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2019-06-10ninja{-fortran}: make pkgs nonvirtual (fix #11628) (#11629)Geoffrey Oxberry3-6/+0
2019-06-10ParaView and Catalyst use python3. (#11485)Dan Lipsa2-13/+65
Use python3 for latest paraview and catalyst versions.
2019-06-10CD: Package Index (#11665)Axel Huebl5-0/+53
Build the docker image for the new package index REST API on each merge/push to develop and master.
2019-06-10Remove gnutls dependency and disable openssl when appropriate (#11646)Chuck Atkins1-4/+9
2019-06-10Define LDFLAGS when using fujitsu compiler (#11669)t-karatsu1-0/+3
2019-06-08dateutils: new package (#11623)Quinn1-0/+19
* Adding the dateutils package * Removing superfluous dependencies
2019-06-08tests: restore `spack spec mpileaks` in test output for Python 2 (#11664)Todd Gamblin1-5/+3
- also remove coverage calls of these commands - we JUST want coverage to tell us what is in the test suite.
2019-06-08concretization: don't apply build-dep constraints for installed packages ↵Peter Scheibel3-5/+85
(#11594) Spack currently tries to unify everything in the DAG, but this is too strict for build dependencies, where it is fine to build a dependency with a tool that conflicts with a version fo that tool for a dependent's build. To enable a workaround for conflicts among build dependencies, so that users can install in multiple steps to avoid these conflicts, make the following changes: * Dont apply package dependency constraints for build deps of installed packages * Avoid applying constraints for installed packages vs. concrete packages * Mark all dependencies of installed packages as visited in normalization method * don't remove dependency links for concrete specs in flat_dependencies Also add tests: * Update test to ensure that link dependencies of installed packages have constraints applied * Add test to check for proper handling of transitive dependencies (which is currently not the case)
2019-06-08fix qt build on gcc8.3 (#11633)Omar Padron3-7/+476
* fix qt build on gcc8.3 * source patches from upstream * remove old code adding the same patch
2019-06-08Add ADIOS2 option to Trilinos (#11609)Francois Budin1-1/+7
ADIOS2 is the latest implementation of the ADaptable Input Output System, ADIOS. This brand new architecture was designed to continue supporting the performance legacy of ADIOS, and extend its current capabilities to address current and future input/output (IO) challenges in the scientific data lifecycle through effective research and development (R&D) activities. ADIOS2 was recently added as a Third Party Library of Trilinos when it was integrated to IOSS, a library inside the SEACAS package.
2019-06-07spack list: latest version (JSON) (#11652)Axel Huebl4-1/+81
List the latest version of each package in JSON encoding. Preparation for consumption for a "spack badge" service.
2019-06-07Compiler search uses a pool of workers (#10190)Massimiliano Culpo17-302/+503
- spack.compilers.find_compilers now uses a multiprocess.pool.ThreadPool to execute system commands for the detection of compiler versions. - A few memoized functions have been introduced to avoid poking the filesystem multiple times for the same results. - Performance is much improved, and Spack no longer fork-bombs the system when doing a `compiler find`
2019-06-07add openmp variant to lammps (#11643)Jeffrey Salmond1-1/+5
* add openmp variant to lammps * add conflict for %gcc@9: and +openmp
2019-06-06commands: remove unused `spack list --format=rst` (#11651)Todd Gamblin2-79/+0
- We use `spack list --foramt=html` now, as it is much faster and doesn't make the docs build take forever. - Remove `spack list --format=rst` as it is no longer used.
2019-06-06added tix package and python variant for tix (#11599)Gregory Lee4-2/+58
* added tix package and python variant for tix * addressing tix review requests * python +tix requires +tkinter
2019-06-06bugfix: StageComposite must include the `expanded` property` (#11647)Todd Gamblin1-0/+4
2019-06-06bugfix: lua-luafilesystem package should use stage.source_path (#11648)Todd Gamblin1-2/+1
2019-06-06tests: package_sanity now checks packages in 3rd-party repos (#11637)Jennifer Herting1-2/+1
2019-06-05travis: disable `spack spec` for python 2.7 as well as 2.6Todd Gamblin1-1/+1
- keep this disabled until the `compiler find` fork bomb is fixed.
2019-06-05tests: add extra coverage for fetch strategy testsTamara Dahlgren4-8/+142
2019-06-05stage: make `source_path` available before stage is builtTamara Dahlgren6-207/+535
- `stage.source_path` was previously overloaded; it returned `None` if it didn't exist and this was used by client code - we want to be able to know the `source_path` before it's created - make stage.source_path available before it exists. - use a well-known stage source path name, `$stage_path/src` that is available when `Stage` is instantiated but does not exist until it's "expanded" - client code can now use the variable before the stage is created. - client code can test whether the tarball is expanded by using the new `stage.expanded` property instead of testing whether `source_path` is `None` - add tests for the new source_path semantics
2019-06-05refactor: remove unused spack.stage._get_mirrors() functionTamara Dahlgren1-37/+24
2019-06-05tty: make tty.* print exception typesTamara Dahlgren15-26/+55
- make tty.msg, tty.info, etc. print the exception type and stringified message if the message argument is an exception. - simplify parts of the code that call tty.debug(str(e)) - add extra tty.debug statements in places where exceptions were previously ignored
2019-06-05nettle: fix broken build (#11611)Justin S1-0/+3
* nettle: force C99 build * nettle: update to use c99_flag from @alalazo Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2019-06-05lammps: added v20190605 (#11638)Christoph Junghans1-0/+1
2019-06-05clang: fix error messages in c11_flag, cxx17_flag (#11632)Justin S1-2/+2
2019-06-05libxpm: revert change made in unrelated PR (#11634)Patrick Gartung1-3/+3
2019-06-05set GUILE env var when building gnutls, fixes issue #11601 (#11607)Gregory Lee1-0/+7
2019-06-05graph: refactor static graphsTodd Gamblin4-100/+73
- `spack graph --static` (and `spack.graph.dot_graph`) now do the "right thing" and print the possible dependency graph of provided packages. - `spack graph --static` no longer concretizes specs, as it only relies on class level metadata - Previously the behavior was not consistent -- `spack graph --static` would graph possible dependencies of concrete specs, but would only include some of them. The new code properly pursues all possible dependencies, and allows traversing by different dependency types.
2019-06-05spack dependencies: support --deptype argumentTodd Gamblin4-10/+47
- `spack dependencies` can now take a --deptype argument to only traverse particular deptypes - add a new "common" argument for deptype in spack.cmd.common.arguments - Database.installed_relatives() can now also take a deptype argument - this is used by `spack dependencies --installed`
2019-06-05package: make possible_dependencies consider deptypesTodd Gamblin3-16/+93
- `PackageBase.possible_dependencies` now: - accepts a deptype param that controls dependency types traversed - returns a dict mapping possible depnames to their immediate possible dependencies (this lets you build a graph easily) - Add tests for PackageBaes
2019-06-05refactor: remove vestigial ALLOWED_URL_SCHEMES from package.pyTodd Gamblin1-4/+0
2019-06-05refactor: make Package.name consistent with other class attributesTodd Gamblin2-11/+18
- The 'name' attribute for packages was being set in DirectiveMeta, which wasn't consistent with other class properties (like fullname, etc.) - Move it to be a class property of `PackageMeta`, and add the corresponding property method wrapper on `PackageBase`
2019-06-05refactor: make PackageBase.possible_dependencies() a class method.Todd Gamblin1-4/+5
2019-06-05add C standard flags to compiler classes (#11618)Justin S7-0/+90
* add c99_flag, c11_flag to compiler class * implement c99_flag, c11_flag for gcc * implement c99_flag, c11_flag for arm * implement c99_flag for cce * implement c99_flag, c11_flag for clang * implement c99_flag, c11_flag for intel * implement c99_flag, c11_flag for xl
2019-06-04Add Google Benchmark version 1.5.0 (#11626)Andrew Gaspar1-1/+3
2019-06-04Revert "Git: patch to make git relocatable with buildcache. (#11596)" (#11625)Patrick Gartung2-58/+0
This reverts commit 30ec13f37584ad2934ecdf5a4e86d93d35b3a76c.
2019-06-04modules: set permissions based on package configuration (#11337)Greg Becker5-52/+99
Previously, module files were not set with the same permissions as the package installation. For world-readable packages, this would not cause a problem. For group readable packages, it does: ``` packages: mypackage: permissions: group: mygroup read: group write: group ``` In this case, the modulefile is unreadable by members of the group other than the one who installed it. Add logic to the modulefile writers to set the permissions based on the configuration in `packages.yaml`
2019-06-04Buildcache relocate.py error fix (#11616)Patrick Gartung3-5/+5
* Add a trailing / if file --mime does not return a mimetype with a / in it * Flake8
2019-06-04hotspot: new package at 6.0 (#11610)Justin S1-0/+21
2019-06-03mesa: Revert updated meson build and restore autotools build (#11595)Chuck Atkins4-130/+68
Due to the large number of issues this migration has caused, this rolls back to the older autotools build. However, it still keeps the updates wrt variants and virtual packages.
2019-05-31Git: patch to make git relocatable with buildcache. (#11596)Patrick Gartung2-0/+58
* Apply patch to git to make it search for config files from its current location instead of the locations hard coded at install. * Add provenance info for patch * Pass needed flags to make * Environment variables need because of relocation
2019-05-31Build cache: relocate path to spack/bin/sbang in text files. (#11592)Patrick Gartung3-13/+35
* Build cache: relocate path to spack/bin/sbang in text files. * Found in testing. * update packaging test * Make sbang replacement including #!/bin/bash. Add an additional spack prefix replacement to fix stage directory references. * flake8 * Use buildinfo.get() so old buildcaches without buildinfo['spackprefix'] can be read.
2019-05-31Package/tau/tau 2.28.1 update (#11591)sameershende2-2/+14
* Updating the TAU package with 2.28 and public repo * Cleaning up TAU package and fixing binutils to install extras The extras variant will install the extra ELF headers needed by the TAU package. The TAU package has been cleaned up and extended. * Adding some comments to the changes in binutils * Adding correct python support, finding include and lib paths. * Added PDT 3.25.1. * Added TAU v2.28.1 with libdwarf and libelf. * When +libdwarf is activated, +libelf is not automatically activated. It checks separately for libelf.
2019-05-30alan: new package at 2.1.1 (#11593)Justin S1-0/+19
2019-05-30Adds the aml memory management library. (#11590)Valentin Reis1-0/+21
AML is a collection of building blocks for explicit memory management on complex architectures. https://xgitlab.cels.anl.gov/argo/aml https://argo-aml.readthedocs.io/en/latest/
2019-05-30r-randomglm: new package at 1.02-1 (#11589)Justin S1-0/+21
2019-05-30Revbayes update (#11559)Nick Booher1-3/+6
* revbayes: new version * revbayes: pep8
2019-05-30mathematica: new package at 12.0.0 (#11509)Justin S1-0/+39
* mathematica: new package at 12.0.0 * mathematica: add missing os import * mathematica: fix url format
2019-05-29precice: add version 1.5.0 (#11577)Frédéric Simonis1-0/+1