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2020-02-18Update and simplify julia package (#14756)Glenn Johnson1-174/+104
* Update and simplify julia package The current Spack Julia package potentially installs a few julia packages, with the installation being controlled by variants. There are a couple of problems with this. First, Julia handles packages very differently from systems such as R and Python. Julia requires write access to the repository directories in order for user installs of packages to work. If spack installs julia packages then there will be a repository, DEPOT_PATH, in the installation directory. If spack is used on an individual basis this would work but would mean that package data is written to the spack installation directory after installation. If spack is used to provide packages for end users then user installs of julia packages will fail due to lack of write access to the repository in the installation directory. It seems best for spack to just install julia without any julia packages, and drop the configuration for those packages. Second, having spack install package as variants seems to be counter to how spack works for other extendable systems, like R and Python. Julia should be an extendable package in spack but it is not clear how to make that work. As pointed out above, installing user packages requires write access to the julia repositories, including the one in the install directory. Essentially, a user package installation will try to update metadata for *all* julia repositories. Furthermore, each of those repositories, assuming one per package with spack, would need to have the Project.toml files merged to present the package stack to julia. Again, it seems best for spack to just install julia itself and not try to install julia packages, at least at this time. A good discussion on this can be found at https://discourse.julialang.org/t/how-does-one-set-up-a-centralized-julia-installation/13922. This PR does the following: - adds versions 1.2.0 and 1.3.1 - removes variants that correspond to julia packages - changes python to build dependency as it seems to only be needed for LLVM - the new versions can use Python-3 - removes dependencies for packages - adds a conflict statement for Intel compiler, with comment - add a setup_build_environment method to find GCC libraries - make formatting consistent - adds JULIA_CPU_TARGET option to correspond with target to help with running julia image on hardware older than build host - added intel build options, for when they can be used - removed code for installing packages - removed code for julia config that was needed for packages Note that versions below 0.5.1 fail to build, with or without these changes. It is not clear why that is. * Update var/spack/repos/builtin/packages/julia/package.py Yes, need to use correct grammar even in the midst of numbers and symbols. Good catch! Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * More cleanup of Julia package This commit does more cleanup and sets more constraints. - Removed release-0.4 and release-0.5. I am not sure if those are actually useful but they are quite old and there are released versions from the same timeframe. - Remove the binutils variant. - Made cmake a build dependency for versions >= 1. - Added git as a dependency for @master. - Limit curl dependency to released versions. - Do not use external curl for master. When I checked, using the external version failed but the internal curl worked. - Versions <= 0.5.0 need an older version of openssl. - Set conflicts directive for cxx variant. - Added conflicts directive for needing +mkl with Intel compiler. - Removed configuration settings as these prevented julia from working properly in all cases that I looked at. * Fix flake8 error Remove 'import sys' that is no longer used. * More dependency tweaks This commit sets further version constraints on dependencies. It really looks like julia requires its internal dependencies more over time. - curl only up to 0.5.0 - openssl only up to 0.5.0 - override with system curl up to version 0.5.0 * Fix spec for curl certs Only depending on curl through 0.5.0. Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18buildcache: Check for tar.bz2 and set tar.gz if not found (#15054)Patrick Gartung1-0/+4
* Check for tar.bz2 and set tar.gz if not found * Move check for tarfile after it is extracted
2020-02-18Add extra version of py-cryptography (#14975)iarspider1-3/+14
* Add extra version of py-cryptography * Update package.py * Update package.py * Update var/spack/repos/builtin/packages/py-cryptography/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-cryptography/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-cryptography/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Flake-8 Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18ROSS: v7.2.0 and branches to match (#15052)Elsa Gonsiorowski, PhD1-1/+5
2020-02-18Fix OpenBLAS 0.3.8 build on darwin (#15041)Seth R. Johnson2-0/+27
* Fix OpenBLAS 0.3.8 build on darwin See https://github.com/xianyi/OpenBLAS/issues/2431, patched in https://github.com/xianyi/OpenBLAS/issues/2431 . * Add references for patchfile
2020-02-18py-hpcbench: new package (#14915)Matthias Wolf1-0/+32
* py-hpcbench: new package * obey the flake8 * address comments, fix versions. * Update var/spack/repos/builtin/packages/py-hpcbench/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18Add extra version of py-graphviz (#14981)iarspider1-1/+4
* Add extra version of py-graphviz * Update package.py * Update package.py * Update var/spack/repos/builtin/packages/py-graphviz/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18npm: Add 6.13.7 (#15034)Michael Kuhn1-2/+3
2020-02-18Add extra version of py-nbconvert (#15044)iarspider1-0/+1
2020-02-18Add extra version of py-pathlib2 (#15048)iarspider1-0/+1
2020-02-18Add extra version of py-pbr (#15049)iarspider1-0/+1
2020-02-18Add extra version of py-pexpect (#15050)iarspider1-0/+2
* Add extra version of py-pexpect * Update package.py Update dependency version
2020-02-18Add extra version of py-ipywidgets (#14987)iarspider1-2/+10
* Add extra version of py-ipywidgets * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update package.py * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-ipywidgets/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18Add extra version of py-defusedxml (#14972)iarspider1-0/+2
* Add extra version of py-defusedxml * Update package.py * Update var/spack/repos/builtin/packages/py-defusedxml/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18Add extra version of py-logilab-common (#14997)iarspider1-2/+5
* Add extra version of py-logilab-common * Update package.py * Update var/spack/repos/builtin/packages/py-logilab-common/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-18Fix allowed python versions of py-tables (#14073)iarspider1-1/+3
* Fix allowed python versions of py-tables * Update package.py * Update package.py * I think I've finally got it * Update package.py * Update package.py * Update package.py
2020-02-18Add extra version of py-more-itertools (#15042)iarspider1-0/+1
2020-02-18Add extra version of py-oauthlib (#15045)iarspider1-0/+1
2020-02-18Add extra version of py-owslib (#15046)iarspider1-0/+1
2020-02-18skip gpg tests when no gpg executable (#14935)Greg Becker4-1/+38
* skip gpg tests when no gpg executable * flake
2020-02-18Update `davix` versions and add version restriction for ROOT (#15038)Seth R. Johnson2-1/+3
From ROOT cmake output: ``` -- Checking for module 'davix>=0.6.4' -- Found davix, version 0.6.8 CMake Warning at cmake/modules/SearchInstalledSoftware.cmake:960 (message): Davix versions 0.6.8 to 0.7.0 have a bug and do not work with ROOT, please upgrade to 0.7.1 or later. ```
2020-02-18an argument 'buf_size' of 'h5fget_file_image_c' should be intent(out). (#15011)h-murai1-0/+16
* an argument 'buf_size' of 'h5fget_file_image_c' should be intent(out). * correct format errors * some modifications based on the comments from the reviewer
2020-02-18pegtl: change to virtual destructor (#14939)noguchi-k2-1/+17
* pegtl: change to virtual destructor * pegtl: fix patch
2020-02-17py-cookiecutter: new package (#14911)Matthias Wolf1-0/+27
* py-cookiecutter: new package * address comments
2020-02-17node-js: Add 12.16.0 and 13.8.0 (#15024)Michael Kuhn1-1/+3
2020-02-17Fix CLHEP fetch URL and add new version (#15032)Seth R. Johnson1-1/+2
2020-02-17spack extensions prints list of extendable packages (#14473)Adam J. Stewart4-3/+23
* spack extensions prints list of extendable packages * Update tab completion scripts
2020-02-17Fix mercurial certificate finding, add latest version (#15026)Adam J. Stewart1-12/+13
2020-02-17Add new version of cairo (#14941)iarspider1-2/+5
* Add new version of cairo * Update var/spack/repos/builtin/packages/cairo/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-17Add new version of ccache; update URL (#14942)iarspider1-2/+3
* Add new version of ccache; update URL * Update var/spack/repos/builtin/packages/ccache/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-17Add new version of davix (#14944)iarspider1-2/+2
* Add new version of davix * Update package.py
2020-02-17Add extra version of py-autopep8 (#14970)iarspider1-1/+3
* Add extra version of py-autopep8 * Update package.py
2020-02-17Add extra version of py-dill (#14971)iarspider1-1/+2
* Add extra version of py-dill * Update package.py
2020-02-17Add extra version of py-futures (#14979)iarspider1-1/+3
* Add extra version of py-futures * Update package.py
2020-02-17libcircle depends on a provider of pkgconfig for build (#15029)eugeneswalker1-1/+1
2020-02-17Qt4 patches (#15025)Seth R. Johnson17-57/+42
* Fix patch applicability * Combine patches for missing qt3 headers and remove krell variant The variant should have always been applied. * Restrict QT patches to actual applicable versions/situations - I researched the associated patches so now their `when=` should more closely match when they're actually needed. - I sorted the patch order so they're grouped by version requirement - I renamed the patches so they're listed by version requirements
2020-02-17Add new version of libunwind (#14947)iarspider1-2/+3
* Add new version of libunwind * Update package.py
2020-02-17Added new default tau version: 2.29. Added explicit zlib build requir… ↵wspear1-0/+5
(#15010) * Added new default tau version: 2.29. Added explicit zlib build requirement. Set up environment to use use elf and libz * Changed zlib to link dependency. Removed elf library path load (wasn't able to reproduce the need for this)
2020-02-17Add extra version of py-matplotlib; fix dependency on six (#15000)iarspider1-2/+4
* Add extra version of py-matplotlib * Update dependency * Update package.py * Update var/spack/repos/builtin/packages/py-matplotlib/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-matplotlib/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-17Add extra version of py-iminuit (#14982)iarspider1-3/+6
* Add extra version of py-iminuit * Update package.py
2020-02-17cmake: Fix spack install inside ctest (#14889)Dr. Christian Tacke1-0/+4
Disable the CMake install tests since they break under certain testing conditions.
2020-02-17Add extra version + variants of py-lxml (#14999)iarspider1-0/+8
* Add extra version of py-lxml * Extra variants for py-lxml * Update var/spack/repos/builtin/packages/py-lxml/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-lxml/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-lxml/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-lxml/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-17libnrm needs pkg-config for build (#15007)eugeneswalker1-0/+1
2020-02-17go: added v1.13.8 and v1.12.17 (#15022)Michael Kuhn1-0/+2
2020-02-16package: Add newer version of PowerAPI package (#15005)Carson Woods1-0/+1
* Add newer commit of PowerAPI package * Update naming scheme to be easier to read
2020-02-16Fix header-only installation of Boost. (#14995)Sergey Kosukhin1-9/+10
2020-02-16gdb: fix installation (#15016)Adam J. Stewart1-0/+2
2020-02-16Use separate build directory for gzip (#14994)Seth R. Johnson1-0/+5
* Use separate build directory for gzip At least on mac systems (perhaps because of a case sensitivity issue?) gzip fails to build inside the source tree: ``` config.status: linking /var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/spack-stage/s3j/spack-stage-gzip-1.10-iatwtuk2l5xgwmuh4pwu5bf27yezpydj/spack-src/GNUmakefile to GNUmakefile config.status: executing depfiles commands ==> Executing phase: 'build' ==> [2020-02-14-09:32:45.502913] 'make' '-j12' make: GNUmakefile: Too many levels of symbolic links make: stat: GNUmakefile: Too many levels of symbolic links make: *** No rule to make target `GNUmakefile'. Stop. ``` * Simplify build directory and add gmake dependency
2020-02-16Remove unneeded dependency on gzip for libmng (#14992)Seth R. Johnson1-1/+0
Libmng only needs gzip to compress man files for distribution, so it builds fine without it. The spack gzip currently fails to compile. ``` config.status: linking /var/folders/fy/x2xtwh1n7fn0_0q2kk29xkv9vvmbqb/T/spack-stage/s3j/spack-stage-gzip-1.10-iatwtuk2l5xgwmuh4pwu5bf27yezpydj/spack-src/GNUmakefile to GNUmakefile config.status: executing depfiles commands ==> Executing phase: 'build' ==> [2020-02-14-09:32:45.502913] 'make' '-j12' make: GNUmakefile: Too many levels of symbolic links make: stat: GNUmakefile: Too many levels of symbolic links make: *** No rule to make target `GNUmakefile'. Stop. ```
2020-02-15Add new version of bison (#14940)iarspider1-0/+1
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