[MRG] add --output-dir as alias for every --outdir

src/sourmash/cli/compute.py

@@ -81,7 +81,7 @@ def subparser(subparsers):
         help='output computed signatures to this file'
     )
     file_args.add_argument(
-        '--outdir', '--output-dir',
+        '--output-dir', '--outdir',
         help='output computed signatures to this directory',
     )
     file_args.add_argument(

src/sourmash/cli/sig/split.py

@@ -12,7 +12,7 @@ def subparser(subparsers):
         help='suppress non-error output'
     )
     subparser.add_argument(
-        '--outdir', '--output-dir',
+        '--output-dir', '--outdir',
         help='output signatures to this directory',
     )
     subparser.add_argument(

src/sourmash/cli/sketch/dna.py

@@ -67,7 +67,7 @@ def subparser(subparsers):
         'specified name'
     )
     file_args.add_argument(
-        '--outdir', '--output-dir',
+        '--output-dir', '--outdir',
         help='output computed signatures to this directory',
     )
     file_args.add_argument(

src/sourmash/cli/sketch/protein.py

@@ -67,7 +67,7 @@ def subparser(subparsers):
         'specified name'
     )
     file_args.add_argument(
-        '--outdir', '--output-dir',
+        '--output-dir', '--outdir',
         help='output computed signatures to this directory',
     )
     file_args.add_argument(

src/sourmash/cli/sketch/translate.py

@@ -67,7 +67,7 @@ def subparser(subparsers):
         'specified name'
     )
     file_args.add_argument(
-        '--outdir', '--output-dir',
+        '--output-dir', '--outdir',
         help='output computed signatures to this directory',
     )
     file_args.add_argument(

src/sourmash/command_compute.py

@@ -114,8 +114,8 @@ def compute(args):
         error("ERROR: must specify -o with --merge")
         sys.exit(-1)
 
-    if args.output and args.outdir:
-        error("ERROR: --outdir doesn't make sense with -o/--output")
+    if args.output and args.output_dir:
+        error("ERROR: --output-dir doesn't make sense with -o/--output")
         sys.exit(-1)
 
     if args.track_abundance:
@@ -162,8 +162,8 @@ def _compute_individual(args, signatures_factory):
         if open_output_each_time:
             # for each input file, construct output filename
             sigfile = os.path.basename(filename) + '.sig'
-            if args.outdir:
-                sigfile = os.path.join(args.outdir, sigfile)
+            if args.output_dir:
+                sigfile = os.path.join(args.output_dir, sigfile)
 
             # does it already exist? skip if so.
             if os.path.exists(sigfile) and not args.force:
@@ -237,7 +237,7 @@ def _compute_individual(args, signatures_factory):
             save_sigs = None
 
 
-    # if --output specified, all collected signatures => args.output,
+    # if --output-dir specified, all collected signatures => args.output,
     # and we need to close here.
     if args.output and save_sigs is not None:
         save_sigs.close()

src/sourmash/command_sketch.py

@@ -186,8 +186,8 @@ def _execute_sketch(args, signatures_factory):
         error("ERROR: must specify -o with --merge")
         sys.exit(-1)
 
-    if args.output and args.outdir:
-        error("ERROR: --outdir doesn't make sense with -o/--output")
+    if args.output and args.output_dir:
+        error("ERROR: --output-dir doesn't make sense with -o/--output")
         sys.exit(-1)
 
     # get number of output sigs:

src/sourmash/sig/__main__.py

@@ -133,10 +133,10 @@ def split(args):
     output_scaled_template = '{md5sum}.k={ksize}.scaled={scaled}.{moltype}.dup={dup}.{basename}.sig'
     output_num_template = '{md5sum}.k={ksize}.num={num}.{moltype}.dup={dup}.{basename}.sig'
 
-    if args.outdir:
-        if not os.path.exists(args.outdir):
-            notify(f'Creating --outdir {args.outdir}')
-            os.mkdir(args.outdir)
+    if args.output_dir:
+        if not os.path.exists(args.output_dir):
+            notify(f'Creating --output-dir {args.output_dir}')
+            os.mkdir(args.output_dir)
 
     progress = sourmash_args.SignatureLoadingProgress()
     loader = sourmash_args.load_many_signatures(args.signatures,
@@ -179,8 +179,8 @@ def split(args):
 
         output_names.add(output_name)
 
-        if args.outdir:
-            output_name = os.path.join(args.outdir, output_name)
+        if args.output_dir:
+            output_name = os.path.join(args.output_dir, output_name)
 
         if os.path.exists(output_name):
             notify(f"** overwriting existing file {format(output_name)}")

tests/test_cmd_signature.py

@@ -1112,6 +1112,28 @@ def test_sig_split_2_outdir(c):
     assert actual_split_sig == test_split_sig
 
 
+@utils.in_tempdir
+def test_sig_split_2_output_dir(c):
+    # split 47 twice, put in outdir via --output-dir instead of --outdir
+    sig47 = utils.get_test_data('47.fa.sig')
+    outdir = c.output('sigout/')
+    c.run_sourmash('sig', 'split', sig47, sig47, '--output-dir', outdir)
+
+    outname1 = 'sigout/09a08691.k=31.scaled=1000.DNA.dup=0.47.fa.sig'
+    outname2 = 'sigout/09a08691.k=31.scaled=1000.DNA.dup=1.47.fa.sig'
+
+    assert os.path.exists(c.output(outname1))
+    assert os.path.exists(c.output(outname2))
+
+    test_split_sig = sourmash.load_one_signature(sig47)
+
+    actual_split_sig = sourmash.load_one_signature(c.output(outname1))
+    assert actual_split_sig == test_split_sig
+
+    actual_split_sig = sourmash.load_one_signature(c.output(outname2))
+    assert actual_split_sig == test_split_sig
+
+
 @utils.in_tempdir
 def test_sig_split_3_multisig(c):
     # split 47 and 47+63-multisig.sig

tests/test_sourmash_compute.py

@@ -178,7 +178,7 @@ def test_do_sourmash_compute_output_and_name_valid_file_outdir(c):
                        '--outdir', c.location)
 
     errmsg = c.last_result.err
-    assert "ERROR: --outdir doesn't make sense with -o/--output" in errmsg
+    assert "ERROR: --output-dir doesn't make sense with -o/--output" in errmsg
 
 
 def test_do_sourmash_compute_singleton():

tests/test_sourmash_sketch.py

@@ -393,6 +393,21 @@ def test_do_sourmash_sketchdna_outdir(c):
     assert str(sig).endswith('short.fa')
 
 
+@utils.in_tempdir
+def test_do_sourmash_sketchdna_output_dir(c):
+    # test via --output-dir not --outdir
+    testdata1 = utils.get_test_data('short.fa')
+    status, out, err = utils.runscript('sourmash',
+                                       ['sketch', 'dna', testdata1,
+                                        '--output-dir', c.location])
+
+    sigfile = os.path.join(c.location, 'short.fa.sig')
+    assert os.path.exists(sigfile)
+
+    sig = next(signature.load_signatures(sigfile))
+    assert str(sig).endswith('short.fa')
+
+
 def test_do_sourmash_sketchdna_output_valid_file(runtmp):
     """ Trigger bug #123 """
     testdata1 = utils.get_test_data('short.fa')
@@ -489,7 +504,7 @@ def test_do_sourmash_sketchdna_output_and_name_valid_file_outdir(c):
                        '--outdir', c.location)
 
     errmsg = c.last_result.err
-    assert "ERROR: --outdir doesn't make sense with -o/--output" in errmsg
+    assert "ERROR: --output-dir doesn't make sense with -o/--output" in errmsg
 
 
 def test_do_sourmash_sketchdna_singleton(runtmp):