Commit graph

25112 commits

Author SHA1 Message Date
Manuela Kuhn
8485474140
py-imageio: add 2.16.0 (#29066)
* py-imageio: add 2.16.0

* Update var/spack/repos/builtin/packages/py-imageio/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-02-21 16:41:28 -07:00
Glenn Johnson
51488dbff5
update bioconductor packages to bioconductor 3.14 (#28900) 2022-02-21 15:38:27 -07:00
Manuela Kuhn
1953d986ae
py-asttokens: add new package (#29073) 2022-02-21 14:47:28 -07:00
Manuela Kuhn
fef58db792
r-brobdingnag: add 1.2-7 (#28997) 2022-02-21 13:57:16 -06:00
Manuela Kuhn
36c64c8012
r-bh: add 1.78.0-0 (#28996) 2022-02-21 13:48:24 -06:00
Manuela Kuhn
8cd95b9f35
r-backports: add 1.4.1 (#28995) 2022-02-21 13:46:58 -06:00
Todd Gamblin
7912a8e90b
bugfix: Not all concrete versions on the CLI should be considered real (#28620)
Some "concrete" versions on the command line, e.g. `qt@5` are really
meant to satisfy some actual concrete version from a package. We should
only assume the user is introducing a new, unknown version on the CLI
if we, well, don't know of any version that satisfies the user's
request.  So, if we know about `5.11.1` and `5.11.3` and they ask for
`5.11.2`, we'd ask the solver to consider `5.11.2` as a solution.  If
they just ask for `5`, though, `5.11.1` or `5.11.3` are fine solutions,
as they satisfy `@5`, so use them.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-02-21 11:46:37 -08:00
Todd Gamblin
2210f84a91
py-numpy, py-scipy: add rgommers as a maintainer (#29109) 2022-02-21 12:41:27 -07:00
Alberto Invernizzi
b8d042273a
Bring back cuda@11.4.0 conflicts for GCC and clang; add 11.4.3:11.4.4 (#29076)
Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2022-02-21 20:28:56 +01:00
Christoph Junghans
9173fd7c61
votca: fix git url and allow build without xtp parts (#29056)
* votca: fix git url
* Votca: add xtp variant
2022-02-21 09:23:00 -08:00
Glenn Johnson
275608e2f2
update CRAN R packages (#28786) 2022-02-21 11:22:33 -06:00
Manuela Kuhn
f744640289
py-importlib-metadata: add 4.11.1 (#29069) 2022-02-21 09:23:32 -07:00
Manuela Kuhn
b9d26caab8
py-executing: add new package (#29074) 2022-02-21 08:56:42 -07:00
Manuela Kuhn
0dd5d493d5
py-pandas: fix tests (#29044) 2022-02-21 08:20:33 -07:00
Seth R. Johnson
e7894b4863
geant4: fix CMake-derived data path (#29091)
* geant4-data: use build+run-only depends

* geant4: point to dependent datadir

This is "used" in the configure step to set up the Geant4Config.cmake
file's persistent pointers to the data directory, but the dependency
is still listed as "run" -- though I'm not sure this is the right behavior
since the geant4 installation really does change as a function of the
data directory, and the installation is incomplete/erroneous
without using one.

* Style
2022-02-21 12:05:59 +00:00
Manuela Kuhn
94d75d0327
py-flit-core: add v3.6.0 (#29009) 2022-02-21 11:35:00 +01:00
Adam J. Stewart
96fceb6e38
py-liblas: add new package (#29027) 2022-02-21 11:23:07 +01:00
h-murai
fc8c3ada56
nwchem: add support for Fujitsu A64FX compilers on v7.0.2 (#28990) 2022-02-21 10:26:51 +01:00
Sebastian Pipping
60fe21ddd7
expat: add v2.4.6, deprecate v2.4.5 (#29100) 2022-02-21 10:24:47 +01:00
Erik Schnetter
0ffce33447
Add c-blosc v1.21.1, c-blosc2 v2.0.4 (#29101) 2022-02-21 10:16:24 +01:00
Seth R. Johnson
043794362a
iwyu: add 0.17 and improve llvm target requirements (#29077)
* iwyu: new version 0.17

* iwyu: allow default llvm target when x86/x86_64
2022-02-21 10:14:21 +01:00
Tom Scogland
f36a6f3fc0
neovim remote: add new package (#29103) 2022-02-21 10:11:57 +01:00
Tom Scogland
7995b7eac4
py-pynvim: add new package (#29102) 2022-02-21 10:11:30 +01:00
Seth R. Johnson
509f1cc00a
git: install keychain helper on macOS (#29090) 2022-02-21 10:09:49 +01:00
Seth R. Johnson
7459aa6c95
Various package fixes for macOS (#29024)
* trilinos: disable dl on macOS

* py-sphinx-argparse: add explicit poetry dependency

* libzmq: fix libbsd dependency

libbsd is *always* required when +libbsd (introduced in #28503) . #20893
had previously removed the macos dependency because libbsd wasn't always
enabled. Libbsd support is only available after 4.3.2 so change it to a
conflict rather than bumping the dependency.

* hdf5: work around GCC11.2 monterey fortran bug

* go-bootstrap: mark conflict for monterey
2022-02-21 09:08:08 +01:00
Olivier Cessenat
2852126196
perl-fth: add the external find feature for perl-fth and new release (#28886) 2022-02-20 23:20:27 -07:00
Sebastian Pipping
9e2d78cffc
expat: Add latest release 2.4.5 with security fixes (#29086) 2022-02-19 15:53:20 -07:00
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