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

[Evgeniy Alekseev]

    Date: Thursday, January 29, 2015 @ 23:28:23
  Author: arcanis
Revision: 126763

upgpkg: pymol 1.7.4.0-2
glew rebuild

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

------------------------+
 ChangeLog              |    3 ++
 PKGBUILD               |   14 +++++----
 numpy-deprecated.patch |   68 +++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 79 insertions(+), 6 deletions(-)

Modified: ChangeLog
===================================================================
--- ChangeLog	2015-01-29 21:39:29 UTC (rev 126762)
+++ ChangeLog	2015-01-29 22:28:23 UTC (rev 126763)
@@ -1,3 +1,6 @@
+1.7.4.0-2:
+glew rebuild
+
 1.7.4.0-1:
 upstream update
 

Modified: PKGBUILD
===================================================================
--- PKGBUILD	2015-01-29 21:39:29 UTC (rev 126762)
+++ PKGBUILD	2015-01-29 22:28:23 UTC (rev 126763)
@@ -5,22 +5,24 @@
 
 pkgname=pymol
 pkgver=1.7.4.0
-pkgrel=1
+pkgrel=2
 pkgdesc="Molecular visualization system on an Open Source foundation"
 arch=('i686' 'x86_64')
 url="http://pymol.org/"
 license=('custom')
-depends=('glew' 'glut' 'libgl' 'python2-numpy' 'python2-pmw' 'tcsh')
+depends=('glew' 'glut' 'libgl' 'libxml2' 'python2-numpy' 'python2-pmw' 'tcsh')
 makedepends=('desktop-file-utils' 'gendesk')
 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")
+        "apbstools_tcltk8.6.patch"
+        "numpy-deprecated.patch")
 install="${pkgname}.install"
 md5sums=('296045ae49b58651f4abe21604996db2'
          '0e9df23150d39cbcb8f79c38ce2a52e5'
          '1f8152c4604ba2939b24e25a022937ca'
-         '138550367b74fd62a7c7bc48d339eb2d')
+         '138550367b74fd62a7c7bc48d339eb2d'
+         '46197cac724b7bce499857891bdd9a0c')
 changelog=ChangeLog
 
 prepare() {
@@ -39,6 +41,8 @@
   # 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"
@@ -52,8 +56,6 @@
 package() {
   cd "${srcdir}/${pkgname}"
   python2 setup.py install --prefix=/usr --root="${pkgdir}"
-  sed -i "s|"${pkgdir}"||g" pymol
-  install -Dm755 "pymol" "${pkgdir}/usr/bin/pymol"
   install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
   install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop"
   install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png"

Added: numpy-deprecated.patch
===================================================================
--- numpy-deprecated.patch	                        (rev 0)
+++ numpy-deprecated.patch	2015-01-29 22:28:23 UTC (rev 126763)
@@ -0,0 +1,68 @@
+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):