Merge pull request #838 from nsoranzo/pkg_resources

Use eggs.require() instead of pkg_resources in lib/galaxy/datatypes/ .

lib/galaxy/datatypes/converters/bgzip.py

@@ -5,13 +5,13 @@ Uses pysam to bgzip a file
 
 usage: %prog in_file out_file
 """
-
-import pkg_resources
-pkg_resources.require( "pysam" )
-import ctabix
-import tempfile
 import optparse
 import subprocess
+import tempfile
+
+from galaxy import eggs
+eggs.require( "pysam" )
+import ctabix
 
 
 def main():

lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py

@@ -6,17 +6,17 @@ Convert from GFF file to interval index file.
 usage:
     python gff_to_interval_index_converter.py [input] [output]
 """
-
 from __future__ import division
 
-import sys
 import fileinput
-import pkg_resources
-pkg_resources.require( "bx-python" )
+import sys
 
-from galaxy.datatypes.util.gff_util import GFFReaderWrapper, GenomicInterval, convert_gff_coords_to_bed
+from galaxy import eggs
+eggs.require( "bx-python" )
 from bx.interval_index_file import Indexes
 
+from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GenomicInterval, GFFReaderWrapper
+
 
 def main():
     # Arguments

lib/galaxy/datatypes/converters/interval_to_bed_converter.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-
 import sys
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 import bx.intervals.io
 
 assert sys.version_info[:2] >= ( 2, 4 )

lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py

@@ -1,9 +1,9 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-
 import sys
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 import bx.intervals.io
 
 assert sys.version_info[:2] >= ( 2, 4 )

lib/galaxy/datatypes/converters/interval_to_coverage.py

@@ -6,14 +6,15 @@ usage: %prog bed_file out_file
     -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in interval file
     -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in coverage file
 """
-import pkg_resources
-pkg_resources.require( "bx-python" )
-from bx.intervals import io
-from bx.cookbook import doc_optparse
 import commands
-from os import environ
 import tempfile
 from bisect import bisect
+from os import environ
+
+from galaxy import eggs
+eggs.require( "bx-python" )
+from bx.cookbook import doc_optparse
+from bx.intervals import io
 
 INTERVAL_METADATA = ('chromCol',
                      'startCol',

lib/galaxy/datatypes/converters/interval_to_fli.py

@@ -14,10 +14,12 @@ where location is formatted as:
 and symbols are sorted in lexigraphical order.
 '''
 import optparse
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 from bx.tabular.io import Comment
-from galaxy.datatypes.util.gff_util import GFFReaderWrapper, read_unordered_gtf, convert_gff_coords_to_bed
+
+from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf
 
 
 def main():

lib/galaxy/datatypes/converters/interval_to_tabix_converter.py

@@ -6,13 +6,13 @@ Supported presets: bed, gff, vcf
 
 usage: %prog in_file out_file
 """
-
-import pkg_resources
-pkg_resources.require( "pysam" )
-import ctabix
-import sys
-import os
 import optparse
+import os
+import sys
+
+from galaxy import eggs
+eggs.require( "pysam" )
+import ctabix
 
 
 def main():

lib/galaxy/datatypes/converters/maf_to_fasta_converter.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-
 import sys
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 import bx.align.maf
+
 from galaxy.tools.util import maf_utilities
 
 assert sys.version_info[:2] >= ( 2, 4 )

lib/galaxy/datatypes/converters/maf_to_interval_converter.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 # Dan Blankenberg
-
 import sys
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 import bx.align.maf
+
 from galaxy.tools.util import maf_utilities
 
 assert sys.version_info[:2] >= ( 2, 4 )

lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py

@@ -3,15 +3,16 @@
 """
 Convert from VCF file to interval index file.
 """
-
 from __future__ import division
 
 import optparse
-import pkg_resources
-pkg_resources.require( "bx-python" )
-import galaxy_utils.sequence.vcf
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 from bx.interval_index_file import Indexes
 
+import galaxy_utils.sequence.vcf
+
 
 def main():
     # Read options, args.

lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py

@@ -7,11 +7,12 @@ Original ordering, which may be specifically needed  by tools or external displa
 
 usage: %prog in_file out_file
 """
-import pkg_resources
-pkg_resources.require( "pysam" )
-import ctabix
 import optparse
 
+from galaxy import eggs
+eggs.require( "pysam" )
+import ctabix
+
 
 def main():
     # Read options, args.

lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py

@@ -7,9 +7,11 @@ Read a wiggle track and print out a series of lines containing
 and fixedStep wiggle lines.
 """
 import sys
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 import bx.wiggle
+
 from galaxy.tools.exception_handling import UCSCOutWrapper, UCSCLimitException
 
 

lib/galaxy/datatypes/display_applications/util.py

@@ -1,5 +1,5 @@
-import pkg_resources
-pkg_resources.require( "pycrypto" )
+from galaxy import eggs
+eggs.require( "pycrypto" )
 from Crypto.Cipher import Blowfish
 
 

lib/galaxy/datatypes/interval.py

@@ -1,25 +1,28 @@
 """
 Interval datatypes
 """
-
-import pkg_resources
-pkg_resources.require( "bx-python" )
-
+import logging
+import math
 import os
 import sys
-import logging
 import tempfile
-import data
-from galaxy import util
-from galaxy.web import url_for
 import urllib
+
+from galaxy import eggs
+eggs.require( "bx-python" )
+eggs.require( "numpy" )
+import numpy
 from bx.intervals.io import GenomicIntervalReader, ParseError
+
+from galaxy import util
 from galaxy.datatypes import metadata
 from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.tabular import Tabular
 from galaxy.datatypes.util.gff_util import parse_gff_attributes
-from galaxy.datatypes.sniff import get_headers
-import math
+from galaxy.web import url_for
+
+import data
 import dataproviders
 
 log = logging.getLogger(__name__)
@@ -1248,11 +1251,6 @@ class Wiggle( Tabular, _RemoteCallMixin ):
         """
         Assumes we have a numpy file.
         """
-        # Maybe if we import here people will still be able to use Galaxy when numpy kills it
-        pkg_resources.require("numpy>=1.2.1")
-
-        import numpy
-
         range = end - start
         # Determine appropriate resolution to plot ~1000 points
         resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )

lib/galaxy/datatypes/tabular.py

@@ -1,23 +1,21 @@
 """
 Tabular datatype
-
 """
-import pkg_resources
-pkg_resources.require( "bx-python" )
+import csv
 import gzip
 import logging
 import os
-import csv
+import re
 from cgi import escape
+
 from galaxy import util
-from galaxy.datatypes import data
-from galaxy.datatypes import metadata
+from galaxy.datatypes import data, metadata
 from galaxy.datatypes.checkers import is_gzip
 from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import get_headers
 from galaxy.util.json import dumps
+
 import dataproviders
-import re
 
 log = logging.getLogger(__name__)
 

lib/galaxy/datatypes/util/gff_util.py

@@ -1,12 +1,13 @@
 """
 Provides utilities for working with GFF files.
 """
-
 import copy
-import pkg_resources
-pkg_resources.require( "bx-python" )
+
+from galaxy import eggs
+eggs.require( "bx-python" )
 from bx.intervals.io import GenomicInterval, MissingFieldError, NiceReaderWrapper, ParseError, GenomicIntervalReader
 from bx.tabular.io import Header, Comment
+
 from galaxy.util.odict import odict