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2019-07-31Update Package Creation Tutorial for PEARC19 (#12209)Adam J. Stewart1-12/+23
* Update Package Creation Tutorial for PEARC19 * A few remaining fixes * Fix section link
2019-07-31Preventing jsoncpp from building tests (#11948)Matthieu Dorier1-1/+6
* Preventing jsoncpp from building tests jsoncpp: making -DJSONCPP_WITH_TESTS=OFF conditioned by self.run_tests
2019-07-31F18: Fix the location to the f18 binary (#12186)Ondřej Čertík1-1/+1
2019-07-31phist: added version 1.8.0 (#12201)jthies1-0/+1
2019-07-31igvtools: fixed query on jdk instead of java (#12195)t-karatsu1-1/+1
2019-07-31kim-api: added version 2.1.2 (#12189)Ryan S. Elliott1-1/+2
2019-07-31genomefinisher: fixed query on jdk instead of java (#12196)t-karatsu1-1/+1
2019-07-30Add pandas 0.25.0 (#12173)Adam J. Stewart1-5/+37
2019-07-30Add tables 3.5.2 (#12172)Adam J. Stewart1-14/+21
2019-07-30Update numexpr dependency version (#12168)Adam J. Stewart1-1/+1
2019-07-30Add py-matplotlib 3.1.1 (#12164)Adam J. Stewart1-73/+98
2019-07-30Add py-wxpython package (#12163)Adam J. Stewart11-9/+47
2019-07-30Add py-cairocffi package (#12161)Adam J. Stewart1-0/+27
2019-07-30Add SIPPackage base class (#12157)Adam J. Stewart10-44/+92
2019-07-30Add Magics 4.1.0 (#12078)Adam J. Stewart1-2/+7
2019-07-30Add eccodes 2.13.0 (#12077)Adam J. Stewart1-1/+4
2019-07-30Allow bsseeker to build with Python 3 (#12075)Adam J. Stewart1-1/+1
2019-07-30Add py-pipits 2.4 (#12074)Adam J. Stewart4-8/+81
* Add py-pipits 2.4 * Flake8 fix
2019-07-30mii: new package at 1.0.2 (#12184)Justin S1-0/+25
* mii: new package at 1.0.2 * mii: fix improper formatting in description * mii: add 1.0.3
2019-07-30gromacs: added version 4.5.5 (#12197)健美猞猁1-0/+1
2019-07-29New package: cgdb (#12154)Ben Bergen1-0/+27
2019-07-29LIBXSMM package: add version 1.13 and optional shared libs (#11998)Hans Pabst1-13/+14
* 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.
2019-07-29hpgmp package: Don't add cpu=native on ARM when using gcc 5.x or before (#12034)Toyohisa Kameyama1-1/+1
2019-07-29CMOR package: add version 3.4.0 (Python3-compatible) (#12076)Adam J. Stewart1-2/+3
2019-07-29Quantum Espresso package: Specify F90 compiler (#12119)Nick Forrington1-0/+1
2019-07-29SimulationIO package: add version 9.0.1 (#12079)Adam J. Stewart1-1/+3
2019-07-29catalyst package: Fix paths used for intermediate code generation (#12082)Chuck Atkins1-5/+5
Fixes #12065
2019-07-29PISM package: add version 1.1.4 (#12083)Adam J. Stewart1-1/+3
2019-07-29Fix some Mac constraint checks (#12138)Adam J. Stewart3-10/+6
* 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.
2019-07-29Add conflicts statement for Python-3.6.7+ and Intel compilerGlenn P Johnson1-0/+5
Python-3.6.7 and up do not build with the Intel compiler - https://bugs.python.org/issue35473 - https://bugs.python.org/issue37415
2019-07-29zeromq package: choose URL based on version; add versions (#12149)Federico Ficarelli1-4/+14
* 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
2019-07-29Gromacs package: add openmp, mdrun_only, double_precision options (#12150)Hironori-Yamaji1-0/+20
2019-07-29New package: py-pytest-isort (#12160)Adam J. Stewart1-0/+19
2019-07-29LLVM package: add optional libomp_tsan support (#11793)Jon Rood1-0/+8
This is only available for LLVM version 6 or greater. So this also adds a conflict statement for earlier versions of LLVM.
2019-07-29update cmake 3.15.1 checksum (#12182)Owen Solberg1-1/+1
2019-07-29OpenGL package: always provides gl (#12158)Adam J. Stewart1-0/+1
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).
2019-07-29py-scipy package: add version 1.3.0 (#12171)Adam J. Stewart1-9/+16
* 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
2019-07-29New package: py-torchvision (#12175)Adam J. Stewart1-0/+33
2019-07-29PyTorch package: add version 1.1.0 (#12174)Adam J. Stewart1-2/+41
* 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
2019-07-29Change dependencies to use virtual jpeg package (#12179)Seth R. Johnson6-6/+6
This prevents conflicts between descendents that depend on an unintentional arbitrary jpeg implementation.
2019-07-28Add a new version (7.2) of draco. (#11852)Kelly (KT) Thompson1-11/+40
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.
2019-07-28Update checksum of fmt 5.3.0 (#12037)Jeongseok Lee1-1/+1
2019-07-28Prevent conflicts between libuuid and Apple Cocoa Framework on Mac (#12166)Seth R. Johnson1-1/+7
* 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
2019-07-27Bump version for BLIS (#12162)Sajid Ali1-0/+2
modified: var/spack/repos/builtin/packages/blis/package.py
2019-07-27cmake: Bump to 3.15.1 (#12151)Chuck Atkins1-0/+1
2019-07-27environment-modules package: add version 4.3.0 (#12155)Xavier Delaruelle1-1/+7
2019-07-26adios2: Patch findmpi for downstream issues. (#12152)Chuck Atkins2-0/+843
2019-07-26kealib: fix incorrect md5sum for v1.4.11 (#12126)Sinan1-6/+8
* fix incorrect md5sum for v1.4.11 * fix url and replace md5 with sha256 * add mainter
2019-07-26update to kim-api-2.1.1 and openkim-models-2019-07-25 (#12137)Ryan S. Elliott2-8/+25
* 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
2019-07-26Add flake8 3.7.8 (#12141)Adam J. Stewart1-43/+34
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