Commit graph

30754 commits

Author SHA1 Message Date
Brian Vanderwende
381f1b76a7
Add RPC lib path to wrapper flags for HDF4 (#35628) 2023-04-20 08:49:04 -07:00
Massimiliano Culpo
1b7cf171ce
Use core API to create a Makefile during bootstrapping (#37023) 2023-04-20 15:11:56 +02:00
Adam J. Stewart
01913d08e7
google-cloud-cli: add new package (#36830)
* google-cloud-cli: add new package

* black fixes

* Less verbose

* [@spackbot] updating style on behalf of adamjstewart

* More robust if ver doesn't exist for platform

* Deprecate ancient GEE

* Fix ppc64le bug

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-04-19 16:12:03 -07:00
Adam J. Stewart
d5fa062e4a
py-einops: add v0.6.1 (#37027) 2023-04-19 15:23:19 -07:00
Erik Schnetter
b164c03b09
coreutils: New version 9.3 (#37021) 2023-04-19 14:18:34 -07:00
Harmen Stoppels
d51af675ef
make version(...) kwargs explicit (#36998)
- [x] Replace `version(ver, checksum=None, **kwargs)` signature with
      `version(ver, checksum=None, *, sha256=..., ...)` explicitly listing all arguments.
- [x] Fix various issues in packages:
  - `tags` instead of `tag`
  - `default` instead of `preferred`
  - `sha26` instead of `sha256`
  - etc

Also, use `sha256=...` consistently.

Note: setting `sha256` currently doesn't validate the checksum length, so you could do
`sha256="a"*32` and it would get checked as `md5`... but that's something for another PR.
2023-04-19 14:17:47 -07:00
Wouter Deconinck
c7508dc216
py-torch: define property cmake_prefix_paths (#37012)
* py-torch: define property cmake_prefix_paths

`py-torch` installs `libtorch` and a cmake config in a non-standard location. This points downstream code to the relevant locations. From there it should pick up the correctly library and include paths for C++ projects.

* py-torch: python_platlib suggestion

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

* [@spackbot] updating style on behalf of wdconinc

* py-torch: back to self.spec["python"].package.platlib

* [@spackbot] updating style on behalf of wdconinc

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-04-19 17:12:45 -04:00
Veselin Dobrev
6ca41cfbcb
Add mfem v4.5.2 and related updates/tweaks in other packages (#36154)
* Add mfem v4.5.2 and related updates/tweaks in other packages

* [mfem] Add the release source link for MFEM v4.5.2

* [mfem] Remove 'goxberry' (his request) from MFEM's maintainers list
2023-04-19 05:55:31 -07:00
Harmen Stoppels
ae909b3688
Extract depfile logic from cli command into a core module (#36995) 2023-04-19 14:36:29 +02:00
Alec Scott
3a5e48f476
installer.py: drop build edges of installed packages by default (#36707)
This means that `spack install` will now build the minimal set of packages
required to install the root(s).

To opt out of build edge pruning, use `spack install --include-build-deps`.

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-04-19 10:00:40 +02:00
Alec Scott
899838b325
apachetop: add v0.23.2 (#37017) 2023-04-19 09:48:52 +02:00
Alec Scott
001bf93ea3
r-rcpptoml: add v0.2.2 (#36886) 2023-04-19 02:07:40 -04:00
Todd Gamblin
b260234faf editing: add higher-precedence SPACK_EDITOR environment variable
Other tools like git support `GIT_EDITOR` which takes higher precedence than the
standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the
`SPACK_EDITOR` env var.

- [x] consolidate editor code from hooks into `spack.util.editor`
- [x] add more editor tests
- [x] add support for `SPACK_EDITOR`
- [x] add a documentation section for controlling the editor and reference it
2023-04-18 16:23:00 -07:00
Todd Gamblin
2f30da1762 refactor: unify use of spack.util.editor
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We
really only want one place where editor search logic is implemented. This consolidates
the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`.

- [x] consolidate editor search logic in spack.util.editor
- [x] add tests for licensing case, where `Executable` is used instead of `os.execv`
- [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg
- [x] add type annotations
2023-04-18 16:23:00 -07:00
Massimiliano Culpo
d92c21ec97
Fix compilation on Cray (target: any) (#37011)
fixes #36628

Fix using compilers that declare "target: any" in their
configuration. This should happen only on Cray with the
module based programming environment.
2023-04-18 15:47:52 -07:00
Benjamin Meyers
5960d74dca
Update and fix py-dgl+cuda (#36823)
* Update and fix py-dgl+cuda

* [@spackbot] updating style on behalf of meyersbs

* Update py-dgl
2023-04-18 15:56:18 -05:00
Jonathon Anderson
c7232f4505
lammps: backport fix for +rocm+kokkos+kspace (#36850)
* lammps: backport hipfft fix for ROCm-based builds

* lammps: Mark incompatibility with Kokkos 4.x for old versions
2023-04-18 15:41:18 -05:00
Jonathon Anderson
08fd8c8d0a
spack ci: preserve custom attributes in build jobs (#36651)
* Simplify test/cmd/ci.py::test_ci_generate_with_custom_scripts

* Rearrange the build-job logic in generate_gitlab_ci_yaml

* Preserve all unknown attributes in build jobs

* Slip tests for custom attributes in the tests for other job types

* Support custom artifacts

* [@spackbot] updating style on behalf of blue42u

* Don't bother sorting needs

---------

Co-authored-by: blue42u <blue42u@users.noreply.github.com>
2023-04-18 15:40:43 -05:00
Alec Scott
eb72217228
r-httpuv: add v1.6.9 (#36951) 2023-04-18 15:12:13 -05:00
Alec Scott
945d032f08
r-git2r: add v0.31.0 (#36864) 2023-04-18 15:08:24 -05:00
Alec Scott
78bfeb11ae
r-highr: add v0.10 (#36867) 2023-04-18 15:06:24 -05:00
kwryankrattiger
9745865250
DaV SDK: Enable ParaView raytracing with in SDK (#36844)
* DaV SDK: Enable ParaView raytracing with in SDK

* CI: Drop swr testing from Data Vis SDK

* ISPC: extend LLVM requirement to main

* DaV SDK: Disallow concretizing develop unifyfs

No longer needed after mochi-margo patch
2023-04-18 13:39:47 -05:00
Benjamin Meyers
accbf2cffc
New packages: py-ogb, py-outdated, py-littleutils (#36824)
* New packages: py-ogb, py-outdated, py-littleutils

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

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

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2023-04-18 11:08:57 -05:00
Annop Wongwathanarat
5d8ca81e82
py-scipy: link with OpenMP version of armpl-gcc when requested (#37002) 2023-04-18 11:08:29 -05:00
Harmen Stoppels
11e5b0cd91
fix typo (#36997) 2023-04-18 08:07:57 -05:00
Todd Gamblin
6845f41d67
Revert addition of SPACK_EDITOR pending review.
This reverts commit d8a26905ee.
This reverts commit 1ee049ccc3.

These were spuriously pushed to `develop`.
2023-04-18 03:57:24 -07:00
Todd Gamblin
1ee049ccc3
editing: add higher-precedence SPACK_EDITOR environment variable
Other tools like git support `GIT_EDITOR` which takes higher precedence than the
standard `VISUAL` or `EDITOR` variables. This adds similar support for Spack, in the
`SPACK_EDITOR` env var.

- [x] consolidate editor code from hooks into `spack.util.editor`
- [x] add more editor tests
- [x] add support for `SPACK_EDITOR`
- [x] add a documentation section for controlling the editor and reference it
2023-04-18 03:42:56 -07:00
Todd Gamblin
d8a26905ee
refactor: unify use of spack.util.editor
Code from `spack.util.editor` was duplicated into our licensing hook in #11968. We
really only want one place where editor search logic is implemented. This consolidates
the logic into `spack.util.editor`, including a special case to run `gvim` with `-f`.

- [x] consolidate editor search logic in spack.util.editor
- [x] add tests for licensing case, where `Executable` is used instead of `os.execv`
- [x] make `_exec_func` argument of `editor()` into public `exec_fn` arg
- [x] add type annotations
2023-04-18 03:00:04 -07:00
Greg Becker
480b7f397e
Allow users to remove items from hierarchy per-path (#31351)
* lmod modules: allow users to remove items from hierarchy per-spec

This allows MPI wrappers that depend on MPI to be removed from the MPI portion of
the hierarchy and be made available when the appropriate compiler is loaded.

module load gcc
module load mpi-wrapper  # implicitly loads mpi
module load hdf5

This allows users to treat an mpi wrapper like an mpi program
2023-04-17 22:17:11 -07:00
Wouter Deconinck
2bc1779a71
py-html5lib, madgraph5amc: correct hashes of empty files (#36979)
* py-html5lib: correct hashes of empty files

Going through and fixing hashes that are due to empty string.
```console
$ grep -Ir $(echo -n | sha256sum | awk '{print$1}') $SPACK_ROOT/var/spack/repos/builtin
/home/wdconinc/git/spack/var/spack/repos/builtin/packages/madgraph5amc/package.py:        sha256="e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855",
/home/wdconinc/git/spack/var/spack/repos/builtin/packages/py-html5lib/package.py:    version("0.99", sha256="e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855")
```

```console
$ spack checksum py-html5lib 0.99
==> Found 1 version of py-html5lib:
  
  0.99  https://files.pythonhosted.org/packages/source/h/html5lib/html5lib-0.99.tar.gz

==> Fetching https://files.pythonhosted.org/packages/source/h/html5lib/html5lib-0.99.tar.gz

    version("0.99", sha256="aff6fd3031c563883197e5a04b7df324086ff5f358278a0386808c463a077e59")
```

* madgraph5: remove incorrectly hashed version
2023-04-17 23:14:10 -04:00
Wouter Deconinck
9ea7937f6d
qt: new version 5.15.9 (#36709)
This adds the new LTS version of Qt5. No build system changes needed.

The bundled libjpeg and sqlite versions were updated, but it is unclear if these are actual build requirements, and we have not been tracking these specific versions in the version dependencies (likely due to exactly this lack of clarity).

Compare: https://github.com/qt/qtbase/compare/v5.15.8-lts-lgpl...v5.15.9-lts-lgpl
2023-04-17 15:06:44 -04:00
Harmen Stoppels
381c0af988
Revert "move depfile logic into its own module, separate traversal logic from model (#36911)" (#36985)
This reverts commit a676f706a8.
2023-04-17 20:58:38 +02:00
Paul Kuberry
4519b42214
xyce: patch issue affecting MPICH (#36826) 2023-04-17 10:19:08 -07:00
Rémi Lacroix
8e50c08b3f
Add NetCDF95 package. (#36959)
* Add NetCDF95 package.
  NetCDF95 is an alternative Fortran interface to the NetCDF library which uses Fortran   2003 features.
* [@spackbot] updating style on behalf of RemiLacroix-IDRIS

---------

Co-authored-by: RemiLacroix-IDRIS <RemiLacroix-IDRIS@users.noreply.github.com>
2023-04-17 10:02:54 -07:00
Tim Haines
121ef695e3
Boost: add version 1.82.0 (#36924) 2023-04-17 18:35:45 +02:00
Sergey Kosukhin
275bfc15b4
netcdf-c: major refactoring, new variants and versions (#36485) 2023-04-17 17:59:10 +02:00
Adam J. Stewart
036695ac94
CI: update Linux images in ML pipelines (#36766)
Add missing openssl/curl/pkgconfig deps to py-tokenizers

Co-authored-by: Harmen Stoppels <harmenstoppels@gmail.com>
2023-04-17 17:42:03 +02:00
Alec Scott
19b55d6b27
r-rstantools: add v2.3.1 (#36890) 2023-04-17 08:53:06 -05:00
Alec Scott
993303f840
r-r-utils: add v2.12.2 (#36884) 2023-04-17 08:29:41 -05:00
Harmen Stoppels
a676f706a8
move depfile logic into its own module, separate traversal logic from model (#36911) 2023-04-17 15:27:01 +02:00
Alec Scott
2081ab8be1
cgl: add v0.60.7 (#36940) 2023-04-17 15:07:34 +02:00
Alec Scott
f2efec7fcc
masurca: add v4.1.0 (#36942) 2023-04-17 15:07:17 +02:00
Alec Scott
e7b549216c
spot: add v2.11.4 (#36943) 2023-04-17 15:06:56 +02:00
Alec Scott
426570fc3f
glab: add v1.28.0 (#36946) 2023-04-17 15:06:32 +02:00
Carlos Bederián
0e55055394
plumed: add 2.8.2, 2.7.6 and their supported gromacs combinations (#36929)
* plumed: Add 2.8.2, 2.7.6

* gromacs: add plumed 2.8.2 and 2.7.6 support
2023-04-17 15:05:31 +02:00
Alec Scott
1bbeb61668
slang: add v2.3.3 (#36952) 2023-04-17 15:04:57 +02:00
Alec Scott
376d87619b
transdecoder: add v5.7.0 (#36953) 2023-04-17 15:04:41 +02:00
Alec Scott
f82b4a68b8
Add "build" stage to many Go packages (#36795) 2023-04-17 15:03:09 +02:00
Adam J. Stewart
abb236e98a
py-lightly: py-torch+distributed required (#36955) 2023-04-17 15:02:13 +02:00
Adam J. Stewart
adf0ce6621
py-sphinx: add new versions (#36938) 2023-04-17 15:01:32 +02:00