Commit graph

27657 commits

Author SHA1 Message Date
kwryankrattiger
117b0af831
Backport fix for buliding vtk-m diy with GCC 11 (#32465) 2022-09-01 11:41:20 -07:00
Peter Scheibel
2968ae667f
New command, spack change, to change existing env specs (#31995)
If you have an environment like

```
$ cat spack.yaml
spack:
  specs: [openmpi@4.1.0+cuda]
```

this PR provides a new command `spack change` that you can use to adjust environment specs from the command line:

```
$ spack change openmpi~cuda
$ cat spack.yaml
spack:
  specs: [openmpi@4.1.0~cuda]
```

in other words, this allows you to tweak the details of environment specs from the command line.

Notes:

* This is only allowed for environments that do not define matrices
  * This is possible but not anticipated to be needed immediately
  * If this were done, it should probably only be done for "named"/not-anonymous specs (i.e. we can change `openmpi+cuda` but not spec like `+cuda` or `@4.0.1~cuda`)
2022-09-01 11:04:01 -07:00
Graeme A Stewart
92b72f186e
root: apply 6.26 COMPILE_DEFINITIONS patch unconditionally (#32472)
This bug isn't per-se tied to the root7 variant and should
be applied always for these ROOT releases
2022-09-01 17:57:50 +02:00
Weiqun Zhang
3d67c58436
amrex: add v22.09 (#32477) 2022-09-01 09:45:49 -06:00
Massimiliano Culpo
01298287f6
Fix CI for package only PRs (#32473) 2022-09-01 14:41:28 +02:00
Jordan Ogas
9dca54fdc8
use bash for autoreconf (#32466) 2022-09-01 02:29:58 -06:00
Massimiliano Culpo
0df0b9a505
Port package sanity unit tests to audits (#32405) 2022-09-01 08:21:12 +02:00
Michael Kuhn
c4647a9c1f
meson: add 0.63.1 (#32441) 2022-08-31 20:45:52 -06:00
marcost2
597af9210f
perl-bignum: Adding perl module (#31590) 2022-08-31 21:07:41 -05:00
Adam J. Stewart
986e8fd6c5
py-black: add v22.8.0 (#32468) 2022-08-31 19:53:46 -06:00
Wouter Deconinck
c75c27c95c
gdk-pixbuf: only build tests when requested (#32452)
The building of tests is optional [as of 2.42.9](801eef111d). This applies this option in the build.

The reason the option was added was to deal with test build failures in sandboxed environments and with certain glibc versions (caused by glib gresources). For example, with the latest version glibc and in the latest version of docker these tests [cannot be built](https://github.com/moby/moby/issues/43595).
2022-08-31 16:16:22 -07:00
Adam J. Stewart
f1f831edef
py-pandas: add v1.4.4 (#32459) 2022-08-31 14:27:15 -07:00
Satish Balay
60f37e8c88
llvm: fix 15.0.0rc builds on MacOS with command-line-tools (#32397)
* llvm: fix 15.0.0rc builds on MacOS with command-line-tools

Ref: https://github.com/llvm/llvm-project/issues/57037

i.e use -DBUILTINS_CMAKE_ARGS=-DCOMPILER_RT_ENABLE_IOS=OFF. But this needs switching "compiler-rt" from "projects" to "runtimes".

Also fixing the warnings below fixes compile errors

CMake Warning at CMakeLists.txt:101 (message):
  Using LLVM_ENABLE_PROJECTS=libcxx is deprecated now, please use
  -DLLVM_ENABLE_RUNTIMES=libcxx or see the instructions at
  https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes.


CMake Warning at CMakeLists.txt:101 (message):
  Using LLVM_ENABLE_PROJECTS=libcxxabi is deprecated now, please use
  -DLLVM_ENABLE_RUNTIMES=libcxxabi or see the instructions at
  https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes.


CMake Warning at CMakeLists.txt:101 (message):
  Using LLVM_ENABLE_PROJECTS=libunwind is deprecated now, please use
  -DLLVM_ENABLE_RUNTIMES=libunwind or see the instructions at
  https://libcxx.llvm.org/BuildingLibcxx.html for building the runtimes.


/private/var/folders/nt/_m1t_x7j76q6sl3xt91tqgs00000gn/T/balay/spack-stage/spack-stage-llvm-15.0.0-rc2-h2t5bohzyy7exz2ub3m42pfycjcmbndk/spack-build-h2t5boh/include/c++/v1/cstdlib:135:9: error: no member named 'at_quick_exit' in the global namespace
using ::at_quick_exit _LIBCPP_USING_IF_EXISTS;
      ~~^

* Update var/spack/repos/builtin/packages/llvm/package.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-31 13:29:07 -07:00
Massimiliano Culpo
0c6e3188ac
ASP-based solver: allow to reuse installed externals (#31558)
fixes #31484

Before this change if anything was matching an external
condition, it was considered "external" and thus something
to be "built".

This was happening in particular to external packages
that were re-read from the DB, which then couldn't be
reused, causing the problems shown in #31484.

This PR fixes the issue by excluding specs with a
"hash" from being considered "external"

* Test that users have a way to select a virtual

This ought to be solved by extending the "require"
attribute to virtual packages, so that one can:
```yaml
mpi:
  require: 'multi-provider-mpi'
```

* Prevent conflicts to be enforced on specs that can be reused.

* Rename the "external_only" fact to "buildable_false", to better reflect its origin
2022-08-31 20:05:55 +00:00
Seth R. Johnson
08261af4ab
py-breathe: add new version and improve version constraints (#31857)
* py-breathe: add new version and improve version constraints

* py-breathe: everyone loves versions

```
py-breathe, py-breathe in the air
don't be afraid to care
````

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

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

* add comment

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-08-31 17:23:19 +00:00
Larry Knox
62e4177e44
hdf5-vol-log: Update package versions and update HDF5 dependency to version 1.13.2 (#32448)
* Add HDF5 version 1.13.2.
Remove HDF5 versions 1.13.0 and 1.13.1.

* Correct formatting.

* Update vol-log-based versions and HDF5 dependency version.
2022-08-31 06:29:15 -07:00
Ivan Maidanski
74506a2a83
bdw-gc: add v8.2.2 (#32453) 2022-08-31 06:18:49 -07:00
Adam J. Stewart
5fcfce18fd
py-gpytorch: add v1.9.0 (#32445) 2022-08-30 11:34:06 -07:00
Adam J. Stewart
c07c4629ff
py-kornia: add v0.6.7 (#32447) 2022-08-30 11:33:49 -07:00
Tamara Dahlgren
3894ceebc9
Environments: Add support for include URLs (#29026)
* Preliminary support for include URLs in spack.yaml (environment) files

This commit adds support in environments for external configuration files obtained from a URL with a preference for grabbing raw text from GitHub and gitlab for efficient downloads of the relevant files. The URL can also be a link to a directory that contains multiple configuration files.

Remote configuration files are retrieved and cached for the environment. Configuration files with the same name will not be overwritten once cached.
2022-08-30 11:13:23 -07:00
Ryan Marcellino
b35a0b1b40
New package: py-mkdocstrings-python (#32421) 2022-08-30 10:27:02 -07:00
Gregory Lee
543a797d1a
added STAT 4.2.0 and updated deps (#32385)
* added STAT 4.2.0 and updated deps

* launchmon package fix and style fixes

* launchmon package fix

* Update var/spack/repos/builtin/packages/launchmon/package.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-30 09:25:55 -06:00
Ivan Maidanski
08c67302fc
libatomic_ops: add v7.6.14 (#32418)
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-30 06:00:09 -07:00
Harmen Stoppels
33cb61afb9
libxml2: fix building with nvhpc (#32440) 2022-08-30 06:13:47 -06:00
Wouter Deconinck
43ae15a887
root: new bugfix version 6.26.06 (#32230) 2022-08-30 10:31:17 +02:00
Toyohisa Kameyama
a735dc027d
oprnmx: fix to build with Fujitsu compiler. (#32389) 2022-08-30 10:26:15 +02:00
Olivier Cessenat
5be9f4dfef
coreutils: add support for external find (#32414) 2022-08-30 02:26:02 -06:00
David M. Rogers
d75234b675
hipsycl: fix building on OSX. Patch boost to be backward-compatible. (#31311)
Co-authored-by: frobnitzem <frobnitzem@users.noreply.github.com>
2022-08-30 10:22:34 +02:00
luker
3779e645b8
scorep: modify configure flags for Cray platforms (#32201) 2022-08-30 00:25:35 -07:00
Olivier Cessenat
7f4799a4a2
visit: actually set the dev env for plugins again (#32427) 2022-08-30 08:02:23 +02:00
Jim Edwards
a09d4ffb4e
esmf: update package for cce (cray) compiler (#32433) 2022-08-30 07:53:45 +02:00
robgics
0c9b4bc3d2
Initial commit for freesurfer package (#32395)
* Initial commit for freesurfer package

* Add myself as maintainer

* Change URLs to https and move url function to proper place.
2022-08-29 14:35:34 -07:00
snehring
778af070f0
snphylo: update to new version (#32425) 2022-08-29 11:56:57 -07:00
Brian Van Essen
bd815fbada
Switched LBANN to using an explicit variant to enable unit testing (#32429)
support rather than relying on the spack install --test root option,
because it doesn't play nice in environments.
2022-08-29 12:53:45 -06:00
Luca Heltai
1c22af8ef4
dealii:: fixed application of stdcxx variant (#32413)
* Fixed imposition of stdcxx.

* Fixed style.
2022-08-29 08:41:17 -07:00
Seth R. Johnson
9687d91d72
celeritas: new version 0.1.1 (#32412) 2022-08-29 08:34:16 -07:00
Wouter Deconinck
a14d228e8b
gdk-pixbuf: new bugfix version 2.42.9 (#32420)
No changes of note. Just bugfixes. Full diff at https://gitlab.gnome.org/GNOME/gdk-pixbuf/-/compare/2.42.6...2.42.9?from_project_id=1548
2022-08-29 07:48:48 -07:00
Ryan Marcellino
b64d2393ea
New package: py-mkdocstrings (#32417) 2022-08-28 14:34:02 -07:00
Ryan Marcellino
d0173a486f
New package: py-mkdocs-jupyter (#32416) 2022-08-28 14:32:50 -07:00
Sergey Kosukhin
215379cc27
libxml2: add new versions (#32394)
* libxml2: add new versions

* libxml2: apply patch preventing SIGFPE
2022-08-27 02:29:49 -06:00
Adam J. Stewart
a7cc58d42c
py-radiant-mlhub: add v0.5 (#32406) 2022-08-26 18:02:02 -06:00
downloadico
430b8ca362
add sra-tools and NCBI-VDT packages (#32403)
* ncbi-vdb: add ncbi-vdb package to spack
ncbi-vdb provides the interface to the NCBI VDB

* sra-tools: add sra-tools to spack
2022-08-26 17:38:27 -06:00
Richard Berger
e6f6de406d
py-sphinx-rtd-theme: add version 1.0.0 (#32379) 2022-08-26 17:38:14 -06:00
Betsy McPhail
ad95719a1d
Use threading.TIMEOUT_MAX when available (#32399)
This value was introduced in Python 3.2. Specifying a timeout greater than
this value will raise an OverflowError.
2022-08-26 17:37:56 -06:00
Jen Herting
59bfa6bcd3
[py-pybedtools] added version 0.9.0 (#32401) 2022-08-26 21:44:53 +00:00
dlkuehn
c7acda0062
New packages: roary plus 5 new perl-* (#32217)
* New package: roary
2022-08-26 14:29:44 -06:00
Massimiliano Culpo
51244abee9
Configuration: Allow requirements for virtual packages (#32369)
Extend the semantics of package requirements to
allow using them also under a virtual package
attribute in packages.yaml

These requirements are enforced whenever that
virtual spec is present in the DAG.
2022-08-26 13:17:40 -07:00
kwryankrattiger
eb1c9c1583
SDK: Option to disable fortran support. (#32319)
This option was requested to support MacOS systems that do not have
fortran installed.
2022-08-26 11:12:13 -07:00
Ryan Marcellino
c227e7ab13
New package: py-mkdocs-material (#32387) 2022-08-26 10:32:03 -07:00
Ryan Marcellino
987c067f68
New package: py-mkdocs-autorefs (#32386) 2022-08-26 10:30:28 -07:00