Scheme creation

.travis.yml

@@ -20,20 +20,13 @@ branches:
   only:
     - master
     - development
-
-# Blacklist of branches to not run CI testing on.
-# branches:
-#  except:
-#   - dontrunme 
-#   - test 
+    - /^.+\/_base$/
 
 before_install:
   - sudo apt-get -qq update;
 
 install:
   - python setup.py install
-  #Install pytest for testing.
-  - pip install pytest
 
 script:
-  - pytest
+  - python setup.py test

MANIFEST.in

@@ -2,6 +2,8 @@ include LICENSE
 include README.rst
 include MANIFEST.in
 include setup.py
-recursive-include *.py *.fasta
+recursive-include biohansel/subtype/data *.fasta
 exclude ipynbs
-exclude venv
+exclude venv
+exclude .venv
+global-exclude *.py[co] __pycache__

README.rst

@@ -43,13 +43,7 @@ Requirements and Dependencies
 
 Each new build of ``biohansel`` is automatically tested on Linux using `Continuous Integration <https://travis-ci.org/phac-nml/bio_hansel/branches>`_. ``biohansel`` has been confirmed to work on Mac OSX (versions 10.13.5 Beta and 10.12.6) when installed with Conda_.
 
-These are the dependencies required for ``biohansel``:
-
-- Python_ (>=v3.6)
-    - numpy_ >=1.12.1
-    - pandas_ >=0.20.1
-    - pyahocorasick_ >=1.1.6
-    - attrs_
+``biohansel`` requires Python 3.6+. Required Python library dependencies can be found in the ``setup.py``.
 
 
 Installation
@@ -259,16 +253,22 @@ Get the latest development code using Git from GitHub:
 
     git clone https://github.com/phac-nml/biohansel.git
     cd biohansel/
+    # checkout the main development branch or some other development branch
     git checkout development
-    # Create a virtual environment (virtualenv) for development
+    # Create a virtual environment (virtualenv) for development; ensure that you're creating a Python virtualenv with Python 3.6!
     virtualenv -p python3 .venv
     # Activate the newly created virtualenv
     source .venv/bin/activate
     # Install biohansel into the virtualenv in "editable" mode
     pip install -e .
+    # install Jupyter for prototyping in a Jupyter Notebook
+    pip install jupyter
+    # launch Jupyter Notebook
+    jupyter notebook
+    # hack away!
 
 
-Run tests with pytest_:
+Run tests with `$ python setup.py test` or pytest_:
 
 .. code-block:: bash
 
@@ -280,7 +280,6 @@ Run tests with pytest_:
     pytest -s tests/test_qc.py
 
 
-
 Legal
 =====