Restructured documentation to be compatible with Sphinx.

docs/Makefile

@@ -61,13 +61,13 @@ fortran-doc:
 	cd .. && ford fortran_docs.md
 
 .PHONY: html
-html: fortran-doc
+html: 
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
 .PHONY: rtdhtml
-rtdhtml: fortran-doc
+rtdhtml: 
 	$(SPHINXBUILD) -T -j auto -E -W --keep-going -b html -d $(BUILDDIR)/doctrees -D language=en . $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

docs/api.rst

@@ -29,6 +29,65 @@ Running a Simulation
 
     Simulation.run
 
+Setting Simulation Parameters
+--------------------------------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    Simulation.set_parameter
+    Simulation.set_simulation_time
+    Simulation.set_integrator
+    Simulation.set_feature
+    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
+
+Retrieving Simulation Parameters
+--------------------------------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    Simulation.get_parameter
+    Simulation.get_simulation_time
+    Simulation.get_integrator
+    Simulation.get_feature
+    Simulation.get_init_cond_files
+    Simulation.get_output_files
+    Simulation.get_unit_system
+    Simulation.get_distance_range
+    Simulation.get_ephemeris_date
+
+Adding Bodies to a Simulation
+-----------------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    Simulation.add_body
+    Simulation.add_solar_system_body
+
+
+File Input and Output
+---------------------
+
+.. autosummary::
+    :toctree: generated/
+
+    Simulation.read_param
+    Simulation.write_param
+    Simulation.read_encounter_file
+    Simulation.read_collision_file
+    Simulation.follow
+    Simulation.save
+    Simulation.initial_conditions_from_bin
+    Simulation.convert
+    Simulation.clean
+
 Fortran API Documentation
 =========================
 

pyproject.toml

@@ -50,6 +50,7 @@ requires = [
     "cmake",
     "pyproject_metadata",
     "pytest",
+    "pathspec",
     "sphinx",
     "sphinx-autosummary-accessors",
     "sphinx-book-theme >= 0.3.0",

src/globals/globals_module.f90

@@ -1,11 +1,11 @@
-! Copyight 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
-! This file is part of Swiftest.
-! Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
-! as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-! Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
-! of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
-! You should have received a copy of the GNU General Public License along with Swiftest. 
-! If not, see: https://www.gnu.org/licenses. 
+!! Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+!! This file is part of Swiftest.
+!! Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+!! as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+!! Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+!! of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+!! You should have received a copy of the GNU General Public License along with Swiftest. 
+!! If not, see: https://www.gnu.org/licenses. 
 
 module globals
    !! author: David A. Minton