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2019-12-13Mirrors: fix cosmetic symlink targetsPeter Josef Scheibel2-1/+34
The targets for the cosmetic paths in mirrrors were being calculated incorrectly as of fb3a3ba: the symlinks used relative paths as targets, and the relative path was computed relative to the wrong directory.
2019-12-13Allow repeated invocations of 'mirror create'Peter Josef Scheibel1-0/+6
When creating a cosmetic symlink for a resource in a mirror, remove it if it already exists. The symlink is removed in case the logic to create the symlink has changed.
2019-12-12fix libev url (#14066)darmac1-2/+1
* fix libev url * remove list_url in libev
2019-12-12compile python with sqlite loadable extensions (#14132)Sinan1-0/+4
2019-12-12cmake: Fix checksum of 4075.patch (#14125)t-karatsu1-1/+1
2019-12-12Fix py-jupyter-client version ranges (#14126)iarspider1-1/+2
2019-12-11charmpp: fix build failing from broken hardlink (#13922)Justin S1-0/+8
* charmpp: fix build failing from broken hardlink * charmpp: use setup_dependent_build_environment
2019-12-11Fix replacement of embedded 'gcc' in augustus (#14116)Glenn Johnson1-25/+25
PR #13975 added makefile filtering to replace gcc/g++ with the spack compiler. This conflicts with other filtering that is done in the package to add paths for dependencies. The text of the dependency paths might have 'gcc' in the path name, depending on the install_path_scheme, and that was being replaced by the new compiler filters. That would mangle the path to the dependecy resulting in a failed build. This PR moves the compiler filters to be before the other filters to make sure that the compiler is set before the dependency paths.
2019-12-11Add missing dependency on setuptools to py-subprocess32 (#14074)iarspider1-0/+3
* Add missing dependency on setuptools to py-subprocess32 * Update package.py * Update var/spack/repos/builtin/packages/py-subprocess32/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py
2019-12-11Bugfix for bad hydrogen tags (#14119)Brian Van Essen1-2/+2
2019-12-11TensorFlow: must specify CUDA compute capabilities (#14118)Adam J. Stewart1-4/+8
* TensorFlow: must specify CUDA compute capabilities * Correctly restrict cuda_arch version ranges
2019-12-11Add try-except for Python installation (#14122)Adam J. Stewart1-2/+6
2019-12-11Fix JDK 8 download URLs (#14120)Adam J. Stewart1-8/+8
2019-12-11Fix py-ppft source extension (#14077)iarspider1-1/+12
* Fix py-ppft source extension * PEP-8 fix * Update package.py * Apply suggestions from code review Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-11Fix py-pox build recipe (#14078)iarspider1-1/+12
* Fix py-pox build recipe * PEP-8 fix * Update package.py * Apply suggestions from code review Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-11Fix py-notebook for Python2 (#14079)iarspider1-11/+13
* Fix py-notebook for Python2 * PEP-8 fix * Update package.py * Update package.py * Syntax fix * Update var/spack/repos/builtin/packages/py-notebook/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-11Fix py-hypothesis (#14084)iarspider1-1/+4
* Fix py-hypothesis * Update package.py * Update package.py * Update package.py
2019-12-11Fix constexpr for llvm 9.0 (#14095)Dan Lipsa2-0/+13
2019-12-11Add grass 7.8.2 (#14115)Adam J. Stewart1-1/+2
2019-12-11Added new versions of hydrogen (#14103)Brian Van Essen1-0/+2
2019-12-11doxygen: Fix libiconv checks (#14106)Michael Kuhn1-0/+10
PR #10589 introduced a libiconv dependency to doxygen. This causes problems on Linux systems, since the iconv symbols are included in libc, which causes CMake to use the external header but not the external library. Work around this by always using the external libiconv.
2019-12-11Build xed CLI for the intel-xed package (#14114)Glenn Johnson1-2/+6
The xed CLI is handy, and can be gotten by building the examples in the intel-xed package. This PR builds the examples and installs the xed CLI. It would also be possible to install more of the example binaries if someone thinks they are useful.
2019-12-11openfoam relocated to https://develop.openfoam.com/Development/openfoam.git ↵Mark Olesen1-3/+3
(#14101)
2019-12-11 diamond: fix narrowing error. (#14064)noguchi-k2-0/+22
* diamond: fix narrowing error * diamond: fix patch * diamond: add link to the patch source
2019-12-11Fix py-pkgconfig recipe (#14081)iarspider1-2/+4
* Fix py-pkgconfig recipe * Update package.py * Proper fix for py-pkgconfig
2019-12-11Fix py-pathos source file extension (#14080)iarspider1-5/+16
* Fix py-pathos source file extension * PEP-8 fix * Add version 0.2.3 to spack * Update package.py
2019-12-11Fix py-llvmlite (#14083)iarspider1-1/+5
* Fix py-llvmlite * Update package.py * Add llvmlite 0.29 * Update package.py
2019-12-11Fix py-dill source archive extension (#14085)iarspider1-1/+13
* Fix py-dill source archive extension * Add py-dill 0.2.7, remove extra str() * Update package.py * Update package.py * Update package.py
2019-12-11llvm: fix for building llvm using Cray PE (#12734)Howard Pritchard1-2/+4
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-12-10Fix json-c package (#14087)iarspider1-1/+2
* Fix json-c package * Fix PEP-8 * Update package.py * Update package.py
2019-12-10Fix libgeotiff dependency of gdal (#14089)iarspider1-3/+3
* Fix libgeotiff dependency of gdal * Update package.py * Fix typo * Update package.py
2019-12-10openmolcas: new package at 19.11 (#14099)Justin S1-0/+37
* openmolcas: new package at 19.11 * openmolcas: fill description * openmolcas: rewrite using CMakePackage * openmolcas: add py-six dep * openmolcas: use setup_build_environment, setup_run_environment * openmolcas: remove redundant cmake dep * openmolcas: explicitly cast Executable to str
2019-12-10pytest: add __init__ files for all test subdirs (#13889)Greg Becker5-6/+22
* pytest: add __init__ files for all test subdirs * add licenses to empty files * Fix Sphinx warning message about comment within docstring * Further fixes to Sphinx docstring
2019-12-10Alternative locations for tclConfig and tkConfig (#14071)iarspider1-0/+6
* Alternative locations for tclConfig and tkConfig * Fix PEP-8
2019-12-10Update tmux to 3.0a (#14096)Eric Berquist1-0/+2
* Add tmux@2.9 and tmux@3.0a * Fix checksums
2019-12-10Better error message when setting unknown variants during concretization ↵Massimiliano Culpo3-8/+17
(#13128) fixes #13124
2019-12-10gromacs-2018.8: fix checksum (#14069)Christoph Junghans1-1/+1
2019-12-10ROOT: +http variant doesn't require any external dependency (#14072)iarspider1-1/+0
2019-12-10Fix py-pyasn1 version for py-pyasn1-modules (#14076)iarspider1-1/+3
2019-12-10Fix for DD4Hep build: can't find boost (#14091)iarspider1-1/+3
2019-12-10More variants for cairo (#14092)iarspider1-3/+13
2019-12-10openfoam-org: Adding openfoam-org versions 6 and 7. (#12859)Simo Tuomisto1-1/+25
This commit adds openfoam-org versions 6 and 7. It also adding new variant for metis and fixes openfoam-org's old environment modification functions.
2019-12-09intel-tbb: fix and cleanup patch version ranges (#14053)Mark W. Krentel1-16/+11
Recent commit e9ee9eaf (#13989) fixed testing version ranges inside patch when clauses. Previously, it was necessary to write all revs individually for packages with multiple length version numbers (2019 and 2019.1). This fixes the build for the old 2017.* versions.
2019-12-09Follow up/11117 fixes and testing (#13607)Omar Padron10-158/+272
* fix docstring in generate_package_index() refering to "public" keys as "signing" keys * use explicit kwargs in push_to_url() * simplify url_util.parse() per tgamblin's suggestion * replace standardize_header_names() with the much simpler get_header() * add some basic tests * update s3_fetch tests * update S3 list code to strip leading slashes from prefix * correct minor warning regression introduced in #11117 * add more tests * flake8 fixes * add capsys fixture to mirror_crud test * add get_header() tests * use get_header() in more places * incorporate review comments
2019-12-09environments: allow 'add' command to add virtuals (#13787)Greg Becker2-2/+26
This PR allows virtual packages to be added to the specs list using the add command. Virtual packages are already allowed in named lists in spack environments/stacks, and they are already allowed in the specs list when added using the yaml directly.
2019-12-09TensorFlow: don't override HOME env var (#14054)Adam J. Stewart1-4/+4
2019-12-09fix incorrect gpu arch map for vtk-m package (#14057)Matt Larsen1-1/+1
2019-12-09Apply URLFetchStrategy to ftp:// and ftps:// url schemes (#13939)Andras Wacha1-1/+3
* Apply URLFetchStrategy to ftp:// and ftps:// url schemes * Corrected trailing whitespace error
2019-12-08Tuneup docs re setting up sphinx for building docs (#14005)George Hartzell1-6/+14
I have, more than once, tried to install the list of things that need to build the docs, only to discover that the list doesn't use Spack's package names. I'm tired of facepalming.... While I was there I touched up the prose about activating the new Python packages; activating a python package doesn't add anything to your PYTHONPATH, it links things into a directory that's *already* on your PYTHONPATH. Note that this all presupposes that you're using that same python....
2019-12-08cbtf-krell: fix missing dependencies (#14021)Adam J. Stewart1-4/+4
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