -m unittest discover test/
+
+.. note::
+
+   This project is under active development.

docs/build/html/_sources/publications.rst.txt

@@ -0,0 +1,7 @@
+Publications
+============
+
+We list the publications that were enabled by the NEMESISPY software in the following.
+
+* Jingxuan Yang, Mark Hammond, Anjali A A Piette, Jasmina Blecic, Taylor J Bell, Patrick G J Irwin, Vivien Parmentier, Shang-Min Tsai, Joanna K Barstow, Nicolas Crouzet, Laura Kreidberg, João M Mendonça, Jake Taylor, Robin Baeyens, Kazumasa Ohno, Lucas Teinturier, Matthew C Nixon, Simultaneous retrieval of orbital phase resolved JWST/MIRI emission spectra of the hot Jupiter WASP-43b: Evidence of water, ammonia and carbon monoxide, Monthly Notices of the Royal Astronomical Society, 2024;, stae1427, https://doi.org/10.1093/mnras/stae1427
+* Jingxuan Yang, Patrick G J Irwin, Joanna K Barstow, Testing 2D temperature models in Bayesian retrievals of atmospheric properties from hot Jupiter phase curves, Monthly Notices of the Royal Astronomical Society, Volume 525, Issue 4, November 2023, Pages 5146–5167, https://doi.org/10.1093/mnras/stad2555

docs/build/html/_sources/tutorial.rst.txt

@@ -0,0 +1,8 @@
+Tutorial
+========
+
+
+
+
+Hot Jupiter emission spectrum
+------------------------------

docs/build/html/_sources/usage.rst.txt

@@ -0,0 +1,46 @@
+Usage
+=====
+
+Installation
+------------
+
+To use NEMESISPY, first clone the `GitHub repository <https://github.com/Jingxuan97/nemesispy>`_
+to your computer. Then, navigate to the directory where you have saved the
+repository and run the command
+
+.. code-block:: console
+
+    $ pip install .
+
+This will install the package and make it available to use in your Python environment.
+In order to install the package but still make it editable, run instead the command
+
+.. code-block:: console
+
+    $ pip install . --editable
+
+NEMESISPY can also by direcly installed from `PyPI <https://pypi.org/project/nemesispy/>`_
+by running
+
+.. code-block:: console
+
+    $ pip install nemesispy
+
+We recommend installing the package from the GitHub repository
+to make sure that you have the latest version of the package.
+
+Opacity data
+------------
+
+NEMESISPY requires opacity data to be provided in the NEMESIS .kta format,
+which can be obtained from the `ExoMol database <https://www.exomol.com/data/data-types/opacity/>`_.
+In addition, the `Exo_k <https://perso.astrophy.u-bordeaux.fr/~jleconte/exo_k-doc/index.html>`_
+package provides many helpful routines for working with opacity data.
+
+Issues and contributions
+------------------------
+To report issues or problems with NEMESISPY, please use the GitHub issue tracker
+`here <https://github.com/Jingxuan97/nemesispy>`_.
+If you would like to contribute to the development of NEMESISPY, or seek scientific
+collaboration, please contact us directly.
+Our contact details can be found `here <https://www.physics.ox.ac.uk/our-people/yangj>`_.

docs/build/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,134 @@
+/*
+ * _sphinx_javascript_frameworks_compat.js
+ * ~~~~~~~~~~
+ *
+ * Compatability shim for jQuery and underscores.js.
+ *
+ * WILL BE REMOVED IN Sphinx 6.0
+ * xref RemovedInSphinx60Warning
+ *
+ */
+
+/**
+ * select a different prefix for underscore
+ */
+$u = _.noConflict();
+
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}