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2022-02-18Add/remove conflicts for Apple silicon (M1/aarch64) (#28850)Seth R. Johnson5-11/+16
* go: remove broken bootstrapping for macos aarch64 * qt: mark apple silicon conflict * trilinos: remove apple silicon conflict * Apply review suggestions * python: add apple silicon conflict for 2.7
2022-02-18r-distributional package: add version 0.3.0 (#29037)Manuela Kuhn1-0/+1
2022-02-18kokkos@:3.5.00 +sycl conflicts with %dpcpp@2022.0.0 (#29055)eugeneswalker1-0/+3
2022-02-18py-humanize: add 4.0.0 (#29034)Manuela Kuhn1-0/+2
2022-02-18py-tensorflow-estimator: new versions (#28093)Glenn Johnson1-1/+9
* py-tensorflow-estimator: new versions * Set proper constraint on py-funcsigs Only needed when the python version is less than 3.3.
2022-02-18py-keras: new versions (#27991)Andrew W Elble2-8/+107
* py-keras: new versions * incorporate feedback * adjust deps, add url_for_version() * change to use pip * remove build phase / remove unnecessary TEST_TMPDIR envvar * switch url_for_version around install, not build
2022-02-18py-tensorflow: add versions 2.5.0 and 2.6.0 (#27138)Glenn Johnson9-83/+373
* py-tensorflow: add versions 2.5.0 and 2.6.0 - add version 2.5.0 - add version 2.6.0 - add patches for newer protobuf - set constraints * Remove import os. left over from testing * Remove unused patch file * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Add py-clang dependency * Adjust py-clang constraint * Build tensorflow with tensorboard - tensorflow - added 2.6.1 and 2.6.2 versions - tensorboard - have bazel use number of jobs set by spack - add versions and constraints - new package: py-tensorboard-data-server - use wheel for py-tensorboard-plugin-wit This package can not build with newer versions of bazel that are needed for newer versions of py-tensorboard. * Update var/spack/repos/builtin/packages/py-clang/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Remove empty line at end of file * Fix import sorting * Adjust python dependencies on py-clang * Add version 2.7.0 of pt-tensorflow and py-tensorboard * Adjust bazel constraints * bazel-4 support begins with py-tensorflow-2.7.0 * Adjust dependencies * Loosen cuda constraint on versions > 2.5 Tensorflow-2.5 and above can use cuda up to version 11.4. * Add constraints to patch The 0008-Fix-protobuf-errors-when-using-system-protobuf.patch patch should only apply to versions 2.5 and above. * Adjust constraints - versions 2.4 and below need protobuf-3.12 and below - versions 2.4 and above can use up to cuda-11.4 - versions 2.2 and below can not use cudnn-8 - the null_linker_bin patch should only be applied to versions 2.5 and above. * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Update var/spack/repos/builtin/packages/py-tensorflow/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Fix py-grpcio dependency for version 2.7 Also, make sure py-h5py mpi specs are consistent. * Add llvm as run dependency. * Fix python spec for py-tensorboard * Fix py-google-auth spec for py-tensorboard * Do not override the pip spec for tensorboard-plugin-wit * Converted py-tensorboard-plugin-wit to wheel only package * Fix bazel dependency spec in tensorflow * Adjust pip masks - allow tensorboard to be specified in pip constraints - mask tensorflow-estimator * Remove blank line at end of file * Adjust pip constraints in setup.py Also, adjust constraint on a patch that is fixed in 2.7 * Fix flake8 error Adjust formatting for consistency. * Get bazel dep right * Fix old cudnn dependency, caught in audit test * Adjust the regex to ensure proper line is changed * Add py-libclang package - Stripped the py-clang package down to just version 5 - added comments to indicate the purpose of py-clang and that py-libclang should be preferred - set dependencies accordingly in py-tensorflow * Remove cap on py-h5py dependency for v2.7 * Add TODO entries for tensorflow-io-gcs-filesystem * Edit some comments * Add phases and select python in PATH for tensorboard-data-server * py-libclang - remove py-wheel dependency - remove raw string notation in filter_file * py-tensorboard-data-server - remove py-wheel dep - remove py-pip dep - use python from package class * py-tensorboard-plugin-wit - switch to PythonPackage - add version 1.8.1 - remove unneeded code * Add comment as to why a wheel is need for tensorboard-plugin-wit * remove which pip from tensorboard-data-server * Fix dependency specs in tensorboard * tweak dependencies for tensorflow * fix python constraint * Use llvm libs property * py-tensorboard-data-server - merge build into install - use std_pip_args * remove py-clang dependency * remove my edits to py-tensorboard-plugin-wit Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-18spack external find: change default behavior (#29031)Massimiliano Culpo23-8/+63
See https://github.com/spack/spack/issues/25353#issuecomment-1041868116 This commit changes the default behavior of ``` $ spack external find ``` from searching all the possible packages Spack knows about to search only for the ones tagged as being a "build-tool". It also introduces a `--all` option to restore the old behavior.
2022-02-18libbson, mongo-c-driver: add 1.21.0 (#28978)Michael Kuhn2-0/+3
2022-02-18curl: add v7.81.0 (#28973)Michael Kuhn1-0/+1
2022-02-18spfft: add version 1.0.6 (#29047)Simon Frasch1-0/+3
2022-02-18py-fasteners: add 0.17.3 (#28988)Manuela Kuhn1-4/+7
2022-02-18util-linux(-uuid): add v2.37.4 (#28985)Michael Kuhn2-0/+2
2022-02-18mariadb-c-client: add v3.2.6 (#28981)Michael Kuhn1-0/+1
2022-02-18sqlite: add v3.37.2 (#28984)Michael Kuhn1-1/+4
2022-02-17pcre: add v8.45 (#28979)Michael Kuhn1-0/+1
2022-02-17pcre2: add v10.39 (#28980)Michael Kuhn1-1/+2
2022-02-17rdma-core: add v39.0 (#28987)Michael Kuhn1-0/+1
2022-02-17darwin: robust macos version detection (#28991)Seth R. Johnson2-7/+49
Prefer `sw_vers` to `platform.mac_ver`. In anaconda3 installation, for example, the latter reports 10.16 on Monterey -- I think this is affected by how and where the python instance was built. Use MACOSX_DEPLOYMENT_TARGET if present to override the operating system choice.
2022-02-17abinit: Add version 9.6.1 and support fujitsu compiler and fujitsu-fftw. ↵Toyohisa Kameyama3-14/+636
(#28474) * abinit: Add version 9.6.1 and support fujitsu compiler and fujitsu-fftw. * fix conflicts +openmp. * Add openmp conflicts.
2022-02-17py-charset-normalizer: add 2.0.12 (#28945)Manuela Kuhn1-0/+1
2022-02-17py-fiscalyear: add v0.4.0 (#29025)Adam J. Stewart1-0/+3
2022-02-17py-fonttools: add 4.29.1 and fix tests (#29032)Manuela Kuhn1-0/+10
2022-02-17py-gevent: add 21.12.0 (#29033)Manuela Kuhn1-0/+1
2022-02-17gitlab: Propagate stack name to downstream build jobs (#29019)Scott Wittenburg1-0/+4
It will be useful for metrics gathering and possibly debugging to have this environment variable available in the runner pods that do the actual rebuilds.
2022-02-17llvm: add libs property (#28621)Glenn Johnson1-2/+8
* llvm: add libs property * Use llvm-config helper for libs property
2022-02-17Testing: optionally run tests on externally installed packages (#28701)Tamara Dahlgren6-9/+65
Since Spack does not install external packages, this commit skips them by default when running stand-alone tests. The assumption is that such packages have likely undergone an acceptance test process. However, the tests can be run against installed externals using ``` % spack test run --externals ... ```
2022-02-17zstd: add v1.5.2 (#28986)Michael Kuhn1-0/+1
2022-02-17Reduce verbosity of patches=... variant (#29015)Harmen Stoppels1-2/+19
* reduce verbosity of patches=... variant * Special-case prefix-matches for satisfies of patches variant
2022-02-17ASP-based solver: don't sort when defining variant possible values (#29013)Massimiliano Culpo1-2/+3
fixes #28260 Since we iterate over different variants from many packages, the variant values may have types which are not comparable, which causes errors at runtime. This is not a real issue though, since we don't need the facts to be ordered. Thus, to avoid needless sorting, the sorted function has been removed and a comment has been added to tip any developer that might need to inspect these clauses for debugging to add back sorting on the first two items only. It's kind of difficult to add a test for this, since the error depends on whether Python sorting algorithm ever needs to compare the third value of a tuple being ordered.
2022-02-17binutils: add external detection (#29022)Tom Scogland1-0/+9
2022-02-16libmd: add v1.0.4 (#28971)Michael Kuhn1-0/+1
2022-02-16libbsd: add v0.11.5 (#28969)Michael Kuhn1-0/+1
2022-02-16extensions: allow multiple "extends" directives (#28853)Tom Scogland2-5/+28
* extensions: allow multiple "extends" directives This will allow multiple extends directives in a package as long as only one of them is selected as a dependency in the concrete spec. * document the option to have multiple extends
2022-02-16libffi: add v3.4.2 (#28970)Michael Kuhn1-4/+5
2022-02-16intel-gtpin: new package (#28542)Mark W. Krentel1-0/+77
2022-02-16concretizer: refactor argument passing for reuseTodd Gamblin6-107/+106
Reuse previously was a very invasive change that required parameters to be added to all the methods that called `concretize()` on a `Spec` object. With the addition of concretizer configuration, we can use the config system to simplify this argument passing and keep the code cleaner. We decided that concretizer config options should be read at `Solver` instantiation time, and if config changes between instnatiation of a particular solver and `solve()` invocation, the `Solver` should use the settings from `__init__()`. - [x] remove `reuse` keyword argument from most concretize functions - [x] refactor usages to use `spack.config.override("concretizer:reuse", True)` - [x] rework argument passing in `Solver` so that parameters are set from config at instantiation time
2022-02-16docs: add section on concretizer configurationTodd Gamblin5-13/+59
* Document `concretizer.yaml`, `--reuse`, and `--fresh`.
2022-02-16commands: refactor `--reuse` handling to use configTodd Gamblin12-40/+140
`--reuse` was previously handled individually by each command that needed it. We are growing more concretization options, and they'll need their own section for commands that support them. Now there are two concretization options: * `--reuse`: Attempt to reuse packages from installs and buildcaches. * `--fresh`: Opposite of reuse -- traditional spack install. To handle thes, this PR adds a `ConfigSetAction` for `argparse`, so that you can write argparse code like this: ``` subgroup.add_argument( '--reuse', action=ConfigSetAction, dest="concretizer:reuse", const=True, default=None, help='reuse installed dependencies/buildcaches when possible' ) ``` With this, you don't need to add logic to pull the argument out and handle it; the `ConfigSetAction` just does it for you. This can probably be used to clean up some other commands later, as well. Code that was previously passing `reuse=True` around everywhere has been refactored to use config, and config is set from the CLI using a new `add_concretizer_args()` function in `spack.cmd.common.arguments`. - [x] Add `ConfigSetAction` to simplify concretizer config on the CLI - [x] Refactor code so that it does not pass `reuse=True` to every function. - [x] Refactor commands to use `add_concretizer_args()` and to pass concretizer config using the config system.
2022-02-16tests: consolidate mock scope creation logic in `conftest.py`Todd Gamblin2-22/+18
Config scopes were different for `config` and `mutable_config`, and `mutable_config` did not have a command line scope. - [x] Fix by consolidating the creation logic for the two fixtures.
2022-02-16config: add a new `concretizer` config sectionTodd Gamblin5-6/+65
The concretizer is going to grow to have many more configuration, and we really need some structured config for that. * We have the `config:concretizer` option that chooses the solver, but extending that is awkward (we'd need to replace a string with a `dict`) and the solver choice will be deprecated eventually. * We have the `concretization` option in environments, but it's not a top-level config section -- it's just for environments, and it also only admits a string right now. To avoid overlapping with either of these and to allow the most extensibility in the future, this adds a new `concretizer` config section that can be used in and outside of environments. There is only one option right now: `reuse`. This can expand to include other options later. Likely, we will soon deprecate `config:concretizer` and warn when the user doesn't use `clingo`, and we will eventually (sometime later) move the `together` / `separately` options from `concretization` into the top-level `concretizer` section. This commit just adds the new section and schema. Fully wiring it up is TBD.
2022-02-16refactor: convert spack.solver.asp.solve() to a classTodd Gamblin4-46/+95
The solver has a lot of configuration associated with it. Rather than adding arguments to everything, we should encapsulate that in a class. This is the start of that work; it replaces `solve()` and its kwargs with a class and properties.
2022-02-16Add 'stable' to the list of infinity version names. (#28772)Mark W. Krentel3-7/+8
* Add 'stable' to the list of infinity version names. Rename libunwind 1.5-head to 1.5-stable. * Add stable to the infinite version list in packaging_guide.rst.
2022-02-16py-etelemetry: add 0.3.0 (#28983)Manuela Kuhn1-0/+2
* py-etelemetry: add 0.3.0 * Update var/spack/repos/builtin/packages/py-etelemetry/package.py Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-16py-filelock: add 3.5.0 (#29006)Manuela Kuhn1-1/+6
2022-02-16py-tomli-w: add new package (#29007)Manuela Kuhn1-0/+18
2022-02-16py-build: python+ensurepip not required (#28562)Adam J. Stewart2-1/+15
* py-build: python+ensurepip not required * Add patch to fix issue when pip is in PYTHONPATH
2022-02-16mesa: enable the `swr` variant if +llvm, instead of using conflicts (#29008)Massimiliano Culpo2-4/+2
* mesa: enable the `swr` variant if +llvm, instead of using conflicts fixes #28994
2022-02-16find_libraries: search for both .so and .dylib on macOS (#28924)Adam J. Stewart1-4/+10
2022-02-16Trilinos: Add UVM variant (#28949)psakievich1-3/+6
13.2+ still supports UVM as an option.