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2019-10-20Add latest version of py-hypothesis (#13314)Adam J. Stewart1-4/+6
2019-10-20Add latest version of py-httpbin (#13315)Adam J. Stewart1-7/+11
2019-10-20Add latest version of py-flask (#13316)Adam J. Stewart1-7/+9
2019-10-20Add latest version of py-torchvision (#13289)Adam J. Stewart1-1/+4
2019-10-20Add latest version of py-typing-extensions (#13288)Adam J. Stewart1-2/+4
2019-10-20Add latest version of py-urllib3 (#13286)Adam J. Stewart1-3/+8
2019-10-20Add latest version of py-virtualenv (#13285)Adam J. Stewart1-3/+4
2019-10-20Add latest version of py-werkzeug (#13284)Adam J. Stewart1-1/+6
2019-10-20Add py-mypy-extensions package (#13283)Adam J. Stewart1-0/+19
2019-10-20Add py-mypy package (#13282)Adam J. Stewart1-0/+26
2019-10-20Add py-pytest-forked package (#13281)Adam J. Stewart1-0/+20
2019-10-20Add py-raven package (#13280)Adam J. Stewart1-0/+21
2019-10-20Add py-flake8-import-order package (#13273)Adam J. Stewart1-0/+20
2019-10-20Add py-sphinxcontrib-devhelp package (#13278)Adam J. Stewart1-0/+23
2019-10-20Add py-sphinxcontrib-applehelp package (#13279)Adam J. Stewart1-0/+23
2019-10-20Add py-sphinxcontrib-htmlhelp package (#13277)Adam J. Stewart1-0/+23
2019-10-20Add py-sphinxcontrib-jsmath package (#13276)Adam J. Stewart1-0/+22
2019-10-20Add py-sphinxcontrib-qthelp package (#13275)Adam J. Stewart1-0/+23
2019-10-20Add py-sphinxcontrib-serializinghtml package (#13274)Adam J. Stewart1-0/+23
2019-10-20Add py-typed-ast package (#13272)Adam J. Stewart1-0/+18
2019-10-20Add py-docutils-stubs package (#13271)Adam J. Stewart1-0/+19
2019-10-20Add py-brotlipy package (#13270)Adam J. Stewart1-0/+23
2019-10-20spack create: http -> https (#13269)Adam J. Stewart1-1/+1
2019-10-19shebangs: don't warn when patching long shebangs (#13266)Todd Gamblin1-1/+1
We've been doing this for quite a while now, and it does not seem to cause issues. - [x] Switch the noisy warning to a debug to make Spack a bit quieter while building.
2019-10-19Microarchitecture specific optimizations for LLVM (#13250)Massimiliano Culpo9-10/+292
* Added architecture specific optimization flags for Clang / LLVM * Disallow compiler optimizations for mixed toolchains * We emit a warning when building for a mixed toolchain * Fixed issues with suffixed versions of compilers; Apple's Clang will, for the time being, fall back on x86-64 for every compilation.
2019-10-19GCC: fix build on macOS Catalina (#13202)Adam J. Stewart1-15/+19
* GCC: speed up build * Add back 3-stage bootstrapping
2019-10-19brotli: fix darwin install name (#13258)Adam J. Stewart1-0/+6
2019-10-18ADIOS2: Dataspaces, libffi, libfabric (#13230)Axel Huebl2-0/+26
* DataSpaces: 1.8.0 Add a newer release of DataSpaces for ADIOS2. Also add missing `-fPIC` flags since this is a static library. * ADIOS2: Dataspaces, libffi, libfabric Add missing dependencies to ADIOS2. Without explicit control, those dependencies might get picked up from the system environment and will cause unstable builds. * Hide transitive SST dependencies * ADIOS2: Simplify SST CMake Flags As proposed by Chuck
2019-10-18Updated to latest version. Removed dependency on node-js (#13055)wspear1-17/+21
* Updated to latest version. Removed dependency on node-js * Refined dependencies * Added dependencies, including version-specific ones. Re-added 0.9.4. * Updated py-jupyterhub requirements. Enabled version 0.9.4 and 1.0.0
2019-10-18fftw: altivec only works for float (#13242)Christoph Junghans1-6/+17
2019-10-18Added package py-python-oauth2, a dependency of py-jupyterhub@0.9.4. … ↵wspear1-0/+18
(#13140) * Added package py-python-oauth2, a dependency of py-jupyterhub@0.9.4. Depends on #13132, #13133 and #13134 * Remove optional dependencies
2019-10-17interproscan: add 5.38-76.0 (#13253)Justin S1-3/+5
2019-10-17satisfaction checks on dependencies should be strict when the parent check ↵Peter Scheibel1-1/+1
is strict (#13243)
2019-10-17Separate setting build environment and run environment in packages (#11115)Massimiliano Culpo14-213/+331
* Methods setting the environment now do it separately for build and run Before this commit the `*_environment` methods were setting modifications to both the build-time and run-time environment simultaneously. This might cause issues as the two environments inherently rely on different preconditions: 1. The build-time environment is set before building a package, thus the package prefix doesn't exist and can't be inspected 2. The run-time environment instead is set assuming the target package has been already installed Here we split each of these functions into two: one setting the build-time environment, one the run-time. We also adopt a fallback strategy that inspects for old methods and executes them as before, but prints a deprecation warning to tty. This permits to port packages to use the new methods in a distributed way, rather than having to modify all the packages at once. * Added a test that fails if any package uses the old API Marked the test xfail for now as we have a lot of packages in that state. * Added a test to check that a package modified by a PR is up to date This test can be used any time we deprecate a method call to ensure that during the first modification of the package we update also the deprecated calls. * Updated documentation
2019-10-17multimethods: avoid calling caller_locals() in Python 3 (#13238)Todd Gamblin2-10/+35
Python 3 metaclasses have a `__prepare__` method that lets us save the class's dictionary before it is constructed. In Python 2 we had to walk up the stack using our `caller_locals()` method to get at this. Using `__prepare__` is much faster as it doesn't require us to use `inspect`. This makes multimethods use the faster `__prepare__` method in Python3, while still using `caller_locals()` in Python 2. We try to reduce the use of caller locals using caching to speed up Python 2 a little bit.
2019-10-17python-editor: added new package at v1.0.4 (#13126)wspear1-0/+19
2019-10-16eospac: avoid conflict with linux's getopt (#13241)Christoph Junghans1-0/+5
* eospac: avoid conflict with linux's getopt * Update package.py
2019-10-16importing: make importlib_importer recognize .pyc cache (#13239)Todd Gamblin1-0/+6
Our importer was always parsing from source (which is considerably slower) because the source size recorded in the .pyc file differed from the size of the input file. Override path_stats in the prepending importer to fool it into thinking that the source size is the size *with* the prepended code.
2019-10-16filter_file: fix multiple invocations on the same file (#13234)Michael Kuhn2-2/+33
Since the backup file is only created on the first invocation, it will contain the original file without any modifications. Further invocations will then read the backup file, effectively reverting prior invocations. This can be reproduced easily by trying to install likwid, which will try to install into /usr/local. Work around this by creating a temporary file to read from.
2019-10-16Bugfix: stage directory permissions and cleaning (#12733)Tamara Dahlgren9-83/+297
* This updates stage names to use "spack-stage-" as a prefix. This avoids removing non-Spack directories in "spack clean" as c141e99 did (in this case so long as they don't contain the prefix "spack-stage-"), and also addresses a follow-up issue where Spack stage directories were not removed. * Spack now does more-stringent checking of expected permissions for staging directories. For a given stage root that includes a user component, all directories before the user component that are created by Spack are expected to match the permissions of their parent; the user component and all deeper directories are expected to be accessible to the user (read/write/execute).
2019-10-16add python version 3.8.0 (#13218)Jeffrey Salmond1-1/+2
2019-10-16expat: don't pick up external docbook (#13228)Christoph Junghans1-2/+2
2019-10-15add latest version of vim (#13203)Jeffrey Salmond1-0/+1
2019-10-15Feature: installed file verification (#12841)Greg Becker13-54/+791
This feature generates a verification manifest for each installed package and provides a command, "spack verify", which can be used to compare the current file checksums/permissions with those calculated at installed time. Verification includes * Checksums of files * File permissions * Modification time * File size Packages installed before this PR will be skipped during verification. To verify such a package you must reinstall it. The spack verify command has three modes. * With the -a,--all option it will check every installed package. * With the -f,--files option, it will check some specific files, determine which package they belong to, and confirm that they have not been changed. * With the -s,--specs option or by default, it will check some specific packages that no files havae changed.
2019-10-15hypre: add version 2.18.1 (#13224)Satish Balay1-0/+1
2019-10-15ADIOS2: Default no Python (#13220)Axel Huebl1-1/+1
Turn off the python variant by default.
2019-10-15lmod: module files are written in a root folder named by target family (#13121)Massimiliano Culpo3-1/+22
fixes #13005 This commit fixes an issue with the name of the root directory for module file hierarchies. Since #3206 the root folder was named after the microarchitecture used for the spec, which is too specific and not backward compatible for lmod hierarchies. Here we compute the root folder name using the target family instead of the target name itself and we add target information in the 'whatis' portion of the module file.
2019-10-15arborx: update v0.8-beta to v0.8-beta2 (#13143)Andrey Prokopenko1-8/+9
- Require Kokkos with c++14 - Update the case of CMake options
2019-10-15kokkos: add cxxstd variant (#13142)Andrey Prokopenko1-1/+10
2019-10-14Add version 0.177 of elfutils (#13129)Tim Haines1-1/+2
* Add version 0.177 * Fix spacing