Fix sourmash_lib import in lca

sourmash/__init__.py

@@ -11,6 +11,7 @@
 from .signature import (load_signatures, load_one_signature, SourmashSignature,
                         save_signatures)
 from .sbtmh import load_sbt_index, search_sbt_index, create_sbt_index
+from . import lca
 
 # retrieve VERSION from sourmash/VERSION.
 thisdir = os.path.dirname(__file__)

sourmash_lib/lca/__main__.py → sourmash/lca/__main__.py

@@ -1,13 +1,13 @@
 """
-Command-line entry point for 'python -m sourmash_lib.lca'
+Command-line entry point for 'python -m sourmash.lca'
 """
 
 import sys
 import argparse
 
 from . import classify, index, summarize_main, rankinfo_main, gather_main
 from .command_compare_csv import compare_csv
-from sourmash_lib.logging import set_quiet, error
+from sourmash.logging import set_quiet, error
 
 usage='''
 sourmash lca <command> [<args>] - work with taxonomic information.

sourmash_lib/lca/command_classify.py → sourmash/lca/command_classify.py

@@ -8,11 +8,11 @@
 import csv
 from collections import Counter
 
-import sourmash_lib
-from sourmash_lib import sourmash_args
-from sourmash_lib.logging import notify, error
-from sourmash_lib.lca import lca_utils
-from sourmash_lib.lca.lca_utils import debug, set_debug
+import sourmash
+from sourmash import sourmash_args
+from sourmash.logging import notify, error
+from sourmash.lca import lca_utils
+from sourmash.lca.lca_utils import debug, set_debug
 
 DEFAULT_THRESHOLD=5                  # how many counts of a taxid at min
 
@@ -132,7 +132,7 @@ def classify(args):
     total_n = len(inp_files)
     for query_filename in inp_files:
         n += 1
-        for query_sig in sourmash_lib.load_signatures(query_filename,
+        for query_sig in sourmash.load_signatures(query_filename,
                                                       ksize=ksize):
             notify(u'\r\033[K', end=u'')
             notify('... classifying {} (file {} of {})', query_sig.name(),

sourmash_lib/lca/command_compare_csv.py → sourmash/lca/command_compare_csv.py

@@ -7,12 +7,12 @@
 import argparse
 from collections import defaultdict
 
-import sourmash_lib
-from sourmash_lib import sourmash_args
-from sourmash_lib.logging import notify, error, print_results
-from sourmash_lib.lca import lca_utils
-from sourmash_lib.lca.lca_utils import debug, set_debug, zip_lineage
-from sourmash_lib.lca.command_index import load_taxonomy_assignments
+import sourmash
+from sourmash import sourmash_args
+from sourmash.logging import notify, error, print_results
+from sourmash.lca import lca_utils
+from sourmash.lca.lca_utils import debug, set_debug, zip_lineage
+from sourmash.lca.command_index import load_taxonomy_assignments
 
 def compare_csv(args):
     p = argparse.ArgumentParser(prog="sourmash lca compare_csv")

sourmash_lib/lca/command_gather.py → sourmash/lca/command_gather.py

@@ -10,12 +10,12 @@
 import csv
 from collections import Counter, defaultdict, namedtuple
 
-import sourmash_lib
-from sourmash_lib import sourmash_args
-from sourmash_lib.logging import notify, error, print_results
-from sourmash_lib.lca import lca_utils
-from sourmash_lib.lca.lca_utils import debug, set_debug
-from sourmash_lib.search import format_bp
+import sourmash
+from sourmash import sourmash_args
+from sourmash.logging import notify, error, print_results
+from sourmash.lca import lca_utils
+from sourmash.lca.lca_utils import debug, set_debug
+from sourmash.search import format_bp
 
 LCAGatherResult = namedtuple('LCAGatherResult',
                              'intersect_bp, f_unique_to_query, f_unique_weighted, average_abund, lineage, f_match, name, n_equal_matches')
@@ -284,7 +284,7 @@ def gather_main(args):
             e = query_sig.minhash.copy_and_clear()
             e.add_many(remaining_mins)
 
-            sourmash_lib.save_signatures([ sourmash_lib.SourmashSignature(e) ],
+            sourmash.save_signatures([ sourmash.SourmashSignature(e) ],
                                          args.output_unassigned)
 
 

sourmash_lib/lca/command_index.py → sourmash/lca/command_index.py

@@ -8,11 +8,11 @@
 import csv
 from collections import defaultdict
 
-import sourmash_lib
-from sourmash_lib import sourmash_args
-from sourmash_lib.logging import notify, error
-from sourmash_lib.lca import lca_utils
-from sourmash_lib.lca.lca_utils import debug, set_debug, LineagePair
+import sourmash
+from sourmash import sourmash_args
+from sourmash.logging import notify, error
+from sourmash.lca import lca_utils
+from sourmash.lca.lca_utils import debug, set_debug, LineagePair
 
 
 def load_taxonomy_assignments(filename, delimiter=',', start_column=2,
@@ -182,7 +182,7 @@ def index(args):
     record_remnants = set(assignments_idx.keys())
     for filename in inp_files:
         n += 1
-        for sig in sourmash_lib.load_signatures(filename, ksize=args.ksize):
+        for sig in sourmash.load_signatures(filename, ksize=args.ksize):
             notify(u'\r\033[K', end=u'')
             notify('... loading signature {} (file {} of {})', sig.name()[:30], n, total_n, end='\r')
             debug(filename, sig.name())

sourmash_lib/lca/command_rankinfo.py → sourmash/lca/command_rankinfo.py

@@ -7,9 +7,9 @@
 import argparse
 from collections import defaultdict
 
-from sourmash_lib.logging import error
-from sourmash_lib.lca import lca_utils
-from sourmash_lib.lca.lca_utils import debug, set_debug
+from sourmash.logging import error
+from sourmash.lca import lca_utils
+from sourmash.lca.lca_utils import debug, set_debug
 
 
 def make_lca_counts(dblist):

sourmash_lib/lca/command_summarize.py → sourmash/lca/command_summarize.py

@@ -8,11 +8,11 @@
 import csv
 from collections import defaultdict, Counter
 
-import sourmash_lib
-from sourmash_lib import sourmash_args
-from sourmash_lib.logging import notify, error, print_results
-from sourmash_lib.lca import lca_utils
-from sourmash_lib.lca.lca_utils import debug, set_debug
+import sourmash
+from sourmash import sourmash_args
+from sourmash.logging import notify, error, print_results
+from sourmash.lca import lca_utils
+from sourmash.lca.lca_utils import debug, set_debug
 
 
 DEFAULT_THRESHOLD=5
@@ -107,7 +107,7 @@ def summarize_main(args):
     hashvals = defaultdict(int)
     for query_filename in inp_files:
         n += 1
-        for query_sig in sourmash_lib.load_signatures(query_filename,
+        for query_sig in sourmash.load_signatures(query_filename,
                                                       ksize=ksize):
             notify(u'\r\033[K', end=u'')
             notify('... loading {} (file {} of {})', query_sig.name(), n,

sourmash_lib/lca/lca_utils.py → sourmash/lca/lca_utils.py

@@ -13,8 +13,8 @@
     from itertools import izip_longest as zip_longest
 import pprint
 
-import sourmash_lib._minhash
-from sourmash_lib.logging import notify
+import sourmash._minhash
+from sourmash.logging import notify
 
 # type to store an element in a taxonomic lineage
 LineagePair = namedtuple('LineagePair', ['rank', 'name'])
@@ -226,7 +226,7 @@ def downsample_scaled(self, scaled):
         elif scaled < self.scaled:
             raise ValueError("cannot decrease scaled from {} to {}".format(self.scaled, scaled))
 
-        max_hash = sourmash_lib._minhash.get_max_hash_for_scaled(scaled)
+        max_hash = sourmash._minhash.get_max_hash_for_scaled(scaled)
         new_hashvals = {}
         for k, v in self.hashval_to_lineage_id.items():
             if k < max_hash: