[arch-commits] Commit in pymol/trunk (ChangeLog PKGBUILD numpy-deprecated.patch)

[Evgeniy Alekseev]

    Date: Wednesday, May 6, 2015 @ 20:17:55
  Author: arcanis
Revision: 132833

upgpkg: pymol 1.7.6.0-1
upstream update

Modified:
  pymol/trunk/ChangeLog
  pymol/trunk/PKGBUILD
Deleted:
  pymol/trunk/numpy-deprecated.patch

------------------------+
 ChangeLog              |    3 ++
 PKGBUILD               |   17 +++++------
 numpy-deprecated.patch |   68 -----------------------------------------------
 3 files changed, 11 insertions(+), 77 deletions(-)

Modified: ChangeLog
===================================================================
--- ChangeLog	2015-05-06 17:18:24 UTC (rev 132832)
+++ ChangeLog	2015-05-06 18:17:55 UTC (rev 132833)
@@ -1,3 +1,6 @@
+1.7.6.0-1:
+upstream update
+
 1.7.4.0-2:
 glew rebuild
 

Modified: PKGBUILD
===================================================================
--- PKGBUILD	2015-05-06 17:18:24 UTC (rev 132832)
+++ PKGBUILD	2015-05-06 18:17:55 UTC (rev 132833)
@@ -4,8 +4,8 @@
 # Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
 
 pkgname=pymol
-pkgver=1.7.4.0
-pkgrel=2
+pkgver=1.7.6.0
+pkgrel=1
 pkgdesc="Molecular visualization system on an Open Source foundation"
 arch=('i686' 'x86_64')
 url="http://pymol.org/"
@@ -15,14 +15,12 @@
 source=("http://downloads.sourceforge.net/project/pymol/pymol/1.7/pymol-v${pkgver}.tar.bz2"
         ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon"
         "${pkgname}-38899.patch"
-        "apbstools_tcltk8.6.patch"
-        "numpy-deprecated.patch")
+        "apbstools_tcltk8.6.patch")
 install="${pkgname}.install"
-md5sums=('296045ae49b58651f4abe21604996db2'
+md5sums=('ec06f784fbb31ab276bb2960c25dc865'
          '0e9df23150d39cbcb8f79c38ce2a52e5'
          '1f8152c4604ba2939b24e25a022937ca'
-         '138550367b74fd62a7c7bc48d339eb2d'
-         '46197cac724b7bce499857891bdd9a0c')
+         '138550367b74fd62a7c7bc48d339eb2d')
 changelog=ChangeLog
 
 prepare() {
@@ -41,8 +39,6 @@
   # fix FS#38899
   patch -p0 -i "${pkgname}-38899.patch"
   mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
-  # fix deprecated API
-  patch -p0 -i "numpy-deprecated.patch"
   # fix FS#39526
   cd "${srcdir}/${pkgname}"
   patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
@@ -50,6 +46,8 @@
 
 build() {
   cd "${srcdir}/${pkgname}"
+  # required c++11
+  export CPPFLAGS="$CPPFLAGS -std=c++11"
   python2 setup.py build
 }
 
@@ -62,3 +60,4 @@
 }
 
 # vim:set ts=2 sw=2 et:
+

Deleted: numpy-deprecated.patch
===================================================================
--- numpy-deprecated.patch	2015-05-06 17:18:24 UTC (rev 132832)
+++ numpy-deprecated.patch	2015-05-06 18:17:55 UTC (rev 132833)
@@ -1,68 +0,0 @@
-diff -ruN pymol.orig/layer0/os_python.h pymol/layer0/os_python.h
---- pymol.orig/layer0/os_python.h	2015-01-29 21:18:47.681749642 +0000
-+++ pymol/layer0/os_python.h	2015-01-29 21:21:07.501148656 +0000
-@@ -30,6 +30,7 @@
- #include<pythread.h>
- 
- #ifdef _PYMOL_NUMPY
-+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
- #include <numpy/arrayobject.h>
- #endif
- 
---- pymol.orig/layer0/Field.cpp	2015-01-29 21:31:36.105141178 +0000
-+++ pymol/layer0/Field.cpp	2015-01-29 21:31:52.655071349 +0000
-@@ -73,7 +73,7 @@
- 
-   if(copy) {
-     if((result = PyArray_SimpleNew(field->n_dim, dims, typenum)))
--      memcpy(PyArray_DATA(result), field->data, field->size);
-+      memcpy(PyArray_DATA((PyArrayObject *)result), field->data, field->size);
-   } else {
-     result = PyArray_SimpleNewFromData(field->n_dim, dims, typenum, field->data);
-   }
---- pymol.orig/layer2/CoordSet.cpp	2015-01-29 21:58:16.588313743 +0000
-+++ pymol/layer2/CoordSet.cpp	2015-01-29 21:59:42.051283150 +0000
-@@ -198,7 +198,7 @@
- 
-   if(copy) {
-     if((result = PyArray_SimpleNew(2, dims, typenum)))
--      memcpy(PyArray_DATA(result), cs->Coord, cs->NIndex * 3 * base_size);
-+      memcpy(PyArray_DATA((PyArrayObject *)result), cs->Coord, cs->NIndex * 3 * base_size);
-   } else {
-     result = PyArray_SimpleNewFromData(2, dims, typenum, cs->Coord);
-   }
---- pymol.orig/layer3/Selector.cpp       2014-12-04 01:50:03.000000000 +0300
-+++ pymol/layer3/Selector.cpp     2015-01-30 00:44:31.622293145 +0300
-@@ -6608,7 +6608,7 @@
-   }
-
-   result = PyArray_SimpleNew(2, dims, typenum);
--  dataptr = (float*) PyArray_DATA(result);
-+  dataptr = (float*) PyArray_DATA((PyArrayObject *)result);
-
-   for(i = 0, iter.reset(); iter.next(); i++) {
-     v_ptr = iter.getCoord();
-@@ -6677,11 +6677,12 @@
-   import_array1(false);
-
-   if(PyArray_Check(coords)) {
--    if(PyArray_NDIM(coords) != 2 || PyArray_DIM(coords, 1) != 3) {
-+    if(PyArray_NDIM((PyArrayObject *)coords) != 2 ||
-+        PyArray_DIM((PyArrayObject *)coords, 1) != 3) {
-       ErrMessage(G, "LoadCoords", "numpy array shape mismatch");
-       return false;
-     }
--    itemsize = PyArray_ITEMSIZE(coords);
-+    itemsize = PyArray_ITEMSIZE((PyArrayObject *)coords);
-     switch(itemsize) {
-       case sizeof(double):
-       case sizeof(float):
-@@ -6700,7 +6701,7 @@
-       // fast implementation for numpy arrays only
- #ifdef _PYMOL_NUMPY
-       for(b = 0; b < 3; b++) {
--        ptr = PyArray_GETPTR2(coords, a, b);
-+        ptr = PyArray_GETPTR2((PyArrayObject *)coords, a, b);
-
-         switch(itemsize) {
-           case sizeof(double):