From edfc98c2fda5110014138f7cfa81e43cf6b75f69 Mon Sep 17 00:00:00 2001
From: Camille Scott <camille.scott.w@gmail.com>
Date: Wed, 13 Sep 2017 15:30:01 -0700
Subject: [PATCH 1/5] Swap to unordered maps where able, for speed

---
 include/oxli/oxli.hh       | 19 ++++++++++---------
 include/oxli/storage.hh    |  3 ++-
 khmer/_oxli/oxli_types.pxd | 11 ++++++-----
 tests/test_subset_graph.py |  2 ++
 4 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/include/oxli/oxli.hh b/include/oxli/oxli.hh
index 1d3a074f9c..1acd65da24 100644
--- a/include/oxli/oxli.hh
+++ b/include/oxli/oxli.hh
@@ -71,6 +71,7 @@ private:\
 
 #include <set>
 #include <map>
+#include <unordered_map>
 #include <queue>
 #include <list>
 #include <functional>
@@ -129,22 +130,22 @@ typedef void (*CallbackFn)(const char * info, void * callback_data,
 typedef unsigned int PartitionID;
 typedef std::set<HashIntoType> SeenSet;
 typedef std::set<PartitionID> PartitionSet;
-typedef std::map<HashIntoType, PartitionID*> PartitionMap;
-typedef std::map<PartitionID, PartitionID*> PartitionPtrMap;
-typedef std::map<PartitionID, SeenSet*> PartitionsToTagsMap;
+typedef std::unordered_map<HashIntoType, PartitionID*> PartitionMap;
+typedef std::unordered_map<PartitionID, PartitionID*> PartitionPtrMap;
+typedef std::unordered_map<PartitionID, SeenSet*> PartitionsToTagsMap;
 typedef std::set<PartitionID *> PartitionPtrSet;
-typedef std::map<PartitionID, PartitionPtrSet*> ReversePartitionMap;
+typedef std::unordered_map<PartitionID, PartitionPtrSet*> ReversePartitionMap;
 typedef std::queue<HashIntoType> NodeQueue;
-typedef std::map<PartitionID, PartitionID*> PartitionToPartitionPMap;
-typedef std::map<HashIntoType, unsigned int> TagCountMap;
-typedef std::map<PartitionID, unsigned int> PartitionCountMap;
+typedef std::unordered_map<PartitionID, PartitionID*> PartitionToPartitionPMap;
+typedef std::unordered_map<HashIntoType, unsigned int> TagCountMap;
+typedef std::unordered_map<PartitionID, unsigned int> PartitionCountMap;
 typedef std::map<unsigned long long, unsigned long long>
 PartitionCountDistribution;
 
 // types used in @camillescott's sparse labeling extension
 typedef unsigned long long int Label;
-typedef std::multimap<HashIntoType, Label> TagLabelMap;
-typedef std::multimap<Label, HashIntoType> LabelTagMap;
+typedef std::unordered_multimap<HashIntoType, Label> TagLabelMap;
+typedef std::unordered_multimap<Label, HashIntoType> LabelTagMap;
 typedef std::pair<HashIntoType, Label> TagLabelPair;
 typedef std::pair<Label, HashIntoType> LabelTagPair;
 typedef std::set<Label> LabelSet;
diff --git a/include/oxli/storage.hh b/include/oxli/storage.hh
index 9a19b0f775..33fb6f7f73 100644
--- a/include/oxli/storage.hh
+++ b/include/oxli/storage.hh
@@ -41,12 +41,13 @@ Contact: khmer-project@idyll.org
 #include <cassert>
 #include <array>
 #include <mutex>
+#include <unordered_map>
 using MuxGuard = std::lock_guard<std::mutex>;
 
 #include "gqf.h"
 
 namespace oxli {
-typedef std::map<HashIntoType, BoundedCounterType> KmerCountMap;
+typedef std::unordered_map<HashIntoType, BoundedCounterType> KmerCountMap;
 
 //
 // base Storage class for hashtable-related storage of information in memory.
diff --git a/khmer/_oxli/oxli_types.pxd b/khmer/_oxli/oxli_types.pxd
index 72e8e8c8f0..899b23a806 100644
--- a/khmer/_oxli/oxli_types.pxd
+++ b/khmer/_oxli/oxli_types.pxd
@@ -1,5 +1,6 @@
 from libcpp cimport bool
 from libcpp.map cimport map
+from libcpp.unordered_map cimport unordered_map
 from libcpp.set cimport set
 from libcpp.string cimport string
 
@@ -13,12 +14,12 @@ cdef extern from "oxli/oxli.hh" namespace "oxli":
 
     ctypedef unsigned int PartitionID
     ctypedef set[PartitionID] PartitionSet
-    ctypedef map[HashIntoType, PartitionID*] PartitionMap
-    ctypedef map[PartitionID, PartitionID*] PartitionPtrMap
-    ctypedef map[PartitionID, HashIntoTypeSet*] PartitionToTagsMap
-    ctypedef map[PartitionID, unsigned int] PartitionCountMap
+    ctypedef unordered_map[HashIntoType, PartitionID*] PartitionMap
+    ctypedef unordered_map[PartitionID, PartitionID*] PartitionPtrMap
+    ctypedef unordered_map[PartitionID, HashIntoTypeSet*] PartitionToTagsMap
+    ctypedef unordered_map[PartitionID, unsigned int] PartitionCountMap
     ctypedef map[unsigned long long, unsigned long long] PartitionCountDistribution
-    ctypedef map[HashIntoType, unsigned int] TagCountMap
+    ctypedef unordered_map[HashIntoType, unsigned int] TagCountMap
     ctypedef unsigned char WordLength
     ctypedef unsigned short int BoundedCounterType
 
diff --git a/tests/test_subset_graph.py b/tests/test_subset_graph.py
index c836801d69..e5db958a4b 100644
--- a/tests/test_subset_graph.py
+++ b/tests/test_subset_graph.py
@@ -700,10 +700,12 @@ def test_partition_overlap_2():
     assert x == ([(3, 8)], 0), x
 
     x = p2.partition_sizes()
+    x[0].sort(key=lambda pair: pair[0])
     assert x == ([(3, 6), (5, 6)], 0), x
 
     x = p1.partition_average_coverages(kh)
     assert x == [(3, 11)]
 
     x = p2.partition_average_coverages(kh)
+    x.sort(key=lambda pair: pair[0])
     assert x == [(3, 5), (5, 10)], x

From ec5171b331403dd3397724c07bd50ee281fefc07 Mon Sep 17 00:00:00 2001
From: Camille Scott <camille.scott.w@gmail.com>
Date: Wed, 13 Sep 2017 15:32:36 -0700
Subject: [PATCH 2/5] Remove unused map includes

---
 include/oxli/hashgraph.hh | 1 -
 include/oxli/hashtable.hh | 1 -
 2 files changed, 2 deletions(-)

diff --git a/include/oxli/hashgraph.hh b/include/oxli/hashgraph.hh
index c8a4156069..f450a42e6b 100644
--- a/include/oxli/hashgraph.hh
+++ b/include/oxli/hashgraph.hh
@@ -43,7 +43,6 @@ Contact: khmer-project@idyll.org
 #include <fstream>
 #include <iostream>
 #include <list>
-#include <map>
 #include <queue>
 #include <set>
 #include <string>
diff --git a/include/oxli/hashtable.hh b/include/oxli/hashtable.hh
index 0ced08d019..1f95605130 100644
--- a/include/oxli/hashtable.hh
+++ b/include/oxli/hashtable.hh
@@ -44,7 +44,6 @@ Contact: khmer-project@idyll.org
 #include <fstream>
 #include <iostream>
 #include <list>
-#include <map>
 #include <queue>
 #include <set>
 #include <string>

From 2c87d813c2e39550ece844db10a9d55b4dadc209 Mon Sep 17 00:00:00 2001
From: Daniel Standage <daniel.standage@gmail.com>
Date: Wed, 13 Sep 2017 22:02:34 -0700
Subject: [PATCH 3/5] Drop __future__ imports

---
 Makefile                                  | 6 +++---
 khmer/__init__.py                         | 1 -
 khmer/_version.py                         | 0
 khmer/kfile.py                            | 1 -
 khmer/khmer_args.py                       | 2 --
 khmer/khmer_logger.py                     | 1 -
 khmer/thread_utils.py                     | 1 -
 khmer/trimming.py                         | 1 -
 khmer/utils.py                            | 1 -
 oxli/build_graph.py                       | 1 -
 oxli/functions.py                         | 1 -
 oxli/partition.py                         | 1 -
 sandbox/assemble-and-track.py             | 1 -
 sandbox/assemble-on-the-go.py             | 1 -
 sandbox/assembly-diff-2.py                | 1 -
 sandbox/assembly-diff.py                  | 2 --
 sandbox/assemstats3.py                    | 2 --
 sandbox/bloom-count.py                    | 2 --
 sandbox/build-sparse-graph.py             | 1 -
 sandbox/calc-best-assembly.py             | 1 -
 sandbox/calc-error-profile.py             | 2 --
 sandbox/calc-median-distribution.py       | 2 --
 sandbox/collect-reads.py                  | 2 --
 sandbox/collect-variants.py               | 1 -
 sandbox/correct-reads.py                  | 1 -
 sandbox/count-kmers-single.py             | 1 -
 sandbox/count-kmers.py                    | 1 -
 sandbox/error-correct-pass2.py            | 1 -
 sandbox/estimate_optimal_hash.py          | 1 -
 sandbox/extract-compact-dbg.py            | 1 -
 sandbox/extract-single-partition.py       | 1 -
 sandbox/extract-unassembled-reads-2.py    | 1 -
 sandbox/extract-unassembled-reads.py      | 1 -
 sandbox/filter-below-abund.py             | 1 -
 sandbox/filter-median-and-pct.py          | 1 -
 sandbox/filter-median.py                  | 1 -
 sandbox/graph-size.py                     | 1 -
 sandbox/link-compact-dbg.py               | 1 -
 sandbox/make-coverage.py                  | 1 -
 sandbox/multi-rename.py                   | 1 -
 sandbox/normalize-by-median-pct.py        | 2 --
 sandbox/optimal_args_hashbits.py          | 1 -
 sandbox/print-tagset.py                   | 1 -
 sandbox/readaligner_pairhmm_train.py      | 2 --
 sandbox/reassemble-contigs.py             | 1 -
 sandbox/renumber-partitions.py            | 1 -
 sandbox/saturate-by-median.py             | 2 --
 sandbox/shuffle-reverse-rotary.py         | 1 -
 sandbox/slice-reads-by-coverage.py        | 1 -
 sandbox/split-fasta.py                    | 1 -
 sandbox/split-sequences-by-length.py      | 1 -
 sandbox/stoptag-abundance-hist.py         | 1 -
 sandbox/stoptags-by-position.py           | 1 -
 sandbox/streaming-assembly-simple.py      | 1 -
 sandbox/strip-partition.py                | 1 -
 sandbox/subset-report.py                  | 1 -
 sandbox/sweep-files.py                    | 1 -
 sandbox/sweep-out-reads-with-contigs.py   | 1 -
 sandbox/sweep-reads.py                    | 1 -
 sandbox/sweep-reads2.py                   | 1 -
 sandbox/sweep-reads3.py                   | 1 -
 sandbox/write-trimmomatic.py              | 1 -
 scripts/abundance-dist-single.py          | 1 -
 scripts/abundance-dist.py                 | 1 -
 scripts/annotate-partitions.py            | 1 -
 scripts/count-median.py                   | 1 -
 scripts/do-partition.py                   | 1 -
 scripts/extract-long-sequences.py         | 1 -
 scripts/extract-paired-reads.py           | 1 -
 scripts/extract-partitions.py             | 1 -
 scripts/fastq-to-fasta.py                 | 1 -
 scripts/filter-abund-single.py            | 1 -
 scripts/filter-abund.py                   | 1 -
 scripts/filter-stoptags.py                | 1 -
 scripts/find-knots.py                     | 1 -
 scripts/interleave-reads.py               | 1 -
 scripts/load-into-counting.py             | 1 -
 scripts/make-initial-stoptags.py          | 1 -
 scripts/merge-partitions.py               | 1 -
 scripts/normalize-by-median.py            | 1 -
 scripts/partition-graph.py                | 1 -
 scripts/readstats.py                      | 1 -
 scripts/sample-reads-randomly.py          | 1 -
 scripts/split-paired-reads.py             | 1 -
 scripts/trim-low-abund.py                 | 1 -
 scripts/unique-kmers.py                   | 1 -
 tests/__init__.py                         | 0
 tests/graph_features.py                   | 2 --
 tests/khmer_tst_utils.py                  | 1 -
 tests/table_fixtures.py                   | 2 --
 tests/test_assembly.py                    | 2 --
 tests/test_banding.py                     | 2 --
 tests/test_countgraph.py                  | 2 --
 tests/test_counting_single.py             | 2 --
 tests/test_counttable.py                  | 2 --
 tests/test_cpython_hierarchy.py           | 2 --
 tests/test_cython_parsing.py              | 2 --
 tests/test_filter_abund.py                | 0
 tests/test_functions.py                   | 2 --
 tests/test_graph.py                       | 2 --
 tests/test_hashset.py                     | 2 --
 tests/test_hll.py                         | 2 --
 tests/test_labelhash.py                   | 2 --
 tests/test_lump.py                        | 1 -
 tests/test_memory.py                      | 2 --
 tests/test_nibblestorage.py               | 2 --
 tests/test_nodegraph.py                   | 2 --
 tests/test_normalize_by_median.py         | 1 -
 tests/test_oxli_functions.py              | 1 -
 tests/test_qfstorage.py                   | 2 --
 tests/test_read_aligner.py                | 2 --
 tests/test_read_handling.py               | 3 ---
 tests/test_read_parsers.py                | 2 --
 tests/test_sandbox_scripts.py             | 3 ---
 tests/test_script_arguments.py            | 2 --
 tests/test_script_output.py               | 2 --
 tests/test_scripts.py                     | 3 ---
 tests/test_sequence_validation.py         | 2 --
 tests/test_streaming_io.py                | 3 ---
 tests/test_subset_graph.py                | 1 -
 tests/test_tabletype.py                   | 0
 tests/test_threaded_sequence_processor.py | 0
 tests/test_version.py                     | 1 -
 123 files changed, 3 insertions(+), 161 deletions(-)
 mode change 100644 => 100755 khmer/__init__.py
 mode change 100644 => 100755 khmer/_version.py
 mode change 100644 => 100755 khmer/kfile.py
 mode change 100644 => 100755 khmer/khmer_args.py
 mode change 100644 => 100755 khmer/khmer_logger.py
 mode change 100644 => 100755 khmer/thread_utils.py
 mode change 100644 => 100755 khmer/trimming.py
 mode change 100644 => 100755 khmer/utils.py
 mode change 100644 => 100755 tests/__init__.py
 mode change 100644 => 100755 tests/graph_features.py
 mode change 100644 => 100755 tests/khmer_tst_utils.py
 mode change 100644 => 100755 tests/table_fixtures.py
 mode change 100644 => 100755 tests/test_assembly.py
 mode change 100644 => 100755 tests/test_banding.py
 mode change 100644 => 100755 tests/test_countgraph.py
 mode change 100644 => 100755 tests/test_counting_single.py
 mode change 100644 => 100755 tests/test_counttable.py
 mode change 100644 => 100755 tests/test_cpython_hierarchy.py
 mode change 100644 => 100755 tests/test_cython_parsing.py
 mode change 100644 => 100755 tests/test_filter_abund.py
 mode change 100644 => 100755 tests/test_functions.py
 mode change 100644 => 100755 tests/test_graph.py
 mode change 100644 => 100755 tests/test_hashset.py
 mode change 100644 => 100755 tests/test_hll.py
 mode change 100644 => 100755 tests/test_labelhash.py
 mode change 100644 => 100755 tests/test_lump.py
 mode change 100644 => 100755 tests/test_memory.py
 mode change 100644 => 100755 tests/test_nibblestorage.py
 mode change 100644 => 100755 tests/test_nodegraph.py
 mode change 100644 => 100755 tests/test_normalize_by_median.py
 mode change 100644 => 100755 tests/test_oxli_functions.py
 mode change 100644 => 100755 tests/test_qfstorage.py
 mode change 100644 => 100755 tests/test_read_aligner.py
 mode change 100644 => 100755 tests/test_read_handling.py
 mode change 100644 => 100755 tests/test_read_parsers.py
 mode change 100644 => 100755 tests/test_sandbox_scripts.py
 mode change 100644 => 100755 tests/test_script_arguments.py
 mode change 100644 => 100755 tests/test_script_output.py
 mode change 100644 => 100755 tests/test_scripts.py
 mode change 100644 => 100755 tests/test_sequence_validation.py
 mode change 100644 => 100755 tests/test_streaming_io.py
 mode change 100644 => 100755 tests/test_subset_graph.py
 mode change 100644 => 100755 tests/test_tabletype.py
 mode change 100644 => 100755 tests/test_threaded_sequence_processor.py
 mode change 100644 => 100755 tests/test_version.py

diff --git a/Makefile b/Makefile
index a7b00c8308..66f15552f6 100644
--- a/Makefile
+++ b/Makefile
@@ -63,9 +63,9 @@ INCLUDESTRING=$(shell gcc -E -x c++ - -v < /dev/null 2>&1 >/dev/null \
 INCLUDEOPTS=$(shell gcc -E -x c++ - -v < /dev/null 2>&1 >/dev/null \
 	    | grep '^ /' | grep -v cc1plus | awk '{print "-I" $$1 " "}')
 
-PYINCLUDE=$(shell python -c "from __future__ import print_function; \
-	    import sysconfig; flags = ['-I' + sysconfig.get_path('include'), \
-	    '-I' + sysconfig.get_path('platinclude')]; print(' '.join(flags))")
+PYINCLUDE=$(shell python -c "import sysconfig; \
+            flags = ['-I' + sysconfig.get_path('include'), \
+            '-I' + sysconfig.get_path('platinclude')]; print(' '.join(flags))")
 
 CPPCHECK_SOURCES=$(filter-out lib/test%, $(wildcard lib/*.cc khmer/_khmer.cc) )
 CPPCHECK=cppcheck --enable=all \
diff --git a/khmer/__init__.py b/khmer/__init__.py
old mode 100644
new mode 100755
index 22d8470f20..c5871e83a4
--- a/khmer/__init__.py
+++ b/khmer/__init__.py
@@ -36,7 +36,6 @@
 """This is khmer; please see http://khmer.readthedocs.io/."""
 
 
-from __future__ import print_function
 from collections import namedtuple
 from math import log
 import json
diff --git a/khmer/_version.py b/khmer/_version.py
old mode 100644
new mode 100755
diff --git a/khmer/kfile.py b/khmer/kfile.py
old mode 100644
new mode 100755
index 92288334b2..ea2b5daa3b
--- a/khmer/kfile.py
+++ b/khmer/kfile.py
@@ -34,7 +34,6 @@
 # Contact: khmer-project@idyll.org
 """File handling/checking utilities for command-line scripts."""
 
-from __future__ import print_function, unicode_literals, division
 
 import os
 import sys
diff --git a/khmer/khmer_args.py b/khmer/khmer_args.py
old mode 100644
new mode 100755
index ea438ffc40..8f233e4efa
--- a/khmer/khmer_args.py
+++ b/khmer/khmer_args.py
@@ -35,8 +35,6 @@
 # Contact: khmer-project@idyll.org
 """Common argparse constructs."""
 
-from __future__ import unicode_literals
-from __future__ import print_function
 
 import sys
 import argparse
diff --git a/khmer/khmer_logger.py b/khmer/khmer_logger.py
old mode 100644
new mode 100755
index bfe64b4a94..aa792f05b4
--- a/khmer/khmer_logger.py
+++ b/khmer/khmer_logger.py
@@ -33,7 +33,6 @@
 # Contact: khmer-project@idyll.org
 """Lightweight logging framework for khmer."""
 
-from __future__ import print_function, unicode_literals
 import sys
 
 __QUIET__ = False
diff --git a/khmer/thread_utils.py b/khmer/thread_utils.py
old mode 100644
new mode 100755
index 55c15eab7c..e5a1fd3068
--- a/khmer/thread_utils.py
+++ b/khmer/thread_utils.py
@@ -35,7 +35,6 @@
 # pylint: disable=missing-docstring,too-few-public-methods
 """Utilities for dealing with multithreaded processing of short reads."""
 
-from __future__ import print_function, unicode_literals
 
 import threading
 import sys
diff --git a/khmer/trimming.py b/khmer/trimming.py
old mode 100644
new mode 100755
index e23679bb0e..ff99756f27
--- a/khmer/trimming.py
+++ b/khmer/trimming.py
@@ -32,7 +32,6 @@
 #
 # Contact: khmer-project@idyll.org
 """Common methods for trimming short reads on k-mer abundance."""
-from __future__ import print_function, unicode_literals
 import screed
 
 
diff --git a/khmer/utils.py b/khmer/utils.py
old mode 100644
new mode 100755
index cee1704e4c..f39689fb39
--- a/khmer/utils.py
+++ b/khmer/utils.py
@@ -33,7 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 """Helpful methods for performing common argument-checking tasks in scripts."""
-from __future__ import print_function, unicode_literals
 from khmer._oxli.parsing import (check_is_left, check_is_right, check_is_pair,
                                  UnpairedReadsError, _split_left_right)
 import itertools
diff --git a/oxli/build_graph.py b/oxli/build_graph.py
index 58674197bd..fbb1e71db6 100755
--- a/oxli/build_graph.py
+++ b/oxli/build_graph.py
@@ -43,7 +43,6 @@
 Use '-h' for parameter help.
 """
 
-from __future__ import print_function, absolute_import, unicode_literals
 
 import sys
 
diff --git a/oxli/functions.py b/oxli/functions.py
index e3608f66da..b252c53fae 100755
--- a/oxli/functions.py
+++ b/oxli/functions.py
@@ -35,7 +35,6 @@
 
 """A collection of functions for use throughout khmer/oxli."""
 
-from __future__ import print_function
 import threading
 import khmer.utils
 
diff --git a/oxli/partition.py b/oxli/partition.py
index 53afe58f55..6cf71febf3 100755
--- a/oxli/partition.py
+++ b/oxli/partition.py
@@ -7,7 +7,6 @@
 #
 # pylint: disable=missing-docstring,no-member
 """Common functions for partitioning."""
-from __future__ import print_function, absolute_import, unicode_literals
 
 import sys
 import gc
diff --git a/sandbox/assemble-and-track.py b/sandbox/assemble-and-track.py
index 429bce66f2..09bbbb1e77 100755
--- a/sandbox/assemble-and-track.py
+++ b/sandbox/assemble-and-track.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-from __future__ import print_function
 import csv
 import screed
 import khmer
diff --git a/sandbox/assemble-on-the-go.py b/sandbox/assemble-on-the-go.py
index 6e5f882dec..a768638e75 100755
--- a/sandbox/assemble-on-the-go.py
+++ b/sandbox/assemble-on-the-go.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-from __future__ import print_function
 import screed
 import khmer
 import argparse
diff --git a/sandbox/assembly-diff-2.py b/sandbox/assembly-diff-2.py
index 74856151db..54ab13bca1 100755
--- a/sandbox/assembly-diff-2.py
+++ b/sandbox/assembly-diff-2.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 import khmer
 import screed
diff --git a/sandbox/assembly-diff.py b/sandbox/assembly-diff.py
index 4c19d7fffb..fae61c0d58 100755
--- a/sandbox/assembly-diff.py
+++ b/sandbox/assembly-diff.py
@@ -33,8 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import division
-from __future__ import print_function
 import sys
 import khmer
 import screed
diff --git a/sandbox/assemstats3.py b/sandbox/assemstats3.py
index 6104231270..176eed2b3f 100755
--- a/sandbox/assemstats3.py
+++ b/sandbox/assemstats3.py
@@ -41,8 +41,6 @@
 You can obtain screed by running
    pip install screed
 '''
-from __future__ import division
-from __future__ import print_function
 
 import screed
 import sys
diff --git a/sandbox/bloom-count.py b/sandbox/bloom-count.py
index 7feefca345..e9e6ce9e4d 100755
--- a/sandbox/bloom-count.py
+++ b/sandbox/bloom-count.py
@@ -34,8 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,no-member
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 import sys
diff --git a/sandbox/build-sparse-graph.py b/sandbox/build-sparse-graph.py
index 8a88f36044..e31a09204f 100755
--- a/sandbox/build-sparse-graph.py
+++ b/sandbox/build-sparse-graph.py
@@ -34,7 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 
-from __future__ import print_function
 import khmer
 import sys
 import screed
diff --git a/sandbox/calc-best-assembly.py b/sandbox/calc-best-assembly.py
index cc11a9bc1a..d06537457c 100755
--- a/sandbox/calc-best-assembly.py
+++ b/sandbox/calc-best-assembly.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import screed
 import argparse
 import sys
diff --git a/sandbox/calc-error-profile.py b/sandbox/calc-error-profile.py
index e4d122a43e..e607ba9688 100755
--- a/sandbox/calc-error-profile.py
+++ b/sandbox/calc-error-profile.py
@@ -41,8 +41,6 @@
 
 Reads FASTQ and FASTA input.
 """
-from __future__ import division
-from __future__ import print_function
 
 import sys
 import argparse
diff --git a/sandbox/calc-median-distribution.py b/sandbox/calc-median-distribution.py
index 78b8e7e563..e502adbdcb 100755
--- a/sandbox/calc-median-distribution.py
+++ b/sandbox/calc-median-distribution.py
@@ -33,8 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import division
-from __future__ import print_function
 import sys
 import khmer
 import argparse
diff --git a/sandbox/collect-reads.py b/sandbox/collect-reads.py
index 6d8e397904..536d0fd40e 100755
--- a/sandbox/collect-reads.py
+++ b/sandbox/collect-reads.py
@@ -43,8 +43,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import division
-from __future__ import print_function
 
 import sys
 import textwrap
diff --git a/sandbox/collect-variants.py b/sandbox/collect-variants.py
index 339e2760ba..a30fed50fb 100755
--- a/sandbox/collect-variants.py
+++ b/sandbox/collect-variants.py
@@ -40,7 +40,6 @@
 
 TODO: add to sandbox README
 """
-from __future__ import print_function
 
 import sys
 import screed
diff --git a/sandbox/correct-reads.py b/sandbox/correct-reads.py
index 7dad20c336..7724185bc6 100755
--- a/sandbox/correct-reads.py
+++ b/sandbox/correct-reads.py
@@ -44,7 +44,6 @@
 
 TODO: add to sandbox/README.
 """
-from __future__ import print_function
 import sys
 import os
 import tempfile
diff --git a/sandbox/count-kmers-single.py b/sandbox/count-kmers-single.py
index aca0d7be2c..fd8aaf5b3d 100755
--- a/sandbox/count-kmers-single.py
+++ b/sandbox/count-kmers-single.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import khmer
diff --git a/sandbox/count-kmers.py b/sandbox/count-kmers.py
index 097e956c59..313b2e400d 100755
--- a/sandbox/count-kmers.py
+++ b/sandbox/count-kmers.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import khmer
diff --git a/sandbox/error-correct-pass2.py b/sandbox/error-correct-pass2.py
index 8e25141cdc..9085232046 100755
--- a/sandbox/error-correct-pass2.py
+++ b/sandbox/error-correct-pass2.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import sys
 import os
 import screed
diff --git a/sandbox/estimate_optimal_hash.py b/sandbox/estimate_optimal_hash.py
index 8c31a7c21d..66dc5f2333 100755
--- a/sandbox/estimate_optimal_hash.py
+++ b/sandbox/estimate_optimal_hash.py
@@ -54,7 +54,6 @@
 Use '-h' for parameter help.
 
 """
-from __future__ import print_function
 import argparse
 import khmer, oxli
 from khmer.khmer_args import info, optimal_size, sanitize_help
diff --git a/sandbox/extract-compact-dbg.py b/sandbox/extract-compact-dbg.py
index dc486e9c9b..bfa44a5c4c 100755
--- a/sandbox/extract-compact-dbg.py
+++ b/sandbox/extract-compact-dbg.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-from __future__ import print_function
 import khmer
 import screed
 import argparse
diff --git a/sandbox/extract-single-partition.py b/sandbox/extract-single-partition.py
index deb84ee531..289609c9dc 100755
--- a/sandbox/extract-single-partition.py
+++ b/sandbox/extract-single-partition.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 from screed.fasta import fasta_iter
 
diff --git a/sandbox/extract-unassembled-reads-2.py b/sandbox/extract-unassembled-reads-2.py
index 56095e0618..be993481a7 100755
--- a/sandbox/extract-unassembled-reads-2.py
+++ b/sandbox/extract-unassembled-reads-2.py
@@ -13,7 +13,6 @@
     erroneous paths from super-high-abundance data
 * run this script with the assembly & the remaining reads.
 """
-from __future__ import print_function
 import sys
 import os.path
 import khmer, khmer.utils
diff --git a/sandbox/extract-unassembled-reads.py b/sandbox/extract-unassembled-reads.py
index 3fc7842e39..478390c669 100755
--- a/sandbox/extract-unassembled-reads.py
+++ b/sandbox/extract-unassembled-reads.py
@@ -8,7 +8,6 @@
     erroneous paths from super-high-abundance data
 * run this script with the assembly & the remaining reads.
 """
-from __future__ import print_function
 import sys
 import os.path
 import khmer, khmer.utils
diff --git a/sandbox/filter-below-abund.py b/sandbox/filter-below-abund.py
index 16a03ba1d9..bead13128d 100755
--- a/sandbox/filter-below-abund.py
+++ b/sandbox/filter-below-abund.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 import os
 import khmer
diff --git a/sandbox/filter-median-and-pct.py b/sandbox/filter-median-and-pct.py
index 20047d5c20..5da4a28182 100755
--- a/sandbox/filter-median-and-pct.py
+++ b/sandbox/filter-median-and-pct.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import sys
 import screed.fasta
 import os
diff --git a/sandbox/filter-median.py b/sandbox/filter-median.py
index c6a4aa2ed1..fd97a5f66a 100755
--- a/sandbox/filter-median.py
+++ b/sandbox/filter-median.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import sys
 import screed.fasta
 import os
diff --git a/sandbox/graph-size.py b/sandbox/graph-size.py
index f9b955345f..44f68fedab 100755
--- a/sandbox/graph-size.py
+++ b/sandbox/graph-size.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import khmer
 import sys
 import screed
diff --git a/sandbox/link-compact-dbg.py b/sandbox/link-compact-dbg.py
index 65372e7efc..2687b45a73 100755
--- a/sandbox/link-compact-dbg.py
+++ b/sandbox/link-compact-dbg.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-from __future__ import print_function
 import khmer
 import screed
 import argparse
diff --git a/sandbox/make-coverage.py b/sandbox/make-coverage.py
index 87767a552e..67f27588d5 100755
--- a/sandbox/make-coverage.py
+++ b/sandbox/make-coverage.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 
 import screed
 
diff --git a/sandbox/multi-rename.py b/sandbox/multi-rename.py
index ea8f595f9f..4fd469d0c4 100755
--- a/sandbox/multi-rename.py
+++ b/sandbox/multi-rename.py
@@ -34,7 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 
-from __future__ import print_function
 import screed
 import sys
 import textwrap
diff --git a/sandbox/normalize-by-median-pct.py b/sandbox/normalize-by-median-pct.py
index 9c03e68464..fa865b4cdd 100755
--- a/sandbox/normalize-by-median-pct.py
+++ b/sandbox/normalize-by-median-pct.py
@@ -41,8 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import division
-from __future__ import print_function
 
 import sys
 import screed
diff --git a/sandbox/optimal_args_hashbits.py b/sandbox/optimal_args_hashbits.py
index 794ad26db5..34fbf5a223 100755
--- a/sandbox/optimal_args_hashbits.py
+++ b/sandbox/optimal_args_hashbits.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import math
diff --git a/sandbox/print-tagset.py b/sandbox/print-tagset.py
index 19a950ce53..0fbf4b3084 100755
--- a/sandbox/print-tagset.py
+++ b/sandbox/print-tagset.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import khmer
 import sys
 import os
diff --git a/sandbox/readaligner_pairhmm_train.py b/sandbox/readaligner_pairhmm_train.py
index e761c402d5..d6105be167 100755
--- a/sandbox/readaligner_pairhmm_train.py
+++ b/sandbox/readaligner_pairhmm_train.py
@@ -33,8 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import division
-from __future__ import print_function
 import khmer
 import argparse
 import collections
diff --git a/sandbox/reassemble-contigs.py b/sandbox/reassemble-contigs.py
index d968b2567a..2c23083cd8 100755
--- a/sandbox/reassemble-contigs.py
+++ b/sandbox/reassemble-contigs.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-from __future__ import print_function
 import argparse
 import screed
 import khmer
diff --git a/sandbox/renumber-partitions.py b/sandbox/renumber-partitions.py
index 895cbc28b1..00f0f47350 100755
--- a/sandbox/renumber-partitions.py
+++ b/sandbox/renumber-partitions.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 import screed
 import gzip
diff --git a/sandbox/saturate-by-median.py b/sandbox/saturate-by-median.py
index 64c1375a33..e784568011 100755
--- a/sandbox/saturate-by-median.py
+++ b/sandbox/saturate-by-median.py
@@ -40,8 +40,6 @@
 reads whether or not they have high coverage.  This is better for
 assessing saturation of (esp) low-coverage data sets.
 """
-from __future__ import division
-from __future__ import print_function
 
 import sys
 import screed
diff --git a/sandbox/shuffle-reverse-rotary.py b/sandbox/shuffle-reverse-rotary.py
index 4b0bd57505..94c76cef35 100755
--- a/sandbox/shuffle-reverse-rotary.py
+++ b/sandbox/shuffle-reverse-rotary.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 import screed
 import os.path
diff --git a/sandbox/slice-reads-by-coverage.py b/sandbox/slice-reads-by-coverage.py
index 61e91c0ec8..2428a4fd98 100755
--- a/sandbox/slice-reads-by-coverage.py
+++ b/sandbox/slice-reads-by-coverage.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import argparse
 import screed
 import sys
diff --git a/sandbox/split-fasta.py b/sandbox/split-fasta.py
index b2f15c39f1..d0488e009e 100755
--- a/sandbox/split-fasta.py
+++ b/sandbox/split-fasta.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 import screed
 
diff --git a/sandbox/split-sequences-by-length.py b/sandbox/split-sequences-by-length.py
index fafa9271ee..a267f24149 100755
--- a/sandbox/split-sequences-by-length.py
+++ b/sandbox/split-sequences-by-length.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import sys
 import screed.fasta
 import os
diff --git a/sandbox/stoptag-abundance-hist.py b/sandbox/stoptag-abundance-hist.py
index 61ee3295d2..4fc6d61791 100755
--- a/sandbox/stoptag-abundance-hist.py
+++ b/sandbox/stoptag-abundance-hist.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import sys
 import khmer
 import os
diff --git a/sandbox/stoptags-by-position.py b/sandbox/stoptags-by-position.py
index 21f0839213..61e5c37063 100755
--- a/sandbox/stoptags-by-position.py
+++ b/sandbox/stoptags-by-position.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import khmer
 import sys
 import screed
diff --git a/sandbox/streaming-assembly-simple.py b/sandbox/streaming-assembly-simple.py
index ea68f71594..c01a26d763 100755
--- a/sandbox/streaming-assembly-simple.py
+++ b/sandbox/streaming-assembly-simple.py
@@ -1,5 +1,4 @@
 #! /usr/bin/env python
-from __future__ import print_function
 import csv
 import screed
 import khmer
diff --git a/sandbox/strip-partition.py b/sandbox/strip-partition.py
index 14c1008e28..a2995304ec 100755
--- a/sandbox/strip-partition.py
+++ b/sandbox/strip-partition.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import screed
 import sys
 
diff --git a/sandbox/subset-report.py b/sandbox/subset-report.py
index 081ae40c0d..21aa695b76 100755
--- a/sandbox/subset-report.py
+++ b/sandbox/subset-report.py
@@ -33,7 +33,6 @@
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # Contact: khmer-project@idyll.org
-from __future__ import print_function
 import khmer
 import sys
 import gc
diff --git a/sandbox/sweep-files.py b/sandbox/sweep-files.py
index 47bf30c51f..e35c9d9e6b 100755
--- a/sandbox/sweep-files.py
+++ b/sandbox/sweep-files.py
@@ -41,7 +41,6 @@
 % sweep-files.py -r <range> --db <fasta/q files> \
 --query <fasta/q files separate>
 """
-from __future__ import print_function
 
 EPILOG = """
 Output will be a collection of fasta/q files, each corresponding to a database
diff --git a/sandbox/sweep-out-reads-with-contigs.py b/sandbox/sweep-out-reads-with-contigs.py
index 0673ddc19a..bf20a6468c 100755
--- a/sandbox/sweep-out-reads-with-contigs.py
+++ b/sandbox/sweep-out-reads-with-contigs.py
@@ -34,7 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 
-from __future__ import print_function
 import sys
 import khmer
 import os.path
diff --git a/sandbox/sweep-reads.py b/sandbox/sweep-reads.py
index 585e260e0a..6c6602810e 100755
--- a/sandbox/sweep-reads.py
+++ b/sandbox/sweep-reads.py
@@ -34,7 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=invalid-name,missing-docstring,no-member
-from __future__ import print_function, unicode_literals
 
 from io import open
 
diff --git a/sandbox/sweep-reads2.py b/sandbox/sweep-reads2.py
index f1a2d8ef2e..f512407c65 100755
--- a/sandbox/sweep-reads2.py
+++ b/sandbox/sweep-reads2.py
@@ -42,7 +42,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import khmer
diff --git a/sandbox/sweep-reads3.py b/sandbox/sweep-reads3.py
index 942c2075dc..1dfda39b72 100755
--- a/sandbox/sweep-reads3.py
+++ b/sandbox/sweep-reads3.py
@@ -42,7 +42,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import os.path
diff --git a/sandbox/write-trimmomatic.py b/sandbox/write-trimmomatic.py
index e18aaf6e02..9fcaac83f2 100755
--- a/sandbox/write-trimmomatic.py
+++ b/sandbox/write-trimmomatic.py
@@ -34,7 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 
-from __future__ import print_function
 import glob
 
 filelist = glob.glob('*R1*.fastq.gz')
diff --git a/scripts/abundance-dist-single.py b/scripts/abundance-dist-single.py
index 56278cbfa1..01ad2a6648 100755
--- a/scripts/abundance-dist-single.py
+++ b/scripts/abundance-dist-single.py
@@ -43,7 +43,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import os
 import sys
 import csv
diff --git a/scripts/abundance-dist.py b/scripts/abundance-dist.py
index 7050c342cb..af8b6c5e8e 100755
--- a/scripts/abundance-dist.py
+++ b/scripts/abundance-dist.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import csv
diff --git a/scripts/annotate-partitions.py b/scripts/annotate-partitions.py
index 91f9996674..3d4e98faa4 100755
--- a/scripts/annotate-partitions.py
+++ b/scripts/annotate-partitions.py
@@ -43,7 +43,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import os
 import textwrap
diff --git a/scripts/count-median.py b/scripts/count-median.py
index 86060e91b4..7d0db34a62 100755
--- a/scripts/count-median.py
+++ b/scripts/count-median.py
@@ -49,7 +49,6 @@
 
 NOTE: All 'N's in the input sequences are converted to 'A's.
 """
-from __future__ import print_function
 import argparse
 import screed
 import sys
diff --git a/scripts/do-partition.py b/scripts/do-partition.py
index 231c0bbbc8..0027270b58 100755
--- a/scripts/do-partition.py
+++ b/scripts/do-partition.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import khmer
 import sys
diff --git a/scripts/extract-long-sequences.py b/scripts/extract-long-sequences.py
index 7de3f6872f..7526c4aedf 100755
--- a/scripts/extract-long-sequences.py
+++ b/scripts/extract-long-sequences.py
@@ -46,7 +46,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import argparse
 import screed
 import textwrap
diff --git a/scripts/extract-paired-reads.py b/scripts/extract-paired-reads.py
index 7ce24ece01..29d7cbe3cb 100755
--- a/scripts/extract-paired-reads.py
+++ b/scripts/extract-paired-reads.py
@@ -44,7 +44,6 @@
 
 Reads FASTQ and FASTA input, retains format for output.
 """
-from __future__ import print_function
 import sys
 import os.path
 import textwrap
diff --git a/scripts/extract-partitions.py b/scripts/extract-partitions.py
index 48e8240a9a..a1d25dcdd6 100755
--- a/scripts/extract-partitions.py
+++ b/scripts/extract-partitions.py
@@ -46,7 +46,6 @@
 @CTB note that if threshold is != 1, those sequences will not be output
 by output_unassigned...
 """
-from __future__ import print_function
 
 import sys
 import screed
diff --git a/scripts/fastq-to-fasta.py b/scripts/fastq-to-fasta.py
index 36ab82377c..ef597d9c39 100755
--- a/scripts/fastq-to-fasta.py
+++ b/scripts/fastq-to-fasta.py
@@ -42,7 +42,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function, unicode_literals
 import sys
 import screed
 from khmer import __version__
diff --git a/scripts/filter-abund-single.py b/scripts/filter-abund-single.py
index a2e44c37c6..6d810df03a 100755
--- a/scripts/filter-abund-single.py
+++ b/scripts/filter-abund-single.py
@@ -45,7 +45,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import os
 import sys
 import threading
diff --git a/scripts/filter-abund.py b/scripts/filter-abund.py
index af2855dbb2..cb729c9b77 100755
--- a/scripts/filter-abund.py
+++ b/scripts/filter-abund.py
@@ -44,7 +44,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 import sys
 import os
 import textwrap
diff --git a/scripts/filter-stoptags.py b/scripts/filter-stoptags.py
index 7d0f744898..a2bc48f170 100755
--- a/scripts/filter-stoptags.py
+++ b/scripts/filter-stoptags.py
@@ -44,7 +44,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import os
 import textwrap
diff --git a/scripts/find-knots.py b/scripts/find-knots.py
index 5eab6c8385..ccfb45a6af 100755
--- a/scripts/find-knots.py
+++ b/scripts/find-knots.py
@@ -41,7 +41,6 @@
 
 % python scripts/find-knots.py <base>
 """
-from __future__ import print_function
 
 import glob
 import os
diff --git a/scripts/interleave-reads.py b/scripts/interleave-reads.py
index fdecd7c72f..65c557d5f2 100755
--- a/scripts/interleave-reads.py
+++ b/scripts/interleave-reads.py
@@ -44,7 +44,6 @@
 
 By default, output is sent to stdout; or use -o. Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import screed
 import sys
diff --git a/scripts/load-into-counting.py b/scripts/load-into-counting.py
index 8164f4e84a..6e797232a8 100755
--- a/scripts/load-into-counting.py
+++ b/scripts/load-into-counting.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function, unicode_literals
 
 import json
 import os
diff --git a/scripts/make-initial-stoptags.py b/scripts/make-initial-stoptags.py
index a56f116661..cbe78657ca 100755
--- a/scripts/make-initial-stoptags.py
+++ b/scripts/make-initial-stoptags.py
@@ -39,7 +39,6 @@
 
 % python scripts/make-initial-stoptags.py <base>
 """
-from __future__ import print_function
 
 import sys
 import textwrap
diff --git a/scripts/merge-partitions.py b/scripts/merge-partitions.py
index efa1b237f2..a0acca36b8 100755
--- a/scripts/merge-partitions.py
+++ b/scripts/merge-partitions.py
@@ -42,7 +42,6 @@
 Load <base>.subset.*.pmap and merge into a single pmap file.  Final
 merged pmap file will be in <base>.pmap.merged.
 """
-from __future__ import print_function
 
 import glob
 import os
diff --git a/scripts/normalize-by-median.py b/scripts/normalize-by-median.py
index b2971ba073..39e387663e 100755
--- a/scripts/normalize-by-median.py
+++ b/scripts/normalize-by-median.py
@@ -45,7 +45,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import sys
 import screed
diff --git a/scripts/partition-graph.py b/scripts/partition-graph.py
index ab81661a0c..f841fe4848 100755
--- a/scripts/partition-graph.py
+++ b/scripts/partition-graph.py
@@ -43,7 +43,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import threading
 import textwrap
diff --git a/scripts/readstats.py b/scripts/readstats.py
index b42cb30556..b6b06d9796 100755
--- a/scripts/readstats.py
+++ b/scripts/readstats.py
@@ -41,7 +41,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import argparse
 import sys
diff --git a/scripts/sample-reads-randomly.py b/scripts/sample-reads-randomly.py
index 5ec2fbb13e..f9206e8d32 100755
--- a/scripts/sample-reads-randomly.py
+++ b/scripts/sample-reads-randomly.py
@@ -45,7 +45,6 @@
 
 Reads FASTQ and FASTA input, retains format for output.
 """
-from __future__ import print_function
 
 import argparse
 import os.path
diff --git a/scripts/split-paired-reads.py b/scripts/split-paired-reads.py
index 22d99ee644..5750100312 100755
--- a/scripts/split-paired-reads.py
+++ b/scripts/split-paired-reads.py
@@ -44,7 +44,6 @@
 
 Reads FASTQ and FASTA input, retains format for output.
 """
-from __future__ import print_function
 import sys
 import os
 import textwrap
diff --git a/scripts/trim-low-abund.py b/scripts/trim-low-abund.py
index a4e34b9fb9..1f1177227d 100755
--- a/scripts/trim-low-abund.py
+++ b/scripts/trim-low-abund.py
@@ -43,7 +43,6 @@
 
 Use -h for parameter help.
 """
-from __future__ import print_function
 import csv
 import sys
 import os
diff --git a/scripts/unique-kmers.py b/scripts/unique-kmers.py
index 61b07c2d85..279da4bdd5 100755
--- a/scripts/unique-kmers.py
+++ b/scripts/unique-kmers.py
@@ -42,7 +42,6 @@
 
 Use '-h' for parameter help.
 """
-from __future__ import print_function
 
 import argparse
 import os
diff --git a/tests/__init__.py b/tests/__init__.py
old mode 100644
new mode 100755
diff --git a/tests/graph_features.py b/tests/graph_features.py
old mode 100644
new mode 100755
index bf7699b688..c2d6912846
--- a/tests/graph_features.py
+++ b/tests/graph_features.py
@@ -36,8 +36,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import itertools
 import random
diff --git a/tests/khmer_tst_utils.py b/tests/khmer_tst_utils.py
old mode 100644
new mode 100755
index e310874d37..dc9c867ddf
--- a/tests/khmer_tst_utils.py
+++ b/tests/khmer_tst_utils.py
@@ -35,7 +35,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring
 
-from __future__ import print_function
 import tempfile
 import os
 import shutil
diff --git a/tests/table_fixtures.py b/tests/table_fixtures.py
old mode 100644
new mode 100755
index 18a9ac2e15..4bc5a9e169
--- a/tests/table_fixtures.py
+++ b/tests/table_fixtures.py
@@ -34,8 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,invalid-name
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 from khmer import Countgraph, SmallCountgraph, Nodegraph
 from khmer import Nodetable, Counttable, SmallCounttable, QFCounttable
diff --git a/tests/test_assembly.py b/tests/test_assembly.py
old mode 100644
new mode 100755
index 8d6fcf95c2..d67f1337bc
--- a/tests/test_assembly.py
+++ b/tests/test_assembly.py
@@ -36,8 +36,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import itertools
 import random
diff --git a/tests/test_banding.py b/tests/test_banding.py
old mode 100644
new mode 100755
index cbd163e07a..3728ba0d8b
--- a/tests/test_banding.py
+++ b/tests/test_banding.py
@@ -32,8 +32,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
-from __future__ import print_function
-from __future__ import absolute_import, division
 
 import screed
 import khmer
diff --git a/tests/test_countgraph.py b/tests/test_countgraph.py
old mode 100644
new mode 100755
index 2c8409ca5a..6b2a9e93d2
--- a/tests/test_countgraph.py
+++ b/tests/test_countgraph.py
@@ -34,8 +34,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
-from __future__ import print_function
-from __future__ import absolute_import, unicode_literals
 
 import gzip
 
diff --git a/tests/test_counting_single.py b/tests/test_counting_single.py
old mode 100644
new mode 100755
index 4532f819cc..585bc0834d
--- a/tests/test_counting_single.py
+++ b/tests/test_counting_single.py
@@ -34,8 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 
diff --git a/tests/test_counttable.py b/tests/test_counttable.py
old mode 100644
new mode 100755
index 15b7808a0b..1873668a35
--- a/tests/test_counttable.py
+++ b/tests/test_counttable.py
@@ -33,8 +33,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 
diff --git a/tests/test_cpython_hierarchy.py b/tests/test_cpython_hierarchy.py
old mode 100644
new mode 100755
index 951f3655b2..a1b1707eb8
--- a/tests/test_cpython_hierarchy.py
+++ b/tests/test_cpython_hierarchy.py
@@ -33,8 +33,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 
diff --git a/tests/test_cython_parsing.py b/tests/test_cython_parsing.py
old mode 100644
new mode 100755
index 1c2aa40bbe..710ae711e2
--- a/tests/test_cython_parsing.py
+++ b/tests/test_cython_parsing.py
@@ -1,5 +1,3 @@
-from __future__ import print_function
-from __future__ import absolute_import
 
 import gc
 import itertools
diff --git a/tests/test_filter_abund.py b/tests/test_filter_abund.py
old mode 100644
new mode 100755
diff --git a/tests/test_functions.py b/tests/test_functions.py
old mode 100644
new mode 100755
index a88fd52b78..ff825b419f
--- a/tests/test_functions.py
+++ b/tests/test_functions.py
@@ -33,8 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,invalid-name,no-member
-from __future__ import print_function
-from __future__ import absolute_import
 
 import screed
 import khmer
diff --git a/tests/test_graph.py b/tests/test_graph.py
old mode 100644
new mode 100755
index c3abd0445c..4eb8e32728
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -34,8 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,no-member,invalid-name,no-self-use
 # pylint: disable=protected-access
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 import screed
diff --git a/tests/test_hashset.py b/tests/test_hashset.py
old mode 100644
new mode 100755
index 1f7a6d89d3..650dfe68c7
--- a/tests/test_hashset.py
+++ b/tests/test_hashset.py
@@ -36,8 +36,6 @@
 """
 Test code for HashSet objects.
 """
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 from . import khmer_tst_utils as utils
diff --git a/tests/test_hll.py b/tests/test_hll.py
old mode 100644
new mode 100755
index 5cad46f2aa..c22a9ae77a
--- a/tests/test_hll.py
+++ b/tests/test_hll.py
@@ -33,8 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
-from __future__ import division, print_function, unicode_literals
-from __future__ import absolute_import
 
 import pickle
 
diff --git a/tests/test_labelhash.py b/tests/test_labelhash.py
old mode 100644
new mode 100755
index c11ba4d2d4..f632d33a66
--- a/tests/test_labelhash.py
+++ b/tests/test_labelhash.py
@@ -33,8 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
-from __future__ import print_function
-from __future__ import absolute_import
 
 import os
 import khmer
diff --git a/tests/test_lump.py b/tests/test_lump.py
old mode 100644
new mode 100755
index b8cf5e0651..a475979a07
--- a/tests/test_lump.py
+++ b/tests/test_lump.py
@@ -33,7 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,no-member,protected-access,invalid-name
-from __future__ import absolute_import
 
 import khmer
 
diff --git a/tests/test_memory.py b/tests/test_memory.py
old mode 100644
new mode 100755
index 826967a16c..7eae28c81e
--- a/tests/test_memory.py
+++ b/tests/test_memory.py
@@ -33,8 +33,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=C0111,C0103,missing-docstring,no-member,protected-access
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 
diff --git a/tests/test_nibblestorage.py b/tests/test_nibblestorage.py
old mode 100644
new mode 100755
index b64bb279bd..24943bb24c
--- a/tests/test_nibblestorage.py
+++ b/tests/test_nibblestorage.py
@@ -32,8 +32,6 @@
 #
 # Contact: khmer-project@idyll.org
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import random
 
diff --git a/tests/test_nodegraph.py b/tests/test_nodegraph.py
old mode 100644
new mode 100755
index 249f901acf..5cd788f49d
--- a/tests/test_nodegraph.py
+++ b/tests/test_nodegraph.py
@@ -34,8 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,protected-access,no-member,invalid-name
 
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 from khmer import Nodegraph, Countgraph
diff --git a/tests/test_normalize_by_median.py b/tests/test_normalize_by_median.py
old mode 100644
new mode 100755
index 3b4b25a222..95ed93fbcf
--- a/tests/test_normalize_by_median.py
+++ b/tests/test_normalize_by_median.py
@@ -32,7 +32,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,invalid-name
-from __future__ import print_function, absolute_import, unicode_literals
 
 import os
 import threading
diff --git a/tests/test_oxli_functions.py b/tests/test_oxli_functions.py
old mode 100644
new mode 100755
index bf1dcef80c..28b06f6051
--- a/tests/test_oxli_functions.py
+++ b/tests/test_oxli_functions.py
@@ -32,7 +32,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,invalid-name,no-member
-from __future__ import print_function, absolute_import, unicode_literals
 
 from . import khmer_tst_utils as utils
 
diff --git a/tests/test_qfstorage.py b/tests/test_qfstorage.py
old mode 100644
new mode 100755
index daaa5eff8e..d12d058e08
--- a/tests/test_qfstorage.py
+++ b/tests/test_qfstorage.py
@@ -1,5 +1,3 @@
-from __future__ import print_function
-from __future__ import absolute_import
 
 import random
 
diff --git a/tests/test_read_aligner.py b/tests/test_read_aligner.py
old mode 100644
new mode 100755
index a2c715e988..da6543e368
--- a/tests/test_read_aligner.py
+++ b/tests/test_read_aligner.py
@@ -33,8 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,no-member,invalid-name,unused-variable
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 from . import khmer_tst_utils as utils
diff --git a/tests/test_read_handling.py b/tests/test_read_handling.py
old mode 100644
new mode 100755
index 81f32c9b3a..020a594098
--- a/tests/test_read_handling.py
+++ b/tests/test_read_handling.py
@@ -34,9 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=C0111,C0103,E1103,W0612
 
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
 
 import gzip
 import os
diff --git a/tests/test_read_parsers.py b/tests/test_read_parsers.py
old mode 100644
new mode 100755
index 032c83d409..0601a888f2
--- a/tests/test_read_parsers.py
+++ b/tests/test_read_parsers.py
@@ -35,8 +35,6 @@
 # pylint: disable=missing-docstring,invalid-name
 
 # Tests for the ReadParser and Read classes.
-from __future__ import print_function
-from __future__ import absolute_import
 from khmer import Read
 from khmer import ReadParser
 from screed import Record
diff --git a/tests/test_sandbox_scripts.py b/tests/test_sandbox_scripts.py
old mode 100644
new mode 100755
index 2ce44574eb..92447b8d98
--- a/tests/test_sandbox_scripts.py
+++ b/tests/test_sandbox_scripts.py
@@ -35,9 +35,6 @@
 
 # pylint: disable=C0111,C0103,E1103,W0612
 
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
 
 import sys
 import os
diff --git a/tests/test_script_arguments.py b/tests/test_script_arguments.py
old mode 100644
new mode 100755
index 14d8b2ef9d..5764ae0fc2
--- a/tests/test_script_arguments.py
+++ b/tests/test_script_arguments.py
@@ -36,8 +36,6 @@
 """
 Tests for various argument-handling code.
 """
-from __future__ import print_function, unicode_literals
-from __future__ import absolute_import
 
 import sys
 import io
diff --git a/tests/test_script_output.py b/tests/test_script_output.py
old mode 100644
new mode 100755
index f1caf3da14..025e6cf2b3
--- a/tests/test_script_output.py
+++ b/tests/test_script_output.py
@@ -37,8 +37,6 @@
 Test code that verifies current script output md5 hashes against recorded
 hashes, to ensure that script function isn't changing.
 """
-from __future__ import print_function
-from __future__ import absolute_import
 
 import khmer
 from . import khmer_tst_utils as utils
diff --git a/tests/test_scripts.py b/tests/test_scripts.py
old mode 100644
new mode 100755
index 945c4739ec..348a521bf3
--- a/tests/test_scripts.py
+++ b/tests/test_scripts.py
@@ -34,9 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=C0111,C0103,E1103,unused-variable,protected-access
 
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
 
 import csv
 import json
diff --git a/tests/test_sequence_validation.py b/tests/test_sequence_validation.py
old mode 100644
new mode 100755
index 5af6187929..192b51286f
--- a/tests/test_sequence_validation.py
+++ b/tests/test_sequence_validation.py
@@ -35,8 +35,6 @@
 # pylint: disable=missing-docstring,invalid-name
 
 # Tests for the ReadParser and Read classes.
-from __future__ import print_function
-from __future__ import absolute_import
 from khmer import Countgraph, SmallCountgraph, Nodegraph
 from khmer import Nodetable, Counttable, SmallCounttable
 from khmer import GraphLabels
diff --git a/tests/test_streaming_io.py b/tests/test_streaming_io.py
old mode 100644
new mode 100755
index 84a66c4e0f..072707a1da
--- a/tests/test_streaming_io.py
+++ b/tests/test_streaming_io.py
@@ -37,9 +37,6 @@
 # of the use of subprocess to execute.  Most script tests should go into
 # test_scripts.py for this reason.
 
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import unicode_literals
 
 import khmer
 from khmer import Nodegraph, Countgraph
diff --git a/tests/test_subset_graph.py b/tests/test_subset_graph.py
old mode 100644
new mode 100755
index c836801d69..bd34e41ba3
--- a/tests/test_subset_graph.py
+++ b/tests/test_subset_graph.py
@@ -34,7 +34,6 @@
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring,invalid-name,no-member,no-self-use
 # pylint: disable=protected-access
-from __future__ import print_function, absolute_import
 
 import khmer
 from khmer._oxli.legacy_partitioning import SubsetPartition, PrePartitionInfo
diff --git a/tests/test_tabletype.py b/tests/test_tabletype.py
old mode 100644
new mode 100755
diff --git a/tests/test_threaded_sequence_processor.py b/tests/test_threaded_sequence_processor.py
old mode 100644
new mode 100755
diff --git a/tests/test_version.py b/tests/test_version.py
old mode 100644
new mode 100755
index d4366699d4..defde717b6
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -33,7 +33,6 @@
 #
 # Contact: khmer-project@idyll.org
 # pylint: disable=missing-docstring
-from __future__ import print_function, unicode_literals
 
 import khmer
 import pytest

From b0db4d4aeeae5947e3bd126465e1fd14d25b6338 Mon Sep 17 00:00:00 2001
From: Daniel Standage <daniel.standage@gmail.com>
Date: Wed, 13 Sep 2017 22:37:32 -0700
Subject: [PATCH 4/5] A couple got left out

---
 doc/dev/guidelines-continued-dev.rst  | 1 -
 examples/python-api/bloom.py          | 1 -
 examples/python-api/consume.py        | 1 -
 examples/python-api/exact-counting.py | 1 -
 4 files changed, 4 deletions(-)

diff --git a/doc/dev/guidelines-continued-dev.rst b/doc/dev/guidelines-continued-dev.rst
index 56f4d97674..a367c1d5c2 100644
--- a/doc/dev/guidelines-continued-dev.rst
+++ b/doc/dev/guidelines-continued-dev.rst
@@ -158,7 +158,6 @@ When wrapping code from liboxli:
 
 For imports,
 
-- `__future__` imports at the top, as usual.
 - `libc` cimports next,
 - then `libcpp` imports and cimports.
 - followed by cimports
diff --git a/examples/python-api/bloom.py b/examples/python-api/bloom.py
index dcfe6bb567..c437e330dc 100755
--- a/examples/python-api/bloom.py
+++ b/examples/python-api/bloom.py
@@ -4,7 +4,6 @@
 # khmer accrues a small false positive rate in order to save substantially on
 # memory requirements.
 
-from __future__ import print_function
 import khmer
 
 ksize = 21
diff --git a/examples/python-api/consume.py b/examples/python-api/consume.py
index cf5fdc52b9..f3050114a7 100755
--- a/examples/python-api/consume.py
+++ b/examples/python-api/consume.py
@@ -2,7 +2,6 @@
 
 # A demonstration of khmer's primary sequence loading function.
 
-from __future__ import print_function
 import khmer
 import sys
 
diff --git a/examples/python-api/exact-counting.py b/examples/python-api/exact-counting.py
index 9656e48318..d4a320d8c8 100755
--- a/examples/python-api/exact-counting.py
+++ b/examples/python-api/exact-counting.py
@@ -3,7 +3,6 @@
 # A demonstration of using khmer for exact k-mer counting. The memory required
 # is 4^k, which limits this to small values of k.
 
-from __future__ import print_function
 import khmer
 
 # Note:

From 079443743ef53bc41599e5ca7f49bdb4cf9d4a67 Mon Sep 17 00:00:00 2001
From: Daniel Standage <daniel.standage@gmail.com>
Date: Wed, 13 Sep 2017 22:43:26 -0700
Subject: [PATCH 5/5] A couple more missed __future__ imports

---
 khmer/_oxli/parsing.pxd | 1 -
 khmer/_oxli/parsing.pyx | 2 --
 khmer/_oxli/utils.pyx   | 1 -
 3 files changed, 4 deletions(-)

diff --git a/khmer/_oxli/parsing.pxd b/khmer/_oxli/parsing.pxd
index d77cfe024e..fe2ad3d57b 100644
--- a/khmer/_oxli/parsing.pxd
+++ b/khmer/_oxli/parsing.pxd
@@ -1,6 +1,5 @@
 # -*- coding: UTF-8 -*-
 
-from __future__ import unicode_literals
 
 from libc.stdint cimport uintptr_t
 
diff --git a/khmer/_oxli/parsing.pyx b/khmer/_oxli/parsing.pyx
index 2cc83a03e1..bf646a5ad9 100644
--- a/khmer/_oxli/parsing.pyx
+++ b/khmer/_oxli/parsing.pyx
@@ -1,7 +1,5 @@
 # -*- coding: UTF-8 -*-
 
-from __future__ import print_function
-from __future__ import unicode_literals
 
 from cython.operator cimport dereference as deref
 cimport cython
diff --git a/khmer/_oxli/utils.pyx b/khmer/_oxli/utils.pyx
index c225a1a490..49d43996f4 100644
--- a/khmer/_oxli/utils.pyx
+++ b/khmer/_oxli/utils.pyx
@@ -1,6 +1,5 @@
 # -*- coding: UTF-8 -*-
 
-from __future__ import unicode_literals
 from cpython.version cimport PY_MAJOR_VERSION
 
 from cython import short, int, long