Commit graph

13926 commits

Author SHA1 Message Date
Adam J. Stewart
354ef2f9ca
Allow bsseeker to build with Python 3 (#12075) 2019-07-30 17:11:14 -05:00
Adam J. Stewart
e13bc0212c
Add py-pipits 2.4 (#12074)
* Add py-pipits 2.4

* Flake8 fix
2019-07-30 17:10:57 -05:00
Justin S
175abecc0b mii: new package at 1.0.2 (#12184)
* mii: new package at 1.0.2

* mii: fix improper formatting in description

* mii: add 1.0.3
2019-07-30 16:16:41 -05:00
健美猞猁
544914f34b gromacs: added version 4.5.5 (#12197) 2019-07-30 16:07:07 +02:00
Ben Bergen
73a9d6556e New package: cgdb (#12154) 2019-07-29 17:19:53 -07:00
Hans Pabst
6db873532c LIBXSMM package: add version 1.13 and optional shared libs (#11998)
* Add +shared variant, which builds shared library in addition to the
  static library.
* Install libraries even when specifying the header-only option
  (header-only is just about installing an additional folder).
* An additional make call is not required to build generator
  executables (they are built by default).
* Streamlined help-line of each variant.
2019-07-29 17:14:41 -07:00
Toyohisa Kameyama
5f716b7ffa hpgmp package: Don't add cpu=native on ARM when using gcc 5.x or before (#12034) 2019-07-29 16:53:59 -07:00
Adam J. Stewart
b8b2fa226e CMOR package: add version 3.4.0 (Python3-compatible) (#12076) 2019-07-29 16:12:37 -07:00
Nick Forrington
6e9f51d1d2 Quantum Espresso package: Specify F90 compiler (#12119) 2019-07-29 15:53:39 -07:00
Adam J. Stewart
c9e5de85fd SimulationIO package: add version 9.0.1 (#12079) 2019-07-29 15:40:57 -07:00
Chuck Atkins
f18c9e0ba5 catalyst package: Fix paths used for intermediate code generation (#12082)
Fixes #12065
2019-07-29 15:31:07 -07:00
Adam J. Stewart
f88636b090 PISM package: add version 1.1.4 (#12083) 2019-07-29 15:26:03 -07:00
Adam J. Stewart
23420a6524 Typo fixes in Environments Tutorial (#12107) 2019-07-29 17:13:56 -05:00
Adam J. Stewart
9af155f0f6 Fix some Mac constraint checks (#12138)
* Fix Mac platform check for dependency in py-ipython package: 'when'
  constraints in Spack directives must be Specs (either a Spec
  object or a Spec in string format)
* Fix Mac version check in py-numpy: platform.mac_ver() returns a
  3-part string as its first tuple item so the check as written would
  never pass; use Spack Version object to simplify check.
* Fix Mac version check in qt package (the check was incorrectly
  comparing ints and strings) and use Spack version object to
  simplify check.
2019-07-29 15:05:02 -07:00
Glenn P Johnson
e7d9a6f426 Add conflicts statement for Python-3.6.7+ and Intel compiler
Python-3.6.7 and up do not build with the Intel compiler

- https://bugs.python.org/issue35473
- https://bugs.python.org/issue37415
2019-07-29 14:38:05 -07:00
Federico Ficarelli
dbd294c204 zeromq package: choose URL based on version; add versions (#12149)
* Add versions 4.3.0, 4.3.1, and 4.3.2
* The URL format changed after 4.1.4, so this adds a url_for_version
  function to choose the URL format based on the version
2019-07-29 14:36:33 -07:00
Hironori-Yamaji
43dd6b3418 Gromacs package: add openmp, mdrun_only, double_precision options (#12150) 2019-07-29 14:29:04 -07:00
Adam J. Stewart
c3dc63ce8f New package: py-pytest-isort (#12160) 2019-07-29 14:02:06 -07:00
Jon Rood
3e02dc258b LLVM package: add optional libomp_tsan support (#11793)
This is only available for LLVM version 6 or greater. So this also
adds a conflict statement for earlier versions of LLVM.
2019-07-29 12:23:15 -07:00
Owen Solberg
ee1c36a2b0 update cmake 3.15.1 checksum (#12182) 2019-07-29 15:13:52 -04:00
Adam J. Stewart
0d0a02b230 OpenGL package: always provides gl (#12158)
With this PR, a user can designate older versions of OpenGL as an
external Spack package, and dependents can use that installation
as long as they do not have version requirements.

MacOS currently comes with OpenGL 2.1; there is currently no
'provides' directive in the OpenGL Spack package which specifies a
gl version provided for versions earlier than OpenGL 3.3, so earlier
versions of OpenGL are not considered to provide any version of gl.
This PR records that any version of OpenGL provides 'gl' (which is
sufficient for any package that does not require a specific version
of gl).
2019-07-29 12:11:53 -07:00
Greg Becker
f78fc30032 intel: Add mpicc wrapper bindir to dependent env (#12132) 2019-07-29 12:04:15 -07:00
Adam J. Stewart
d1752d8640 py-scipy package: add version 1.3.0 (#12171)
* Version 1.3.0 requires python 3.5 or later (no Python 2 support)
* Remove test of scipy.weave import (not available since 1.0)
* Add more-sensitive py-numpy constraints based on py-scipy version
* Replace py-nose dependency with py-pytest
* Add adamjstewart as maintainer
2019-07-29 11:57:59 -07:00
Adam J. Stewart
249f571556 New package: py-torchvision (#12175) 2019-07-29 11:42:08 -07:00
Adam J. Stewart
18bd189876 PyTorch package: add version 1.1.0 (#12174)
* Rename py-pytorch to py-torch
* Add versions 1.1.0 and 1.0.1
* Define modules to test import of after installation (import_modules)
* py-typing dependency is only needed for older versions of Python
  (3.4 or before)
* Newer versions of py-torch depend on newer versions of CUDA
* Add adamjstewart as maintainer
2019-07-29 11:39:05 -07:00
Seth R. Johnson
3d0b5bd541 Change dependencies to use virtual jpeg package (#12179)
This prevents conflicts between descendents that depend on an unintentional
arbitrary jpeg implementation.
2019-07-29 12:08:55 -05:00
Kelly (KT) Thompson
a3f6f52622 Add a new version (7.2) of draco. (#11852)
This change also
+ Makes the `build_type` user settable and
+ Adds support for running tests.
+ Provide depends_on('cmake') for versions prior to 7.0.
2019-07-28 22:15:21 -05:00
Jeongseok Lee
e23d613ee6 Update checksum of fmt 5.3.0 (#12037) 2019-07-28 22:07:51 -05:00
Seth R. Johnson
95985e0798 Prevent conflicts between libuuid and Apple Cocoa Framework on Mac (#12166)
* Remove libuuid dependency for python on Darwin

Python 2.7 includes Carbon, which requires a proprietary typedef defined in
the system `/usr/include/uuid/uuid.h`:
```
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Python/mactoolboxglue.c:27:
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Include/pymactoolbox.h:10:
In file included from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:23:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
```

Similarly, even with Python 3, having Spack's libuuid in the toolchain
causes matplotlib to fail to build downstream because its `osx` backend
links against Carbon:
```
building 'matplotlib.backends._macosx' extension
/rnsdhpc/code/spack/lib/spack/env/clang/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include -I/usr/X11/include -I/opt/X11/include -I. -I/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.2-bipx24oyxqxowqc75o5vfih7dljiaohz/include/python3.7m -c src/_macosx.m -o build/temp.macosx-10.14.5-x86_64-3.7/src/_macosx.o
In file included from src/_macosx.m:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
        uuid_string_t   ext_jnl_uuid;
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char                    io_string_t[512];
```

MacOS version 10.14.5
Xcode 10.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)

* Mark libuuid as conflicting with Darwin due to framework

If Spack's libuuid is included by any other package that tests for or
requires the Cocoa or Carbon frameworks, the build will *fail* becuse it
appears that Apple's libraries require a special version of libuuid and
uuid.h.

```
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
        uuid_string_t   ext_jnl_uuid;
        ^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char                    io_string_t[512];
```

* Revert "Mark libuuid as conflicting with Darwin due to framework"

This reverts commit 9a68b75202005fc265abe2033e4ad36312a9a34d.

* Document libuuid exception in python package
2019-07-28 14:58:09 -05:00
Sajid Ali
9afd5113bc Bump version for BLIS (#12162)
modified:   var/spack/repos/builtin/packages/blis/package.py
2019-07-27 18:32:06 -05:00
Chuck Atkins
8d0c3e482f cmake: Bump to 3.15.1 (#12151) 2019-07-27 12:21:03 -05:00
Xavier Delaruelle
398c53eaa2 environment-modules package: add version 4.3.0 (#12155) 2019-07-27 12:20:39 -05:00
Chuck Atkins
18e41f9959 adios2: Patch findmpi for downstream issues. (#12152) 2019-07-26 13:17:31 -07:00
Sinan
511f84dd8c kealib: fix incorrect md5sum for v1.4.11 (#12126)
* fix incorrect md5sum for v1.4.11

* fix url and replace md5 with sha256

* add mainter
2019-07-26 15:14:46 -05:00
Ryan S. Elliott
12055acccc update to kim-api-2.1.1 and openkim-models-2019-07-25 (#12137)
* update to kim-api-2.1.1 and openkim-models-2019-07-25

* openkim-models provide needed dependency constraints and settings

* add maintainers and fixup flake8 errors
2019-07-26 13:06:10 -05:00
Adam J. Stewart
fbb04ece43
Add flake8 3.7.8 (#12141) 2019-07-26 12:11:07 -05:00
t-karatsu
21daa41dd6 libxc: Make configure recognize Fujitsu compiler (#12147) 2019-07-26 12:09:52 -05:00
Justin S
e2d16429ae py-pyomo: new package at 5.6.6 (#12134)
* py-pyomo: new package at 5.6.6

* py-pyomo: add missing deps, python constraint
2019-07-26 10:38:25 -05:00
Rémi Lacroix
9caba3e072 Small fixes for font-util package (#12148)
* font-util: Remove duplicated dependencies.

* font-util: Fix path handling for font resources.

The "join_path" call made no sense but still managed to work somehow most of the times.
2019-07-26 10:32:39 -05:00
Adam J. Stewart
0babdab8f0 Add GDAL 3.0.1 (#12140) 2019-07-26 09:25:35 +02:00
Adam J. Stewart
07fefea52d Add Python 3.7.4 (#12142) 2019-07-26 09:18:46 +02:00
Oliver Breitwieser
867ba9d7fe googletest: Fix reversed +pthreads option (#12128)
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.

If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.

Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
2019-07-25 19:50:23 -05:00
Justin S
94af6cad5f interproscan: new package at 5.36-75.0 (#12130) 2019-07-25 19:49:42 -05:00
Matthias Diener
7cc1292202 git-lfs: add version 2.8.0 (#12131) 2019-07-25 19:46:03 -05:00
Glenn Johnson
7ad8061cbb Patches for graphviz (#12133)
- patch to build with qt5, enabling gvedit to build
- two patches to compile graphviz with icc
2019-07-25 19:45:10 -05:00
Satish Balay
7bd3b66f6e
xsdk: phist has a conflict with gcc version <= gcc-4.9.1 (#11946)
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds

This is triggered by #11677

* fix typo
2019-07-25 14:01:00 -05:00
Gregory Lee
e8a71089a6 use Excecutable instead of exec for editing licenses (#11968)
* fix defunct editor exit in #11691
2019-07-25 11:48:32 -07:00
Elizabeth Fischer
fff99a8a3a Make OpenJDK the default (#12106) 2019-07-25 10:25:26 -07:00
Chuck Atkins
e614d4b481 cmake: Add a patch to revert a findmpi regression (#12129) 2019-07-25 10:23:01 -07:00
Chris Green
c20c153d16
catch: more versions, new and older. (#12123)
New versions 2.9.0, 2.9.1, older versions 2.2.2, 2.2.3, 2.4.1, 2.4.2, 2.7.0, 2.7.1, 2.7.2.
2019-07-25 11:33:03 -05:00