<pre style='margin:0'>
Zero King (l2dy) pushed a commit to branch master
in repository macports-ports.

</pre>
<p><a href="https://github.com/macports/macports-ports/commit/db431b451844f18ddab8623c28cd4f301715e171">https://github.com/macports/macports-ports/commit/db431b451844f18ddab8623c28cd4f301715e171</a></p>
<pre style="white-space: pre; background: #F8F8F8"><span style='display:block; white-space:pre;color:#808000;'>commit db431b451844f18ddab8623c28cd4f301715e171
</span>Author: David Seifert <SoapZA@users.noreply.github.com>
AuthorDate: Mon Oct 2 18:30:06 2017 +0200

<span style='display:block; white-space:pre;color:#404040;'>    pysam: Update to latest 0.12.0.1 release
</span><span style='display:block; white-space:pre;color:#404040;'>    
</span><span style='display:block; white-space:pre;color:#404040;'>    * Also add myself as a maintainer
</span><span style='display:block; white-space:pre;color:#404040;'>    See https://trac.macports.org/ticket/53467
</span>---
 python/py-pysam/Portfile                           | 55 +++++++++++++++-------
 .../py-pysam/files/patch-pysam-remove-RPATH.diff   | 11 +++++
 2 files changed, 49 insertions(+), 17 deletions(-)

<span style='display:block; white-space:pre;color:#808080;'>diff --git a/python/py-pysam/Portfile b/python/py-pysam/Portfile
</span><span style='display:block; white-space:pre;color:#808080;'>index 154b478..3da5392 100644
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>--- a/python/py-pysam/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/python/py-pysam/Portfile
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -1,27 +1,48 @@
</span> # -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-PortSystem              1.0
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-PortGroup               python 1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortSystem          1.0
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+PortGroup           python 1.0
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-name                    py-pysam
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-version                 0.5
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-categories-append       science
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-license                 MIT BSD
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-maintainers             nomaintainer
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-description             Python interface for the SAM/BAM sequence alignment and mapping format
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-long_description        Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API.
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-platforms               darwin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+name                py-pysam
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+set realname        pysam
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+version             0.12.0.1
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+categories-append   science
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+platforms           darwin
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+license             MIT BSD
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+maintainers         @SoapZA
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-homepage                http://code.google.com/p/pysam/
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-master_sites            googlecode:pysam
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-distname                pysam-${version}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+description         Python interface for the SAM/BAM sequence \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    alignment and mapping format
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+long_description    Pysam is a python module for reading and manipulating \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    Samfiles. It's a lightweight wrapper of the samtools C-API.
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-checksums           rmd160  2a72beb9724bf193361fc042a72201be9837a290 \
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>-                    sha256  d74d1bfc462ec4f0f120be2ef0af2205d9964ec73e365f2c4ac6de3d810b6ef9
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+homepage            http://pypi.python.org/pypi/${realname}
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-python.versions         27
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+master_sites        pypi:p/${realname}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+distname            ${realname}-${version}
</span> 
<span style='display:block; white-space:pre;background:#ffe0e0;'>-if {${name} eq ${subport}} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+checksums           rmd160  315bdf74c211fad5372c1eb43751eff3609d3d27 \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    sha256  04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+python.versions     27 34 35 36
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+patchfiles          patch-pysam-remove-RPATH.diff
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+if {${name} ne ${subport}} {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_build       port:py${python.version}-setuptools \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                        port:py${python.version}-cython
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    depends_lib-append  port:htslib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    livecheck.type      none
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+} else {
</span>     livecheck.name      pysam
     livecheck.regex     pysam-(\\d+(\\.\\d+)+)${extract.suffix}
 }
<span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+post-patch {
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    # delete htslib, just to be safe
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+    file delete -force htslib
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+}
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+configure.env       HTSLIB_MODE="external" \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    HTSLIB_INCLUDE_DIR="${prefix}"/include \
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                    HTSLIB_LIBRARY_DIR="${prefix}"/lib
</span><span style='display:block; white-space:pre;color:#808080;'>diff --git a/python/py-pysam/files/patch-pysam-remove-RPATH.diff b/python/py-pysam/files/patch-pysam-remove-RPATH.diff
</span>new file mode 100644
<span style='display:block; white-space:pre;color:#808080;'>index 0000000..1506978
</span><span style='display:block; white-space:pre;background:#ffe0e0;'>--- /dev/null
</span><span style='display:block; white-space:pre;background:#e0e0ff;'>+++ b/python/py-pysam/files/patch-pysam-remove-RPATH.diff
</span><span style='display:block; white-space:pre;background:#e0e0e0;'>@@ -0,0 +1,11 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+prevent setup.py from adding RPATHs
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+--- cy_build.py
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>++++ cy_build.py
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+@@ -81,6 +81,5 @@
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+             if not ext.extra_link_args:
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                 ext.extra_link_args = []
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+ 
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+-            ext.extra_link_args += ['-Wl,-rpath,$ORIGIN']
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+                                     
</span><span style='display:block; white-space:pre;background:#e0ffe0;'>+         build_ext.build_extension(self, ext)
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