From 6bea62fadc6ba82a7cba21c8024c7a31e66c3e98 Mon Sep 17 00:00:00 2001
From: Robert Edwards <raedwards@gmail.com>
Date: Mon, 17 Aug 2020 17:21:02 +0930
Subject: [PATCH] updating version handling and adding version to log

---
 PhiSpy.py                         | 3 ++-
 PhiSpyModules/__init__.py         | 4 ++--
 PhiSpyModules/helper_functions.py | 6 +-----
 VERSION                           | 2 +-
 4 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/PhiSpy.py b/PhiSpy.py
index 674b709..abf3ec2 100755
--- a/PhiSpy.py
+++ b/PhiSpy.py
@@ -2,6 +2,7 @@
 import os
 import sys
 import gzip
+import pkg_resources
 from functools import reduce
 
 from Bio import SeqIO
@@ -11,13 +12,13 @@
 
 import PhiSpyModules
 
-
 def main(argv):  #organismPath, output_dir, trainingFlag, INSTALLATION_DIR, evaluateOnly, threshold_for_FN, phageWindowSize, quietMode, keep):
 
     ######################################
     #         parse the options          #
     ######################################
     args_parser = PhiSpyModules.get_args()
+    PhiSpyModules.log_and_message(f"Welcome to PhiSpy.py version {PhiSpyModules.__version__}\n")
     PhiSpyModules.log_and_message(f"Starting PhiSpy.py with the following arguments\n{args_parser}")
 
     # if we get here we need an input file
diff --git a/PhiSpyModules/__init__.py b/PhiSpyModules/__init__.py
index 508d068..75bfdd6 100644
--- a/PhiSpyModules/__init__.py
+++ b/PhiSpyModules/__init__.py
@@ -12,7 +12,6 @@
 from .search_phmms import search_phmms
 from .log_and_message import log_and_message, message
 from .errors import ColorNotFoundError, NoBasesCounted
-
 from .version import __version__
 
 __all__ = ['SeqioFilter',
@@ -26,5 +25,6 @@
            'prophage_measurements_to_tbl', 'write_all_outputs', 'write_prophage_information', 'log_and_message',
            'search_phmms',
            'message',
-            'ColorNotFoundError', 'NoBasesCounted'
+            'ColorNotFoundError', 'NoBasesCounted',
+            '__version__'
            ]
diff --git a/PhiSpyModules/helper_functions.py b/PhiSpyModules/helper_functions.py
index 5493343..c64ccf7 100755
--- a/PhiSpyModules/helper_functions.py
+++ b/PhiSpyModules/helper_functions.py
@@ -8,11 +8,7 @@
 import logging
 
 from .log_and_message import message
-
-try:
-    __version__ = pkg_resources.get_distribution('phispy').version
-except Exception:
-    __version__ = 'unknown'
+from .version import __version__
 
 def print_list():
     f = None
diff --git a/VERSION b/VERSION
index 1b94a07..73274fd 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-4.1.16
+4.1.17