Commit graph

27935 commits

Author SHA1 Message Date
Seth R. Johnson
e19f29da66
silo package: fix patch for 4.11-bsd (#29075)
There's a check to skip for version '10.2-bsd', but the patch
does not apply to '11-bsd' either.
2022-02-19 07:26:32 -07:00
Harmen Stoppels
39fcafaf45
binutils: add v2.38 (#29067) 2022-02-19 06:02:34 -07:00
downloadico
22d07b328e
New package: ovito (#28787) 2022-02-19 05:05:11 -07:00
Manuela Kuhn
f37855f5bb
py-ipykernel: add 6.9.1 (#29071)
* py-ipykernel: add 6.9.1

* Add py-jupyter-core version restriction
2022-02-18 22:54:07 -07:00
Seth R. Johnson
f33770553f
Add/remove conflicts for Apple silicon (M1/aarch64) (#28850)
* 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
2022-02-18 21:56:32 -07:00
Manuela Kuhn
e886a61a6c
r-distributional package: add version 0.3.0 (#29037) 2022-02-18 18:38:19 -08:00
eugeneswalker
bbb81d5d68
kokkos@:3.5.00 +sycl conflicts with %dpcpp@2022.0.0 (#29055) 2022-02-18 14:33:59 -08:00
Manuela Kuhn
99707beae7
py-humanize: add 4.0.0 (#29034) 2022-02-18 16:28:28 -06:00
Glenn Johnson
be53b5db96
py-tensorflow-estimator: new versions (#28093)
* py-tensorflow-estimator: new versions

* Set proper constraint on py-funcsigs

Only needed when the python version is less than 3.3.
2022-02-18 14:19:05 -06:00
Andrew W Elble
45f3b2fc52
py-keras: new versions (#27991)
* 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
2022-02-18 14:18:11 -06:00
Glenn Johnson
e5f6914bd2
py-tensorflow: add versions 2.5.0 and 2.6.0 (#27138)
* 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>
2022-02-18 14:10:00 -06:00
Massimiliano Culpo
7fd94fc4bc
spack external find: change default behavior (#29031)
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.
2022-02-18 11:51:01 -07:00
Michael Kuhn
2ed52d32c7
libbson, mongo-c-driver: add 1.21.0 (#28978) 2022-02-18 07:08:48 -07:00
Michael Kuhn
31e538795e
curl: add v7.81.0 (#28973) 2022-02-18 03:59:52 -07:00
Simon Frasch
0ad3319243
spfft: add version 1.0.6 (#29047) 2022-02-18 10:58:52 +01:00
Manuela Kuhn
4efd47d0c3
py-fasteners: add 0.17.3 (#28988) 2022-02-18 02:57:04 -07:00
Michael Kuhn
43016d0ff4
util-linux(-uuid): add v2.37.4 (#28985) 2022-02-18 02:08:48 -07:00
Michael Kuhn
5796de8bcb
mariadb-c-client: add v3.2.6 (#28981) 2022-02-18 01:08:58 -07:00
Michael Kuhn
60e9af6e0f
sqlite: add v3.37.2 (#28984) 2022-02-18 00:23:57 -07:00
Michael Kuhn
ae84ce535b
pcre: add v8.45 (#28979) 2022-02-17 23:03:38 -07:00
Michael Kuhn
5bdc72e2ed
pcre2: add v10.39 (#28980) 2022-02-17 22:53:47 -07:00
Michael Kuhn
7a1364fcb2
rdma-core: add v39.0 (#28987) 2022-02-17 22:44:52 -07:00
Seth R. Johnson
6c61c2695a
darwin: robust macos version detection (#28991)
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.
2022-02-17 20:50:41 -07:00
Toyohisa Kameyama
b768fb85c6
abinit: Add version 9.6.1 and support fujitsu compiler and fujitsu-fftw. (#28474)
* abinit: Add version 9.6.1 and support fujitsu compiler and fujitsu-fftw.
* fix conflicts +openmp.
* Add openmp conflicts.
2022-02-17 15:42:49 -08:00
Manuela Kuhn
b3f5f55f95
py-charset-normalizer: add 2.0.12 (#28945) 2022-02-17 15:44:38 -07:00
Adam J. Stewart
00f0d11b8f
py-fiscalyear: add v0.4.0 (#29025) 2022-02-17 22:10:47 +01:00
Manuela Kuhn
e6142e8183
py-fonttools: add 4.29.1 and fix tests (#29032) 2022-02-17 15:06:57 -06:00
Manuela Kuhn
98fa2c6f10
py-gevent: add 21.12.0 (#29033) 2022-02-17 15:05:47 -06:00
Scott Wittenburg
38643dcd7e
gitlab: Propagate stack name to downstream build jobs (#29019)
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.
2022-02-17 15:36:48 -05:00
Glenn Johnson
e7e6a16064
llvm: add libs property (#28621)
* llvm: add libs property

* Use llvm-config helper for libs property
2022-02-17 13:52:49 -06:00
Tamara Dahlgren
fefe65a35b
Testing: optionally run tests on externally installed packages (#28701)
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 ...
```
2022-02-17 19:47:42 +01:00
Michael Kuhn
4d669bfdf4
zstd: add v1.5.2 (#28986) 2022-02-17 07:05:23 -07:00
Harmen Stoppels
d93f9b82ac
Reduce verbosity of patches=... variant (#29015)
* reduce verbosity of patches=... variant

* Special-case prefix-matches for satisfies of patches variant
2022-02-17 11:06:32 +01:00
Massimiliano Culpo
fa132614e0
ASP-based solver: don't sort when defining variant possible values (#29013)
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.
2022-02-17 08:50:50 +01:00
Tom Scogland
a0bd6c8817
binutils: add external detection (#29022) 2022-02-17 08:45:24 +01:00
Michael Kuhn
dcdf5022ad
libmd: add v1.0.4 (#28971) 2022-02-16 19:50:38 -07:00
Michael Kuhn
b021cf39aa
libbsd: add v0.11.5 (#28969) 2022-02-16 19:50:15 -07:00
Tom Scogland
8f5fcc6e95
extensions: allow multiple "extends" directives (#28853)
* 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
2022-02-16 21:23:12 +00:00
Michael Kuhn
e8c5f195a7
libffi: add v3.4.2 (#28970) 2022-02-16 13:41:29 -07:00
Mark W. Krentel
36020d69d7
intel-gtpin: new package (#28542) 2022-02-16 18:22:26 +00:00
Todd Gamblin
b1ff9c05bc concretizer: refactor argument passing for reuse
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
2022-02-16 10:17:18 -08:00
Todd Gamblin
d33973df6c docs: add section on concretizer configuration
* Document `concretizer.yaml`, `--reuse`, and `--fresh`.
2022-02-16 10:17:18 -08:00
Todd Gamblin
a2b8e0c3e9 commands: refactor --reuse handling to use config
`--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.
2022-02-16 10:17:18 -08:00
Todd Gamblin
f155de7462 tests: consolidate mock scope creation logic in conftest.py
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.
2022-02-16 10:17:18 -08:00
Todd Gamblin
800ed16e7a config: add a new concretizer config section
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.
2022-02-16 10:17:18 -08:00
Todd Gamblin
1903e45eec refactor: convert spack.solver.asp.solve() to a class
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.
2022-02-16 10:17:18 -08:00
Mark W. Krentel
87a3b72ef0
Add 'stable' to the list of infinity version names. (#28772)
* 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.
2022-02-16 09:08:51 -08:00
Manuela Kuhn
884da5e326
py-etelemetry: add 0.3.0 (#28983)
* 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>
2022-02-16 10:22:38 -06:00
Manuela Kuhn
9fc9386944
py-filelock: add 3.5.0 (#29006) 2022-02-16 10:22:16 -06:00
Manuela Kuhn
e84a2db23d
py-tomli-w: add new package (#29007) 2022-02-16 10:21:09 -06:00