[med-svn] [Git][med-team/virulencefinder][master] 8 commits: Make the build reproducible

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / virulencefinder


Commits:
5556ed47 by Andreas Tille at 2019-09-02T07:37:32Z
Make the build reproducible

- - - - -
c58d1058 by Andreas Tille at 2019-09-02T07:37:53Z
New upstream version

- - - - -
9c83e55a by Andreas Tille at 2019-09-02T07:37:53Z
New upstream version 0.0+git20190809.dde157a
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f381a51d by Andreas Tille at 2019-09-02T07:37:54Z
Update upstream source from tag 'upstream/0.0+git20190809.dde157a'

Update to upstream version '0.0+git20190809.dde157a'
with Debian dir 283137f871d3efbc6e05cb9cc333a97511af1f44
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2d20a950 by Andreas Tille at 2019-09-02T07:52:37Z
Upstream is now tagging releases but currently provided Git commit is younger.  Just change watch file to pick only releases in the future.

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683e5a79 by Andreas Tille at 2019-09-02T07:54:36Z
New upstream version 2.0.3+git20190809.dde157a
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a59ab9e4 by Andreas Tille at 2019-09-02T07:54:37Z
Update upstream source from tag 'upstream/2.0.3+git20190809.dde157a'

Update to upstream version '2.0.3+git20190809.dde157a'
with Debian dir 5b36294651f29f4270c87d793feabab8a11a455e
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4ce2a988 by Andreas Tille at 2019-09-02T07:56:29Z
Upload to unstable

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6 changed files:

- Dockerfile
- README.md
- debian/changelog
- + debian/patches/reproducible_build.patch
- + debian/patches/series
- debian/watch


Changes:

=====================================
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
=====================================
@@ -21,7 +21,8 @@ isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and L
 
 ## Installation
 
-Setting up VirulenceFinder program
+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
=====================================
@@ -1,9 +1,17 @@
-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 at debian.org>  Fri, 02 Aug 2019 23:36:25 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 02 Sep 2019 09:54:48 +0200
 
 virulencefinder (0.0+git20190402.4812325-1) unstable; urgency=medium
 


=====================================
debian/patches/reproducible_build.patch
=====================================
@@ -0,0 +1,18 @@
+Description: Make the build reproducible
+Author: Chris Lamb <lamby at 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
=====================================
@@ -0,0 +1 @@
+reproducible_build.patch


=====================================
debian/watch
=====================================
@@ -1,4 +1,6 @@
 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



View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/compare/aca7f1399a136bac8275f432ce71a0ac85d75ee3...4ce2a988fa041eccf3ba94b3be91f82fa4b8bcd3

-- 
View it on GitLab: https://salsa.debian.org/med-team/virulencefinder/compare/aca7f1399a136bac8275f432ce71a0ac85d75ee3...4ce2a988fa041eccf3ba94b3be91f82fa4b8bcd3
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