down to 32 warnings

src/sourmash/commands.py

@@ -248,7 +248,8 @@ def plot(args):
     D_filename = args.distances
 
     notify(f'loading comparison matrix from {D_filename}...')
-    D = numpy.load(open(D_filename, 'rb'))
+    with open(D_filename, 'rb') as f:
+        D = numpy.load(f)
     # not sure how to change this to use f-strings
     notify('...got {} x {} matrix.', *D.shape)
 
@@ -274,7 +275,8 @@ def plot(args):
             labelfilename = D_filename + '.labels.txt'
 
         notify(f'loading labels from {labelfilename}')
-        labeltext = [ x.strip() for x in open(labelfilename) ]
+        with open(labelfilename) as f:
+            labeltext = [ x.strip() for x in f ]
 
         if len(labeltext) != D.shape[0]:
             error('{} labels != matrix size, exiting', len(labeltext))

src/sourmash/save_load.py

@@ -229,7 +229,7 @@ def _error_on_fastaq(filename, **kwargs):
     success = False
     try:
         with screed.open(filename) as it:
-            _ = next(iter(it))
+            _ = next(it)
 
             success = True
     except:
@@ -288,7 +288,7 @@ def _get_signatures_from_rust(siglist):
     # Rust supports multiple. For now, go through serializing
     # and deserializing the signature! See issue #1167 for more.
     json_str = sourmash.save_signatures(siglist)
-    for ss in sourmash.load_signatures(json_str):
+    for ss in sourmash.signature.load_signatures(json_str):
         yield ss
 
 

tests/test_lca.py

@@ -6,6 +6,7 @@
 import csv
 import pytest
 import glob
+from pathlib import Path
 
 import sourmash_tst_utils as utils
 import sourmash
@@ -1830,7 +1831,7 @@ def test_single_summarize_to_output_check_filename(runtmp):
     print(runtmp.last_result.out)
     print(runtmp.last_result.err)
 
-    outdata = open(runtmp.output('output.txt'), 'rt').read()
+    outdata = Path(runtmp.output('output.txt')).read_text()
 
     assert 'loaded 1 signatures from 1 files total.' in runtmp.last_result.err
     assert 'count,superkingdom,phylum,class,order,family,genus,species,strain,filename,sig_name,sig_md5,total_counts\n' in outdata

tests/test_picklist.py

@@ -31,7 +31,7 @@ def test_load_empty_picklist_allow():
 def test_dup_md5_picked(runtmp):
     # load a sig, duplicate, and see if a picklist gets the right one
     sig47 = utils.get_test_data('47.fa.sig')
-    ss = sourmash.load_signatures(sig47)
+    ss = sourmash.load_file_as_signatures(sig47)
     sig = list(ss)[0]
 
     # save a manifest with one entry
@@ -69,7 +69,7 @@ def test_dup_md5_picked_mf_to_picklist(runtmp):
     # load a sig, duplicate, and see if a picklist gets the right one
     # uses an in memory picklist
     sig47 = utils.get_test_data('47.fa.sig')
-    ss = sourmash.load_signatures(sig47)
+    ss = sourmash.load_file_as_signatures(sig47)
     sig = list(ss)[0]
 
     # save a manifest with one entry
@@ -101,7 +101,7 @@ def test_dup_md5_picked_mf_to_picklist_sqlite(runtmp):
     # load a sig, duplicate, and see if a picklist gets the right one
     # use a sqlite db with its own to_picklist behavior.
     sig47 = utils.get_test_data('47.fa.sig')
-    ss = sourmash.load_signatures(sig47)
+    ss = sourmash.load_file_as_signatures(sig47)
     sig = list(ss)[0]
 
     # save a manifest with one entry
@@ -126,4 +126,4 @@ def test_dup_md5_picked_mf_to_picklist_sqlite(runtmp):
     ml3 = ml2.select(picklist=pl)
     print('picked:', len(ml3))
 
-    assert len(pl.pickset) == len(ml3)
+    assert len(pl.pickset) == len(ml3)

tests/test_sourmash.py

@@ -11,6 +11,9 @@
 import pytest
 import zipfile
 import random
+import warnings
+from pathlib import Path
+
 import numpy
 
 import sourmash_tst_utils as utils
@@ -1658,8 +1661,7 @@ def test_do_sourmash_sbt_search_output(runtmp):
 
     runtmp.sourmash('search', 'short.fa.sig', 'zzz', '-o', 'foo')
 
-    outfile = open(runtmp.output('foo'))
-    output = outfile.read()
+    output = Path(runtmp.output('foo')).read_text()
     print(output)
     assert 'e26a306d26512' in output
     assert '914591cd1130aa915' in output
@@ -1733,8 +1735,7 @@ def test_do_sourmash_sbt_move_and_search_output(runtmp):
                                         'zzz.sbt.json', '-o', 'foo'],
                                         in_directory=newpath)
 
-    outfile = open(os.path.join(newpath, 'foo'))
-    output = outfile.read()
+    output = Path(os.path.join(newpath, 'foo')).read_text()
     print(output)
     assert '914591cd1130aa91' in output
     assert 'e26a306d2651' in output
@@ -2090,11 +2091,11 @@ def test_search_gzip(runtmp):
 
     runtmp.sourmash('sketch','dna','-p','k=31,num=500', testdata1, testdata2)
 
-    data = open(runtmp.output('short.fa.sig'), 'rb').read()
+    data = Path(runtmp.output('short.fa.sig')).read_bytes()
     with gzip.open(runtmp.output('zzz.gz'), 'wb') as fp:
         fp.write(data)
 
-    data = open(runtmp.output('short2.fa.sig'), 'rb').read()
+    data = Path(runtmp.output('short2.fa.sig')).read_bytes()
     with gzip.open(runtmp.output('yyy.gz'), 'wb') as fp:
         fp.write(data)
 
@@ -3199,10 +3200,11 @@ def test_compare_with_abundance_1(runtmp):
     s1 = signature.SourmashSignature(E1, filename='e1', name='e1')
     s2 = signature.SourmashSignature(E2, filename='e2', name='e2')
 
-    signature.save_signatures([s1],
-                                open(runtmp.output('e1.sig'), 'w'))
-    signature.save_signatures([s2],
-                                open(runtmp.output('e2.sig'), 'w'))
+    with open(runtmp.output('e1.sig'), 'w') as f:
+        signature.save_signatures([s1], f)
+
+    with open(runtmp.output('e2.sig'), 'w') as f:
+        signature.save_signatures([s2], f)
 
     runtmp.sourmash('search', 'e1.sig', 'e2.sig', '-k', '5')
 
@@ -3224,10 +3226,11 @@ def test_compare_with_abundance_2(runtmp):
     s1 = signature.SourmashSignature(E1, filename='e1', name='e1')
     s2 = signature.SourmashSignature(E2, filename='e2', name='e2')
 
-    signature.save_signatures([s1],
-                                open(runtmp.output('e1.sig'), 'w'))
-    signature.save_signatures([s2],
-                                open(runtmp.output('e2.sig'), 'w'))
+    with open(runtmp.output('e1.sig'), 'w') as f:
+        signature.save_signatures([s1], f)
+
+    with open(runtmp.output('e2.sig'), 'w') as f:
+        signature.save_signatures([s2], f)
 
     runtmp.sourmash('search', 'e1.sig', 'e2.sig', '-k', '5')
 
@@ -3250,10 +3253,11 @@ def test_compare_with_abundance_3(runtmp):
     s1 = signature.SourmashSignature(E1, filename='e1', name='e1')
     s2 = signature.SourmashSignature(E2, filename='e2', name='e2')
 
-    signature.save_signatures([s1],
-                                open(runtmp.output('e1.sig'), 'w'))
-    signature.save_signatures([s2],
-                                open(runtmp.output('e2.sig'), 'w'))
+    with open(runtmp.output('e1.sig'), 'w') as f:
+        signature.save_signatures([s1], f)
+
+    with open(runtmp.output('e2.sig'), 'w') as f:
+        signature.save_signatures([s2], f)
 
     runtmp.sourmash('search', 'e1.sig', 'e2.sig', '-k', '5')
 
@@ -5346,7 +5350,7 @@ def test_sbt_categorize(runtmp):
     # yields 521/1000 ==> ~0.5
     assert 'for genome-s10+s11, found: 0.50 genome-s10' in runtmp.last_result.err
 
-    out_csv = open(runtmp.output('out.csv')).read()
+    out_csv = Path(runtmp.output('out.csv')).read_text()
     print(out_csv)
     assert '4.sig,genome-s10+s11,genome-s10,0.504' in out_csv
 
@@ -5399,7 +5403,7 @@ def test_sbt_categorize_ignore_abundance_3(runtmp):
 
     assert 'for 1-1, found: 0.88 1-1' in runtmp.last_result.err
 
-    out_csv4 = open(runtmp.output('out4.csv')).read()
+    out_csv4 = Path(runtmp.output('out4.csv')).read_text()
     assert 'reads-s10x10-s11.sig,1-1,1-1,0.87699' in out_csv4
 
 
@@ -5787,7 +5791,7 @@ def test_do_sourmash_index_zipfile_append(c):
     # should be no overlap
     assert not set(first_half).intersection(set(second_half))
 
-    with pytest.warns(None) as record:
+    with warnings.catch_warnings(record=True) as record:
         c.run_sourmash('index', '-k', '31', 'zzz.sbt.zip',
                        *first_half)
     # UserWarning is raised when there are duplicated entries in the zipfile
@@ -5800,7 +5804,7 @@ def test_do_sourmash_index_zipfile_append(c):
     assert c.last_result.status == 0
     assert 'Finished saving SBT index, available at' in c.last_result.err
 
-    with pytest.warns(None) as record:
+    with warnings.catch_warnings(record=True) as record:
         c.run_sourmash('index', "--append", '-k', '31', 'zzz.sbt.zip',
                        *second_half)
     # UserWarning is raised when there are duplicated entries in the zipfile