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2019-11-01Documentation: Database.query methods share docstrings (#13515)Greg Becker1-41/+53
Currently, query arguments in the Spack core are documented on the Database._query method, where the functionality is defined. For users of the spack python command, this makes the python builtin method help less than ideally useful, as help(spack.store.db.query) and help(spack.store.db.query_local) do not show relevant information. This PR updates the doc attributes for the Database.query and Database.query_local arguments to mirror everything after the first line of the Database._query docstring.
2019-11-01cuda: fix conflict statements for x86-64 targets (#13472)Massimiliano Culpo1-4/+6
* cuda: fix conflict statements for x86-64 targets fixes #13462 This build system mixin was not updated after the support for specific targets has been merged. * Updated the version range of cuda that conflicts with gcc@8: * Updated the version range of cuda that conflicts with gcc@8: for ppc64le * Relaxed conflicts for version > 10.1 * Updated versions in conflicts Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
2019-11-01cpu: fix clang flags for generic x86_64 (#13491)Greg Becker2-8/+16
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-11-01syaml_int type should use int.__repr__ rather than str.__repr__ (#13487)Peter Scheibel1-1/+1
2019-10-31elpa: prefer 2016.05.004 until sse/avx/avx2 issues are resolved (#13530)eugeneswalker1-1/+1
- configuration fails on newer versions when enabling sse/avx/avx2 - prefer an older version that will build with these features
2019-10-31trilinos: temporarily constrain netcdf@:4.7.1 (#13526)eugeneswalker1-1/+1
remove this when issues are resolved with `trilinos^netcdf@4.7.2`
2019-10-25Add top-level `CHANGELOG.md` with release notes.v0.13.0Todd Gamblin1-0/+262
2019-10-25version bump: 0.13.0Todd Gamblin1-1/+1
2019-10-25tutorial: move tutorial to standalone site (#13450)Todd Gamblin31-7565/+28
* docs: add a spack environment for building the docs * docs: remove tutorial and link to spack-tutorial.readthedocs.io The tutorial now has its own standalone website, versioned by instances of the tutorial. Link to that instead of versioning it directly with Spack.
2019-10-25`mirror create --all` can mirror everything (#12940)Peter Scheibel11-228/+465
Support mirroring all packages with `spack mirror create --all`. In this mode there is no concretization: * Spack pulls every version of every package into the created mirror. * It also makes multiple attempts for each package/version combination (if there is a temporary connection failure). * Continues if all attempts fail. i.e., this makes its best effort to fetch evrerything, even if all attempts to fetch one package fail. This also changes mirroring logic to prefer storing sources by their hash or by a unique name derived from the source. For example: * Archives with checksums are named by the sha256 sum, i.e., `archive/f6/f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8.tar.gz` vs the previous `<package-name>-package-version>.tar.gz` * VCS repositories are stored by a path derived from their URL, e.g. `git/google/leveldb.git/master.tar.gz`. The new mirror layout allows different packages to refer to the same resource or source without duplicating that download in the mirror/cache. This change is not essential to mirroring everything but is expected to save space when mirroring packages that all use the same resource. The new structure of the mirror is: ``` <base directory>/ _source-cache/ <-- the _source-cache directory is new archive/ <-- archives/resources/patches stored by hash 00/ <-- 2-letter sha256 prefix 002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056.tar.gz 01/ 0154c25c45b5506b6d618ca8e18d0ef093dac47946ac0df464fb21e77b504118.tar.gz 0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea.tar.gz ... git/ OpenFAST/ openfast.git/ master.tar.gz <-- repo by branch name PHASTA/ phasta.git/ 11f431f2d1a53a529dab4b0f079ab8aab7ca1109.tar.gz <-- repo by commit ... svn/ <-- each fetch strategy has its own subdirectory ... openmpi/ <-- the remaining package directories have the old format openmpi-1.10.1.tar.gz <-- human-readable name is symlink to _source-cache ``` In addition to the archive names as described above, `mirror create` now also creates symlinks with the old format to help users understand which package each mirrored archive is associated with, and to allow mirrors to work with old spack versions. The symlinks are relative so the mirror directory can still itself be archived. Other improvements: * `spack mirror create` will not re-download resources that have already been placed in it. * When creating a mirror, the resources downloaded to the mirror will not be cached (things are not stored twice).
2019-10-25Add py-twine package (#13449)Adam J. Stewart1-0/+22
2019-10-25Add py-pkginfo package (#13448)Adam J. Stewart1-0/+19
2019-10-25Add latest version of py-tqdm (#13446)Adam J. Stewart1-2/+7
2019-10-25Add latest version of py-requests-toolbelt (#13445)Adam J. Stewart1-2/+3
2019-10-25Add latest version of py-readme-renderer (#13444)Adam J. Stewart1-3/+5
2019-10-25New package: gpu-burn (#13108)Glenn Johnson2-0/+73
2019-10-25bugfix: restore upstream lock safety; update testsPeter Scheibel2-19/+48
Restore upstream lock safety; avoid calling methods directly on upstream DB in test.
2019-10-25py-nbformat package: add version 4.4.0 (#13421)Andreas Baumbach1-0/+1
2019-10-25New package: py-defusedxml (#13419)Andreas Baumbach1-0/+17
2019-10-25New package: OSQP (#13432)Sinan1-0/+22
2019-10-25LIBXSMM package: add version 1.14 (#13436)Hans Pabst1-1/+2
2019-10-25lmdb package: add version 0.9.24 (#13437)Michael Kuhn1-0/+1
2019-10-25sqlite package: add version 3.30.1 (#13438)Michael Kuhn1-0/+1
2019-10-25py-gensim: new package at 3.8.0 (#13136)Justin S1-0/+28
* py-gensim: new package at 3.8.0 * py-gensim: add 3.8.1
2019-10-25completion: add bash completion for `spack spec --json` (#13433)Todd Gamblin1-1/+2
2019-10-25Make error msg of test_api_for_build_and_run_environment more informative ↵Andreas Baumbach1-1/+2
(#13435)
2019-10-25bugfix: reindexing is not necessary for DB v0.9.3 to v5 upgrade (#13434)Todd Gamblin1-3/+25
reindexing takes a significant amount of time, and there's no reason to do it from DB version 0.9.3 to version 5. The only difference is that v5 can contain "deprecated_for" fields. - [x] Add a `_skip_reindex` list at the start of `database.py` - [x] Skip the reindex for upgrades in this list. The new version will just be written to the file the first time we actually have to write the DB out (e.g., after an install), and reads will still work fine.
2019-10-24bugfix: allow fetching no-code packages (#13429)Todd Gamblin3-22/+12
Previously, spack would error out if we tried to fetch something with no code, but that would prevent fetching dependencies. In particular, this would fail: spack fetch --dependencies xsdk - [x] Instead of raising an error, just print a message that there is nothing to be fetched for packages like xsdk that do not have code. - [x] Make BundleFetchStrategy a bit more quiet about doing nothing.
2019-10-24commands: Add `--json` argument to `spack spec` (#13431)Todd Gamblin2-5/+23
We've had `spack spec --yaml` for a while, and we've had methods for JSON for a while as well. We just haven't has a `--json` argument for `spack spec`. - [x] Add a `--json` argument to `spack spec`, just like `--yaml`
2019-10-24Improvements to detection of AMD architectures. (#13407)Chris Green6-4/+142
New entry for K10 microarchitecture. Reorder Zen* microarchitectures to avoid triggering as k10. Remove some desktop-specific flags that were preventing Opteron Bulldozer/Piledriver/Steamroller/Excavator CPUs from being recognized as such. Remove one or two flags which weren't produced in /proc/cpuinfo on older OS (RHEL6 and friends).
2019-10-24Views: fix python in views when python prefix is under a symlink (#12575)Greg Becker1-1/+12
* Fix python in views when python prefix is under a symlink * Add todo for future generalization
2019-10-24Add latest version of NetCDF libraries (#13416)Adam J. Stewart3-5/+9
2019-10-24Extend HPX package (#13219)Mikael Simberg1-6/+24
* Add master branch as version to HPX package * Remove C++98 option from HPX package * Add option to turn off examples in HPX package * Add MPI variant to HPX package
2019-10-24New package: py-cdsapi (#13363)Jannek Squar1-0/+19
* New package py-cdsapi to access Climate Data Store for downloading climate and weather reanalysis data * Improvements
2019-10-24mfem: add version 4.0 (without cuda) (#11880)Geoffrey Oxberry2-7/+84
* mfem: add version 4.0.0 (without cuda, raja, etc) * mfem@4.0.0: add occa variant * mfem@4.0.0: add raja variant * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2019-10-24Correctly identify Skylake CPUs on Darwin. (#13377)Chris Green4-1/+12
* Correctly identify Skylake CPUs on Darwin. * Add a test for haswell on Mojave.
2019-10-24database: update DB version and change to integer database versions (#13410)Greg Becker1-1/+3
Update on version format: change to an integer database format version for simplicity, instead of tracking the Spack version.
2019-10-24Patch libtool when using the Arm compiler (#12004)Nick Forrington1-0/+24
* Patch libtool when using the arm, clang, and fujitsu compilers If libtool does not have values for linker/pic flags, patch them in
2019-10-23blast-legacy: fix build issues (#13370)Eric Martin1-1/+2
2019-10-23subread: add version 2.0.0 (#13368)Eric Martin1-0/+1
2019-10-23sundials: add version 5.0.0 and new variant (#13375)Cody Balos1-66/+106
* sundials: add version 5.0.0 and new variant plus some cleanup * sundiaks: fix formatting * sundials: fix dependencies
2019-10-23vt: add version 0.5772 (#13367)Eric Martin1-0/+1
2019-10-23add `spack dev-build` command; deprecate `spack diy` (#13374)Greg Becker7-86/+216
Rename the `spack diy` command to `spack dev-build` to make the use case clearer. The `spack diy` command has some useful functionality for developers using Spack to build their dependencies and configure/build/install the code they are developing. Developers do not notice it, partly because of the obscure name. The `spack dev-build` command has a `-u/--until PHASE` option to stop after a given phase of the build. This can be used to configure your project, run cmake on your project, or similarly stop after any stage of the build the user wants. These options are analogous to the existing `spack configure` and `spack build` commands, but for developer builds. To unify the syntax, we have deprecated the `spack configure` and `spack build` commands, and added a `-u/--until PHASE` option to the `spack install` command as well. The functionality in `spack dev-build` (specifically `spack dev-build -u cmake`) may be able to supersede the `spack setup` command, but this PR does not deprecate that command as that will require slightly more thought.
2019-10-23bugfix: web.push_to_url should not format the local path that is passed to ↵Peter Scheibel1-6/+1
it (#13408) fd58c98 formats the `Stage`'s `archive_path` in `Stage.archive` (as part of `web.push_to_url`). This is not needed and if the formatted differs from the original path (for example if the archive file name contains a URL query suffix), then the copy fails. This removes the formatting that occurs in `web.push_to_url`. We should figure out a way to handle bad cases like this *and* to have nicer filenames for downloaded files. One option that would work in this particular case would be to also pass `-J` / `--remote-header-name` to `curl`. We'll need to do follow-up work to determine if we can use `-J` everywhere. See also: https://github.com/spack/spack/pull/11117#discussion_r338301058
2019-10-23bison: Fix parallel build (#13402)Michael Kuhn2-4/+88
2019-10-23syaml.dump now allows representing all syaml_ objects (originally this was ↵Peter Scheibel1-10/+5
only available for syaml.dump_config) (#13403)
2019-10-23Users can configure use of RPATH or RUNPATH (#9168)Massimiliano Culpo9-2/+172
Add a new entry in `config.yaml`: config: shared_linking: 'rpath' If this variable is set to `rpath` (the default) Spack will set RPATH in ELF binaries. If set to `runpath` it will set RUNPATH. Details: * Spack cc wrapper explicitly adds `--disable-new-dtags` when linking * cc wrapper also strips `--enable-new-dtags` from the compile line when disabling (and vice versa) * We specifically do *not* add any dtags flags on macOS, which uses Mach-O binaries, not ELF, so there's no RUNPATH)
2019-10-23commands: add `spack deprecate` command (#12933)Greg Becker13-63/+789
`spack deprecate` allows for the removal of insecure packages with minimal impact to their dependents. It allows one package to be symlinked into the prefix of another to provide seamless transition for rpath'd and hard-coded applications using the old version. Example usage: spack deprecate /hash-of-old-openssl /hash-of-new-openssl The spack deprecate command is designed for use only in extroardinary circumstances. The spack deprecate command makes no promises about binary compatibility. It is up to the user to ensure the replacement is suitable for the deprecated package.
2019-10-23mysql: Use correct python command (#13393)Michael Kuhn1-9/+10
* mysql: Use correct python command python~pythoncmd does not provide a python symlink for python3, so make sure we pick the right command. * mysql: Adapt to build env changes
2019-10-23hypre: Add new variants to expose existing features. (#13373)Sarah Osborn1-5/+36
* hypre: Add new variants to expost existing features. * hypre: Add new variants to expose existing features. * hypre: Shorten description line. * hypre: Add an explicit else clause to disable some features.