Add first tests for helpers.py

Covers the initiation of SQLiteBroker class
Includes the various extras needed to run the py.test/coverage scripts

rdmcl/helpers.py

@@ -9,6 +9,7 @@
 from copy import copy
 from hashlib import md5
 from multiprocessing import SimpleQueue, Process, Pipe
+from buddysuite.buddy_resources import pretty_time
 
 
 class SQLiteBroker(object):
@@ -117,30 +118,6 @@ def total_elapsed(self, prefix="", postfix=""):
         return "%s%s%s" % (prefix, pretty_time(round(time()) - self.start), postfix)
 
 
-def pretty_time(seconds):
-    if seconds < 60:
-        output = "%i sec" % seconds
-    elif seconds < 3600:
-        minutes = floor(seconds / 60)
-        seconds -= minutes * 60
-        output = "%i min, %i sec" % (minutes, seconds)
-    elif seconds < 86400:
-        hours = floor((seconds / 60) / 60)
-        seconds -= hours * 60 * 60
-        minutes = floor(seconds / 60)
-        seconds -= minutes * 60
-        output = "%i hrs, %i min, %i sec" % (hours, minutes, seconds)
-    else:
-        days = floor(((seconds / 60) / 60) / 24)
-        seconds -= (days * 60 * 60 * 24)
-        hours = floor((seconds / 60) / 60)
-        seconds -= (hours * 60 * 60)
-        minutes = floor(seconds / 60)
-        seconds -= (minutes * 60)
-        output = "%i days, %i hrs, %i min, %i sec" % (days, hours, minutes, seconds)
-    return output
-
-
 def md5_hash(in_str):
     in_str = str(in_str).encode()
     return md5(in_str).hexdigest()

rdmcl/run_tests.sh

@@ -8,6 +8,10 @@ echo "test_fixtures.py"
 TEST_SCRIPTS=${DIR}'/tests/test_fixtures.py '
 py.test ${TEST_SCRIPTS} --cov ${DIR}/tests/__init__.py --cov-report html -n 4 -p no:cacheprovider --durations=10 $@
 
+echo "test_helpers.py"
+TEST_SCRIPTS=${DIR}'/tests/test_helpers.py '
+py.test ${TEST_SCRIPTS} --cov ${DIR}/helpers.py --cov-report html -n 1 -p no:cacheprovider --durations=10 $@
+
 echo "test_rdmcl.py"
 TEST_SCRIPTS=${DIR}'/tests/test_rdmcl.py '
 py.test ${TEST_SCRIPTS} --cov ${DIR}/rdmcl.py --cov-report html -n 8 -p no:cacheprovider --durations=10 $@

rdmcl/tests/test_helpers.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import pytest
+from .. import helpers
+import os
+import buddysuite.SeqBuddy
+import buddysuite.buddy_resources as br
+from hashlib import md5
+import sqlite3
+from multiprocessing.queues import SimpleQueue
+
+
+def test_sqlitebroker_init(hf):
+    tmpdir = br.TempDir()
+    broker = helpers.SQLiteBroker("%s%sdb.sqlite" % (tmpdir.path, hf.sep))
+    assert broker.db_file == "%s%sdb.sqlite" % (tmpdir.path, hf.sep)
+    assert type(broker.connection) == sqlite3.Connection
+    assert type(broker.cursor) == sqlite3.Cursor
+    assert type(broker.broker_queue) == SimpleQueue
+    assert broker.broker is None

rdmcl/tests/test_rdmcl.py

@@ -2,10 +2,10 @@
 # -*- coding: utf-8 -*-
 
 import pytest
+from .. import rdmcl
 import os
 import pandas as pd
 from collections import OrderedDict
-from .. import rdmcl
 from buddysuite import buddy_resources as br
 
 

test.sh

@@ -14,6 +14,14 @@ then
     FAILURE=1
 fi
 
+#### Helper tests
+TEST_SCRIPTS='test_helpers.py '
+py.test ${TEST_SCRIPTS} --cache-clear -p no:cacheprovider --cov --cov-report= --cov-config ../.coveragerc --durations=10
+if [ $? -ne 0 ]
+then
+    FAILURE=1
+fi
+
 #### RD-MCL tests
 TEST_SCRIPTS='test_rdmcl.py '
 py.test ${TEST_SCRIPTS} --cache-clear -p no:cacheprovider --cov --cov-report= --cov-config ../.coveragerc --durations=10