Merge pull request #55 from gbouras13/jossreviews

Clean up CONTRIBUTING.md

CONTRIBUTING.md

@@ -1,19 +1,15 @@
-.. highlight:: shell
+# Contributing
 
-============
-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
-----------------------
+## Types of Contributions
+
+#### Report Bugs
 
-Report Bugs
-~~~~~~~~~~~
 
 Report bugs at https://github.com/gbouras13/dnaapler/issues.
 
@@ -23,27 +19,23 @@ If you are reporting a bug, please include:
 * Any details about your local setup that might be helpful in troubleshooting.
 * Detailed steps to reproduce the bug.
 
-Fix Bugs
-~~~~~~~~
+#### 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
-~~~~~~~~~~~~~~~~~~
+#### 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
-~~~~~~~~~~~~~~~~~~~
+#### Write Documentation
 
 dnaapler could always use more documentation, whether as part of the
 official dnaapler docs, in docstrings, or even on the web in blog posts,
 articles, and such.
 
-Submit Feedback
-~~~~~~~~~~~~~~~
+#### Submit Feedback
 
 The best way to send feedback is to file an issue at https://github.com/gbouras13/dnaapler/issues.
 
@@ -54,47 +46,57 @@ If you are proposing a feature:
 * Remember that this is a volunteer-driven project, and that contributions
   are welcome :)
 
-Get Started!
-------------
+## Get Started!
 
 Ready to contribute? Here's how to set up `dnaapler` for local development.
 
 1. Fork the `dnaapler` repo on GitHub.
 2. Clone your fork locally::
 
-    $ git clone [email protected]:gbouras13/dnaapler.git
+```
+    git clone [email protected]:gbouras13/dnaapler.git
+```
+
 
 3. Install your local copy into a virtual environment. You will also need blast available. Assuming you have mamba installed::
 
-    $ mamba create -n dnaaplerDEV pip blast
-    $ conda activate dnaaplerDEV
-    $ cd dnaapler/
+```
+    mamba create -n dnaaplerDEV pip blast
+    conda activate dnaaplerDEV
+    cd dnaapler/
+```
+
 
 4. Create a branch for local development::
 
-    $ git checkout -b name-of-your-bugfix-or-feature
+```
+    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 black and isort and the
    tests::
 
-    $ black . 
-    $ isort . 
-    $ poetry run pytest tests/
+```
+    black . 
+    isort . 
+    pytest tests/
+```
 
    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
+```
+    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
------------------------
+## Pull Request Guidelines
 
 Before you submit a pull request, check that it meets these guidelines: