Purge references to preview mode. Clean up some deprecated code block…

…s in demux.

ipyrad/__main__.py

@@ -358,8 +358,6 @@ def parse_command_line():
   * Documentation: http://ipyrad.readthedocs.io
     """)
 
-    #* Preview mode (subsamples data)
-    #  ipyrad -p params-data.txt -s --preview  
 
     ## add arguments 
     parser.add_argument('-v', '--version', action='version', 
@@ -408,10 +406,6 @@ def parse_command_line():
     parser.add_argument("--MPI", action='store_true',
         help="connect to parallel CPUs across multiple nodes")
 
-    parser.add_argument("--preview", action='store_true',
-        help="run ipyrad in preview mode. Subset the input file so it'll run"\
-            + "quickly so you can verify everything is working")
-
     parser.add_argument("--ipcluster", metavar="ipcluster", dest="ipcluster",
         type=str, nargs="?", const="default",
         help="connect to ipcluster profile (default: 'default')")
@@ -604,7 +598,6 @@ def main():
             data.run(
                 steps=steps, 
                 force=args.force, 
-                preview=args.preview, 
                 show_cluster=1, 
                 ipyclient=ipyclient)
 

ipyrad/assemble/cluster_within.py

@@ -53,9 +53,10 @@ def get_quick_depths(data, sample):
     if sample.files.clusters:
         pass
     else:
-        ## set cluster file handles
-        sample.files.clusters = os.path.join(
-            data.dirs.clusts, sample.name+".clustS.gz")
+        pass
+    ## set cluster file handles
+    sample.files.clusters = os.path.join(
+        data.dirs.clusts, sample.name+".clustS.gz")
 
     ## get new clustered loci
     fclust = data.samples[sample.name].files.clusters
@@ -1413,7 +1414,7 @@ def cleanup_and_die(async_results):
 
 
 
-def run(data, samples, noreverse, maxindels, force, preview, ipyclient):
+def run(data, samples, noreverse, maxindels, force, ipyclient):
     """ run the major functions for clustering within samples """
 
     ## list of samples to submit to queue
@@ -1563,9 +1564,7 @@ def run(data, samples, noreverse, maxindels, force, preview, ipyclient):
 
 
 NO_UHITS_ERROR = """\
-    No clusters (.utemp hits) found for {}. If you are running preview mode and
-    the size of the truncated input file isn't big enough try increasing the
-    size of <your_assembly>._hackersonly[\"preview_truncate_length\"
+    No clusters (.utemp hits) found for {}.
     """