Fix a few tracebacks when building docs with 'make -C doc/ html' .

.ci/pep8_sources.txt

@@ -2,6 +2,7 @@ cron/parse_builds.py
 lib/galaxy/auth
 lib/galaxy/config.py
 lib/galaxy/datatypes/{data,proteomics}.py
+lib/galaxy/datatypes/converters/{bedgraph_to_array_tree_converter,wiggle_to_array_tree_converter}.py
 lib/galaxy/exceptions/error_codes.py
 lib/galaxy/jobs/{__init__,error_level,manager,stock_rules}.py
 lib/galaxy/main.py

doc/source/conf.py

@@ -274,6 +274,6 @@ class Mock(object):
             return Mock()
 
 # adding pbs_python, DRMAA_python, markupsafe, and drmaa here had no effect.
-MOCK_MODULES = ['tables', 'decorator', 'numpy']
+MOCK_MODULES = ['tables', 'decorator']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py

@@ -3,13 +3,16 @@
 from __future__ import division
 
 import sys
+
 from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.arrays.array_tree import *
-# from bx.arrays.wiggle import BedReader
+
+eggs.require('numpy')  # noqa
+eggs.require('bx-python')  # noqa
+from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
 
 BLOCK_SIZE = 100
 
+
 class BedGraphReader:
     def __init__( self, f ):
         self.f = f
@@ -36,6 +39,8 @@ class BedGraphReader:
                 chrom_end = int(feature[2])
                 score = float(feature[3])
                 return chrom, chrom_start, chrom_end, None, score
+
+
 def main():
 
     input_fname = sys.argv[1]
@@ -44,7 +49,7 @@ def main():
     reader = BedGraphReader( open( input_fname ) )
 
     # Fill array from reader
-    d = array_tree_dict_from_reader( reader, {}, block_size = BLOCK_SIZE )
+    d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )
 
     for array_tree in d.itervalues():
         array_tree.root.build_summary()

lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py

@@ -3,13 +3,16 @@
 from __future__ import division
 
 import sys
+
 from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.arrays.array_tree import *
+eggs.require('numpy')  # noqa
+eggs.require('bx-python')  # noqa
+from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
 from bx.arrays.wiggle import WiggleReader
 
 BLOCK_SIZE = 100
 
+
 def main():
 
     input_fname = sys.argv[1]
@@ -18,7 +21,7 @@ def main():
     reader = WiggleReader( open( input_fname ) )
 
     # Fill array from reader
-    d = array_tree_dict_from_reader( reader, {}, block_size = BLOCK_SIZE )
+    d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )
 
     for array_tree in d.itervalues():
         array_tree.root.build_summary()

lib/galaxy/visualization/data_providers/genome.py

@@ -2,25 +2,27 @@
 Data providers for genome visualizations.
 """
 
-import os, sys, re
-import pkg_resources
 import itertools
-import random
 import math
+import os
+import random
+import re
+import sys
 
-pkg_resources.require( "numpy" )
-pkg_resources.require( "bx-python" )
-pkg_resources.require( "pysam" )
+from galaxy import eggs
+eggs.require('numpy')  # noqa
+eggs.require('bx-python')  # noqa
 from bx.interval_index_file import Indexes
-from bx.bbi.bigwig_file import BigWigFile
 from bx.bbi.bigbed_file import BigBedFile
+from bx.bbi.bigwig_file import BigWigFile
+eggs.require('pysam')  # noqa
 from pysam import csamtools, ctabix
 
+from galaxy.datatypes.interval import Bed, Gff, Gtf
 from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFFeature, GFFInterval, GFFReaderWrapper, parse_gff_attributes
 from galaxy.util.json import loads
 from galaxy.visualization.data_providers.basic import BaseDataProvider
 from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and_cigar
-from galaxy.datatypes.interval import Bed, Gff, Gtf
 
 #
 # Utility functions.