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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/6425cf520a1d420659f665cecc066324d6e33ce7">6425cf52</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-06T11:15:37+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Avoid calling Git - use Debian version to specify the code version
</pre>
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<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/af46d81468e074a16cc2d7124a6bdea9bbb19067">af46d814</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-11-06T11:19:55+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#2e4ef98b13fea86cbd5d1dcb52d04fbf5f4852c1">
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+
debian/patches/do_not_use_git.patch
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</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bcbio/-/compare/83db5e8f405d4b774235f814a7edbd6020aa15aa...af46d81468e074a16cc2d7124a6bdea9bbb19067#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio (1.2.4-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Avoid calling Git - use Debian version to specify the code version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #973804</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 06 Nov 2020 11:16:33 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">bcbio (1.2.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<li id="2e4ef98b13fea86cbd5d1dcb52d04fbf5f4852c1">
<a href="https://salsa.debian.org/med-team/bcbio/-/compare/83db5e8f405d4b774235f814a7edbd6020aa15aa...af46d81468e074a16cc2d7124a6bdea9bbb19067#2e4ef98b13fea86cbd5d1dcb52d04fbf5f4852c1"><strong>debian/patches/do_not_use_git.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 06 Nov 2020 11:09:40 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/973804</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: Avoid calling Git - use Debian version to specify the code version</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/973804</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/setup.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span> VERSION = '1.2.4'</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # add bcbio version number and git commit hash of the current revision to version.py</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- git_run = subprocess.run(['git', 'rev-parse', '--short', 'HEAD'], stdout=subprocess.PIPE)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ git_run = subprocess.run(['dpkg-parsechangelog', '-SVersion'], stdout=subprocess.PIPE)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> git_run.check_returncode()</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> except subprocess.SubprocessError:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> commit_hash = ''</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span> else:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> here = os.path.dirname(os.path.abspath(__file__))</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> with open(os.path.join(here, 'bcbio', 'pipeline', 'version.py'), 'w') as version_file:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> version_file.writelines([f'__version__ = "{VERSION}"\n',</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f'__git_revision__ = "{commit_hash}"\n'])</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ f'__debian_revision__ = "{commit_hash}"\n'])</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> # dependencies are installed via Conda from</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bcbio/provenance/programs.py</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bcbio/provenance/programs.py</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -147,8 +147,8 @@</span> def _get_versions(config=None):</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> from bcbio.pipeline import version</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> if hasattr(version, "__version__"):</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bcbio_version = ("%s-%s" % (version.__version__, version.__git_revision__)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if version.__git_revision__ else version.__version__)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bcbio_version = ("%s-%s" % (version.__version__, version.__debian_revision__)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if version.__debian_revision__ else version.__version__)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> bcbio_version = ""</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> except ImportError:</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/compare/83db5e8f405d4b774235f814a7edbd6020aa15aa...af46d81468e074a16cc2d7124a6bdea9bbb19067#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#spelling</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">include_tests</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#add_installed_dir_paths.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">do_not_use_git.patch</span></pre>
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