[MRG] alias sig fileinfo to sig summarize; minor docs, test cleanup

doc/command-line.md

@@ -1026,6 +1026,9 @@ databases, LCA databases, and directory hierarchies.
 `sourmash sig fileinfo` provides optional JSON and YAML output, and
 those formats are under semantic versioning.
 
+Note: `sourmash signature summarize` is an alias for `fileinfo`; they are
+the same command.
+
 ### `sourmash signature split` - split signatures into individual files
 
 Split each signature in the input file(s) into individual files, with
@@ -1315,8 +1318,14 @@ sourmash sig manifest tests/test-data/prot/all.zip -o manifest.csv
 will create a CSV file, `manifest.csv`, in the internal sourmash
 manifest format.  The manifest will contain an entry for every
 signature in the file, database, or collection. This format is largely
-meant for internal use, but it can serve as a picklist pickfile for
-subsetting large collections.
+meant for internal use, but it can serve as a
+[picklist pickfile](#using-picklists-to-subset-large-collections-of-signatures)
+for subsetting large collections.
+
+By default, `sourmash sig manifest` will rebuild the manifest by
+iterating over the signatures in the input file. This can be slow for
+large collections. Use `--no-rebuild-manifest` to load an existing
+manifest if it is available.
 
 ## Advanced command-line usage
 

src/sourmash/cli/sig/__init__.py

@@ -12,6 +12,7 @@
 from . import filter
 from . import flatten
 from . import fileinfo
+from . import fileinfo as summarize
 from . import kmers
 from . import intersect
 from . import manifest

src/sourmash/cli/sig/fileinfo.py

@@ -1,8 +1,23 @@
 """provide summary information on the given file"""
 
+usage="""
+
+    sourmash sig fileinfo <filename>
+
+This will provide a summary of the sketch contents in the given file.
+
+JSON output can be generated in place of the normal human-readable output
+with '--json-out'.
+
+'sig summarize' and 'sig fileinfo' are aliases for the same command.
+
+"""
+
+
 
 def subparser(subparsers):
-    subparser = subparsers.add_parser('fileinfo')
+    subparser = subparsers.add_parser('fileinfo', aliases=['summarize'],
+                                      usage=usage)
     subparser.add_argument('path')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',

src/sourmash/cli/sig/manifest.py

@@ -1,8 +1,23 @@
 """create a manifest for a collection of signatures"""
 
+usage="""
+
+    sourmash sig manifest <filename> -o manifest.csv
+
+This will output a sourmash manifest in CSV format. This manifest
+can be used as a picklist with --picklist manifest.csv::manifest.
+
+The manifest will be rebuilt by iterating over the signatures in the
+file unless --no-rebuild-manifest is specified; for large
+collections, rebuilding the manifest can take a long time!
+
+See also the 'describe' and 'fileinfo' commands under 'sourmash sig'.
+
+"""
+
 
 def subparser(subparsers):
-    subparser = subparsers.add_parser('manifest')
+    subparser = subparsers.add_parser('manifest', usage=usage)
     subparser.add_argument('location')
     subparser.add_argument(
         '-q', '--quiet', action='store_true',

src/sourmash/sig/__main__.py

@@ -284,15 +284,18 @@ def manifest(args):
 
     rebuild = True
     if args.no_rebuild_manifest:
+        debug("sig manifest: not forcing rebuild.")
         rebuild = False
+    else:
+        debug("sig manifest: forcing rebuild.")
 
     manifest = sourmash_args.get_manifest(loader, require=True,
                                           rebuild=rebuild)
 
     with open(args.output, "w", newline='') as csv_fp:
         manifest.write_to_csv(csv_fp, write_header=True)
 
-    notify(f"built manifest for {len(manifest)} signatures total.")
+    notify(f"manifest contains {len(manifest)} signatures total.")
     notify(f"wrote manifest to '{args.output}'")
 
 

tests/test_cmd_signature.py

@@ -1231,7 +1231,7 @@ def test_sig_extract_1(runtmp):
     assert actual_extract_sig == test_extract_sig
 
 
-def test_sig_extract_1(runtmp):
+def test_sig_extract_1_from_file(runtmp):
     # run sig extract with --from-file
     c = runtmp
 
@@ -2366,7 +2366,7 @@ def test_sig_flatten_1(runtmp):
     assert test_flattened.minhash == siglist[0].minhash
 
 
-def test_sig_flatten_1(runtmp):
+def test_sig_flatten_1_from_file(runtmp):
     c = runtmp
 
     # extract matches to several names from among several signatures & flatten

tests/test_cmd_signature_fileinfo.py

@@ -1,19 +1,13 @@
 """
 Tests for the 'sourmash signature fileinfo' command line.
 """
-import csv
 import shutil
 import os
-import glob
 
 import pytest
-import screed
 import json
 
 import sourmash_tst_utils as utils
-import sourmash
-from sourmash.signature import load_signatures
-from sourmash.manifest import CollectionManifest
 from sourmash_tst_utils import SourmashCommandFailed
 
 ## command line tests
@@ -43,6 +37,30 @@ def test_fileinfo_1_sig(runtmp):
         assert line.strip() in out
 
 
+def test_fileinfo_1_sig_summarize(runtmp):
+    # get basic info on a signature with 'summarize' as alias for fileinfo
+    sig47 = utils.get_test_data('47.fa.sig')
+
+    shutil.copyfile(sig47, runtmp.output('sig47.sig'))
+    runtmp.run_sourmash('sig', 'summarize', 'sig47.sig')
+
+    out = runtmp.last_result.out
+    print(runtmp.last_result.out)
+
+    expected_output = """\
+path filetype: MultiIndex
+location: sig47.sig
+is database? no
+has manifest? yes
+num signatures: 1
+total hashes: 5177
+summary of sketches:
+   1 sketches with DNA, k=31, scaled=1000             5177
+""".splitlines()
+    for line in expected_output:
+        assert line.strip() in out
+
+
 def test_fileinfo_1_sig_abund(runtmp):
     # get basic info on a signature with abundance
     sig47 = utils.get_test_data('47.abunds.fa.sig')
@@ -126,7 +144,7 @@ def test_fileinfo_4_zip(runtmp):
     print(runtmp.last_result.out)
 
     # 'location' will be fully resolved, ignore it for now
-    expected_output = f"""\
+    expected_output = """\
 path filetype: ZipFileLinearIndex
 is database? yes
 has manifest? yes
@@ -187,7 +205,7 @@ def test_fileinfo_4_zip_rebuild(runtmp):
     # CTB: note we're missing one of the 8 in the rebuilt, dna-sig.noext,
     # because it is not automatically included unless you load the zipfile
     # with traverse. This is intentional.
-    expected_output = f"""\
+    expected_output = """\
 path filetype: ZipFileLinearIndex
 is database? yes
 has manifest? yes

tests/test_sourmash_args.py

@@ -285,7 +285,7 @@ def test_save_signatures_to_location_3_zip_add_with_manifest(runtmp):
 
         # construct & save manifest
         mf = manifest.CollectionManifest([row])
-        mf_name = f"SOURMASH-MANIFEST.csv"
+        mf_name = "SOURMASH-MANIFEST.csv"
 
         manifest_fp = io.StringIO()
         mf.write_to_csv(manifest_fp, write_header=True)
@@ -461,8 +461,8 @@ def _signatures_with_internal(self):
     assert m.rows[0]['internal_location'] == "fakeiloc"
 
 
-def test_get_manifest_3_build():
-    # check that manifest is building
+def test_get_manifest_3_build_2():
+    # check that manifest is building, but only when asked
     sig47 = utils.get_test_data('47.fa.sig')
     ss47 = sourmash.load_one_signature(sig47)