Dockerfile

@@ -17,7 +17,7 @@ RUN apt-get update -qq; \
 ENV DEBIAN_FRONTEND Teletype
 
 # Install python dependencies
-RUN pip3 install -U biopython tabulate cgecore==1.4.2;
+RUN pip3 install -U biopython==1.73 tabulate cgecore==1.4.2;
 
 # Install kma
 RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \

README.md

@@ -22,6 +22,7 @@ isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and L
 ## Installation
 
 Setting up VirulenceFinder program   
+**Warning:** Due to bugs in BioPython 1.74, if you are not using the Docker container, do not use that version if not using Python 3.7.
 ```bash
 # Go to wanted location for virulencefinder
 cd /path/to/some/dir

debian/changelog

-virulencefinder (0.0+git20190402.4812325-2) UNRELEASED; urgency=medium
+virulencefinder (2.0.3+git20190809.dde157a-1) unstable; urgency=medium
 
+  [ Chris Lamb ]
+  * Make the build reproducible
+    Closes: #933783
+
+  [ Andreas Tille ]
+  * New upstream version
   * debhelper-compat 12
   * Standards-Version: 4.4.0
+  * Upstream is now tagging releases but currently provided Git commit is
+    younger.  Just change watch file to pick only releases in the future.
 
- -- Andreas Tille <tille@debian.org>  Fri, 02 Aug 2019 23:36:25 +0200
+ -- Andreas Tille <tille@debian.org>  Mon, 02 Sep 2019 09:54:48 +0200
 
 virulencefinder (0.0+git20190402.4812325-1) unstable; urgency=medium
 

debian/patches/reproducible_build.patch

+Description: Make the build reproducible
+Author: Chris Lamb <lamby@debian.org>
+Last-Update: 2019-08-03
+Bug-Debian: https://bugs.debian.org/933783
+
+--- virulencefinder-0.0+git20190402.4812325.orig/virulencefinder.py
++++ virulencefinder-0.0+git20190402.4812325/virulencefinder.py
+@@ -473,8 +473,8 @@ for db in results:
+ 
+ # Get run info for JSON file
+ service = os.path.basename(__file__).replace(".py", "")
+-date = time.strftime("%d.%m.%Y")
+-time = time.strftime("%H:%M:%S")
++date = time.strftime("%d.%m.%Y", time.gmtime(int(os.environ.get('SOURCE_DATE_EPOCH', time.time()))))
++time = time.strftime("%H:%M:%S", time.gmtime(int(os.environ.get('SOURCE_DATE_EPOCH', time.time()))))
+ 
+ # Make JSON output file
+ data = {service: {}}

debian/patches/series

+reproducible_build.patch

debian/watch

 version=4
 
-opts="mode=git,pretty=0.0+git%cd.%h" \
-    https://bitbucket.org/genomicepidemiology/virulencefinder/ HEAD
+https://bitbucket.org/genomicepidemiology/virulencefinder/downloads/?tab=tags .*/virulencefinder/get/@ANY_VERSION@\.tar\.gz
+
+#opts="mode=git,pretty=2.0.3+git%cd.%h" \
+#    https://bitbucket.org/genomicepidemiology/virulencefinder/ HEAD