major refactoring; updated docs; formatted with isort & black

.circleci/config.yml

@@ -7,11 +7,6 @@ jobs:
     steps:
       - checkout
 
-      - restore_cache:
-          keys:
-            - v1-dependencies-{{ checksum "/home/circleci/project/Pipfile.lock" }}
-            - v1-dependencies-
-
       - run:
           name: install dependencies
           command: |
@@ -23,17 +18,9 @@ jobs:
             sudo apt install gawk libgfortran4 python2
             python3.8 -m pip install --user pytest numpy coverage psutil
 
-      - save_cache:
-          paths:
-            - ".venv"
-            - "/usr/local/bin"
-            - "/usr/local/lib/python3.8/site-packages"
-            - "/home/circleci/.local/share/virtualenvs/"
-          key: v1-dependencies-{{ checksum "/home/circleci/project/Pipfile.lock" }}
-
       - run:
           name: run tests
           command: |
             set -e
-            cd pypka/tests/
+            cd ./tests/
             python3.8 -m pytest test.py

.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

.gitignore

@@ -8,32 +8,132 @@ LOG*
 *eback.xvg
 *.prm
 P_*.pdb
-.nfs*
+*.nfs*
 TMP.pdb
 clean*.pdb
+*.pqr
+*.sh
 
-__pycache__
-.vscode/
-pypka/.vscode/
-build/
-.eggs/
-pypKa.egg-info/
 pypka/build/
 .pytest_cache/
 dist/
-pypka.egg-info/
-pypka/__pycache__/
 pypka/build/
 pypka/*.pyc
 pypka/delphi4py/*.pyc
 pypka/delphi4py/*.pyc
-pypka/delphi4py/__pycache__/
 pypka/delphi4py/readFiles/*f
 pypka/delphi4py/rundelphi/*f
-pypka/delphi4py/readFiles/__pycache__/
-pypka/delphi4py/rundelphi/__pycache__/
 pypka/delphi4py/rundelphi/benchmark
-pypka/example/test/
-pypka/.nfs*
+examples/test/
+
+Dockerfile
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+
+!pypka/mc/*so
+!pypka/delphi4py/*/*.so
 
-Dockerfile

CONTRIBUTING.rst

@@ -0,0 +1,110 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/mms-fcul/pypka/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* PypKa's version and parameters used for the calculation
+* Origin of the input structure:  Protein Data Bank or simulation (please specify the FF)
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+PypKa could always use more documentation, whether as part of the
+official PypKa docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/mms-fcul/pypka/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `pypka` for local development.
+
+1. Fork the `pypka` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone git@github.com:your_name_here/pypka.git
+
+3. Install your local copy into a virtualenv. Assuming you have pipenv installed, this is how you set up your fork for local development::
+    
+    $ cd pypka/
+    $ pipenv install pypka
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass the tests::
+
+    $ make tests
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy.
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed.
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+

MANIFEST.in

@@ -1,16 +1,20 @@
-include LICENSE README.md 
+include LICENSE 
+include README.md
+include CONTRIBUTING.rst
 global-include *.so addHtaut
 
 graft pypka/G54A7
 graft pypka/CHARMM36m
 graft pypka/pdb2pqr
 graft pypka/delphi4py
 
-prune pypka/tests/
-prune pypka/docs/
-prune pypka/scripts/
-prune __pycache__
-
 global-exclude .vscode .circleci
-global-exclude *.out .nfs*
-exclude .gitignore
+global-exclude *.out .nfs* P_*.pdb *frc *.profl *eback.xvg *.prm clean*.pdb *sh
+exclude .gitignore
+
+recursive-enclude tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
+