Merge pull request #86 from OMaraLab/adjustments

Final adjustments resulting from manuscript revision

Author: recombinatrix

.DS_Store

@@ -3,8 +3,8 @@
 * @lunamorrow @khiron @recombinatrix @RangikaM
 
 /polyconf/ @lunamorrow @recombinatrix
-/polytop/ @lunamorrow @khiron
-/polybuild/ @lunamorrow @RangikaM
+/polytop/ @lunamorrow @khiron @recombinatrix
+/polybuild/ @lunamorrow @RangikaM @recombinatrix
 
 # information on how to adjust the code owners can be found here:
-# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners

.github/CODEOWNERS

@@ -2,19 +2,19 @@
 
 *PolyConstruct* contains three python tools for generating polymer coordinate and topolgy files for molecular dynamics simulations.  
 
-*PolyConf* is a tool for generating ensembles of polymer conformations by combining monomer coordinate files.
+* *PolyConf* is a tool for generating ensembles of polymer conformations by combining monomer coordinate files.
 
-*PolyBuild* is a tool for generating polymer topology files for simulaton from polymer coordinate files, leveraging the functionality of the gromacs tool pdb2gmx.
+* *PolyBuild* is a tool for generating polymer topology files for simulaton from polymer coordinate files, leveraging the functionality of the gromacs tool pdb2gmx.
 
-*PolyTop* is a tool for generating polymer topology files from monomer topology files.
+* *PolyTop* is a tool for generating polymer topology files from monomer topology files.
 
 *PolyConstruct* was published in the paper *PolyConstruct: adapting biomolecular simulation pipelines for polymers with PolyBuild, PolyConf and PolyTop*.
 
 ## Getting started
 
-Detailed documentation is available at the [PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html).  This includes installation instructions, tutorials and worked examples, and api documentation for all polyconstruct methods.
+Detailed documentation is available at the [PolyConstruct ReadTheDocs](https://polyconstruct.readthedocs.io/en/latest/index.html).  This includes installation instructions, tutorials and worked examples, and api documentation for all *PolyConstruct* methods.
 
-There are also detailed tutorials for PolyConf in the folder [polyconf_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polyconf_examples), and detailed tutorials for PolyTop in the folder [polytop_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polytop_examples)
+There is a series of detailed tutorials for *PolyConf* in the folder [polyconf_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polyconf_examples), and for *PolyTop* in the folder [polytop_examples](https://github.com/OMaraLab/polyconstruct/tree/main/polytop_examples).  A set of example input and output files for *PolyBuild* are presented in the folder [polybuild_examples/RTP_entries](https://github.com/OMaraLab/polyconstruct/tree/main/polybuild_examples/RTP_entries)
 
 ## Quick and dirty installation
 

README.md

@@ -3,8 +3,8 @@
 * @lunamorrow @khiron @recombinatrix @RangikaM
 
 /polyconf/ @lunamorrow @recombinatrix
-/polytop/ @lunamorrow @khiron
-/polybuild/ @lunamorrow @RangikaM
+/polytop/ @lunamorrow @khiron @recombinatrix
+/polybuild/ @lunamorrow @RangikaM @recombinatrix
 
 # information on how to adjust the code owners can be found here:
-# https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners

docs/CODEOWNERS

@@ -24,12 +24,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "polyconstruct"
+project = "PolyConstruct"
 copyright = (
-    "2024, Luna Morrow. "
+    "2024, Rangika Munaweera, Ada Quinn, Luna Morrow, Megan O'Mara. "
     "A Python library for constructing polymer topologies and coordinates"
 )
-author = "Luna Morrow"
+author = "Rangika Munaweera, Ada Quinn, Luna Morrow, Megan O'Mara"
 add_module_names = False
 
 # The short X.Y version
@@ -195,7 +195,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     (master_doc, "polyconstruct", "PolyConstruct Documentation",
-     author, "polyconstruct", "A group of packages to construct polymer topologies and coordinates for molecular dynamics simulation with GROMACS",
+     author, "polyconstruct", "A python library to generate polymer topology and coordinate files for molecular dynamics simulation with GROMACS",
      "Miscellaneous"),
 ]