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 - - - - - 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 - - - - - 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. - - - - - 683e5a79 by Andreas Tille at 2019-09-02T07:54:36Z New upstream version 2.0.3+git20190809.dde157a - - - - - 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 - - - - - 4ce2a988 by Andreas Tille at 2019-09-02T07:56:29Z Upload to unstable - - - - - 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 <[email protected]> Fri, 02 Aug 2019 23:36:25 +0200 + -- Andreas Tille <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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