From d88811ed7d052516e696fb2020d685d2c4df806a Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 29 Sep 2016 17:34:48 +0200
Subject: [PATCH] Added a seed option to the obi test command for reproducible
 tests

---
 python/obitools3/commands/test.pyx | 37 ++++++++++++++++++------------
 1 file changed, 22 insertions(+), 15 deletions(-)

diff --git a/python/obitools3/commands/test.pyx b/python/obitools3/commands/test.pyx
index 7875694..8e81e5f 100644
--- a/python/obitools3/commands/test.pyx
+++ b/python/obitools3/commands/test.pyx
@@ -2,13 +2,9 @@ from obitools3.apps.progress cimport ProgressBar  # TODO I absolutely don't unde
 from obitools3.obidms._obidms import OBIDMS       # TODO cimport doesn't work
 from obitools3.utils cimport str2bytes
 
-import os
-import sys
 import shutil
-import unittest
-import random
 import string
-import psutil
+import random
 
 
 VIEW_TYPES = [None, "NUC_SEQS_VIEW"]
@@ -65,7 +61,7 @@ def random_str_with_max_len(max_len):
 
 
 def random_column(infos):
-    return random.choice(list(infos['view'].columns))
+    return random.choice(sorted(list(infos['view'].columns)))
 
 
 def random_unique_name(infos):
@@ -117,7 +113,7 @@ def test_add_col(config, infos):
     #existing_col = random_bool(config)    # TODO doesn't work because of line count problem. See obiview.c line 1737
     #if existing_col and infos["view_names"] != [] :
     #    random_view = infos['dms'].open_view(random.choice(infos["view_names"]))
-    #    random_column = random_view[random.choice(list(random_view.columns)]
+    #    random_column = random_view[random.choice(sorted(list(random_view.columns))]
     #    random_column_refs = random_column.refs
     #    if random_column_refs['name'] in infos['view'] :
     #        alias = random_unique_name(infos)
@@ -230,7 +226,7 @@ def random_new_view(config, infos, first=False):
             line_selection = []
             for i in range(random.randint(1, v_to_clone.line_count)) :
                 line_selection.append(random.randint(0, v_to_clone.line_count-1))
-            print_test(config, "New line selection: "+str(line_selection))
+            #print_test(config, "New line selection: "+str(line_selection))
     else :
         v_type = random_view_type()
     infos['view'] = infos['dms'].new_view(random_unique_name(infos), 
@@ -288,7 +284,7 @@ def addOptions(parser):
                        metavar='<SEQ_MAX_LEN>',
                        default=200,
                        type=int,
-                       help="Maximum length of DNA sequences."
+                       help="Maximum length of DNA sequences. "
                             "Default: 200")
 
     group.add_argument('--str_max_len','-t',
@@ -296,7 +292,7 @@ def addOptions(parser):
                        metavar='<STR_MAX_LEN>',
                        default=200,
                        type=int,
-                       help="Maximum length of character strings."
+                       help="Maximum length of character strings. "
                             "Default: 200")
 
     group.add_argument('--comments_max_len','-c',
@@ -304,7 +300,7 @@ def addOptions(parser):
                        metavar='<COMMENTS_MAX_LEN>',
                        default=10000,
                        type=int,
-                       help="Maximum length of view comments."
+                       help="Maximum length of view comments. "
                             "Default: 10000")
 
     group.add_argument('--max_ini_col_count','-o',
@@ -312,7 +308,7 @@ def addOptions(parser):
                        metavar='<MAX_INI_COL_COUNT>',
                        default=10,
                        type=int,
-                       help="Maximum number of columns in the initial view."
+                       help="Maximum number of columns in the initial view. "
                             "Default: 10")
 
     group.add_argument('--max_line_nb','-l',
@@ -320,7 +316,7 @@ def addOptions(parser):
                        metavar='<MAX_LINE_NB>',
                        default=10000,
                        type=int,
-                       help="Maximum number of lines in a column."
+                       help="Maximum number of lines in a column. "
                             "Default: 10000")
 
     group.add_argument('--max_elts_per_line','-e',
@@ -328,17 +324,27 @@ def addOptions(parser):
                        metavar='<MAX_ELTS_PER_LINE>',
                        default=20,
                        type=int,
-                       help="Maximum number of elements per line in a column."
+                       help="Maximum number of elements per line in a column. "
                             "Default: 20")
 
     group.add_argument('--verbose','-v',
                        action="store_true", dest="test:verbose",
                        default=False,
-                       help="Print the tests."
+                       help="Print the tests. "
                             "Default: Don't print the tests")
 
+    group.add_argument('--seed','-g',
+                       action="store", dest="test:seed",
+                       metavar='<SEED>',
+                       default=None,
+                       help="Seed (use for reproducible tests). "
+                            "Default: Seed is determined by Python")
+
 def run(config):
     
+    if 'seed' in config['test'] :
+        random.seed(config['test']['seed'])
+    
     infos = {'dms': None, 
              'view': None, 
              'view_names': None, 
@@ -352,6 +358,7 @@ def run(config):
     print("Initializing the DMS and the first view...")
             
     ini_dms_and_first_view(config, infos)
+    print_test(config, repr(infos['view']))
     
     i = 0
     for t in range(config['test']['nbtests']):