From b1565e7df5917a386dd1f89ae643cf4894d599bc Mon Sep 17 00:00:00 2001
From: Luiz Irber <luiz.irber@gmail.com>
Date: Mon, 1 Oct 2018 16:50:42 -0700
Subject: [PATCH] make 10x support optional

---
 requirements.txt     | 2 --
 setup.py             | 1 +
 sourmash/commands.py | 5 +++--
 sourmash/tenx.py     | 3 ++-
 tox.ini              | 3 ++-
 5 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index 5d4c9724fb..18a36ed08b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -9,5 +9,3 @@ sphinx
 alabaster
 recommonmark
 sphinxcontrib-napoleon
-pathos
-bamnostic>=0.9.2
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 00839520be..085824e8dd 100644
--- a/setup.py
+++ b/setup.py
@@ -76,6 +76,7 @@
         'test' : ['pytest', 'pytest-cov', 'numpy', 'matplotlib', 'scipy','recommonmark'],
         'demo' : ['jupyter', 'jupyter_client', 'ipython'],
         'doc' : ['sphinx'],
+        '10x': ['pathos', 'bamnostic>=0.9.2'],
         },
     "include_package_data": True,
     "package_data": {
diff --git a/sourmash/commands.py b/sourmash/commands.py
index e5ebc32c46..4eb3f1ca1e 100644
--- a/sourmash/commands.py
+++ b/sourmash/commands.py
@@ -4,7 +4,6 @@
 import csv
 import itertools
 import multiprocessing
-import pathos.multiprocessing as mp
 import os
 import os.path
 import sys
@@ -16,7 +15,6 @@
 from . import sourmash_args
 from .logging import notify, error, print_results, set_quiet
 from .sbtmh import SearchMinHashesFindBest, SigLeaf
-from .tenx import read_10x_folder
 
 from .sourmash_args import DEFAULT_LOAD_K
 DEFAULT_COMPUTE_K = '21,31,51'
@@ -267,6 +265,9 @@ def maybe_add_alignment(alignment, cell_seqs, args, barcodes):
                 notify('calculated {} signatures for {} sequences in {}',
                        len(siglist), n + 1, filename)
             elif args.input_is_10x:
+                import pathos.multiprocessing as mp
+                from .tenx import read_10x_folder
+
                 barcodes, bam_file = read_10x_folder(filename)
                 manager = multiprocessing.Manager()
 
diff --git a/sourmash/tenx.py b/sourmash/tenx.py
index 9fde7374f8..32fecf0d4e 100644
--- a/sourmash/tenx.py
+++ b/sourmash/tenx.py
@@ -1,5 +1,4 @@
 import os
-import bamnostic as bs
 
 
 def read_single_column(filename):
@@ -11,6 +10,8 @@ def read_single_column(filename):
 
 def read_10x_folder(folder):
     """Get QC-pass barcodes, genes, and bam file from a 10x folder"""
+    import bamnostic as bs
+
     barcodes = read_single_column(os.path.join(folder, 'barcodes.tsv'))
 
     bam_file = bs.AlignmentFile(
diff --git a/tox.ini b/tox.ini
index 7331de4ed2..2ab46bf267 100644
--- a/tox.ini
+++ b/tox.ini
@@ -9,7 +9,8 @@ deps=
     codecov
     ipfsapi
     redis
-    pysam
+    bamnostic
+    pathos
 commands=
     pip install -r requirements.txt
     pip install -e .[test]