Restructured project and improved docstrings for the documentation pa…

…ge. Changed the structure of the imports so that the _bindings module is only imported when it needs to be run, so that the documentation can be built without it.

docs/api.rst

@@ -42,7 +42,6 @@ Setting Simulation Parameters
     Simulation.set_init_cond_files
     Simulation.set_output_files
     Simulation.set_unit_system
-    Simulation.update_param_units
     Simulation.set_distance_range
     Simulation.set_ephemeris_date
 
@@ -88,6 +87,123 @@ File Input and Output
     Simulation.convert
     Simulation.clean
 
+
+Initial Conditions Generation Functions
+=======================================
+
+.. autosummary::
+    :toctree: generated/
+
+    swiftest.init_cond.solar_system_horizons
+    swiftest.init_cond.horizons_query
+    swiftest.init_cond.horizons_get_physical_properties
+    swiftest.init_cond.vec2xr
+
+
+Input/Output Processing Functions
+==================================
+
+A collection of functions for processing simulation files.
+
+Reading and writing simulation parameter and initial conditions files
+---------------------------------------------------------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    swiftest.io.process_netcdf_input
+    swiftest.io.read_swiftest_param
+    swiftest.io.read_swifter_param
+    swiftest.io.read_swift_param
+    swiftest.io.write_swift_param
+    swiftest.io.write_labeled_param
+    swiftest.io.select_active_from_frame
+    swiftest.io.swiftest_xr2infile
+
+Tools for fixing differences between NetCDF-Fortran and xarray data structures
+------------------------------------------------------------------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    swiftest.io.swiftest2xr
+    swiftest.io.reorder_dims
+    swiftest.io.fix_types
+
+
+Conversions between legacy integrator formats and Swiftest
+----------------------------------------------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    swiftest.io.swifter2swiftest
+    swiftest.io.swifter2xr
+    swiftest.io.swifter_xr2infile
+    swiftest.io.swiftest2swifter_param
+    swiftest.io.swift2swifter
+    swiftest.io.swift2swiftest
+
+Tools
+=====
+
+Miscellaneous helper functions 
+
+.. autosummary::
+    :toctree: generated/
+
+    swiftest.tool.magnitude
+    swiftest.tool.wrap_angle
+    swiftest.tool.follow_swift
+    swiftest.tool.danby
+    swiftest.tool.el2xv_one
+    swiftest.tool.el2xv_vec
+    swiftest.tool.xv2el_one
+    swiftest.tool.xv2el_vec
+
+Constants
+=========
+
+The `constants` module defines several astronomical and physical constants. Below is a description of each constant:
+
+.. list-table::
+   :widths: 25 75
+   :header-rows: 1
+
+   * - Constant
+     - Description
+   * - ``GC``
+     - The gravitational constant (G) from Astropy constants, in SI units (m^3 kg^-1 s^-2).
+   * - ``AU2M``
+     - Astronomical Unit in meters, representing the average distance from the Earth to the Sun.
+   * - ``GMSun``
+     - Standard gravitational parameter for the Sun in m^3 s^-2.
+   * - ``MSun``
+     - Mass of the Sun in kilograms.
+   * - ``RSun``
+     - Radius of the Sun in meters.
+   * - ``MEarth``
+     - Mass of the Earth in kilograms.
+   * - ``REarth``
+     - Radius of the Earth in meters.
+   * - ``GMEarth``
+     - Standard gravitational parameter for the Earth in m^3 s^-2.
+   * - ``JD2S``
+     - Number of seconds in a Julian day.
+   * - ``YR2S``
+     - Number of seconds in a Julian year (365.25 days).
+   * - ``einsteinC``
+     - Speed of light in vacuum in meters per second.
+   * - ``J2Sun``
+     - Solar quadrupole moment coefficient (J2), indicating the extent of the Sun's equatorial bulge.
+   * - ``J4Sun``
+     - Higher order coefficient (J4) for the Sun's shape, indicating asymmetry in its mass distribution.
+   * - ``rotpoleSun``
+     - SkyCoord object representing the rotation pole of the Sun in right ascension (ra) and declination (dec), converted to Cartesian coordinates.
+   * - ``rotSun``
+     - Angular velocity of the Sun's rotation in radians per second, considering an average rotational period of 25.05 days.
+
+
 Fortran API Documentation
 =========================
 

docs/conf.py

@@ -9,9 +9,8 @@
 from sphinx.util import logging
 
 # Disable import of swiftest._bindings so that we don't have to build the Fortran code when building the docs
-import swiftest
 autodoc_mock_imports = ['swiftest._bindings']
-
+import swiftest
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 project = 'Swiftest'

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "swiftest"
-version = "2023.12.0"
+version = "2023.12.1"
 authors=[
     {name = 'David A. Minton', email='daminton@purdue.edu'},
     {name = 'Carlisle Wishard'},
@@ -115,12 +115,7 @@ before-all = [
     "LIBS=\"\" buildscripts/build_dependencies.sh -p ${PREFIX} -d ${HOME}/Downloads -m ${MACOSX_DEPLOYMENT_TARGET}"
 ]
 
-[tool.cibuildwheel.linux]
-skip = "cp312-* pp* -manylinux_i686* *-musllinux*"
-before-all = [
-    "yum install doxygen libxml2-devel libcurl-devel -y",
-    "buildscripts/build_dependencies.sh -p /usr/local"
-]
+
 [tool.cibuildwheel.linux.environment]
 PREFIX="/usr/local"
 NCDIR="${PREFIX}"
@@ -138,22 +133,14 @@ HDF5_DIR="${HDF5_ROOT}/cmake"
 PATH="${HDF5_ROOT}/bin:${PATH}"
 CMAKE_INSTALL_LIBDIR="lib"
 
+[tool.cibuildwheel.linux]
+skip = "cp312-* pp* -manylinux_i686* *-musllinux*"
+before-all = [
+    "yum install doxygen libxml2-devel libcurl-devel -y",
+    "buildscripts/build_dependencies.sh -p /usr/local"
+]
+
 [[tool.scikit-build.generate]]
 path = "version.txt"
 location = "source"
 template = '''${version}'''
-
-[project.optional-dependencies]
-docs = [
-    "sphinx",
-    "sphinx-autosummary-accessors",
-    "sphinx-book-theme >= 0.3.0",
-    "sphinx-copybutton",
-    "sphinx-design",
-    "sphinx-inline-tabs",
-    "sphinxext-rediraffe",
-    "sphinxext-opengraph",
-    "nbsphinx",
-    "ipython",
-    "ford"
-]

src/globals/globals_module.f90

@@ -48,7 +48,7 @@ module globals
    integer(I4B), parameter :: UPPERCASE_OFFSET = iachar('A') - iachar('a') !! ASCII character set parameter for lower to upper 
                                                                            !! conversion - offset between upper and lower
 
-   character(*), parameter :: VERSION = "2023.12.0" !! Swiftest version
+   character(*), parameter :: VERSION = "2023.12.1" !! Swiftest version
 
    !> Symbolic name for integrator types
    character(*), parameter :: UNKNOWN_INTEGRATOR = "UKNOWN INTEGRATOR"

swiftest/init_cond.py

@@ -37,7 +37,6 @@ def horizons_get_physical_properties(altid,**kwargs):
     **kwargs: Any
             Additional keyword arguments to pass to the query method (see https://astroquery.readthedocs.io/en/latest/jplhorizons/jplhorizons.html)
 
-
     Returns
     -------
     MSun_over_Mpl : float
@@ -184,7 +183,6 @@ def horizons_query(id, ephemerides_start_date, exclude_spacecraft=True, verbose=
         An astroquery.jplhorizons HorizonsClass object. Or None if no match was found.
     altid: string list | None
         A list of alternate ids if more than one object matches the list
-        
     """
 
     def get_altid(errstr,exclude_spacecraft=True):
@@ -416,6 +414,7 @@ def solar_system_horizons(name: str,
 
     return id,name,a,e,inc,capom,omega,capm,rh,vh,Gmass,Rpl,rhill,Ip,rot,J2,J4
 
+
 def vec2xr(param: Dict, **kwargs: Any):
     """
     Converts and stores the variables of all bodies in an xarray dataset.
@@ -458,9 +457,11 @@ def vec2xr(param: Dict, **kwargs: Any):
         instead of passing Ip1, Ip2, and Ip3 separately
     time : array of floats
         Time at start of simulation
+        
     Returns
     -------
     ds : xarray dataset
+        Dataset containing the variables of all bodies passed in kwargs
     """
     scalar_dims = ['id']
     vector_dims = ['id','space']