Adding tox, pytest, flake8, and travis configurations

Lets test some tests!

.travis.yml

@@ -0,0 +1,11 @@
+language: python
+python:
+  - "3.3"
+  - "3.6"
+  - "3.7"  # 3.7 development branch
+# command to install dependencies
+install:
+  - pip install tox-travis
+# command to run tests
+script:
+  - tox

docs/install.rst

@@ -29,3 +29,18 @@ or mv the TRAL configuration directory from your root dir to your home, e.g.::
     $ cd ~
     $ sudo mv /root/.tral ./
     $ sudo chown -R $(whoami) .tral
+
+
+Development
+-----------
+
+To compile locally, run
+
+    $ pip install -r requirements_dev.py
+    $ python setup.py install
+
+TRAL uses tox and pytest for testing. The following commands relate to testing and code style:
+
+    $ flake8  # check code style
+    $ python setup.py test  # Run tests
+    $ tox  # Run comprehensive test suite on multiple python versions

requirements.txt

@@ -0,0 +1,3 @@
+--index-url https://pypi.python.org/simple/
+
+-e .

requirements_dev.txt

@@ -0,0 +1,3 @@
+--index-url https://pypi.python.org/simple/
+
+-e .[develop,docs]

setup.cfg

@@ -0,0 +1,6 @@
+[aliases]
+test=pytest
+
+[flake8]
+exclude = docs
+max-line-length = 120

setup.py

@@ -59,15 +59,30 @@ def read(*paths):
         "Operating System :: OS Independent",
         ],
     install_requires=[
-        "Biopython >= 1.64",
+        "biopython >= 1.64",
         "configobj >= 5.0.6",
-        #"docutils >= 0.11", # Uncomment if you wish to create the documentation locally.
         "numpy >= 1.6.1",
-        #"pypandoc >= 0.9.6" # Uncomment if you wish to convert the markdown readme to a rest readme for upload on Pypi.
-        #"pytest >= 2.5.2", # Uncomment if you wish to run the tests locally.
         "scipy >=0.12.0",
-        #"Sphinx >= 1.2.2", # Uncomment if you wish to create the documentation locally.
     ],
+    setup_requires=["pytest-runner"],
+    tests_require=[
+        "pytest >= 2.5.2",
+    ],
+    # Install with e.g. `python setup.py install tral[docs]`
+    extras_require={
+        'docs': [
+            "docutils >= 0.11",
+            "pypandoc >= 0.9.6",
+            "Sphinx >= 1.2.2",
+            ],
+        'develop': [
+            "flake8 >= 3.6",
+            "tox >= 3.5",
+        ],
+        'workflow': [
+            "pyfaidx==0.4.7.1",  # Used by the workflow example for fasta indexing
+        ]
+    },
     # package_data: None-module files, which should still be distributed are mentioned here:
     package_data={"tral": ["tral_configuration/*.ini",
                            "tral_configuration/data/hhrepid/*",

tox.ini

@@ -0,0 +1,24 @@
+[tox]
+; could add some more environments in the future
+envlist = py37, flake8
+
+[travis]
+python =
+    3.7: py37
+    3.6: py36
+    3.5: py35
+    3.4: py34
+    3.3: py33
+
+[testenv:flake8]
+basepython = python
+deps = flake8
+commands = flake8 tral
+
+[testenv]
+deps =
+    -r{toxinidir}/requirements_dev.txt
+
+commands =
+    pip install -U pip
+    python setup.py test