Making changes required to make pebl suitable for rpm packaging

Author: abhik

docs/src/intro.rst

@@ -32,7 +32,7 @@ include :term:`prior models` and :term:`task controllers`.
         This is the set of observations that is used to score a given network.
         The data can include missing values and hidden/unobserved variables and
         observations can be marked as being the result of specific
-        interventions. Data can be read from a file or created progrmatically.
+        interventions. Data can be read from a file or created programatically.
 
     Learner
         A learner implements a specific learning algorithm. It is given some

docs/src/tutorial.rst

@@ -242,8 +242,8 @@ taskcontroller package to run these learners in parallel::
 >>>            [ simanneal.SimulatedAnnealingLearner(dataset) for i in range(5) ]
 >>> tc = multiprocess.MultiProcessController(poolsize=2)
 >>> results = tc.run(learners)
->>> merged_results = results.merge(merged_results)
->>> merged_results.tohtml("example4-result")
+>>> merged_result = results.merge(results)
+>>> merged_result.tohtml("example4-result")
 
 In this example, we import the multiprocess module (line 3), create a
 multiprocess task controller with a pool size of two processes (line 7), run

setup.cfg

@@ -6,3 +6,8 @@ doctest-tests=1
 [apydia]
 modules = pebl
 
+[build_sphinx]
+source-dir = docs/src
+build-dir  = docs/build
+all_files  = 1
+

setup.py

@@ -63,7 +63,7 @@ def _unavailable(self, exc):
 
 setup(
     name='pebl',
-    version='1.01',
+    version='1.0.1',
     description='Python Environment for Bayesian Learning',
     long_description = long_desc,
     package_dir={'': 'src'},
@@ -77,7 +77,7 @@ def _unavailable(self, exc):
     license='MIT',
     zip_safe=False,
     classifiers=[
-        'Development Status :: 4 - Beta',
+        'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
         'Intended Audience :: Science/Research',
         'License :: OSI Approved :: MIT License',

src/pebl/test/testfiles/testdata1.txt

@@ -1,4 +1,4 @@
-var1	var2	var3
-2.5!	!X	1.7
-1.1	    !1.7	2.3
-4.2	999.3	12
+var1	var2	var3
+2.5!	!X	1.7
+1.1	    !1.7	2.3
+4.2	999.3	12

src/pebl/test/testfiles/testdata10.txt

@@ -1,8 +1,8 @@
-# some calculations with this dataset derived manually in pebl/test/test_cpd.py
-
-"v1,discrete(2)"	"v2,discrete(2)"	"v3,discrete(2)"	"v4,discrete(2)"
-0	1	1	0
-1	0	0	1
-1	1	1	0
-1	1	1	0
-0	0	1	1
+# some calculations with this dataset derived manually in pebl/test/test_cpd.py
+
+"v1,discrete(2)"	"v2,discrete(2)"	"v3,discrete(2)"	"v4,discrete(2)"
+0	1	1	0
+1	0	0	1
+1	1	1	0
+1	1	1	0
+0	0	1	1

src/pebl/test/testfiles/testdata11.txt

@@ -1,6 +1,6 @@
-"v1,discrete(2)"	"v2,discrete(2)"	"v3,discrete(2)"	"v4,discrete(2)"
-0	X	1	0
-1	X	0	1
-1	X	1	0
-1	X	1	0
-0	X	1	1
+"v1,discrete(2)"	"v2,discrete(2)"	"v3,discrete(2)"	"v4,discrete(2)"
+0	X	1	0
+1	X	0	1
+1	X	1	0
+1	X	1	0
+0	X	1	1

src/pebl/test/testfiles/testdata2.txt

@@ -1,7 +1,7 @@
-# comment line			
-"shh,discrete(2)"	"ptchp,discrete(3)"	"smo,continuous"	"outcome,class(good, bad)"
-
-0!	!0	1.25	good
-#comment in the data section			
-1	!1	1.1	bad
-1	2	0.45	bad
+# comment line			
+"shh,discrete(2)"	"ptchp,discrete(3)"	"smo,continuous"	"outcome,class(good, bad)"
+
+0!	!0	1.25	good
+#comment in the data section			
+1	!1	1.1	bad
+1	2	0.45	bad

src/pebl/test/testfiles/testdata3.txt

@@ -1,4 +1,4 @@
-	"shh,discrete(2)"	"ptchp,discrete(3)"
-sample1	0!	!0
-sample2	1	!1
-sample3	1	2
+	"shh,discrete(2)"	"ptchp,discrete(3)"
+sample1	0!	!0
+sample2	1	!1
+sample3	1	2

src/pebl/test/testfiles/testdata4.txt

@@ -1,4 +1,4 @@
-"shh,discrete(2)"	"ptchp,discrete(3)"	
-sample1	0!	!0
-sample2	1	!1
-sample3	1	2
+"shh,discrete(2)"	"ptchp,discrete(3)"	
+sample1	0!	!0
+sample2	1	!1
+sample3	1	2

src/pebl/test/testfiles/testdata5.txt

@@ -1,10 +1,10 @@
-v1	v2	v3	v4	v5
-1.2	1.4	2.1	2.2	1.1
-2.3	1.1	2.1	3.2	1.3
-3.2	0	1.2	2.5	1.6
-4.2	2.4	3.2	2.1	2.8
-2.7	1.5	0	1.5	1.1
-1.1	2.3	2.1	1.7	3.2
-2.3	1.1	4.3	2.3	1.1
-3.2	2.6	1.9	1.7	1.1
-2.1	1.5	3	1.4	1.1
+v1	v2	v3	v4	v5
+1.2	1.4	2.1	2.2	1.1
+2.3	1.1	2.1	3.2	1.3
+3.2	0	1.2	2.5	1.6
+4.2	2.4	3.2	2.1	2.8
+2.7	1.5	0	1.5	1.1
+1.1	2.3	2.1	1.7	3.2
+2.3	1.1	4.3	2.3	1.1
+3.2	2.6	1.9	1.7	1.1
+2.1	1.5	3	1.4	1.1

src/pebl/test/testfiles/testdata6.txt

@@ -1,6 +1,6 @@
-"v1,discrete(2)"	"v2,discrete(2)"	"v3,discrete(2)"	"v4,discrete(2)"
-0	1	1	0
-1	0	0	2
-1	1	2	0
-1	1	1	0
-0	0	1	1
+"v1,discrete(2)"	"v2,discrete(2)"	"v3,discrete(2)"	"v4,discrete(2)"
+0	1	1	0
+1	0	0	2
+1	1	2	0
+1	1	1	0
+0	0	1	1

src/pebl/test/testfiles/testdata7.txt

@@ -1,31 +1,31 @@
-"v1,discrete(3)"	"v2,discrete(4)"	"v3,discrete(3)"	"v4,discrete(6)"
-0	2	1	2
-1	2	1	1
-2	1	0	2
-2	1	1	1
-1	1	2	1
-1	1	0	1
-2	0	1	0
-1	2	1	1
-1	0	0	2
-1	2	2	0
-2	1	0	2
-1	2	0	2
-0	2	0	1
-1	2	1	2
-1	2	0	0
-1	0	1	0
-1	2	0	0
-1	2	0	1
-2	0	2	2
-1	1	0	1
-1	0	0	2
-0	1	1	1
-2	2	2	2
-2	2	1	0
-2	0	2	2
-2	1	0	0
-0	2	0	1
-1	0	2	2
-1	2	1	1
-0	0	2	1
+"v1,discrete(3)"	"v2,discrete(4)"	"v3,discrete(3)"	"v4,discrete(6)"
+0	2	1	2
+1	2	1	1
+2	1	0	2
+2	1	1	1
+1	1	2	1
+1	1	0	1
+2	0	1	0
+1	2	1	1
+1	0	0	2
+1	2	2	0
+2	1	0	2
+1	2	0	2
+0	2	0	1
+1	2	1	2
+1	2	0	0
+1	0	1	0
+1	2	0	0
+1	2	0	1
+2	0	2	2
+1	1	0	1
+1	0	0	2
+0	1	1	1
+2	2	2	2
+2	2	1	0
+2	0	2	2
+2	1	0	0
+0	2	0	1
+1	0	2	2
+1	2	1	1
+0	0	2	1

src/pebl/test/testfiles/testdata8.txt

@@ -1,31 +1,31 @@
-"v1,discrete(3),"	"v2,discrete(3)"	"v3,discrete(3)"	"v4,discrete(3)"	"v5,discrete(3)"
-0	0	X	1	2
-0	0	X	1	1
-2	1	X	0	0
-2	1	X	1	1
-1	1	X	2	0
-1	1	X	0	0
-2	0	X	1	0
-1	2	X	1	1
-1	0	X	0	2
-1	2	X	2	0
-2	1	X	0	2
-1	2	X	0	2
-0	2	X	2	1
-1	2	X	1	2
-1	2	X	0	0
-0	0	X	1	0
-0	1	X	0	0
-0	1	X	0	1
-2	0	X	2	2
-2	1	X	2	1
-1	0	X	0	2
-0	1	X	1	1
-2	2	X	2	2
-2	2	X	1	0
-2	0	X	2	2
-2	1	X	2	0
-0	2	X	0	1
-0	0	X	2	2
-1	2	X	1	1
-0	0	X	2	1
+"v1,discrete(3),"	"v2,discrete(3)"	"v3,discrete(3)"	"v4,discrete(3)"	"v5,discrete(3)"
+0	0	X	1	2
+0	0	X	1	1
+2	1	X	0	0
+2	1	X	1	1
+1	1	X	2	0
+1	1	X	0	0
+2	0	X	1	0
+1	2	X	1	1
+1	0	X	0	2
+1	2	X	2	0
+2	1	X	0	2
+1	2	X	0	2
+0	2	X	2	1
+1	2	X	1	2
+1	2	X	0	0
+0	0	X	1	0
+0	1	X	0	0
+0	1	X	0	1
+2	0	X	2	2
+2	1	X	2	1
+1	0	X	0	2
+0	1	X	1	1
+2	2	X	2	2
+2	2	X	1	0
+2	0	X	2	2
+2	1	X	2	0
+0	2	X	0	1
+0	0	X	2	2
+1	2	X	1	1
+0	0	X	2	1