ipyparallel now called in ipyrad/__init__.py with ipcontroller functi…

…on to modifiy controller types.

ipyrad/__init__.py

@@ -4,10 +4,23 @@
 from . import plotting
 from . import dstats
 #from . import core
+
+## create an ipyparallel controller with an exit call to close at sys
+## exit, and a unique cluster-id name
+from ipyrad.core.parallel import ipcontroller_init
+from ipyrad.core.parallel import ipcontroller_set
+
+global __IPNAME__
+ipcontroller_init()
+
+## load the functional modules
 from ipyrad.core.assembly import Assembly
 from ipyrad.core.assembly import merge
 from ipyrad.core.sample import Sample
 from ipyrad.core.paramsinfo import get_params_info
 from ipyrad.core.load_dataobj import load_assembly
 
-__version__ = "0.0.65"
+
+__version__ = "0.0.66"
+
+

ipyrad/__main__.py

@@ -2,12 +2,30 @@
 """ the main CLI for calling ipyrad """
 
 from __future__ import print_function, division  # Requires Python 2.7+ 
+import optparse
 
 
-def main():
+def parse_params():
     """ a toy func """
+    ## create a default Assembly object
+    data = 
+    params = open(paramsfile).readlines()
+
     xpoint = 3
     print(xpoint, "CLI not ready yet")
 
+
+def parse_command_line():
+	""" Parse CLI. Only three options now. """
+	## -p  choose params file
+	## -s  subselect steps
+	## -n  create new params file
+	print("not yet")
+
+
 if __name__ == "__main__": 
-    main()
+
+    ## parse params file input
+    parse_params()
+
+    ## 

ipyrad/assemble/__init__.py

@@ -5,3 +5,5 @@
 from . import jointestimate
 from . import consens_se
 
+
+

ipyrad/assemble/cluster_within.py

@@ -62,7 +62,7 @@ def cleanup(data, sample):
         sample.depths.mjmin = keepmj
         sample.depths.statmin = keepstat
 
-        data.stamp("s3 clustering on "+sample.name)        
+        data._stamp("s3 clustering on "+sample.name)        
     else:
         print("no clusters found for {}".format(sample.name))
 

ipyrad/assemble/demultiplex.py

@@ -469,16 +469,16 @@ def parallel_chunker(data, raws, paired, ipyclient):
 
 
 
-def parallel_sorter(data, rawfilename, chunks, cutter, longbar, filenum, ipyclient):
+def parallel_sorter(data, rawtups, chunks, cutter, longbar, filenum, ipyclient):
     """ takes list of chunk files and runs barmatch function
-    on them across N processors and outputs temp file results.
+    on them across all engines and outputs temp file results.
     This is parallelized on N chunks.
     """
     ## send file to multiprocess queue"
     chunknum = 0
     submitted_args = []
     for tmptuple in chunks:
-        submitted_args.append([data, rawfilename, tmptuple, cutter,
+        submitted_args.append([data, rawtups, tmptuple, cutter,
                                longbar, chunknum, filenum])
         chunknum += 1
 
@@ -754,15 +754,15 @@ def run(data, preview, ipyclient):
 
     ## run test
     import ipyrad as ip
-    from ipyrad.core.assembly import Assembly
+    #from ipyrad.core.assembly import Assembly
 
     ## get current location
     PATH = os.path.abspath(os.path.dirname(__file__))
     ## get location of test files
     IPATH = os.path.dirname(os.path.dirname(PATH))
 
     DATA = os.path.join(IPATH, "tests", "test_rad")
-    TEST = Assembly("test-demultiplex")
+    TEST = ip.Assembly("test-demultiplex")
     #TEST = ip.load_assembly(os.path.join(DATA, "testrad"))
     TEST.set_params(1, "./")
     TEST.set_params(2, "./tests/data/sim_rad_test_R1_.fastq.gz")

ipyrad/assemble/jointestimate.py

@@ -7,11 +7,8 @@
 import scipy.optimize
 import numpy as np
 import itertools
-import glob
 import os
-import multiprocessing
 import gzip
-from ipyrad.assemble import worker
 from collections import Counter
 
 
@@ -246,7 +243,7 @@ def run(data, samples, ipyclient, force):
         lbview = ipyclient.load_balanced_view()
         results = lbview.map_async(optim, submitted_args)
         fakeres = results.get()
-        print(fakeres)
+        #print(fakeres)
 
         ## get results and remove temp files
         cleanup(data, samples)
@@ -273,7 +270,7 @@ def cleanup(data, samples):
             sampobj.stats["state"] = 4
             sampobj.stats["hetero_est"] = est_h
             sampobj.stats["error_est"] = est_e
-            data.stamp("s4 params estimated on "+sampobj.name)
+            data._stamp("s4 params estimated on "+sampobj.name)
             os.remove(tempres)
         else:
             pass

ipyrad/assemble/rawedit.py

@@ -473,7 +473,7 @@ def cleanup(data, sample, submitted, results, force):
     sample.stats.reads_filtered = fcounts["keep"]
 
     ## save stats to the sample??
-    data.stamp("s2 rawediting on "+sample.name)        
+    data._stamp("s2 rawediting on "+sample.name)