MRG: misc cleanup (#424)

* refactor & rename & consolidate

* remove 'lower'

src/python/sourmash_plugin_branchwater/__init__.py

@@ -69,7 +69,6 @@ def __init__(self, p):
     def main(self, args):
         print_version()
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold: {args.threshold}")
-        args.moltype = args.moltype.lower()
         num_threads = set_thread_pool(args.cores)
 
         notify(f"searching all sketches in '{args.query_paths}' against '{args.against_paths}' using {num_threads} threads")
@@ -117,7 +116,6 @@ def __init__(self, p):
     def main(self, args):
         print_version()
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold bp: {args.threshold_bp}")
-        args.moltype = args.moltype.lower()
 
         num_threads = set_thread_pool(args.cores)
 
@@ -165,7 +163,6 @@ def __init__(self, p):
     def main(self, args):
         print_version()
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold bp: {args.threshold_bp} / save matches: {args.save_matches}")
-        args.moltype = args.moltype.lower()
 
         num_threads = set_thread_pool(args.cores)
 
@@ -212,7 +209,6 @@ def __init__(self, p):
 
     def main(self, args):
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} ")
-        args.moltype = args.moltype.lower()
 
         num_threads = set_thread_pool(args.cores)
 
@@ -277,7 +273,6 @@ def __init__(self, p):
     def main(self, args):
         print_version()
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold: {args.threshold}")
-        args.moltype = args.moltype.lower()
 
         num_threads = set_thread_pool(args.cores)
 
@@ -324,7 +319,6 @@ def __init__(self, p):
     def main(self, args):
         print_version()
         notify(f"ksize: {args.ksize} / scaled: {args.scaled} / moltype: {args.moltype} / threshold: {args.threshold}")
-        args.moltype = args.moltype.lower()
 
         num_threads = set_thread_pool(args.cores)
 

src/python/tests/conftest.py

@@ -16,6 +16,10 @@ def toggle_internal_storage(request):
 def zip_query(request):
     return request.param
 
+@pytest.fixture(params=[True, False])
+def zip_db(request):
+    return request.param
+
 @pytest.fixture(params=[True, False])
 def zip_against(request):
     return request.param

src/python/tests/sourmash_tst_utils.py

@@ -14,6 +14,23 @@
 from io import StringIO
 
 
+def get_test_data(filename):
+    thisdir = os.path.dirname(__file__)
+    return os.path.join(thisdir, 'test-data', filename)
+
+
+def make_file_list(filename, paths):
+    with open(filename, 'wt') as fp:
+        fp.write("\n".join(paths))
+        fp.write("\n")
+
+
+def zip_siglist(runtmp, siglist, db):
+    runtmp.sourmash('sig', 'cat', siglist,
+                    '-o', db)
+    return db
+
+
 def scriptpath(scriptname='sourmash'):
     """Return the path to the scripts, in both dev and install situations."""
     # note - it doesn't matter what the scriptname is here, as long as

src/python/tests/test_cluster.py

@@ -2,15 +2,7 @@
 import pytest
 
 from . import sourmash_tst_utils as utils
-
-def get_test_data(filename):
-    thisdir = os.path.dirname(__file__)
-    return os.path.join(thisdir, 'test-data', filename)
-
-def make_file_list(filename, paths):
-    with open(filename, 'wt') as fp:
-        fp.write("\n".join(paths))
-        fp.write("\n")
+from .sourmash_tst_utils import get_test_data, make_file_list
 
 
 def test_installed(runtmp):

src/python/tests/test_gather.py → src/python/tests/test_fastgather.py

@@ -4,23 +4,7 @@
 
 import sourmash
 from . import sourmash_tst_utils as utils
-
-
-def get_test_data(filename):
-    thisdir = os.path.dirname(__file__)
-    return os.path.join(thisdir, 'test-data', filename)
-
-
-def make_file_list(filename, paths):
-    with open(filename, 'wt') as fp:
-        fp.write("\n".join(paths))
-        fp.write("\n")
-
-
-def zip_siglist(runtmp, siglist, db):
-    runtmp.sourmash('sig', 'cat', siglist,
-                    '-o', db)
-    return db
+from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist)
 
 
 def test_installed(runtmp):
@@ -30,7 +14,6 @@ def test_installed(runtmp):
     assert 'usage:  fastgather' in runtmp.last_result.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_simple(runtmp, zip_against):
     # test basic execution!
     query = get_test_data('SRR606249.sig.gz')
@@ -58,7 +41,6 @@ def test_simple(runtmp, zip_against):
     assert {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'gather_result_rank', 'intersect_bp'}.issubset(keys)
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_simple_with_prefetch(runtmp, zip_against):
     # test basic execution!
     query = get_test_data('SRR606249.sig.gz')
@@ -93,7 +75,6 @@ def test_simple_with_prefetch(runtmp, zip_against):
     assert keys == {'query_filename', 'query_name', 'query_md5', 'match_name', 'match_md5', 'intersect_bp'}
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_missing_query(runtmp, capfd, zip_against):
     # test missing query
     query = runtmp.output('no-such-file')
@@ -122,7 +103,6 @@ def test_missing_query(runtmp, capfd, zip_against):
     assert 'Error: No such file or directory' in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_bad_query(runtmp, capfd, zip_against):
     # test non-sig query
     query = runtmp.output('no-such-file')
@@ -154,7 +134,6 @@ def test_bad_query(runtmp, capfd, zip_against):
     assert 'Error: Fastgather requires a single query sketch. Check input:' in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_missing_against(runtmp, capfd, zip_against):
     # test missing against
     query = get_test_data('SRR606249.sig.gz')
@@ -278,7 +257,6 @@ def test_bad_against_3(runtmp, capfd):
     assert 'InvalidArchive' in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_against_multisigfile(runtmp, zip_against):
     # test against a sigfile that contains multiple sketches
     query = get_test_data('SRR606249.sig.gz')
@@ -311,7 +289,6 @@ def test_against_multisigfile(runtmp, zip_against):
     # @CTB this is a bug :(. It should load multiple sketches properly!
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_query_multisigfile(runtmp, capfd, zip_against):
     # test with a sigfile that contains multiple sketches
     against_list = runtmp.output('against.txt')
@@ -341,7 +318,6 @@ def test_query_multisigfile(runtmp, capfd, zip_against):
     assert "Error: Fastgather requires a single query sketch. Check input:" in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_against_nomatch(runtmp, capfd, zip_against):
     # test with 'against' file containing a non-matching ksize
     query = get_test_data('SRR606249.sig.gz')
@@ -370,7 +346,6 @@ def test_against_nomatch(runtmp, capfd, zip_against):
     assert 'WARNING: skipped 1 search paths - no compatible signatures.' in captured.err
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_md5s(runtmp, zip_against):
     # check that the correct md5sums (of the original sketches) are in
     # the output files
@@ -424,7 +399,6 @@ def test_md5s(runtmp, zip_against):
             assert ss.md5sum() in md5s
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_csv_columns_vs_sourmash_prefetch(runtmp, zip_against):
     # the column names should be strict subsets of sourmash prefetch cols
     query = get_test_data('SRR606249.sig.gz')
@@ -466,7 +440,6 @@ def test_csv_columns_vs_sourmash_prefetch(runtmp, zip_against):
     assert diff_keys == set(['unique_intersect_bp', 'median_abund', 'f_match_orig', 'std_abund', 'average_abund', 'f_unique_to_query', 'remaining_bp', 'f_unique_weighted', 'sum_weighted_found', 'total_weighted_hashes', 'n_unique_weighted_found', 'f_orig_query', 'f_match'])
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_fastgather_gatherout_as_picklist(runtmp, zip_against):
     # should be able to use fastgather gather output as picklist
     query = get_test_data('SRR606249.sig.gz')
@@ -508,7 +481,6 @@ def test_fastgather_gatherout_as_picklist(runtmp, zip_against):
     assert picklist_df.equals(full_df)
 
 
-@pytest.mark.parametrize('zip_against', [False, True])
 def test_fastgather_prefetchout_as_picklist(runtmp, zip_against):
     # should be able to use fastgather prefetch output as picklist
     query = get_test_data('SRR606249.sig.gz')

src/python/tests/test_multigather.py → src/python/tests/test_fastmultigather.py

@@ -8,17 +8,7 @@
 
 import sourmash
 from . import sourmash_tst_utils as utils
-
-
-def get_test_data(filename):
-    thisdir = os.path.dirname(__file__)
-    return os.path.join(thisdir, 'test-data', filename)
-
-
-def make_file_list(filename, paths):
-    with open(filename, 'wt') as fp:
-        fp.write("\n".join(paths))
-        fp.write("\n")
+from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist)
 
 
 def index_siglist(runtmp, siglist, db, *, ksize=31, scaled=1000, moltype='DNA',
@@ -37,11 +27,6 @@ def test_installed(runtmp):
     assert 'usage:  fastmultigather' in runtmp.last_result.err
 
 
-def zip_siglist(runtmp, siglist, db):
-    runtmp.sourmash('sig', 'cat', siglist,
-                    '-o', db)
-    return db
-
 def test_simple(runtmp, zip_against):
     # test basic execution!
     query = get_test_data('SRR606249.sig.gz')

src/python/tests/test_index.py

@@ -5,17 +5,7 @@
 import shutil
 
 from . import sourmash_tst_utils as utils
-
-
-def get_test_data(filename):
-    thisdir = os.path.dirname(__file__)
-    return os.path.join(thisdir, 'test-data', filename)
-
-
-def make_file_list(filename, paths):
-    with open(filename, 'wt') as fp:
-        fp.write("\n".join(paths))
-        fp.write("\n")
+from .sourmash_tst_utils import (get_test_data, make_file_list, zip_siglist)
 
 
 def test_installed(runtmp):