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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.
2020-04-15Environments/views: only override spec prefix for non-external packages (#15475)Peter Scheibel2-1/+49
* only override spec prefix for non-external packages * add test that environment shell modifications respect explicitly-specified prefixes for external packages * add clarifying comment
2020-04-15Source devnull in environment_after_sourcing_files (closes #15775) (#15791)Jonathon Anderson1-1/+2
spack.util.environment_after_sourcing_files compares the local environment against a shell environment after having sourced a file; but this ends up including the default shell profile and rc, which might differ from the local environment. To change this, compare against the default shell environment, expressed here as 'source /dev/null'.
2020-04-15bugfix: TERM may not be in the environment on Cray (#15630)Todd Gamblin1-3/+7
2020-04-15Blacklist Lmod variable modifications when sourcing files (#15778)Massimiliano Culpo3-1/+24
fixes #15775 Add all the variables listed here: https://lmod.readthedocs.io/en/latest/090_configuring_lmod.html to the list of those blacklisted when constructing environment modifications by sourcing files.
2020-04-15Tests: Mirror Mixin ClassesAxel Huebl8-0/+174
2020-04-15x.org: mirror mixinAxel Huebl3-2/+40
According to my nightly CI/CD tests, x.org is another large provider of software in common build chains that is often down. Added a hand-selected amount of mirrors that is well up-to-sync. Tested with `util-macros` that has a quite "recent" patch release. Other packages to follow in an individual PR.
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>
2020-04-15Fix grcp@1.27.0: (#16052)Federico Ficarelli1-0/+5
Current default version was missing a dependency.
2020-04-15Add new package: mrbench (#16062)darmac1-0/+23
2020-04-15Add new package: kinesis (#16063)darmac1-0/+27
2020-04-15Added Laghos v3 to Proxy Apps v3 (#16070)Robert Pavel1-2/+3
Also fixed upper bound for v2 apps
2020-04-15julea: New package (#16071)Michael Kuhn1-0/+42
2020-04-15IQ-TREE: added new package at v1.6.12 (#16064)ilbiondo1-0/+51
2020-04-15Phylobayes MPI: added new package at v1.8b (#16065)ilbiondo1-0/+31
2020-04-15openfoam: set run environment by sourcing bashrc (#15949)Massimiliano Culpo1-11/+9
2020-04-15py-sonlib: added new package (#16058)ilbiondo1-0/+28
Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-04-14Apply same patch to version 10. (#15963)Dan Lipsa1-1/+1
2020-04-14libssh2: fix linking on macOS (#16012)Adam J. Stewart2-0/+7
* libssh2: fix linking on macOS * Fix libgit2 linkage to libssh2
2020-04-14MAINT: Charliecloud OSX error (#16049)Tyler Reddy1-0/+2
* MAINT: Charliecloud OSX error * raise an appropriate error when attempting to build Charliecloud on Mac OSX, since it will otherwise fail with a more confusing configure stage link check failure * Update var/spack/repos/builtin/packages/charliecloud/package.py Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * MAINT: PR 16049 revision * remove an unused import Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-04-14fix typo (#16043)Sajid Ali1-1/+1
2020-04-14new package: py-torch-nvidia-apex (#16050)Andrew W Elble1-0/+41
2020-04-14Add new variants (#16047)Carson Woods1-0/+59
2020-04-14py-memory-profiler: add new version (#16048)Adam J. Stewart1-3/+4
2020-04-14cp2k: add version 7.1 (#16037)Tiziano Müller1-1/+16
* cp2k: add version 7.1 * cp2k: add option to use COSMA for CP2K 8+
2020-04-14tau: remove deprecated variants (#16041)Carson Woods1-16/+0
* Add more tau variants * Add more tau variants * Remove deprecated packages * Fix flake8 issue
2020-04-14Package extensions: fixed a link in docs (#16040)Massimiliano Culpo3-7/+9
* Moved link to the right place in the docs * Fixed a few minor issues in extensions docs Fixed a typo, added a subsubsection for better navigation, reworded "modules in Python" as "Python packages"
2020-04-14Add support for pre-release builds of Rust (beta, master, nightly) (#16042)Andrew Gaspar1-3/+73
2020-04-14py-tokenizers: add 0.5.2 (#16039)Adam J. Stewart1-0/+7
2020-04-14libtree: new package at 1.0.3 (#16036)Harmen Stoppels1-0/+18
* Add new package libtree * Fix linter issues
2020-04-14pfft: fix to handle 'precision' variant in fftw (#16029)Tom Payerle1-12/+16
* pfft: fix to handle 'precision' variant in fftw pfft had been checking for +double, etc. in fftw spec, which no longer are present (replaced by Multivalued variant precision). * pfft: fix to handle 'precision' variant in fftw pfft had been checking for +double, etc. in fftw spec, which no longer are present (replaced by Multivalued variant precision). (amended to use more idiomatic checks as suggested by @alalazo)
2020-04-14muscle: add 3.8.31 (#15974)Justin S1-3/+24
* muscle: add 3.8.31 * muscle: use build_directory property * muscle: add url_for_version, fix version comparison
2020-04-14sourceware.org: mirror urls (#15992)Axel Huebl7-26/+49
sourceware.org is often quite overrun and times out or results in certificate errors. Since libffi, bzip2, elfutils, etc. are quite fundamental in build chains, lets add some official mirrors. libffi, bzip2, elfutils, lvm2, valgrind: add mirrors
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