EXP: update sig manifest default rebuilding behavior for v5.

src/sourmash/cli/sig/manifest.py

@@ -37,17 +37,29 @@ def subparser(subparsers):
         "-f", "--force", action="store_true", help="try to load all files as signatures"
     )
     subparser.add_argument(
-        "--no-rebuild-manifest",
+        "--rebuild-manifest",
         help="use existing manifest if available",
         action="store_true",
+        default=None,
     )
+    subparser.add_argument(
+        "--no-rebuild-manifest",
+        help="force rebuilding manifest if available",
+        action="store_false",
+        dest="rebuild_manifest",
+    )
+
     subparser.add_argument(
         "-F",
         "--manifest-format",
         help="format of manifest output file; default is 'csv')",
         default="csv",
         choices=["csv", "sql"],
     )
+    subparser.add_argument(
+        "--v4", dest="cli_version", action="store_const", const="v4", default="v4"
+    )
+    subparser.add_argument("--v5", dest="cli_version", action="store_const", const="v5")
 
 
 def main(args):

src/sourmash/sig/__main__.py

@@ -360,12 +360,22 @@
         error("Use -d/--debug for details.")
         sys.exit(-1)
 
-    rebuild = True
-    if args.no_rebuild_manifest:
-        debug("sig manifest: not forcing rebuild.")
+    # behavior switch: in v4, manifests were rebuilt by default; in v5, not.
+    if args.cli_version == "v4":
+        rebuild = True
+
+        # was --no-rebuild-manifest specified?
+        if args.rebuild_manifest is False:
+            debug("sig manifest: not forcing rebuild.")
+            rebuild = False
+        else:
+            # either left as default (None) or set (True) - rebuild
+            debug("sig manifest: forcing rebuild.")
+    else:  # args.cli_version == 'v5':
         rebuild = False
-    else:
-        debug("sig manifest: forcing rebuild.")
+        if args.rebuild_manifest:
+            debug("sig manifest: forcing rebuild.")
+            rebuild = True
 
     manifest = sourmash_args.get_manifest(loader, require=True, rebuild=rebuild)
 

tests/test_cmd_signature.py

@@ -3952,7 +3952,7 @@ def test_sig_manifest_1_zipfile_csv_gz(runtmp):
 
 
 def test_sig_manifest_1_zipfile_already_exists(runtmp):
-    # make a manifest from a .zip file; f
+    # make a manifest from a .zip file;
     protzip = utils.get_test_data("prot/protein.zip")
 
     mf_csv = runtmp.output("mf.csv")
@@ -4098,10 +4098,16 @@ def test_sig_manifest_does_not_exist(runtmp):
     )
 
 
-def test_sig_manifest_7_allzip_1(runtmp):
+def test_sig_manifest_7_allzip_1(runtmp, cli_v4_only):
     # the rebuilt manifest w/o '-f' will miss dna-sig.noext
+    # note: default in v4 is to rebuild manifest
     allzip = utils.get_test_data("prot/all.zip")
-    runtmp.sourmash("sig", "manifest", allzip, "-o", "xyz.csv")
+    runtmp.sourmash(
+        "sig", "manifest", allzip, "-o", "xyz.csv", "-d", version=cli_v4_only
+    )
+
+    print(runtmp.last_result.out)
+    print(runtmp.last_result.err)
 
     manifest_fn = runtmp.output("xyz.csv")
     with open(manifest_fn, newline="") as csvfp:
@@ -4126,11 +4132,28 @@ def test_sig_manifest_7_allzip_2(runtmp):
     assert "dna-sig.noext" in filenames
 
 
-def test_sig_manifest_7_allzip_3(runtmp):
-    # the existing manifest contains 'dna-sig.noext' whther or not -f is
-    # used.
+def test_sig_manifest_7_allzip_3_no_rebuild(runtmp, cli_v4_only):
+    # the manifest contains 8 entries.
+    # note: --no-rebuild-manifest is default behavior on v4, but not on v5.
+    allzip = utils.get_test_data("prot/all.zip")
+    runtmp.sourmash(
+        "sig", "manifest", allzip, "-o", "xyz.csv", "--no-rebuild", version=cli_v4_only
+    )
+
+    manifest_fn = runtmp.output("xyz.csv")
+    with open(manifest_fn, newline="") as csvfp:
+        manifest = CollectionManifest.load_from_csv(csvfp)
+
+    assert len(manifest) == 8
+    filenames = set(row["internal_location"] for row in manifest.rows)
+    assert "dna-sig.noext" in filenames
+
+
+def test_sig_manifest_7_allzip_3_no_rebuild_is_default_v5(runtmp, cli_v5_only):
+    # by default, do not rebuild the manifest.
+    # note: --no-rebuild-manifest is on by default in v5
     allzip = utils.get_test_data("prot/all.zip")
-    runtmp.sourmash("sig", "manifest", allzip, "-o", "xyz.csv", "--no-rebuild")
+    runtmp.sourmash("sig", "manifest", allzip, "-o", "xyz.csv", version=cli_v5_only)
 
     manifest_fn = runtmp.output("xyz.csv")
     with open(manifest_fn, newline="") as csvfp: