Updates documentation

README.md

@@ -1,6 +1,6 @@
 [![Actions Status](https://github.com/cabb99/open3spn2/workflows/CI/badge.svg)](https://github.com/cabb99/open3spn2/actions)
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-[![Anaconda-Server Badge](https://anaconda.org/wolynes-lab/open3spn2/badges/version.svg)](https://conda.anaconda.org/wolynes-lab/open3spn2)
+[![Anaconda-Server Badge](https://anaconda.org/conda-forge/open3spn2/badges/version.svg)](https://anaconda.org/conda-forge/open3spn2)
 
 # Open-3SPN2
 A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA in OpenMM.
@@ -9,11 +9,9 @@ A Implementation of the 3SPN.2 and 3SPN.2C coarse-grained molecular model of DNA
 
 ## Installation
 
-Installation of the open3SPN2 repository is available through anaconda. Some of the dependencies  are contained in the omnia channel (openmm, pdbfixer) or in the conda-forge channel (mdtraj).
+Installation of the open3SPN2 repository is available through anaconda.
 
-```conda config --append channels conda-forge```
-
-```conda install -c wolynes-lab open3spn2```
+```conda install -c conda-forge open3spn2```
 
 For protein-DNA simulations you will also need to install [openAWSEM](https://github.com/npschafer/openawsem) and add the openAWSEM path to the `$PYTHONPATH` environment variable. In linux you can set the path variables on `~/.bashrc`.
 
@@ -30,8 +28,8 @@ If you publish any work using the open3SPN2 package, please include the followin
 Open3SPN2
 Lu, W., Bueno, C., Schafer, N. P., Moller, J., Jin, S., Chen, X., ... & Wolynes, P. G. (2021). OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLoS computational biology, 17(2), e1008308. https://doi.org/10.1371/journal.pcbi.1008308
 
-3SPN.2
-Hinckley, D. M., Freeman, G. S., Whitmer, J. K., & De Pablo, J. J. (2013). An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization. Journal of Chemical Physics, 139(14). https://doi.org/10.1063/1.4822042
-
 3SPN.2C
 Freeman, G. S., Hinckley, D. M., Lequieu, J. P., Whitmer, J. K., & De Pablo, J. J. (2014). Coarse-grained modeling of DNA curvature. Journal of Chemical Physics, 141(16). https://doi.org/10.1063/1.4897649
+
+3SPN.2
+Hinckley, D. M., Freeman, G. S., Whitmer, J. K., & De Pablo, J. J. (2013). An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization. Journal of Chemical Physics, 139(14). https://doi.org/10.1063/1.4822042

docs/source/api.rst

@@ -1,25 +1,31 @@
-Classes and functions
-===============================
+open3SPN2 Module Documentation
+==============================
 
 .. automodule:: open3SPN2
     :noindex:
-
-DNA
-------------------
+
+Classes and Functions
+---------------------
+
+DNA Class
+^^^^^^^^^^^^^^^^^^^^^^^
+
 .. autoclass:: open3SPN2.DNA
     :member-order: bysource
     :members:
 
-System
-------------------
+System Class
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 .. autoclass:: open3SPN2.System
 
     .. automethod:: __init__
 
     .. rubric:: Methods
-    
+
 DNA Forces
-------------------
+^^^^^^^^^^
+
 .. autoclass:: open3SPN2.Bond
     :member-order: bysource
     :members:
@@ -35,7 +41,7 @@ DNA Forces
 .. autoclass:: open3SPN2.Stacking
     :member-order: bysource
     :members:
-    
+
 .. autoclass:: open3SPN2.BasePair
     :member-order: bysource
     :members:
@@ -52,8 +58,9 @@ DNA Forces
     :member-order: bysource
     :members:
 
-DNA - Protein Forces
---------------------
+DNA-Protein Forces
+^^^^^^^^^^^^^^^^^^
+
 .. autoclass:: open3SPN2.ExclusionProteinDNA
     :member-order: bysource
     :members:
@@ -62,28 +69,31 @@ DNA - Protein Forces
     :member-order: bysource
     :members:
 
-Utils
------
+Utility Functions
+^^^^^^^^^^^^^^^^^
+
 .. autofunction:: open3SPN2.parseConfigTable
-    
+
 .. autofunction:: open3SPN2.parsePDB
-    
+
 .. autofunction:: open3SPN2.fixPDB
-    
+
 .. autofunction:: open3SPN2.pdb2table
 
-Tests
------
-.. autoclass:: open3SPN2.TestEnergies
+Tests Functions
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: tests.TestEnergies
     :member-order: bysource
     :members:
-    
-.. autofunction:: open3SPN2.test_DNA_from_xyz
-    
-.. autofunction:: open3SPN2.test_parse_xyz
-    
-.. autofunction:: open3SPN2.test_parse_log
-    
+
+.. autofunction:: tests.test_DNA_from_xyz
+
+.. autofunction:: tests.test_parse_xyz
+
+.. autofunction:: tests.test_parse_log
+
 Exceptions
-----------
-.. autoclass:: open3SPN2.DNATypeError
+^^^^^^^^^^
+
+.. autoclass:: open3SPN2.DNATypeError

docs/source/conf.py

@@ -74,7 +74,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.

tests/__init__.py

@@ -0,0 +1,2 @@
+from .test_energies import *
+from .test_IO import *

tests/test_energies.py

@@ -12,7 +12,9 @@
 
 # Define a fixture to load the test sets
 # Define a module-level variable to store the test sets
-_test_sets = pd.read_csv('tests/test_cases.csv', comment='#')
+
+test_path = Path(__file__).parent 
+_test_sets = pd.read_csv(test_path/'test_cases.csv', comment='#')
 _ef = 1 * unit.kilocalorie / unit.kilojoule  # energy scaling factor
 
 @pytest.fixture