Commit graph

12393 commits

Author SHA1 Message Date
Christoph Junghans
4ea5e177cd
CMake: make ninja verbose as well (#12200) 2019-07-31 08:41:58 -06:00
Ondřej Čertík
7e61527f9e F18: Fix the location to the f18 binary (#12186) 2019-07-31 15:43:08 +02:00
jthies
ae1524821e phist: added version 1.8.0 (#12201) 2019-07-31 15:35:59 +02:00
t-karatsu
b744accaf6 igvtools: fixed query on jdk instead of java (#12195) 2019-07-31 14:49:51 +02:00
Javier Cervantes
a948954886 Print environment name when removing active env (#12198) 2019-07-31 14:40:11 +02:00
Adam J. Stewart
d973fca00e Fix Sphinx deprecation warning when building docs (#12205)
* Fix Sphinx deprecation warning when building docs

* Set minimum required version of Sphinx
2019-07-31 10:23:56 +02:00
Ryan S. Elliott
86ff5baed7 kim-api: added version 2.1.2 (#12189) 2019-07-31 09:13:13 +02:00
t-karatsu
268c806111 genomefinisher: fixed query on jdk instead of java (#12196) 2019-07-31 08:55:56 +02:00
Adam J. Stewart
db2bbbcecf
Add pandas 0.25.0 (#12173) 2019-07-30 17:16:32 -05:00
Adam J. Stewart
59e9541386
Add tables 3.5.2 (#12172) 2019-07-30 17:16:15 -05:00
Adam J. Stewart
60da9303c6
Update numexpr dependency version (#12168) 2019-07-30 17:15:38 -05:00
Adam J. Stewart
70512b8ba2
Add py-matplotlib 3.1.1 (#12164) 2019-07-30 17:15:20 -05:00
Adam J. Stewart
482152e092
Add py-wxpython package (#12163) 2019-07-30 17:13:32 -05:00
Adam J. Stewart
c1c5f58d12
Add py-cairocffi package (#12161) 2019-07-30 17:13:02 -05:00
Adam J. Stewart
b34da4e108
Add SIPPackage base class (#12157) 2019-07-30 17:12:48 -05:00
Adam J. Stewart
f487f87e3e
Add Magics 4.1.0 (#12078) 2019-07-30 17:11:47 -05:00
Adam J. Stewart
e728883c71
Add eccodes 2.13.0 (#12077) 2019-07-30 17:11:29 -05:00
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