[MRG] refactor and simplify sourmash sig subcommand signature loadi…

…ng (#1672)

* add -f and --from-file to downsample

* upgrade downsample error handling and output

* more better status output for downsample

* use new sig loading in cat, describe, and split

* support --from-file and force for rest of sig subcommands

* remove unused import

* trap expected errors and print out nicely

* turn LoadManySignatures into a generator

* test force

* add num test for sig split

* add some flatten tests for code cov

* add test for both --num and --scaled

* add picklist checks to everything

* minor cleanup

* minor cleanup

* factor out common argparse

* clean up and test error output

* add many more tests etc.

* add picklist test for sig cat

* remove picklists from subtract for now

Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>

src/sourmash/cli/categorize.py

@@ -1,7 +1,5 @@
 "'sourmash categorize' - query an SBT for bes match, with many signatures."
 
-import argparse
-
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
 

src/sourmash/cli/compute.py

@@ -29,8 +29,6 @@
 ---
 """
 
-from argparse import FileType
-
 from sourmash.minhash import get_minhash_default_seed
 from sourmash.cli.utils import add_construct_moltype_args
 

src/sourmash/cli/import_csv.py

@@ -1,6 +1,5 @@
 """'sourmash import_csv' description goes here"""
 
-import sys
 from sourmash.logging import notify
 
 

src/sourmash/cli/sig/cat.py

@@ -1,7 +1,7 @@
 """concatenate signature files"""
 
-import sourmash
-from sourmash.logging import notify, print_results, error
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
@@ -27,6 +27,9 @@ def subparser(subparsers):
         '-f', '--force', action='store_true',
         help='try to load all files as signatures'
     )
+    add_ksize_arg(subparser, 31)
+    add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/describe.py

@@ -1,12 +1,12 @@
 """show details of signature"""
 
-import sourmash
-from sourmash.logging import notify, print_results, error
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('describe')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
@@ -15,6 +15,17 @@ def subparser(subparsers):
         '--csv', metavar='FILE',
         help='output information to a CSV file'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
+    add_ksize_arg(subparser, 31)
+    add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/downsample.py

@@ -1,17 +1,20 @@
 """downsample one or more signatures"""
 
-import sys
-
-from sourmash.cli.utils import add_moltype_args, add_ksize_arg
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('downsample')
-    subparser.add_argument('signatures', nargs="+")
+    subparser.add_argument('signatures', nargs="*")
     subparser.add_argument(
         '--scaled', type=int, default=0,
         help='scaled value to downsample to'
     )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     subparser.add_argument(
         '--num', metavar='N', type=int, default=0,
         help='num value to downsample to'
@@ -25,8 +28,13 @@ def subparser(subparsers):
         help='output signature to this file (default stdout)',
         default='-',
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
     add_ksize_arg(subparser, 31)
     add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/export.py

@@ -1,7 +1,5 @@
 """export a signature, e.g. to mash"""
 
-import sys
-
 from sourmash.cli.utils import add_ksize_arg, add_moltype_args
 
 

src/sourmash/cli/sig/extract.py

@@ -1,14 +1,12 @@
 """extract one or more signatures"""
 
-import sys
-
 from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
                                 add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('extract')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
@@ -26,6 +24,14 @@ def subparser(subparsers):
         '--name', default=None,
         help='select signatures whose name contains this substring'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     add_ksize_arg(subparser, 31)
     add_moltype_args(subparser)
     add_picklist_args(subparser)

src/sourmash/cli/sig/filter.py

@@ -1,7 +1,5 @@
 """filter k-mers on abundance"""
 
-import sys
-
 from sourmash.cli.utils import add_moltype_args, add_ksize_arg
 
 

src/sourmash/cli/sig/flatten.py

@@ -1,13 +1,12 @@
 """remove abundances"""
 
-import sys
-
-from sourmash.cli.utils import add_moltype_args, add_ksize_arg
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('flatten')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
@@ -25,8 +24,17 @@ def subparser(subparsers):
         '--name', default=None,
         help='select signatures whose name contains this substring'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     add_ksize_arg(subparser, 31)
     add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/ingest.py

@@ -1,7 +1,5 @@
 """ingest/import a mash or other signature"""
 
-import sys
-
 
 def subparser(subparsers):
     # Dirty hack to simultaneously support new and previous interface

src/sourmash/cli/sig/intersect.py

@@ -1,13 +1,12 @@
 """intersect one or more signatures"""
 
-import sys
-
-from sourmash.cli.utils import add_moltype_args, add_ksize_arg
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('intersect')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
@@ -20,8 +19,17 @@ def subparser(subparsers):
         '-A', '--abundances-from', metavar='FILE',
         help='intersect with & take abundances from this signature'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     add_ksize_arg(subparser, 31)
     add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/manifest.py

@@ -1,8 +1,5 @@
 """create a manifest for a collection of signatures"""
 
-import sourmash
-from sourmash.logging import notify, print_results, error
-
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('manifest')

src/sourmash/cli/sig/merge.py

@@ -1,13 +1,12 @@
 """merge one or more signatures"""
 
-import sys
-
-from sourmash.cli.utils import add_moltype_args, add_ksize_arg
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('merge')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
@@ -24,8 +23,17 @@ def subparser(subparsers):
         '--name',
         help='rename merged signature'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     add_ksize_arg(subparser, 31)
     add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/rename.py

@@ -1,11 +1,12 @@
 """rename signature"""
 
-from sourmash.cli.utils import add_ksize_arg, add_moltype_args
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('rename')
-    subparser.add_argument('sigfiles', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument('name')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
@@ -20,8 +21,17 @@ def subparser(subparsers):
         help='output renamed signature to this file (default stdout)',
         default='-'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
     add_ksize_arg(subparser, 31)
     add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/split.py

@@ -1,18 +1,30 @@
 """concatenate signature files"""
 
-import sourmash
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg,
+                                add_picklist_args)
 
 
 def subparser(subparsers):
     subparser = subparsers.add_parser('split')
-    subparser.add_argument('signatures', nargs='+')
+    subparser.add_argument('signatures', nargs='*')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',
         help='suppress non-error output'
     )
     subparser.add_argument(
         '--outdir', help='output signatures to this directory'
     )
+    subparser.add_argument(
+        '-f', '--force', action='store_true',
+        help='try to load all files as signatures'
+    )
+    subparser.add_argument(
+        '--from-file',
+        help='a text file containing a list of files to load signatures from'
+    )
+    add_ksize_arg(subparser, 31)
+    add_moltype_args(subparser)
+    add_picklist_args(subparser)
 
 
 def main(args):

src/sourmash/cli/sig/subtract.py

@@ -1,8 +1,6 @@
 """subtract one or more signatures"""
 
-import sys
-
-from sourmash.cli.utils import add_moltype_args, add_ksize_arg
+from sourmash.cli.utils import (add_moltype_args, add_ksize_arg)
 
 
 def subparser(subparsers):