Merge branch 'v1.2'

biologyguy · Feb 3, 2017 · e52d0bb · e52d0bb
2 parents 58520b8 + d1fd2ca
commit e52d0bb
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Showing 6 changed files with 22 additions and 10 deletions.
diff --git a/buddysuite/AlignBuddy.py b/buddysuite/AlignBuddy.py
@@ -70,7 +70,7 @@
 
 # ################################################ GLOBALS ###################################################### #
 GAP_CHARS = ["-", ".", " "]
-VERSION = br.Version("AlignBuddy", 1, "2.4", br.contributors, {"year": 2017, "month": 2, "day": 2})
+VERSION = br.Version("AlignBuddy", 1, "2.5", br.contributors, {"year": 2017, "month": 2, "day": 3})
 
 
 # #################################################### ALIGNBUDDY #################################################### #
@@ -90,7 +90,11 @@ def __init__(self, _input, in_format=None, out_format=None):
         # Handles
         if str(type(_input)) == "<class '_io.TextIOWrapper'>":
             if not _input.seekable():  # Deal with input streams (e.g., stdout pipes)
-                temp = StringIO(br.utf_encode(_input.read()))
+                input_txt = _input.read()
+                if re.search("Buddy::.* has crashed with the following traceback", input_txt):
+                    print(input_txt)
+                    sys.exit()
+                temp = StringIO(br.utf_encode(input_txt))
                 _input = temp
             _input.seek(0)
             in_handle = _input.read()

diff --git a/buddysuite/DatabaseBuddy.py b/buddysuite/DatabaseBuddy.py
@@ -80,7 +80,7 @@
            "fastq-solexa", "fastq-illumina", "genbank", "gb", "imgt", "nexus", "phd", "phylip", "seqxml",
            "stockholm", "tab", "qual"]
 CONFIG = br.config_values()
-VERSION = br.Version("DatabaseBuddy", 1, "2.4", br.contributors, {"year": 2017, "month": 2, "day": 2})
+VERSION = br.Version("DatabaseBuddy", 1, "2.5", br.contributors, {"year": 2017, "month": 2, "day": 3})
 
 GREY = "\033[90m"
 RED = "\033[91m"

diff --git a/buddysuite/PhyloBuddy.py b/buddysuite/PhyloBuddy.py
@@ -147,7 +147,7 @@ def ascending_order(phylobuddy):
 
 # ##################################################### GLOBALS ###################################################### #
 CONFIG = br.config_values()
-VERSION = br.Version("PhyloBuddy", 1, "2.4", br.contributors, {"year": 2017, "month": 2, "day": 2})
+VERSION = br.Version("PhyloBuddy", 1, "2.5", br.contributors, {"year": 2017, "month": 2, "day": 3})
 OUTPUT_FORMATS = ["newick", "nexus", "nexml"]
 PHYLO_INFERENCE_TOOLS = ["raxml", "phyml", "fasttree"]
 
@@ -167,7 +167,11 @@ def __init__(self, _input, _in_format=None, _out_format=None):
         # Handles
         if str(type(_input)) == "<class '_io.TextIOWrapper'>":
             if not _input.seekable():  # Deal with input streams (e.g., stdout pipes)
-                temp = StringIO(br.utf_encode(_input.read()))
+                input_txt = _input.read()
+                if re.search("Buddy::.* has crashed with the following traceback", input_txt):
+                    print(input_txt)
+                    sys.exit()
+                temp = StringIO(br.utf_encode(input_txt))
                 _input = temp
             _input.seek(0)
             in_from_handle = _input.read()

diff --git a/buddysuite/SeqBuddy.py b/buddysuite/SeqBuddy.py
@@ -157,7 +157,7 @@ def incremental_rename(query, replace):
 # - Try to speed things up by reading in all sequence data only when necessary
 
 # ###################################################### GLOBALS ##################################################### #
-VERSION = br.Version("SeqBuddy", 1, "2.4", br.contributors, {"year": 2017, "month": 2, "day": 2})
+VERSION = br.Version("SeqBuddy", 1, "2.5", br.contributors, {"year": 2017, "month": 2, "day": 3})
 OUTPUT_FORMATS = ["ids", "accessions", "summary", "full-summary", "clustal", "embl", "fasta", "fastq", "fastq-sanger",
                   "fastq-solexa", "fastq-illumina", "genbank", "gb", "imgt", "nexus", "phd", "phylip", "phylip-relaxed",
                   "phylipss", "phylipsr", "raw", "seqxml", "sff", "stockholm", "tab", "qual"]
@@ -185,7 +185,11 @@ def __init__(self, sb_input, in_format=None, out_format=None, alpha=None):
         # Handles
         if str(type(sb_input)) == "<class '_io.TextIOWrapper'>":
             if not sb_input.seekable():  # Deal with input streams (e.g., stdout pipes)
-                temp = StringIO(br.utf_encode(sb_input.read()))
+                input_txt = sb_input.read()
+                if re.search("Buddy::.* has crashed with the following traceback", input_txt):
+                    print(input_txt)
+                    sys.exit()
+                temp = StringIO(br.utf_encode(input_txt))
                 sb_input = temp
             sb_input.seek(0)
             in_handle = sb_input.read()

diff --git a/buddysuite/buddy_resources.py b/buddysuite/buddy_resources.py
@@ -772,7 +772,7 @@ def check_garbage_flags(in_args, tool):
         flag_list = in_args.sequence
 
     for flag in flag_list:
-        if flag and re.match(" -", flag):
+        if flag and re.match(" -", str(flag)):
             _stderr("%s.py: error: unrecognized arguments: %s\n" % (tool, flag))
             sys.exit()
     return True
@@ -1370,7 +1370,7 @@ def isfile_override(path):
 
 # #################################################### VARIABLES ##################################################### #
 
-contributors = [Contributor("Stephen", "Bond", commits=1023, github="https://github.com/biologyguy"),
+contributors = [Contributor("Stephen", "Bond", commits=1033, github="https://github.com/biologyguy"),
                 Contributor("Karl", "Keat", commits=392, github="https://github.com/KarlKeat"),
                 Contributor("Jeremy", "Labarge", commits=26, github="https://github.com/biojerm"),
                 Contributor("Dustin", "Mitchell", commits=12, github="https://github.com/djmitche"),

diff --git a/setup.py b/setup.py
@@ -61,7 +61,7 @@ def run():
 }
 
 setup(name='buddysuite',
-      version='1.2.4',
+      version='1.2.5',
       description='BuddySuite is a collection of command line utilities written in Python for '
                   'working with biological data.',
       long_description=open(os.path.join(os.path.dirname(__file__), 'README.rst'), encoding="utf-8").read(),