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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/cyvcf2">Debian Med / cyvcf2</a>
</h3>
<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/6635001399760fde56e134d40e356041d8b6a204">66350013</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-07-09T23:15:12+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not import numpy during clean
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<h4>1 changed file:</h4>
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<a href="#9dc58384c9cd04e644e5798125752d075fe16e70">
debian/patches/add_htslib_link_dependency.patch
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<h4>Changes:</h4>
<li id="9dc58384c9cd04e644e5798125752d075fe16e70">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/6635001399760fde56e134d40e356041d8b6a204#9dc58384c9cd04e644e5798125752d075fe16e70"><strong>debian/patches/add_htslib_link_dependency.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,9 +5,46 @@ Description: Add missing link dependency on htslib, cythonize modules</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC7" 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="LC8" class="line" lang="diff"><span class="p">@@ -56,15 +56,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -11,11 +11,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> sys.stderr.write("ERROR: cyvcf2 is only for python 2.7 or greater you are running %d.%d\n", (sys.version_info.major, sys.version_info.minor))</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> extensions = [Extension("cyvcf2.cyvcf2",</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Install numpy right now</span></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;">-dist.Distribution().fetch_build_eggs(['numpy'])</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import numpy as np</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> def get_version():</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> """Get the version info from the mpld3 package without importing it"""</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> import ast</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -44,27 +39,27 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> return extensions</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Build the Cython extension by statically linking to the bundled htslib</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sources = [</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x for x in glob.glob('htslib/*.c') </span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not any(e in x for e in ['irods', 'plugin'])</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-]</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sources += glob.glob('htslib/cram/*.c')</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Exclude the htslib sources containing main()'s</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))]</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sources.append('cyvcf2/helpers.c')</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+extensions = []</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if "clean" not in sys.argv:</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ import numpy as np</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Build the Cython extension by statically linking to the bundled htslib</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sources = [</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ x for x in glob.glob('htslib/*.c') </span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if not any(e in x for e in ['irods', 'plugin'])</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ]</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sources += glob.glob('htslib/cram/*.c')</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # Exclude the htslib sources containing main()'s</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))]</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sources.append('cyvcf2/helpers.c')</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-extensions = [Extension("cyvcf2.cyvcf2",</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ extensions = [Extension("cyvcf2.cyvcf2",</span></span>
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11
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> ["cyvcf2/cyvcf2.pyx"] + sources,</span>
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12
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- libraries=['z', 'bz2', 'lzma', 'curl', 'ssl'] + (['crypt'] if platform.system() != 'Darwin' else []),</span></span>
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13
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libraries=['z', 'bz2', 'lzma', 'curl', 'ssl', 'hts'] + (['crypt'] if platform.system() != 'Darwin' else []),</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,14 +53,13 @@ Description: Add missing link dependency on htslib, cythonize modules</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="diff"> "-Wno-unused-result", "-Wno-discarded-qualifiers"],</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> include_dirs=['htslib', 'cyvcf2', np.get_include()])]</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span></span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CYTHONIZE = bool(int(os.getenv("CYTHONIZE", 0)))</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if CYTHONIZE:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if "clean" not in sys.argv:</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> try:</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> from Cython.Build import cythonize</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> except ImportError:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -75,8 +7<span class="idiff left right">4</span>,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="p">@@ -75,8 +7<span class="idiff left right">0</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> sys.exit(1)</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> compiler_directives = {"language_level": 2, "embedsignature": True}</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> extensions = cythonize(extensions, compiler_directives=compiler_directives)</span>
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