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MRG: fix deprecations (rm use of sourmash.load_one_signature) #245

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Merged
merged 4 commits into from
Apr 15, 2025
Merged

MRG: fix deprecations (rm use of sourmash.load_one_signature) #245

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27e632b
replace sourmash.load_one_signature with sourmash.signature.load_one_…
bluegenes Apr 14, 2025
49dfd46
Merge branch 'main' into fix-deprecations
bluegenes Apr 14, 2025
9ec763e
fix typo in test name
bluegenes Apr 14, 2025
006f7da
Merge branch 'main' into fix-deprecations
bluegenes Apr 15, 2025
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114 changes: 57 additions & 57 deletions tests/test_gbsketch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,11 @@

import sourmash
from sourmash import sourmash_args
from sourmash.signature import load_one_signature_from_json
import sourmash_tst_utils as utils
from sourmash_tst_utils import SourmashCommandFailed



def get_test_data(filename):
thisdir = os.path.dirname(__file__)
return os.path.join(thisdir, 'test-data', filename)
Expand All @@ -35,10 +35,10 @@ def test_gbsketch_simple(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -89,10 +89,10 @@ def test_gbsketch_simple_default_failed(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'-r', '3',
Expand Down Expand Up @@ -129,10 +129,10 @@ def test_gbsketch_manifest(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -170,8 +170,8 @@ def test_gbsketch_genomes_only(runtmp):

sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--genomes-only',
Expand Down Expand Up @@ -202,7 +202,7 @@ def test_gbsketch_proteomes_only(runtmp):

sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--proteomes-only',
Expand All @@ -229,8 +229,8 @@ def test_gbsketch_genomes_only_via_params(runtmp, capfd):

sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -263,7 +263,7 @@ def test_gbsketch_proteomes_only_via_params(runtmp, capfd):

sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3',
Expand Down Expand Up @@ -296,10 +296,10 @@ def test_gbsketch_save_fastas(runtmp):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--fastas', out_dir, '--keep-fasta',
Expand Down Expand Up @@ -433,10 +433,10 @@ def test_gbsketch_bad_acc(runtmp):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
# why does this need ksize =30 and not ksize = 10!???
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_mod, '-o', output,
'--failed', failed, '-r', '3', #'--fastas', output_fastas,
Expand Down Expand Up @@ -600,7 +600,7 @@ def test_gbsketch_version_bug(runtmp):
ch_fail = runtmp.output('checksum_dl_failed.csv')

sig1 = get_test_data('GCA_000193795.2.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss1 = load_one_signature_from_json(sig1, ksize=31)

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -662,9 +662,9 @@ def test_zip_file_permissions(runtmp):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -693,9 +693,9 @@ def test_gbsketch_protein_dayhoff_hp(runtmp):
sig1 = get_test_data('GCA_000961135.2.protein.sig.gz')
sig2 = get_test_data('GCA_000961135.2.dayhoff.sig.gz')
sig3 = get_test_data('GCA_000961135.2.hp.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=30, select_moltype='protein')
ss2 = sourmash.load_one_signature(sig2, ksize=30, select_moltype='dayhoff')
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='hp')
ss1 = load_one_signature_from_json(sig1, ksize=30, select_moltype='protein')
ss2 = load_one_signature_from_json(sig2, ksize=30, select_moltype='dayhoff')
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='hp')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3',
Expand Down Expand Up @@ -756,8 +756,8 @@ def test_gbsketch_simple_batched_single_acc(runtmp, capfd):

sig1 = get_test_data('GCA_000961135.2.sig.gz')
sig2 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=30, select_moltype='protein')
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc1, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -801,9 +801,9 @@ def test_gbsketch_simple_batched_multiple(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
'--failed', failed, '-r', '3', '--checksum-fail', ch_fail,
Expand Down Expand Up @@ -855,11 +855,11 @@ def test_gbsketch_simple_batch_restart(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig2, ksize=21)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig2, ksize=21)
# why does this need ksize =30 and not ksize = 10!???
ss4 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss4 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

# first, cat sig2 into an output file that will trick gbsketch into thinking it's a prior batch
runtmp.sourmash('sig', 'cat', sig2, '-o', out1)
Expand Down Expand Up @@ -971,11 +971,11 @@ def test_gbsketch_simple_batch_restart_sig_zip(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig2, ksize=21)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig2, ksize=21)
# why does this need ksize =30 and not ksize = 10!???
ss4 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss4 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

# first, cat sig2 into an output file that will trick gbsketch into thinking it's a prior batch
runtmp.sourmash('sig', 'cat', sig2, '-o', out1)
Expand Down Expand Up @@ -1034,11 +1034,11 @@ def test_gbsketch_simple_batch_restart_incomplete_sig_zip(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig2, ksize=21)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig2, ksize=21)
# why does this need ksize =30 and not ksize = 10!???
ss4 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss4 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

# first, cat sig2 into an output file that will trick gbsketch into thinking it's a prior batch
runtmp.sourmash('sig', 'cat', sig2, '-o', out1)
Expand Down Expand Up @@ -1100,9 +1100,9 @@ def test_gbsketch_simple_batch_restart_skipcount(runtmp, capfd):

sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig2, ksize=21)
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig2, ksize=21)

# first, cat sig2 into an output file that will trick gbsketch into thinking it's a prior batch
runtmp.sourmash('sig', 'cat', sig2, '-o', out1)
Expand Down Expand Up @@ -1176,10 +1176,10 @@ def test_gbsketch_simple_batch_restart_with_incomplete_zip(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss3 = sourmash.load_one_signature(sig2, ksize=21)
ss4 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
ss3 = load_one_signature_from_json(sig2, ksize=21)
ss4 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

# first, cat sig2 into an output file that will trick gbsketch into thinking it's a prior batch
runtmp.sourmash('sig', 'cat', sig2, '-o', out1)
Expand Down Expand Up @@ -1260,10 +1260,10 @@ def test_gbsketch_overwrite(runtmp, capfd):
sig1 = get_test_data('GCA_000175535.1.sig.gz')
sig2 = get_test_data('GCA_000961135.2.sig.gz')
sig3 = get_test_data('GCA_000961135.2.protein.sig.gz')
ss1 = sourmash.load_one_signature(sig1, ksize=31)
ss2 = sourmash.load_one_signature(sig2, ksize=31)
# ss3 = sourmash.load_one_signature(sig2, ksize=21)
ss4 = sourmash.load_one_signature(sig3, ksize=30, select_moltype='protein')
ss1 = load_one_signature_from_json(sig1, ksize=31)
ss2 = load_one_signature_from_json(sig2, ksize=31)
# ss3 = load_one_signature_from_json(sig2, ksize=21)
ss4 = load_one_signature_from_json(sig3, ksize=30, select_moltype='protein')

# run the workflow once - write all to single output
runtmp.sourmash('scripts', 'gbsketch', acc_csv, '-o', output,
Expand Down
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