Adding cookie_cutter template

.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

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* bam_collapsing version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 
 # Distribution / packaging
 .Python
+env/
 build/
 develop-eggs/
 dist/
@@ -23,7 +24,6 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -54,7 +54,6 @@ coverage.xml
 # Django stuff:
 *.log
 local_settings.py
-db.sqlite3
 
 # Flask stuff:
 instance/
@@ -81,14 +80,13 @@ celerybeat-schedule
 # SageMath parsed files
 *.sage.py
 
-# Environments
+# dotenv
 .env
+
+# virtualenv
 .venv
-env/
 venv/
 ENV/
-env.bak/
-venv.bak/
 
 # Spyder project settings
 .spyderproject

.travis.yml

@@ -0,0 +1,29 @@
+# Config file for automatic testing at travis-ci.org
+
+language: python
+python:
+  - 3.6
+  - 3.5
+  - 3.4
+  - 2.7
+
+# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+install: pip install -U tox-travis
+
+# Command to run tests, e.g. python setup.py test
+script: tox
+
+# Assuming you have installed the travis-ci CLI tool, after you
+# create the Github repo and add it to Travis, run the
+# following command to finish PyPI deployment setup:
+# $ travis encrypt --add deploy.password
+deploy:
+  provider: pypi
+  distributions: sdist bdist_wheel
+  user: rhshah
+  password:
+    secure: PLEASE_REPLACE_ME
+  on:
+    tags: true
+    repo: rhshah/bam_collapsing
+    python: 3.6

AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Ronak Shah <[email protected]>
+
+Contributors
+------------
+
+None yet. Why not be the first?

CONTRIBUTING.rst

@@ -0,0 +1,128 @@
+.. 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/rhshah/bam_collapsing/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+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
+~~~~~~~~~~~~~~~~~~~
+
+bam_collapsing could always use more documentation, whether as part of the
+official bam_collapsing 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/rhshah/bam_collapsing/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.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `bam_collapsing` for local development.
+
+1. Fork the `bam_collapsing` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/bam_collapsing.git
+
+3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+
+    $ mkvirtualenv bam_collapsing
+    $ cd bam_collapsing/
+    $ python setup.py develop
+
+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 flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ flake8 bam_collapsing tests
+    $ python setup.py test or py.test
+    $ tox
+
+   To get flake8 and tox, just pip install them into your virtualenv.
+
+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 2.7, 3.4, 3.5 and 3.6, and for PyPy. Check
+   https://travis-ci.org/rhshah/bam_collapsing/pull_requests
+   and make sure that the tests pass for all supported Python versions.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ py.test tests.test_bam_collapsing
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bumpversion patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

HISTORY.rst

@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.1.0 (2019-08-09)
+------------------
+
+* First release on PyPI.