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2020-04-17oneDNN: add new version (#16129)Adam J. Stewart1-1/+2
2020-04-17singularity: new variants to enable non-suid and non-network builds (#16088)Andrew W Elble1-23/+32
Defaults are left as they are currently
2020-04-17New package: Biopandas python package (#16066)ilbiondo1-0/+24
* Biopandas python package * Update var/spack/repos/builtin/packages/py-biopandas/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-biopandas/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * remove scipy dependency Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-17magma: added v2.5.3 (#16097)Stan Tomov1-1/+2
Also updated maintainer list
2020-04-17py-gcovr: added new package at v4.2 (#16100)Michael Kuhn1-0/+23
2020-04-17open-iscsi: added new package at v2.1.1 (#16113)darmac1-0/+32
2020-04-17aespipe: added new package at v2.4f (#16114)darmac1-0/+22
2020-04-17sz: run "make clean" after configure (#15759)Kai Germaschewski1-0/+3
At least the v2.0.2.0 tar ball contains compiled object files etc, which cause the build to fail on other architectures (ppc64le in particular), so this patch adds a `make clean` after configuring first.
2020-04-17asdcplib: added new package at v2.10.35 (#16118)darmac1-0/+23
2020-04-17libtree: added v1.1.2 (#16119)Harmen Stoppels1-0/+1
2020-04-16SourceForge: Mirror Mixin (#16112)Axel Huebl39-68/+162
* SourceForge: Mirror Mixin Add a mixing class for direct `CNAME`s to sourceforge mirrors. Since the main gateway servers are often down, this could reduce timeouts and fetch errors for sourceforge.net hosted software. * SourceForge: unspectacular mirror replacement add mirrors to all sourceforge packages with trivial download logic. tested fetch of latest version of each of these packages with various mirrors before committing. * SourceForge: xz the author homepage is chronocially overrun and this is the offical upload with many mirrors.
2020-04-16bugfix: fix emacs support on macOS (#16110)Todd Gamblin1-1/+1
- fix missing self.spec
2020-04-16macOS: Fix emacs Linking (#16106)Axel Huebl2-1/+9
* macOS: Fix emacs Linking Fix linking issue of emacs on macOS (clang and gcc). Applies the same work-around as conda-forge: https://github.com/conda-forge/emacs-feedstock/blob/b051f6c928d8b99fed3fabd9a8d67be993f94494/recipe/build.sh Homebrew avoids this by linking against the system ncurses lib: https://github.com/Homebrew/homebrew-core/blob/master/Formula/emacs.rb * ncurses: fix outdated variant comment this comment was build on the assumption that gnutls triggers a termlib dependency in emacs. that's not the case, ncurses itself depends on termlib when build with this feature.
2020-04-16libpng: github downloadAxel Huebl1-5/+4
libpng still has its sourceforge page but is actively been developed on github. since the sourceforge urls are too often down (as seen in my nightly CI/CD tests), just switch the download source to GitHub instead.
2020-04-16macos: use DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATHTodd Gamblin5-10/+14
`DYLD_LIBRARY_PATH` can frequently break builtin macOS software when pointed at Spack libraries. This is because it takes *higher* precedence than the default library search paths, which are used by system software. `DYLD_FALLBACK_LIBRARY_PATH`, on the other hand, takes lower precedence. At first glance, this might seem bad, because the software installed by Spack in an environment needs to find *its* libraries, and it should not use the defaults. However, Spack's isntallations are always `RPATH`'d, so they do not have this problem. `DYLD_FALLBACK_LIBRARY_PATH` is thus useful for things built in an environment that need to use Spack's libraries, that don't set *their* RPATHs correctly for whatever reason. We now prefer it to `DYLD_LIBRARY_PATH` in modules and in environments because it helps a little bit, and it is much less intrusive.
2020-04-16darwin: cut DYLD_LIBRARY_PATH from default modulesGeoffrey Malcolm Oxberry1-2/+0
This commit removes the DYLD_LIBRARY_PATH variable from the default modules.yaml for darwin. The rationale behind deleting this environment variable is that paths in this environment variable take precedence over the default locations of libraries (usually the install path of the library), which can lead to linking errors in some circumstances. For example, executables intended to link with Apple's system BLAS and LAPACK will instead link to a spack-installed implementation (e.g., OpenBLAS), causing runtime errors. These errors are resolved by instead relying on paths set in DYLD_FALLBACK_LIBRARY_PATH, which is lower in precedence than default locations of libraries.
2020-04-16ncurses: forward termlib libs (#16101)Axel Huebl1-1/+5
These libs need to be forwarded, as in ncurses `pkg-config` file.
2020-04-16emacs: libxml2 deps (#16103)Axel Huebl1-0/+1
emacs depends on libxml2.
2020-04-16Bugfix: For spack buildcache check, Handle specs where only the hash is (#15663)Marc Allen1-1/+1
provided (#15662). Prior to this fix, the checked Spec object would not be populated, and concretization would fail. Co-authored-by: Marc Allen <mrcall@amazon.com>
2020-04-16Add ncurses+termlib dependency to mesa (#16038)Glenn Johnson1-0/+2
Mesa links against libtinfo so needs to depend on ncurses. It also needs a little help finding the library directory so an LDFLAGS configure option is added.
2020-04-16New version xrootd-4.11.3 (#16092)Amjad Kotobi1-0/+1
2020-04-16singularity: updated maintainer list (#16093)Carlos Arango Gutierrez1-1/+1
2020-04-16openbabel: fix compilation errors (#16090)athanasio1-0/+6
- Disable maeparser as it is broken with CMake - Added missing dependencies
2020-04-16New package bonniepp added (#16091)Amjad Kotobi1-0/+21
2020-04-16Add new version 1.1.1 (#16087)Harmen Stoppels1-0/+1
2020-04-16New matlab versions (#16086)Antonio Arena1-4/+20
2020-04-16MPark.Variant: GCC 7.3.1 Conflict (#16081)Axel Huebl1-2/+11
* MPark.Variant: GCC 7.3.1 Conflict Due to an ICE in this specific patch-release of GCC, compile errors in downstream packages should be avoided with a clean conflict. * Fix superfluous spaces Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Fix typo Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-16dbcsr: expose all options, check openblas feats (#16034)Tiziano Müller1-7/+60
* dbcsr: expose all options, check openblas feats * dbcsr: use Ninja to build, ensure serialized tests * dbcsr: add myself as maintainer
2020-04-16Add Cubist (#16069)asmaahassan901-0/+32
* Add Cubist * enhance recipe * Not using OS module anymore * remove white space * Fix build shell * make Flake8 happy * use bash shell for build * Convert it To MakefilePackage as per peer-review
2020-04-16HAL: added new package at v2.1 (#16085)ilbiondo1-0/+102
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-15Add new package: zookeeper-benchmark (#16067)darmac1-0/+25
* Add new package: zookeeper-benchmark * refine zookeeper version * refine zookeeper version variant * remove unused variant
2020-04-15Neo4j (#16068)darmac1-0/+31
* Update var/spack/repos/builtin/packages/neo4j/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Add new package: neo4j * refine neo4j package * fix flake8 warning Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15update: memsurfer with python3 (#15636)Harsh Bhatia1-17/+19
* update: memsurfer with python3 * flake8 compliance * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/memsurfer/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * removed build_type preferences at adamjstewart's suggestion * Added build/run dependency on python3.7 as suggested by adam stewart * more flake8 horror! Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15Upgrade MSTK versions (#16079)Rao Garimella1-0/+3
2020-04-15netcdf-cxx4: bugfix (#16080)Carson Woods1-0/+1
* Add new variants * Fix missing config_args variable
2020-04-15Merge branch 'releases/v0.14' into developTodd Gamblin2-1/+16
2020-04-15Make tags case insensitiveMichael Kuhn2-0/+10
Currently, tags are case sensitive, which is unintuitive: ```console $ spack list -t hpc ==> 2 packages. nek5000 nektools $ spack list -t HPC ==> 1 packages. mfem $ spack list -t Hpc ==> 0 packages. ``` This change makes them case insensitive: ```console $ spack list -t hpc ==> 3 packages. mfem nek5000 nektools $ spack list -t HPC ==> 3 packages. mfem nek5000 nektools $ spack list -t Hpc ==> 3 packages. mfem nek5000 nektools ```
2020-04-15x.org packages: mirror mixinAxel Huebl200-400/+401
overhaul all x.org packages to use available mirrors.
2020-04-15update CHANGELOG.md for 0.14.2v0.14.2Todd Gamblin1-0/+15
2020-04-15version bump: 0.14.2Todd Gamblin1-1/+1
2020-04-15bugfix: spack test should not output [+] for mock installs (#15609)Todd Gamblin1-3/+2
`spack test` has a spurious '[+] ' in the output: ``` lib/spack/spack/test/install.py .........[+] ...... ``` Output is properly suppressed: ``` lib/spack/spack/test/install.py ............... ```
2020-04-15Added maintainers (#16078)wspear1-0/+1
Co-authored-by: Wyatt Spear <wspear@cs.uoregon.edu>
2020-04-15Sonlib (#16060)ilbiondo1-0/+47
* sonLib package as required by the HAL toolkit * cleanup * Update var/spack/repos/builtin/packages/sonlib/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/sonlib/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15New package: py-cmake-format (#16055)Kelly (KT) Thompson2-0/+21
* New package py-cmake-format * wrap long lines * Fix package description formatting.
2020-04-15Bump version of libtree (#16051)Harmen Stoppels1-1/+3
2020-04-15`spack install` terminal output handling in foreground/background (#15723)Todd Gamblin7-224/+1155
Makes the following changes: * (Fixes #15620) tty configuration was failing when stdout was redirected. The implementation now creates a pseudo terminal for stdin and checks stdout properly, so redirections of stdin/out/err should be handled now. * Handles terminal configuration when the Spack process moves between the foreground and background (possibly multiple times) during a build. * Spack adjusts terminal settings to allow users to to enable/disable build process output to the terminal using a "v" toggle, abnormal exit cases (like CTRL-C) could leave the terminal in an unusable state. This is addressed here with a special-case handler which restores terminal settings. Significantly extend testing of process output logger: * New PseudoShell object for setting up a master and child process and configuring file descriptor inheritance between the two * Tests for "v" verbosity toggle making use of the added PseudoShell object * Added `uniq` function which takes a list of elements and replaces any consecutive sequence of duplicate elements with a single instance (e.g. "112211" -> "121") Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-15database: maintain in-memory consistency on remove (#15777)Massimiliano Culpo2-1/+21
The performance improvements done in #14693 where leaving the DB in an inconsistent state when specs were removed from it. This PR updates the DB internal state whenever the DB is written to a file. Note that we still cannot properly enumerate installed dependents, so there is a TODO in this code. Fixing that will require the dependents dictionaries in specs to be re-keyed (either by hash, or not keyed at all -- a list would do). See #11983 for details.
2020-04-15performance: add a verification file to the database (#14693)Andrew W Elble3-3/+52
Reading the database repeatedly can be quite slow. We need a way to speed up Spack when it reads the DB multiple times, but the DB has not been modified between reads (which is nearly all the time). - [x] Add a file containing a unique uuid that is regenerated at database write time. Use this uuid to suppress re-parsing the database contents if we know a previous uuid and the uuid has not changed. - [x] Fix mutable_database fixture so that it resets the last seen verifier when it resets. - [x] Enable not rereading the database immediately after a write. Make the tests reset the last seen verifier in between tests that use the database fixture. - [x] make presence of uuid module optional
2020-04-15Remove DB conversion of old index.yaml (#15298)Peter Scheibel1-84/+45
Removed the code that was converting the old index.yaml format into index.json. Since the change happened in #2189 it should be considered safe to drop this (untested) code.
2020-04-15Allow Spack Environments with '-h' in the name (#15429)Adam J. Stewart2-32/+63
If a user invoked "spack env activate example-henv", Spack would mistakenly interpret the "-h" from "example-henv" as the "-h" option. This commit allows users to create and activate environments with "-h" in the name. This issue existed for bash shell support as well as csh support, and this commit addresses both, along with some other unrelated csh support issues.