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10 changed files with 1344 additions and 21 deletions
7
.gitignore
vendored
Normal file
7
.gitignore
vendored
Normal file
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@ -0,0 +1,7 @@
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apbs-1.2.1-source.tar.gz
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/apbs-1.3-source.tar.gz
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/APBS-1.4-source.tar.gz
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/apbs-1.5.tar.gz
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/apbs-pdb2pqr-dfb858d32674438fb8c21421acc86e21667eb8cb.tar.gz
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/apbs-pdb2pqr-vAPBS-3.0.0.tar.gz
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/apbs-3.0.0.tar.gz
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21
Makefile
21
Makefile
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@ -1,21 +0,0 @@
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# Makefile for source rpm: apbs
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# $Id$
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NAME := apbs
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||||
SPECFILE = $(firstword $(wildcard *.spec))
|
||||
|
||||
define find-makefile-common
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for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done
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endef
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||||
|
||||
MAKEFILE_COMMON := $(shell $(find-makefile-common))
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||||
|
||||
ifeq ($(MAKEFILE_COMMON),)
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||||
# attept a checkout
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define checkout-makefile-common
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test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2
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||||
endef
|
||||
|
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MAKEFILE_COMMON := $(shell $(checkout-makefile-common))
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endif
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|
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include $(MAKEFILE_COMMON)
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482
apbs-LGPL_V2
Normal file
482
apbs-LGPL_V2
Normal file
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@ -0,0 +1,482 @@
|
|||
GNU LIBRARY GENERAL PUBLIC LICENSE
|
||||
Version 2, June 1991
|
||||
|
||||
Copyright (C) 1991 Free Software Foundation, Inc.
|
||||
51 Franklin Street, Fifth Floor
|
||||
Boston, MA 02110-1301, USA.
|
||||
Everyone is permitted to copy and distribute verbatim copies
|
||||
of this license document, but changing it is not allowed.
|
||||
|
||||
[This is the first released version of the library GPL. It is
|
||||
numbered 2 because it goes with version 2 of the ordinary GPL.]
|
||||
|
||||
Preamble
|
||||
|
||||
The licenses for most software are designed to take away your
|
||||
freedom to share and change it. By contrast, the GNU General Public
|
||||
Licenses are intended to guarantee your freedom to share and change
|
||||
free software--to make sure the software is free for all its users.
|
||||
|
||||
This license, the Library General Public License, applies to some
|
||||
specially designated Free Software Foundation software, and to any
|
||||
other libraries whose authors decide to use it. You can use it for
|
||||
your libraries, too.
|
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|
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When we speak of free software, we are referring to freedom, not
|
||||
price. Our General Public Licenses are designed to make sure that you
|
||||
have the freedom to distribute copies of free software (and charge for
|
||||
this service if you wish), that you receive source code or can get it
|
||||
if you want it, that you can change the software or use pieces of it
|
||||
in new free programs; and that you know you can do these things.
|
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|
||||
To protect your rights, we need to make restrictions that forbid
|
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anyone to deny you these rights or to ask you to surrender the rights.
|
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These restrictions translate to certain responsibilities for you if
|
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you distribute copies of the library, or if you modify it.
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For example, if you distribute copies of the library, whether gratis
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or for a fee, you must give the recipients all the rights that we gave
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you. You must make sure that they, too, receive or can get the source
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code. If you link a program with the library, you must provide
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Our method of protecting your rights has two steps: (1) copyright
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Also, for each distributor's protection, we want to make certain
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|
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Finally, any free program is threatened constantly by software
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Most GNU software, including some libraries, is covered by the ordinary
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|
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one; be sure to read it in full, and don't assume that anything in it is
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The reason we have a separate public license for some libraries is that
|
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they blur the distinction we usually make between modifying or adding to a
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|
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analogous to running a utility program or application program. However, in
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a textual and legal sense, the linked executable is a combined work, a
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treats it as such.
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Because of this blurred distinction, using the ordinary General
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However, unrestricted linking of non-free programs would deprive the
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The precise terms and conditions for copying, distribution and
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works together with the library.
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Note that it is possible for a library to be covered by the ordinary
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|
||||
GNU LIBRARY GENERAL PUBLIC LICENSE
|
||||
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
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|
||||
0. This License Agreement applies to any software library which
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A "library" means a collection of software functions and/or data
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The "Library", below, refers to any such software library or work
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"Source code" for a work means the preferred form of the work for
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Activities other than copying, distribution and modification are not
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1. You may copy and distribute verbatim copies of the Library's
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You may charge a fee for the physical act of transferring a copy,
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and you may at your option offer warranty protection in exchange for a
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in the event an application does not supply such function or
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(For example, a function in a library to compute square roots has
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a purpose that is entirely well-defined independent of the
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application. Therefore, Subsection 2d requires that any
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application-supplied function or table used by this function must
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be optional: if the application does not supply it, the square
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root function must still compute square roots.)
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These requirements apply to the modified work as a whole. If
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Thus, it is not the intent of this section to claim rights or contest
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In addition, mere aggregation of another work not based on the Library
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that they refer to the ordinary GNU General Public License, version 2,
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If distribution of object code is made by offering access to copy
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distribute the source code, even though third parties are not
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However, linking a "work that uses the Library" with the Library
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creates an executable that is a derivative of the Library (because it
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contains portions of the Library), rather than a "work that uses the
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Section 6 states terms for distribution of such executables.
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When a "work that uses the Library" uses material from a header file
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Otherwise, if the work is a derivative of the Library, you may
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Any executables containing that work also fall under Section 6,
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You must give prominent notice with each copy of the work that the
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|
||||
facilities. This must be distributed under the terms of the
|
||||
Sections above.
|
||||
|
||||
b) Give prominent notice with the combined library of the fact
|
||||
that part of it is a work based on the Library, and explaining
|
||||
where to find the accompanying uncombined form of the same work.
|
||||
|
||||
8. You may not copy, modify, sublicense, link with, or distribute
|
||||
the Library except as expressly provided under this License. Any
|
||||
attempt otherwise to copy, modify, sublicense, link with, or
|
||||
distribute the Library is void, and will automatically terminate your
|
||||
rights under this License. However, parties who have received copies,
|
||||
or rights, from you under this License will not have their licenses
|
||||
terminated so long as such parties remain in full compliance.
|
||||
|
||||
9. You are not required to accept this License, since you have not
|
||||
signed it. However, nothing else grants you permission to modify or
|
||||
distribute the Library or its derivative works. These actions are
|
||||
prohibited by law if you do not accept this License. Therefore, by
|
||||
modifying or distributing the Library (or any work based on the
|
||||
Library), you indicate your acceptance of this License to do so, and
|
||||
all its terms and conditions for copying, distributing or modifying
|
||||
the Library or works based on it.
|
||||
|
||||
10. Each time you redistribute the Library (or any work based on the
|
||||
Library), the recipient automatically receives a license from the
|
||||
original licensor to copy, distribute, link with or modify the Library
|
||||
subject to these terms and conditions. You may not impose any further
|
||||
restrictions on the recipients' exercise of the rights granted herein.
|
||||
You are not responsible for enforcing compliance by third parties to
|
||||
this License.
|
||||
|
||||
11. If, as a consequence of a court judgment or allegation of patent
|
||||
infringement or for any other reason (not limited to patent issues),
|
||||
conditions are imposed on you (whether by court order, agreement or
|
||||
otherwise) that contradict the conditions of this License, they do not
|
||||
excuse you from the conditions of this License. If you cannot
|
||||
distribute so as to satisfy simultaneously your obligations under this
|
||||
License and any other pertinent obligations, then as a consequence you
|
||||
may not distribute the Library at all. For example, if a patent
|
||||
license would not permit royalty-free redistribution of the Library by
|
||||
all those who receive copies directly or indirectly through you, then
|
||||
the only way you could satisfy both it and this License would be to
|
||||
refrain entirely from distribution of the Library.
|
||||
|
||||
If any portion of this section is held invalid or unenforceable under any
|
||||
particular circumstance, the balance of the section is intended to apply,
|
||||
and the section as a whole is intended to apply in other circumstances.
|
||||
|
||||
It is not the purpose of this section to induce you to infringe any
|
||||
patents or other property right claims or to contest validity of any
|
||||
such claims; this section has the sole purpose of protecting the
|
||||
integrity of the free software distribution system which is
|
||||
implemented by public license practices. Many people have made
|
||||
generous contributions to the wide range of software distributed
|
||||
through that system in reliance on consistent application of that
|
||||
system; it is up to the author/donor to decide if he or she is willing
|
||||
to distribute software through any other system and a licensee cannot
|
||||
impose that choice.
|
||||
|
||||
This section is intended to make thoroughly clear what is believed to
|
||||
be a consequence of the rest of this License.
|
||||
|
||||
12. If the distribution and/or use of the Library is restricted in
|
||||
certain countries either by patents or by copyrighted interfaces, the
|
||||
original copyright holder who places the Library under this License may add
|
||||
an explicit geographical distribution limitation excluding those countries,
|
||||
so that distribution is permitted only in or among countries not thus
|
||||
excluded. In such case, this License incorporates the limitation as if
|
||||
written in the body of this License.
|
||||
|
||||
13. The Free Software Foundation may publish revised and/or new
|
||||
versions of the Library General Public License from time to time.
|
||||
Such new versions will be similar in spirit to the present version,
|
||||
but may differ in detail to address new problems or concerns.
|
||||
|
||||
Each version is given a distinguishing version number. If the Library
|
||||
specifies a version number of this License which applies to it and
|
||||
"any later version", you have the option of following the terms and
|
||||
conditions either of that version or of any later version published by
|
||||
the Free Software Foundation. If the Library does not specify a
|
||||
license version number, you may choose any version ever published by
|
||||
the Free Software Foundation.
|
||||
|
||||
14. If you wish to incorporate parts of the Library into other free
|
||||
programs whose distribution conditions are incompatible with these,
|
||||
write to the author to ask for permission. For software which is
|
||||
copyrighted by the Free Software Foundation, write to the Free
|
||||
Software Foundation; we sometimes make exceptions for this. Our
|
||||
decision will be guided by the two goals of preserving the free status
|
||||
of all derivatives of our free software and of promoting the sharing
|
||||
and reuse of software generally.
|
||||
|
||||
NO WARRANTY
|
||||
|
||||
15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO
|
||||
WARRANTY FOR THE LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
|
||||
EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR
|
||||
OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT WARRANTY OF ANY
|
||||
KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
|
||||
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
|
||||
PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
|
||||
LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
|
||||
THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
|
||||
|
||||
16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
|
||||
WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
|
||||
AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
|
||||
FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
|
||||
CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
|
||||
LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
|
||||
RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
|
||||
FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
|
||||
SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
|
||||
DAMAGES.
|
||||
|
||||
END OF TERMS AND CONDITIONS
|
||||
|
||||
How to Apply These Terms to Your New Libraries
|
||||
|
||||
If you develop a new library, and you want it to be of the greatest
|
||||
possible use to the public, we recommend making it free software that
|
||||
everyone can redistribute and change. You can do so by permitting
|
||||
redistribution under these terms (or, alternatively, under the terms of the
|
||||
ordinary General Public License).
|
||||
|
||||
To apply these terms, attach the following notices to the library. It is
|
||||
safest to attach them to the start of each source file to most effectively
|
||||
convey the exclusion of warranty; and each file should have at least the
|
||||
"copyright" line and a pointer to where the full notice is found.
|
||||
|
||||
<one line to give the library's name and a brief idea of what it does.>
|
||||
Copyright (C) <year> <name of author>
|
||||
|
||||
This library is free software; you can redistribute it and/or
|
||||
modify it under the terms of the GNU Lesser General Public
|
||||
License as published by the Free Software Foundation; either
|
||||
version 2 of the License, or (at your option) any later version.
|
||||
|
||||
This library is distributed in the hope that it will be useful,
|
||||
but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
|
||||
Lesser General Public License for more details.
|
||||
|
||||
You should have received a copy of the GNU Lesser General Public
|
||||
License along with this library; if not, write to the Free Software
|
||||
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
|
||||
Also add information on how to contact you by electronic and paper mail.
|
||||
|
||||
You should also get your employer (if you work as a programmer) or your
|
||||
school, if any, to sign a "copyright disclaimer" for the library, if
|
||||
necessary. Here is a sample; alter the names:
|
||||
|
||||
Yoyodyne, Inc., hereby disclaims all copyright interest in the
|
||||
library `Frob' (a library for tweaking knobs) written by James Random Hacker.
|
||||
|
||||
<signature of Ty Coon>, 1 April 1990
|
||||
Ty Coon, President of Vice
|
||||
|
||||
That's all there is to it!
|
||||
23
apbs-c99.patch
Normal file
23
apbs-c99.patch
Normal file
|
|
@ -0,0 +1,23 @@
|
|||
Partial backport of this commit, to avoid an implicit declaration of
|
||||
getpid and future build failures:
|
||||
|
||||
Author: Noah Oblath <nsoblath@gmail.com>
|
||||
Date: Mon Jan 24 15:33:56 2022 -0800
|
||||
|
||||
Nsoblath/issue 163 (#171)
|
||||
|
||||
diff -ur apbs-3.0.0.orig/contrib/iapbs/src/apbs_driver.c apbs-3.0.0/contrib/iapbs/src/apbs_driver.c
|
||||
--- apbs-3.0.0.orig/contrib/iapbs/src/apbs_driver.c 2020-05-30 03:47:30.000000000 +0200
|
||||
+++ apbs-3.0.0/contrib/iapbs/src/apbs_driver.c 2023-02-06 07:58:46.215007012 +0100
|
||||
@@ -18,6 +18,11 @@
|
||||
|
||||
#include "apbs_driver.h"
|
||||
|
||||
+#ifdef WIN32
|
||||
+#include <process.h>
|
||||
+#else
|
||||
+#include <unistd.h>
|
||||
+#endif
|
||||
|
||||
/*! \def MAX_BUF_SIZE
|
||||
\brief Buffer size for internal APBS string input.
|
||||
325
apbs-cmake.patch
Normal file
325
apbs-cmake.patch
Normal file
|
|
@ -0,0 +1,325 @@
|
|||
--- a/apbs/CMakeLists.txt_orig 2018-05-20 13:00:17.451341064 -0400
|
||||
+++ b/apbs/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400
|
||||
@@ -1,4 +1,5 @@
|
||||
-cmake_minimum_required (VERSION 3.12)
|
||||
+cmake_minimum_required(VERSION 3.13...4.0)
|
||||
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
|
||||
|
||||
################################################################################
|
||||
# TODO: Add licensing and authorship information
|
||||
@@ -7,7 +8,6 @@
|
||||
# (configure.ac:1306)
|
||||
################################################################################
|
||||
set(CMAKE_VERBOSE_MAKEFILE true)
|
||||
-cmake_policy(SET CMP0054 OLD)
|
||||
cmake_policy(SET CMP0042 NEW)
|
||||
set(CMAKE_MACOSX_RPATH 1)
|
||||
|
||||
@@ -70,10 +71,10 @@
|
||||
set(TOOLS_PATH ${APBS_BUILD}/tools)
|
||||
set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
|
||||
|
||||
-set(LIBRARY_INSTALL_PATH lib)
|
||||
-set(HEADER_INSTALL_PATH include/apbs)
|
||||
+set(LIBRARY_INSTALL_PATH ${LIB_INSTALL_DIR})
|
||||
+set(HEADER_INSTALL_PATH ${INCLUDE_INSTALL_DIR}/apbs)
|
||||
set(EXECUTABLE_INSTALL_PATH bin)
|
||||
-set(SHARE_INSTALL_PATH share/apbs)
|
||||
+set(SHARE_INSTALL_PATH ${SHARE_INSTALL_PREFIX}/apbs)
|
||||
|
||||
set(APBS_LIBS)
|
||||
set(APBS_LIB_DIRS)
|
||||
@@ -85,7 +86,7 @@
|
||||
PATHS "${APBS_ROOT}"
|
||||
DOC "The path to the external git submodules")
|
||||
|
||||
-set(SYS_LIBPATHS /usr/lib64)
|
||||
+#set(SYS_LIBPATHS /usr/lib64)
|
||||
#list(APPEND SYS_LIBPATHS /usr/lib64)
|
||||
|
||||
|
||||
@@ -139,11 +140,6 @@
|
||||
################################################################################
|
||||
message(STATUS "Setting lookup paths for headers and libraries")
|
||||
|
||||
-set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
|
||||
-list(APPEND CMAKE_INCLUDE_PATH /usr/include)
|
||||
-list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
|
||||
-
|
||||
-
|
||||
################################################################################
|
||||
# Enable ansi pedantic compiling #
|
||||
################################################################################
|
||||
@@ -307,12 +303,12 @@
|
||||
################################################################################
|
||||
if(NOT ENABLE_FETK)
|
||||
# We'll use autotools to build MALOC if FETK is enabled.
|
||||
- add_subdirectory(${EXTERNALS_PATH}/fetk/maloc)
|
||||
- include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base
|
||||
- ${EXTERNALS_PATH}/fetk/maloc/src/vsys
|
||||
- ${EXTERNALS_PATH}/fetk/maloc/src/vsh
|
||||
- ${EXTERNALS_PATH}/fetk/maloc/src/psh)
|
||||
- list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
|
||||
+ #add_subdirectory(${EXTERNALS_PATH}/fetk/maloc)
|
||||
+ #include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base
|
||||
+ # ${EXTERNALS_PATH}/fetk/maloc/src/vsys
|
||||
+ # ${EXTERNALS_PATH}/fetk/maloc/src/vsh
|
||||
+ # ${EXTERNALS_PATH}/fetk/maloc/src/psh)
|
||||
+ #list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
|
||||
list(APPEND APBS_LIBS maloc)
|
||||
endif()
|
||||
|
||||
@@ -778,10 +774,10 @@
|
||||
################################################################################
|
||||
# Set up additional directories to install #
|
||||
################################################################################
|
||||
-install(DIRECTORY ${APBS_ROOT}/doc
|
||||
- DESTINATION ${SHARE_INSTALL_PATH}
|
||||
- PATTERN "programmer" EXCLUDE
|
||||
- PATTERN "CMakeLists.txt" EXCLUDE)
|
||||
+#install(DIRECTORY ${APBS_ROOT}/doc
|
||||
+# DESTINATION ${SHARE_INSTALL_PATH}
|
||||
+# PATTERN "programmer" EXCLUDE
|
||||
+# PATTERN "CMakeLists.txt" EXCLUDE)
|
||||
|
||||
if(BUILD_DOC)
|
||||
install(DIRECTORY ${APBS_BUILD}/doc/programmer
|
||||
@@ -791,27 +787,11 @@
|
||||
PATTERN "mainpage.h" EXCLUDE)
|
||||
endif()
|
||||
|
||||
-install(DIRECTORY ${APBS_ROOT}/examples
|
||||
- DESTINATION ${SHARE_INSTALL_PATH})
|
||||
-
|
||||
-install(DIRECTORY ${APBS_ROOT}/tests
|
||||
- DESTINATION ${SHARE_INSTALL_PATH}
|
||||
- FILES_MATCHING
|
||||
- PATTERN "*.py"
|
||||
- PATTERN "README")
|
||||
-
|
||||
-if(BUILD_TOOLS)
|
||||
- install(DIRECTORY ${APBS_ROOT}/tools
|
||||
- DESTINATION ${SHARE_INSTALL_PATH}
|
||||
- USE_SOURCE_PERMISSIONS
|
||||
- PATTERN "CMakeLists.txt"
|
||||
- PATTERN "matlab" EXCLUDE)
|
||||
-
|
||||
- if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
|
||||
- install(DIRECTORY ${APBS_BUILD}/tools/bin
|
||||
+if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
|
||||
+ install(
|
||||
+ DIRECTORY ${APBS_BUILD}/tools/bin
|
||||
DESTINATION ${SHARE_INSTALL_PATH}/tools
|
||||
USE_SOURCE_PERMISSIONS)
|
||||
- endif()
|
||||
endif()
|
||||
|
||||
################################################################################
|
||||
@@ -880,7 +860,7 @@
|
||||
set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}")
|
||||
set(CPACK_PACKAGE_DESCRIPTION "APBS - Adaptive Poisson Boltzmann Solver")
|
||||
|
||||
-set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/../LICENSE.md")
|
||||
+set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE.md")
|
||||
set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md")
|
||||
|
||||
set(CPACK_SOURCE_IGNORE_FILES "${PROJECT_BINARY_DIR};/.git/;.gitignore;/tools/matlab/")
|
||||
--- a/apbs/src/CMakeLists.txt_orig 2018-05-20 13:00:20.518351049 -0400
|
||||
+++ b/apbs/src/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400
|
||||
@@ -1,4 +1,4 @@
|
||||
-cmake_minimum_required(VERSION 2.8)
|
||||
+cmake_minimum_required(VERSION 3.13...4.0)
|
||||
|
||||
macro(add_items TYPE)
|
||||
|
||||
@@ -32,11 +32,11 @@
|
||||
message(STATUS "With external header files ${EXTERNAL_HEADERS}")
|
||||
message(STATUS "With internal header files ${INTERNAL_HEADERS}")
|
||||
message(STATUS "With library dependencies ${LIBRARY_DEPENDENCIES}")
|
||||
- add_library(${LIBRARY_NAME} ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS})
|
||||
- target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES})
|
||||
+ add_library(${LIBRARY_NAME} OBJECT ${SOURCES} ${EXTERNAL_HEADERS} ${INTERNAL_HEADERS})
|
||||
+ # target_link_libraries(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES})
|
||||
#add_dependencies(${LIBRARY_NAME} ${LIBRARY_DEPENDENCIES})
|
||||
INSTALL(FILES ${EXTERNAL_HEADERS} DESTINATION ${HEADER_INSTALL_PATH}/${LIBRARY})
|
||||
- INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH})
|
||||
+ # INSTALL(TARGETS ${LIBRARY_NAME} DESTINATION ${LIBRARY_INSTALL_PATH})
|
||||
list(APPEND APBS_INTERNAL_LIBS ${LIBRARY_NAME})
|
||||
set(APBS_INTERNAL_LIBS ${APBS_INTERNAL_LIBS} PARENT_SCOPE)
|
||||
message(STATUS "Added ${LIBRARY_NAME}")
|
||||
@@ -45,6 +45,11 @@
|
||||
add_subdirectory(generic)
|
||||
add_subdirectory(pmgc)
|
||||
add_subdirectory(mg)
|
||||
+add_library(apbs SHARED $<TARGET_OBJECTS:apbs_generic> $<TARGET_OBJECTS:apbs_pmgc> $<TARGET_OBJECTS:apbs_mg>)
|
||||
+# set a SOVERSION to keep packager happy
|
||||
+SET_TARGET_PROPERTIES(apbs PROPERTIES SOVERSION "1")
|
||||
+target_link_libraries(apbs ${LIBRARY_DEPENDENCIES})
|
||||
+INSTALL(TARGETS apbs LIBRARY DESTINATION ${LIBRARY_INSTALL_PATH})
|
||||
|
||||
if(ENABLE_FETK)
|
||||
add_subdirectory(fem)
|
||||
@@ -56,7 +61,7 @@
|
||||
message(STATUS "External Headers: ${EXTERNAL_HEADERS}")
|
||||
|
||||
#add_executable(apbs main.c routines.c)
|
||||
-add_executable(apbs main.c apbs.h routines.c routines.h)
|
||||
+add_executable(apbs-bin main.c apbs.h routines.c routines.h)
|
||||
message(STATUS " ")
|
||||
message(STATUS "APBS Libraries: ${APBS_LIBS}")
|
||||
message(STATUS "Internal Libraries: ${APBS_INTERNAL_LIBS}")
|
||||
@@ -64,7 +69,8 @@
|
||||
|
||||
#add_dependencies(apbs ${BEM_LIB})
|
||||
#target_include_directories(apbs PRIVATE apbs.h routines.h)
|
||||
-target_link_libraries(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS})
|
||||
+target_link_libraries(apbs-bin ${APBS_LIBS} apbs)
|
||||
+SET_TARGET_PROPERTIES(apbs-bin PROPERTIES OUTPUT_NAME apbs)
|
||||
#add_dependencies(apbs ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${APBS_LIBS})
|
||||
|
||||
configure_file(
|
||||
@@ -79,6 +85,6 @@
|
||||
endif()
|
||||
|
||||
INSTALL(FILES apbs.h routines.h DESTINATION ${HEADER_INSTALL_PATH})
|
||||
-INSTALL(TARGETS apbs DESTINATION ${EXECUTABLE_INSTALL_PATH})
|
||||
+INSTALL(TARGETS apbs-bin DESTINATION ${EXECUTABLE_INSTALL_PATH})
|
||||
|
||||
message(STATUS ${CMAKE_C_FLAGS})
|
||||
--- a/apbs/tools/manip/CMakeLists.txt_orig 2018-05-20 13:00:31.831387880 -0400
|
||||
+++ b/apbs/tools/manip/CMakeLists.txt 2018-05-20 13:07:07.742714938 -0400
|
||||
@@ -1,9 +1,10 @@
|
||||
message(STATUS "Building manip")
|
||||
|
||||
set(LIBS "")
|
||||
-list(APPEND LIBS "apbs_generic")
|
||||
-list(APPEND LIBS "apbs_mg")
|
||||
-list(APPEND LIBS "apbs_pmgc")
|
||||
+#list(APPEND LIBS "apbs_generic")
|
||||
+#list(APPEND LIBS "apbs_mg")
|
||||
+#list(APPEND LIBS "apbs_pmgc")
|
||||
+list(APPEND LIBS "apbs")
|
||||
if(FETK_ENABLED)
|
||||
list(APPEND LIBS "apbs_fem")
|
||||
endif(FETK_ENABLED)
|
||||
@@ -11,7 +12,9 @@
|
||||
message(STATUS "libraries: ${LIBS}")
|
||||
|
||||
add_executable(coulomb coulomb.c)
|
||||
-target_link_libraries(coulomb ${LIBS})
|
||||
+target_link_libraries(coulomb ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(born born.c)
|
||||
-target_link_libraries(born ${LIBS})
|
||||
+target_link_libraries(born ${LIBS} ${APBS_LIBS})
|
||||
+
|
||||
+INSTALL(TARGETS coulomb born DESTINATION ${EXECUTABLE_INSTALL_PATH})
|
||||
--- a/apbs/tools/mesh/CMakeLists.txt_orig 2018-05-20 13:00:26.966372042 -0400
|
||||
+++ b/apbs/tools/mesh/CMakeLists.txt 2018-05-20 13:00:47.917440250 -0400
|
||||
@@ -1,9 +1,10 @@
|
||||
message(STATUS "Building mesh")
|
||||
|
||||
set(LIBS "")
|
||||
-list(APPEND LIBS "apbs_generic")
|
||||
-list(APPEND LIBS "apbs_mg")
|
||||
-list(APPEND LIBS "apbs_pmgc")
|
||||
+#list(APPEND LIBS "apbs_generic")
|
||||
+#list(APPEND LIBS "apbs_mg")
|
||||
+#list(APPEND LIBS "apbs_pmgc")
|
||||
+list(APPEND LIBS "apbs")
|
||||
if(FETK_ENABLED)
|
||||
list(APPEND LIBS "apbs_fem")
|
||||
endif(FETK_ENABLED)
|
||||
@@ -11,46 +12,48 @@
|
||||
message(STATUS "libraries: ${LIBS}")
|
||||
|
||||
add_executable(mgmesh mgmesh.c)
|
||||
-target_link_libraries(mgmesh ${LIBS})
|
||||
+target_link_libraries(mgmesh ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(smooth smooth.c)
|
||||
-target_link_libraries(smooth ${LIBS})
|
||||
+target_link_libraries(smooth ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(dxmath dxmath.c)
|
||||
-target_link_libraries(dxmath ${LIBS})
|
||||
+target_link_libraries(dxmath ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(mergedx mergedx.c)
|
||||
-target_link_libraries(mergedx ${LIBS})
|
||||
+target_link_libraries(mergedx ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(mergedx2 mergedx2.c)
|
||||
-target_link_libraries(mergedx2 ${LIBS})
|
||||
+target_link_libraries(mergedx2 ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(value value.c)
|
||||
-target_link_libraries(value ${LIBS})
|
||||
+target_link_libraries(value ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(multivalue multivalue.c)
|
||||
-target_link_libraries(multivalue ${LIBS})
|
||||
+target_link_libraries(multivalue ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(benchmark benchmark.c)
|
||||
-target_link_libraries(benchmark ${LIBS})
|
||||
+target_link_libraries(benchmark ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(similarity similarity.c)
|
||||
-target_link_libraries(similarity ${LIBS})
|
||||
+target_link_libraries(similarity ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(analysis analysis.c)
|
||||
-target_link_libraries(analysis ${LIBS})
|
||||
+target_link_libraries(analysis ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(dx2mol dx2mol.c)
|
||||
-target_link_libraries(dx2mol ${LIBS})
|
||||
+target_link_libraries(dx2mol ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(dx2uhbd dx2uhbd.c)
|
||||
-target_link_libraries(dx2uhbd ${LIBS})
|
||||
+target_link_libraries(dx2uhbd ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(del2dx del2dx.c)
|
||||
-target_link_libraries(del2dx ${LIBS})
|
||||
+target_link_libraries(del2dx ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(tensor2dx tensor2dx.c)
|
||||
-target_link_libraries(tensor2dx ${LIBS})
|
||||
+target_link_libraries(tensor2dx ${LIBS} ${APBS_LIBS})
|
||||
|
||||
add_executable(uhbd_asc2bin uhbd_asc2bin.c)
|
||||
-target_link_libraries(uhbd_asc2bin ${LIBS})
|
||||
+target_link_libraries(uhbd_asc2bin ${LIBS} ${APBS_LIBS})
|
||||
+
|
||||
+INSTALL(TARGETS mgmesh smooth dxmath mergedx mergedx2 value multivalue benchmark similarity analysis dx2mol dx2uhbd del2dx tensor2dx uhbd_asc2bin DESTINATION ${EXECUTABLE_INSTALL_PATH})
|
||||
--- a/a/tools/python/CMakeLists.orig.txt 2020-05-30 03:47:30.000000000 +0200
|
||||
+++ b/b/tools/python/CMakeLists.txt 2025-07-24 20:56:31.152039088 +0200
|
||||
@@ -1,3 +1,4 @@
|
||||
+cmake_minimum_required(VERSION 3.13...4.0)
|
||||
if (${CMAKE_VERSION} VERSION_GREATER "3.13")
|
||||
CMAKE_POLICY(SET CMP0078 OLD)
|
||||
CMAKE_POLICY(SET CMP0086 OLD)
|
||||
@@ -23,18 +24,16 @@
|
||||
SET(CMAKE_SWIG_FLAGS "")
|
||||
|
||||
SWIG_ADD_LIBRARY(apbslib
|
||||
- #TYPE USE_BUILD_SHARED_LIBS
|
||||
+ TYPE USE_BUILD_SHARED_LIBS
|
||||
TYPE SHARED
|
||||
LANGUAGE python
|
||||
SOURCES apbslib.i)
|
||||
|
||||
# Hack to get the correct shared library extensions. Why does Python suck so hard wrt to this?
|
||||
-if(APPLE)
|
||||
- set(CMAKE_SHARED_LIBRARY_SUFFIX ".so")
|
||||
-endif(APPLE)
|
||||
+set(CMAKE_SHARED_LIBRARY_SUFFIX ".so")
|
||||
|
||||
# Another hack to get SWIG to use the the correct library extension!
|
||||
-#SET_TARGET_PROPERTIES(${SWIG_MODULE_apbslib_REAL_NAME} PROPERTIES SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX})
|
||||
+SET_TARGET_PROPERTIES(${SWIG_MODULE_apbslib_REAL_NAME} PROPERTIES SUFFIX ${CMAKE_SHARED_LIBRARY_SUFFIX})
|
||||
|
||||
SWIG_LINK_LIBRARIES(apbslib ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${Python3_LIBRARIES})
|
||||
|
||||
60
apbs-exclude_tests.patch
Normal file
60
apbs-exclude_tests.patch
Normal file
|
|
@ -0,0 +1,60 @@
|
|||
--- a/tests/test_cases.orig.cfg 2020-05-30 03:47:30.000000000 +0200
|
||||
+++ b/tests/test_cases.cfg 2021-11-01 11:30:08.175043842 +0100
|
||||
@@ -74,57 +74,3 @@
|
||||
apbs-mol : 1.847663548071E+03 1.883912182952E+03 2.732623683321E+03 3.123035854133E+03 -3.624863445503E+01 -3.904121297757E+02 -3.541635359318E+02
|
||||
apbs-smol : 1.847860440020E+03 1.885436377745E+03 2.734040568569E+03 3.125279428954E+03 -3.757593797629E+01 -3.912388198513E+02 -3.536628818750E+02
|
||||
|
||||
-
|
||||
-[geoflow]
|
||||
-input_dir : ../examples/geoflow
|
||||
-imidazole : -1.030222099963E+01 5.417419E-01
|
||||
-
|
||||
-
|
||||
-[bem]
|
||||
-input_dir : ../examples/bem
|
||||
-451c_order1 : -1.172906546441e+03
|
||||
-451c_order5 : -1.175936034727E+03
|
||||
-
|
||||
-[bem-pKa]
|
||||
-input_dir : ../examples/bem-pKa
|
||||
-ASH66 : -9.954199102140E-01
|
||||
-2LZT-ASH66 : -8.620097356247E+01
|
||||
-2LZT-noASH66 : -8.601110775968E+01
|
||||
-
|
||||
-[bem-binding-energy]
|
||||
-input_dir : ../examples/bem-binding-energy
|
||||
-1d30 : -5.249027161163E+03
|
||||
-1d30_monomer1 : -6.232145066905E+03
|
||||
-1d30_monomer2 : -1.821470879387E+02
|
||||
-
|
||||
-
|
||||
-[pbam]
|
||||
-input_dir : ../examples/pbam
|
||||
-toy_energyforce : -4.965018552290E+01 -4.965018552290E+01
|
||||
-
|
||||
-[pbsam]
|
||||
-input_dir : ../examples/pbsam-gly
|
||||
-gly_energyforce : 6.176608555569E-05 6.210593742215E-05
|
||||
-
|
||||
-
|
||||
-[protein-rna]
|
||||
-input_dir : ../examples/protein-rna
|
||||
-setup : python apbs_dx.py
|
||||
-apbs-0.025 : 3.186122223752E+04 3.662855899462E+04 8.477786964834E+03 1.000545153104E+04 2.329205982055E+04 2.653636629928E+04 8.674116429353E+01
|
||||
-apbs-0.050 : 3.184763478312E+04 3.661493366846E+04 8.475252516617E+03 1.000292179294E+04 2.327168361816E+04 2.651594350839E+04 9.606836713866E+01
|
||||
-apbs-0.075 : 3.184033569905E+04 3.660761530545E+04 8.473669396547E+03 1.000134276339E+04 2.326088212207E+04 2.650511882057E+04 1.011537214883E+02
|
||||
-apbs-0.100 : 3.183548000794E+04 3.660274809589E+04 8.472507235893E+03 1.000018407412E+04 2.325372656922E+04 2.649794981016E+04 1.046142116108E+02
|
||||
-apbs-0.125 : 3.183190100647E+04 3.659916161996E+04 8.471585837513E+03 9.999265654586E+03 2.324845847155E+04 2.649267328362E+04 1.072226817610E+02
|
||||
-apbs-0.150 : 3.182909678356E+04 3.659635228953E+04 8.470821300868E+03 9.998503715551E+03 2.324433086171E+04 2.648854016160E+04 1.093084123761E+02
|
||||
-apbs-0.175 : 3.182680817429E+04 3.659406006570E+04 8.470167484600E+03 9.997852199372E+03 2.324096101131E+04 2.648516662194E+04 1.110412443877E+02
|
||||
-apbs-0.200 : 3.182488501939E+04 3.659213428941E+04 8.469596195763E+03 9.997282974485E+03 2.323812822097E+04 2.648233134327E+04 1.125199716537E+02
|
||||
-apbs-0.225 : 3.182323306491E+04 3.659048040133E+04 8.469088900775E+03 9.996777552566E+03 2.323569434544E+04 2.647989580221E+04 1.138070465620E+02
|
||||
-apbs-0.250 : 3.182178954360E+04 3.658903543806E+04 8.468632740499E+03 9.996323108319E+03 2.323356752071E+04 2.647776789284E+04 1.149444369078E+02
|
||||
-apbs-0.275 : 3.182051070674E+04 3.658775551975E+04 8.468218414737E+03 9.995910367297E+03 2.323168374787E+04 2.647588345522E+04 1.159616972338E+02
|
||||
-apbs-0.300 : 3.181936493519E+04 3.658660893678E+04 8.467838971928E+03 9.995532397856E+03 2.322999676177E+04 2.647419611346E+04 1.168804254687E+02
|
||||
-apbs-0.325 : 3.181832869046E+04 3.658557208654E+04 8.467489074881E+03 9.995183878464E+03 2.322847209567E+04 2.647267132259E+04 1.177168854906E+02
|
||||
-apbs-0.400 : 3.181571629593E+04 3.658295870300E+04 8.466578740909E+03 9.994277216885E+03 2.322463613929E+04 2.646883588223E+04 1.198456038803E+02
|
||||
-apbs-0.500 : 3.181302243781E+04 3.658026461575E+04 8.465598755475E+03 9.993301332440E+03 2.322070101887E+04 2.646490251594E+04 1.220607673699E+02
|
||||
-apbs-0.600 : 3.181090090954E+04 3.657814345443E+04 8.464799341688E+03 9.992505379555E+03 2.321762631365E+04 2.646183001839E+04 1.238080564885E+02
|
||||
-apbs-0.700 : 3.180915789156E+04 3.657640108752E+04 8.464126109756E+03 9.991835140855E+03 2.321512352191E+04 2.645932953757E+04 1.252364090878E+02
|
||||
-apbs-0.800 : 3.180768241803E+04 3.657492640520E+04 8.463546035019E+03 9.991257699113E+03 2.321302636223E+04 2.645723464562E+04 1.264340604647E+02
|
||||
11
apbs-python311.patch
Normal file
11
apbs-python311.patch
Normal file
|
|
@ -0,0 +1,11 @@
|
|||
--- a/tools/manip/inputgen.orig.py 2020-05-30 03:47:30.000000000 +0200
|
||||
+++ b/tools/manip/inputgen.py 2021-12-26 12:13:08.819979543 +0100
|
||||
@@ -266,7 +266,7 @@
|
||||
file (string)
|
||||
"""
|
||||
nproc = 0
|
||||
- file = open(filename, 'rU')
|
||||
+ file = open(filename)
|
||||
text = ""
|
||||
while 1:
|
||||
line = file.readline()
|
||||
435
apbs.spec
Normal file
435
apbs.spec
Normal file
|
|
@ -0,0 +1,435 @@
|
|||
# Workaround for GCC-10
|
||||
%define _legacy_common_support 1
|
||||
|
||||
%global commit %{nil}
|
||||
%global shortcommit %{nil}
|
||||
%global datecommit %{nil}
|
||||
|
||||
# To perform all tests, APBS needs to be compiled together additional sub-modules
|
||||
%bcond_without check
|
||||
|
||||
Name: apbs
|
||||
Summary: Adaptive Poisson Boltzmann Solver
|
||||
Version: 3.0.0
|
||||
Release: 32%{datecommit}%{shortcommit}%{?dist}
|
||||
# iAPBS looks licensed with a LGPLv2+, APBS is released under BSD license.
|
||||
License: LGPL-2.0-or-later AND BSD-3-Clause
|
||||
URL: https://www.poissonboltzmann.org/
|
||||
Source0: https://github.com/Electrostatics/apbs/archive/refs/tags/v%{version}/%{name}-%{version}.tar.gz
|
||||
Source1: %{name}-LGPL_V2
|
||||
|
||||
Patch0: %{name}-cmake.patch
|
||||
|
||||
# Exclude tests because they are for features inactivated
|
||||
Patch1: %{name}-exclude_tests.patch
|
||||
|
||||
# Porting to Python-3.11
|
||||
Patch2: %{name}-python311.patch
|
||||
|
||||
Patch3: apbs-c99.patch
|
||||
|
||||
BuildRequires: gcc-c++
|
||||
BuildRequires: cmake3
|
||||
BuildRequires: chrpath
|
||||
BuildRequires: make
|
||||
BuildRequires: doxygen
|
||||
BuildRequires: graphviz
|
||||
BuildRequires: maloc-devel
|
||||
BuildRequires: zlib-devel
|
||||
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
|
||||
Requires: python3-%{name}
|
||||
|
||||
%description
|
||||
APBS is a software package for the numerical solution of the
|
||||
Poisson-Boltzmann equation (PBE), one of the most popular continuum
|
||||
models for describing electrostatic interactions between molecular
|
||||
solutes in salty, aqueous media. APBS was designed to efficiently
|
||||
evaluate electrostatic properties for such simulations for a wide
|
||||
range of length scales to enable the investigation of molecules with
|
||||
tens to millions of atoms. It is also widely used in molecular
|
||||
visualization (in such applications as PyMOL).
|
||||
|
||||
%package tools
|
||||
Summary: Utility programs that utilize the APBS package
|
||||
Requires: %{name}%{?_isa} = %{version}-%{release}
|
||||
%description tools
|
||||
The apbs-tools package contains several utility programs for
|
||||
conversion, analysis and preparation of files that use the adaptive
|
||||
poisson boltzmann solver library.
|
||||
|
||||
%package libs
|
||||
Summary: Libraries for APBS
|
||||
%description libs
|
||||
APBS solver libraries.
|
||||
|
||||
%package devel
|
||||
Summary: Libraries and header files for the APBS package
|
||||
Requires: %{name}-libs%{?_isa} = %{version}-%{release}
|
||||
%description devel
|
||||
The apbs-devel package contains the header files and libraries
|
||||
necessary for developing programs using the adaptive poisson boltzmann
|
||||
(APBS) solver library.
|
||||
|
||||
%package doc
|
||||
Summary: Documentation for the APBS package
|
||||
BuildRequires: tex(latex)
|
||||
BuildRequires: texlive-multirow
|
||||
BuildRequires: texlive-hanging
|
||||
BuildRequires: texlive-adjustbox
|
||||
BuildRequires: texlive-stackengine
|
||||
BuildRequires: texlive-sectsty
|
||||
BuildRequires: texlive-etoc
|
||||
BuildRequires: texlive-tocloft
|
||||
BuildRequires: texlive-ulem
|
||||
BuildRequires: texlive-newunicodechar
|
||||
BuildRequires: texlive-wasy
|
||||
BuildRequires: texlive-wasysym
|
||||
BuildArch: noarch
|
||||
%description doc
|
||||
The apbs-doc package contains API reference inforemation for
|
||||
development using the adaptive poisson boltzmann (APBS) solver
|
||||
library.
|
||||
|
||||
%package -n python3-apbs
|
||||
Summary: Python interface of APBS
|
||||
BuildRequires: python3-devel
|
||||
BuildRequires: python3-numpy
|
||||
BuildRequires: python3-sphinx
|
||||
BuildRequires: swig
|
||||
%{?python_provide:%python_provide python3-%{name}}
|
||||
Obsoletes: %{name}-libs < 0:3.0.0-11
|
||||
%description -n python3-apbs
|
||||
Python interface of APBS.
|
||||
|
||||
%prep
|
||||
%autosetup -n %{name}-%{version} -N
|
||||
%patch -P 0 -p2 -b .apbs-cmake
|
||||
%patch -P 1 -p1 -b .exclude_tests
|
||||
|
||||
%if 0%{?python3_version_nodots} >= 311
|
||||
%patch -P 2 -p1 -b .python311
|
||||
%endif
|
||||
|
||||
%patch -P 3 -p1
|
||||
|
||||
cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING
|
||||
cp -p %{SOURCE1} contrib/iapbs/iapbs-LGPLv2
|
||||
|
||||
%build
|
||||
export CFLAGS="%{build_cflags} -fopenmp -lm"
|
||||
export CXXFLAGS="%{build_cxxflags} -fopenmp -lm"
|
||||
%cmake -DCMAKE_BUILD_TYPE:STRING=Release \
|
||||
-DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF \
|
||||
-DENABLE_FETK:BOOL=OFF -DCMAKE_C_FLAGS:STRING="%{build_cflags} -fopenmp -lm -DNDEBUG" \
|
||||
-DCMAKE_CXX_FLAGS:STRING="%{build_cxxflags} -fopenmp -lm -DNDEBUG" \
|
||||
-DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON \
|
||||
-DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON \
|
||||
-DCMAKE_INSTALL_PREFIX:PATH=%{_prefix} \
|
||||
-DINCLUDE_INSTALL_DIR:PATH=%{_includedir} \
|
||||
-DLIB_INSTALL_DIR:PATH=%{_libdir} \
|
||||
-DSHARE_INSTALL_PREFIX:PATH=%{_datadir}
|
||||
|
||||
%cmake_build
|
||||
|
||||
%install
|
||||
%cmake_install
|
||||
|
||||
# Tools
|
||||
for bin in %{buildroot}%{_bindir}/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do
|
||||
cp -p $bin %{buildroot}%{_bindir}/apbs-`basename $bin`
|
||||
rm -f $bin
|
||||
done
|
||||
|
||||
# Remove rpaths
|
||||
for bin in %{buildroot}%{_bindir}/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx}; do
|
||||
chrpath -d $bin
|
||||
chrpath -d %{buildroot}%{_bindir}/apbs
|
||||
done
|
||||
|
||||
chrpath -d %{buildroot}%{_libdir}/libapbs.so.1
|
||||
|
||||
# Move Python libraries under Python's tree directories
|
||||
mkdir -p %{buildroot}%{python3_sitearch}/apbs
|
||||
install -pm 755 tools/manip/psize.py %{buildroot}%{python3_sitearch}/apbs/
|
||||
%{__python3} %{_rpmconfigdir}/redhat/pathfix.py -pn -i "%{__python3}" %{buildroot}%{python3_sitearch}/apbs/psize.py
|
||||
ln -s %{python3_sitearch}/apbs/psize.py %{buildroot}%{_bindir}/apbs-psize.py
|
||||
install -pm 755 %_vpath_builddir/lib/_apbslib.so %{buildroot}%{python3_sitearch}/apbs/
|
||||
|
||||
# Remove redundant tools binary files in /usr/share
|
||||
rm -rf %{buildroot}%{_datadir}/apbs
|
||||
|
||||
# Remove static libraries
|
||||
for i in `find %{buildroot} -type f \( -name "*.a" \)`; do
|
||||
rm -f $i
|
||||
done
|
||||
|
||||
%if %{with check}
|
||||
%check
|
||||
pushd tests
|
||||
export LD_LIBRARY_PATH=%{buildroot}%{_libdir}
|
||||
export PATH=%{buildroot}%{_bindir}
|
||||
%{__python3} ./apbs_tester.py
|
||||
%endif
|
||||
|
||||
%files
|
||||
%{_bindir}/apbs
|
||||
|
||||
%files libs
|
||||
%license LICENSE.md COPYING contrib/iapbs/iapbs-COPYING contrib/iapbs/iapbs-LGPLv2
|
||||
%doc README.md
|
||||
%{_libdir}/libapbs.so.1
|
||||
|
||||
%files -n python3-apbs
|
||||
%{python3_sitearch}/apbs/
|
||||
|
||||
%files devel
|
||||
%{_libdir}/libapbs.so
|
||||
%{_includedir}/iapbs/
|
||||
%{_includedir}/apbs
|
||||
|
||||
%files tools
|
||||
%{_bindir}/apbs-psize.py
|
||||
%{_bindir}/apbs-coulomb
|
||||
%{_bindir}/apbs-born
|
||||
%{_bindir}/apbs-mgmesh
|
||||
%{_bindir}/apbs-dxmath
|
||||
%{_bindir}/apbs-mergedx2
|
||||
%{_bindir}/apbs-mergedx
|
||||
%{_bindir}/apbs-value
|
||||
%{_bindir}/apbs-uhbd_asc2bin
|
||||
%{_bindir}/apbs-smooth
|
||||
%{_bindir}/apbs-dx2mol
|
||||
%{_bindir}/apbs-dx2uhbd
|
||||
%{_bindir}/apbs-similarity
|
||||
%{_bindir}/apbs-multivalue
|
||||
%{_bindir}/apbs-benchmark
|
||||
%{_bindir}/apbs-analysis
|
||||
%{_bindir}/apbs-del2dx
|
||||
%{_bindir}/apbs-tensor2dx
|
||||
|
||||
%files doc
|
||||
%license LICENSE.md
|
||||
%doc %_vpath_builddir/doc
|
||||
|
||||
%changelog
|
||||
* Fri Jan 16 2026 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-32
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_44_Mass_Rebuild
|
||||
|
||||
* Fri Sep 19 2025 Python Maint <python-maint@redhat.com> - 3.0.0-31
|
||||
- Rebuilt for Python 3.14.0rc3 bytecode
|
||||
|
||||
* Fri Aug 15 2025 Python Maint <python-maint@redhat.com> - 3.0.0-30
|
||||
- Rebuilt for Python 3.14.0rc2 bytecode
|
||||
|
||||
* Thu Jul 24 2025 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-29
|
||||
- Fix rhbz#2380463
|
||||
|
||||
* Wed Jul 23 2025 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-28
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild
|
||||
|
||||
* Tue Jun 03 2025 Python Maint <python-maint@redhat.com> - 3.0.0-27
|
||||
- Rebuilt for Python 3.14
|
||||
|
||||
* Thu Jan 16 2025 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-26
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild
|
||||
|
||||
* Wed Jul 17 2024 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-25
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
|
||||
|
||||
* Sat Jun 08 2024 Python Maint <python-maint@redhat.com> - 3.0.0-24
|
||||
- Rebuilt for Python 3.13
|
||||
|
||||
* Sat May 25 2024 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-23
|
||||
- Fix patch commands
|
||||
|
||||
* Mon Jan 22 2024 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-22
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
|
||||
|
||||
* Fri Jan 19 2024 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-21
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
|
||||
|
||||
* Wed Jul 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-20
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
|
||||
|
||||
* Wed Jun 14 2023 Python Maint <python-maint@redhat.com> - 3.0.0-19
|
||||
- Rebuilt for Python 3.12
|
||||
|
||||
* Mon Feb 06 2023 Florian Weimer <fweimer@redhat.com> - 3.0.0-18
|
||||
- Fix C99 compatibility issue
|
||||
|
||||
* Wed Jan 18 2023 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-17
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
|
||||
|
||||
* Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-16
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
|
||||
|
||||
* Mon Jun 13 2022 Python Maint <python-maint@redhat.com> - 3.0.0-15
|
||||
- Rebuilt for Python 3.11
|
||||
|
||||
* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-14
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
|
||||
|
||||
* Tue Jan 04 2022 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-13
|
||||
- Patched for Python-3.11
|
||||
|
||||
* Mon Nov 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-12
|
||||
- Re-enable tests
|
||||
|
||||
* Mon Nov 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-11
|
||||
- Fix installation conflict of python package
|
||||
|
||||
* Sun Oct 31 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-10
|
||||
- Compile from a new source archive
|
||||
|
||||
* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-9
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
|
||||
|
||||
* Fri Jun 04 2021 Python Maint <python-maint@redhat.com> - 3.0.0-8
|
||||
- Rebuilt for Python 3.10
|
||||
|
||||
* Tue Jan 26 2021 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-7
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
|
||||
|
||||
* Fri Jan 01 2021 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-6
|
||||
- Use cmake3 options
|
||||
|
||||
* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-5
|
||||
- Second attempt - Rebuilt for
|
||||
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
|
||||
|
||||
* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 3.0.0-4
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
|
||||
|
||||
* Wed Jun 17 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-3
|
||||
- Use cmake3 macro
|
||||
|
||||
* Wed Jun 17 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-2
|
||||
- Use cmake3
|
||||
|
||||
* Sun May 31 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-1
|
||||
- Release 3.0.0
|
||||
|
||||
* Tue May 26 2020 Miro Hrončok <mhroncok@redhat.com> - 3.0.0-0.3.20200512gitdfb858d
|
||||
- Rebuilt for Python 3.9
|
||||
|
||||
* Wed May 13 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-0.2.20200512gitdfb858d
|
||||
- Fix release tag
|
||||
|
||||
* Wed May 13 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.0.0-0.1.20200512.gitdfb858d
|
||||
- Pre-release 3.0.0 (rhbz#1752306, rhbz#1799157)
|
||||
- Add libs sub-package
|
||||
- Add workaround for GCC-10
|
||||
- Use Python3
|
||||
|
||||
* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-5
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
|
||||
|
||||
* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-4
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
|
||||
|
||||
* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-3
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
|
||||
|
||||
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.5-2
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
|
||||
|
||||
* Sat May 19 2018 Tim Fenn <tim.fenn@gmail.com> - 1.5-1
|
||||
- update to 1.5
|
||||
|
||||
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-8
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
|
||||
|
||||
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-7
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
|
||||
|
||||
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-6
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
|
||||
|
||||
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-5
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
|
||||
|
||||
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.4-4
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
|
||||
|
||||
* Wed Jun 17 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4-3
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
|
||||
|
||||
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.4-2
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
|
||||
|
||||
* Thu Jun 19 2014 Tim Fenn <tim.fenn@gmail.com> - 1.4-1
|
||||
- update to 1.4
|
||||
|
||||
* Wed Jun 18 2014 Tim Fenn <tim.fenn@gmail.com> - 1.3-8
|
||||
- fix for bug 1105956 (apbslib.c patch for format-security error)
|
||||
|
||||
* Sat Jun 07 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.3-8
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
|
||||
|
||||
* Wed Oct 30 2013 Tim Fenn <tim.fenn@gmail.com> - 1.3-7
|
||||
- rebuild for atlas 3.10.1 (consolidates lapack and blas)
|
||||
|
||||
* Sat Aug 03 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.3-6
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
|
||||
|
||||
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.3-5
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
|
||||
|
||||
* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.3-4
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
|
||||
|
||||
* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.3-3
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
|
||||
|
||||
* Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.3-2
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild
|
||||
|
||||
* Mon Nov 15 2010 Tim Fenn <fenn@stanford.edu> - 1.3-1
|
||||
- update to 1.3
|
||||
|
||||
* Wed Jul 21 2010 David Malcolm <dmalcolm@redhat.com> - 1.2.1-3
|
||||
- Rebuilt for https://fedoraproject.org/wiki/Features/Python_2.7/MassRebuild
|
||||
|
||||
* Tue Dec 01 2009 Tim Fenn <fenn@stanford.edu> - 1.2.1-2
|
||||
- add RPM_OPT_FLAGS
|
||||
|
||||
* Wed Nov 25 2009 Tim Fenn <fenn@stanford.edu> - 1.2.1-1
|
||||
- update to 1.2.1
|
||||
|
||||
* Tue Nov 24 2009 Tim Fenn <fenn@stanford.edu> - 1.2.0-2
|
||||
- fix broken source
|
||||
|
||||
* Thu Nov 04 2009 Tim Fenn <fenn@stanford.edu> - 1.2.0-1
|
||||
- update to 1.2.0
|
||||
|
||||
* Mon Jul 27 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-7
|
||||
- remove python byte compiled files in bindir
|
||||
- loop to add tools
|
||||
|
||||
* Sun Jul 26 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-6
|
||||
- remove check macro
|
||||
|
||||
* Fri Jul 24 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-5
|
||||
- enable and add arpack, python to buildrequires, fix files section accordingly
|
||||
- add check macro
|
||||
- move tools to a subpackage
|
||||
- move doc into subpackage
|
||||
- spec cleanup
|
||||
|
||||
* Thu Jul 23 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-4
|
||||
- merge aqua and pmgZ into libapbs
|
||||
|
||||
* Fri Jul 10 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-3
|
||||
- separate aqua and pmgZ into separate libraries/packages
|
||||
- add maloc BuildRequires
|
||||
|
||||
* Mon May 04 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-2
|
||||
- fix RPM_BUILD_ROOT
|
||||
- rename patches
|
||||
- add "-q" to setup
|
||||
- add README to doc
|
||||
- edit description
|
||||
- edit license
|
||||
|
||||
* Fri Apr 24 2009 Tim Fenn <fenn@stanford.edu> - 1.1.0-1
|
||||
- initial build
|
||||
1
sources
1
sources
|
|
@ -0,0 +1 @@
|
|||
SHA512 (apbs-3.0.0.tar.gz) = 9107acf5fb591cd7a822dc3cb0be58b5d3142e85951585749068e748459bceb0c7503ecfd95b6b4370378d619c30aedb04f5e3ca5c1ad15683533171cb7208fb
|
||||
Loading…
Add table
Add a link
Reference in a new issue