From 33a09ebef856ed4f88911d3d949274bebf390cdc Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <mcrusoe@msu.edu>
Date: Fri, 28 Mar 2014 20:51:24 -0400
Subject: [PATCH] demote nose & sphinx to extra dependencies.

Auto-install Python developer tools as needed
---
 ChangeLog |  5 +++++
 Makefile  | 23 +++++++++++++++++------
 setup.py  |  4 ++--
 3 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 87c674fd30..10e0875aff 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -9,6 +9,11 @@
     * .ycm_extra_conf.py: Update our custom YouCompleteMe configuration to
     query the package configuration for the proper compilation flags.
 
+2014-03-28  Michael R. Crusoe  <mcrusoe@msu.edu>
+
+    * Makefile,setup.py: demote nose & sphinx to extra dependencies.
+    Auto-install Python developer tools as needed.
+
 2013-03-27  Michael R. Crusoe  <mcrusoe@msu.edu>
 
     * The system zlib and bzip2 libraries are now used instead of the bundled
diff --git a/Makefile b/Makefile
index b70b659671..9b06efb04e 100644
--- a/Makefile
+++ b/Makefile
@@ -23,6 +23,7 @@ debug:
 		--inplace
 
 doc: FORCE
+	pip install --user sphinx || pip install sphinx
 	./setup.py build_sphinx --fresh-env
 	@echo ''
 	@echo '--> docs in build/sphinx/html <--'
@@ -39,31 +40,40 @@ cppcheck: FORCE
 		--platform=unix64 --std=posix --quiet
 
 pep8: FORCE
-	pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/
+	pip install --user --quiet pep8==1.5 || pip install --quiet pep8==1.5
+	pep8 --exclude=_version.py setup.py khmer/ scripts/ tests/ || true
 
 autopep8: FORCE
+	pip install --user autopep8 || pip install autopep8
 	autopep8 --recursive --in-place --exclude _version.py --ignore E309 setup.py \
 		khmer/ scripts/ tests/
 
 pylint: all FORCE
+	pip install --user pylint || pip install pylint
 	pylint -f parseable khmer/[!_]*.py khmer/__init__.py scripts/*.py tests \
 		|| true
 
-coverage.xml: FORCE
+# We need to get coverage to look at our scripts. Since they aren't in a
+# python module we can't tell nosetests to look for them (via an import
+# statement). So we run nose inside of coverage.
+.coverage: FORCE
+	pip install --user coverage || pip install coverage
 	coverage run --branch --source=scripts,khmer -m nose --with-xunit \
 		--attr=\!known_failing --processes=0
+
+coverage.xml: .coverage
 	coverage xml
 
-coverage.html: FORCE
-	coverage run --branch --source=scripts,khmer -m nose --with-xunit \
-		--attr=\!known_failing --processes=0
-	coverage html 
+coverage.html: .coverage
+	coverage html
 
 coverage-gcovr.xml: FORCE
+	pip install --user gcovr || pip install gcovr
 	gcovr --root=. --branches --gcov-exclude='.*zlib.*|.*bzip2.*' --xml \
 		--output=coverage-gcovr.xml
 
 nosetests.xml: all
+	pip install --user nose || pip install nose
 	./setup.py nosetests --with-xunit
 
 doxygen: FORCE
@@ -76,6 +86,7 @@ lib:
 	$(MAKE)
 
 test: all
+	pip install --user nose || pip install nose
 	./setup.py nosetests
 
 FORCE:
diff --git a/setup.py b/setup.py
index 310da10249..8e4c9218fa 100755
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 """ Setup for khmer project. """
 
 import ez_setup
-ez_setup.use_setuptools(version="0.6c11")
+ez_setup.use_setuptools(version="0.7.2")
 
 import os
 from os import listdir as os_listdir
@@ -98,7 +98,7 @@
         "url": 'http://ged.msu.edu/',
         "packages": ['khmer'],
         "install_requires": ["screed >= 0.7.1", 'argparse >= 1.2.1', ],
-        "setup_requires": ['nose >= 1.0', 'sphinx', ],
+        "extras_require": {'docs': ['sphinx'], 'tests': ['nose >= 1.0']},
         "scripts": SCRIPTS,
         "ext_modules": [EXTENSION_MOD, ],
         # "platforms": '', # empty as is conveyed by the classifiers below