Commit graph

27518 commits

Author SHA1 Message Date
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
Dom Heinzeller
26a16dc5bb
Add pic variant to bacio (#32388)
* Add pic variant to bacio

* Fix black style error
2022-08-26 09:24:34 -07:00
François Trahay
e41f9aad38
add eztrace 2.0 release (#32350)
* [EZTrace] Version uptate to 2.0

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

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-26 08:45:05 -07:00
Massimiliano Culpo
b6ea2a46d1
Update archspec to latest commit (#32368)
Modifications:

- [x] Add graviton3
- [x] Optimize __eq__ for microarchitectures
2022-08-26 12:58:20 +02:00
Tom Scogland
a2f0588004
calculate make_jobs in ninja (#32384)
This is in case ninja's setup_dependent_package is called before its
module is initialized by build_environment
2022-08-26 03:37:53 -06:00
Chris White
b31cd189a7
Improve error message for yaml config file (#32382)
* improve error message

* Update lib/spack/spack/config.py

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-26 02:43:03 +00:00
Wouter Deconinck
3ba58d85e2
libzmq: add patch for gcc-12; conflict for older gcc-11 versions (#32381)
Per #32214, the existing patch `92b2c...` for `gcc@11:` only applies
cleanly for `libzmq@4.3.3:4.3.4`. This PR adds a conflict for earlier
versions, as they cannot be patched due to different context.

For `gcc@11`, this leaves the most recent two versions available (a
satisfactory compromise).

For `gcc@12`, however, there is another existing conflict that makes
these most recent two versions unavailable. This PR adds an upstream
patch for the single most recent version that allows compilation with
`gcc@12` for that most recent version.

Starting point:
- `gcc@11` concretizes on all versions, attempts to apply patch on
`@4.2.3:4.3.4`, and only succeeds to apply patch on `@4.3.3:4.3.4`,
- `gcc@12` concretizes on `@:4.3.1` (and `@master`), attempts to apply
patch on `@4.2.3:4.3.1`, fails to apply patch on all.

Ending point:
- `gcc@11` concretizes on `@4.3.3:4.3.4` (and `@master`), attempts and
succeeds to apply patch on `@4.3.3:4.3.4`,
- `gcc@12` concretizes on `@4.3.4` (and `@master`), attempts and
succeeds to apply patch on `@4.3.4`.

Verified with environment build:
```yaml
spack:
  specs:
  - libzmq@4.3.4%gcc@12.1.0
  - libzmq@4.3.4%gcc@11.3.0
  - libzmq@4.3.3%gcc@11.3.0
  view: false
```
which returns the following:
```console
16:14:47 wdconinc@menelaos ~/git/spack (libzmq-patch-gcc12 *+$%=) $
spack install --fresh
==> Installing environment libzmq
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libmd-1.0.4-egpgd6eoaqtsl5fja2iwsl6gyc4o32p5
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libsodium-1.0.18-af3rsfnvck6anxf7eeog3f2bph44tjia
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/pkgconf-1.8.0-z5of2hj2c6ygd3kxr4cwv7u7t42sxair
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libmd-1.0.4-tec234gco2sd7n52dkwbrad43sdhaw4o
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libsodium-1.0.18-uljf675u3yrn5c7fdjdpa5c7qnnkynke
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/pkgconf-1.8.0-l4hzc2g4pnn7dwyttphmxivt3xghvpoq
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libbsd-0.11.5-fi3ri64moy45ksr4sf5pcwd6k23dsa4o
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libbsd-0.11.5-2matmm7im7oygrr77k7wznttv4rbupfz
==> Installing libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr
==> No binary for libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr found:
installing from source
==> Fetching
c593001a89.tar.gz
==> Fetching
310b8aa57a
==> Fetching
https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1
==> Applied patch
92b2c38a2c.patch?full_index=1
==> Applied patch
https://github.com/zeromq/libzmq/pull/4334.patch?full_index=1
==> libzmq: Executing phase: 'autoreconf'
==> libzmq: Executing phase: 'configure'
==> libzmq: Executing phase: 'build'
==> libzmq: Executing phase: 'install'
==> libzmq: Successfully installed
libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr
  Fetch: 0.61s.  Build: 1m 31.57s.  Total: 1m 32.18s.
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-12.1.0/libzmq-4.3.4-t7ad54q3atrnte4rzq7g7cfjcw5227pr
==> Installing libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz
==> No binary for libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz found:
installing from source
==> Fetching
9d9285db37.tar.gz
==> Using cached archive:
/home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239
==> Applied patch
92b2c38a2c.patch?full_index=1
==> libzmq: Executing phase: 'autoreconf'
==> libzmq: Executing phase: 'configure'
==> libzmq: Executing phase: 'build'
==> libzmq: Executing phase: 'install'
==> libzmq: Successfully installed
libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz
  Fetch: 0.93s.  Build: 11.55s.  Total: 12.48s.
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.3-pxrd6piprucu65bkro2ixms6d3x2eudz
==> Installing libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h
==> No binary for libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h found:
installing from source
==> Using cached archive:
/home/wdconinc/.spack/cache/_source-cache/archive/c5/c593001a89f5a85dd2ddf564805deb860e02471171b3f204944857336295c3e5.tar.gz
==> Using cached archive:
/home/wdconinc/.spack/cache/_source-cache/archive/31/310b8aa57a8ea77b7ac74debb3bf928cbafdef5e7ca35beaac5d9c61c7edd239
==> Applied patch
92b2c38a2c.patch?full_index=1
==> libzmq: Executing phase: 'autoreconf'
==> libzmq: Executing phase: 'configure'
==> libzmq: Executing phase: 'build'
==> libzmq: Executing phase: 'install'
==> libzmq: Successfully installed
libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h
  Fetch: 0.01s.  Build: 10.77s.  Total: 10.78s.
[+]
/opt/software/linux-ubuntu22.04-skylake/gcc-11.3.0/libzmq-4.3.4-hiil6dzy2reb4nk555zztwh44rpbyv4h
```
2022-08-25 19:13:41 -06:00
Adam J. Stewart
c6842605ac
py-pytorch-lightning: add v1.7.3 (#32383) 2022-08-25 18:01:50 -06:00
snehring
4d10cdb7e8
phylip: adding workarounds for gcc10+ (#32376)
* phylip: adding workarounds for gcc10+

* phylip: switch to spec.satisfies
2022-08-25 16:29:40 -06:00
Massimiliano Culpo
1bffa46d4d
zig: add v0.9.1 (#32380) 2022-08-25 14:38:26 -07:00
Richard Berger
6e420c3556
charliecloud: add versions 0.28 and 0.29 (#32378) 2022-08-25 13:21:27 -07:00
Ryan Marcellino
a476f0fa59
New package: py-mkdocs (#32363) 2022-08-25 12:37:20 -07:00
AMD Toolchain Support
6fb13c0fc5
fixed cp2k libcp2k.pc (#32349)
Co-authored-by: Prasanthi <pdonthir@amd.com>
2022-08-25 12:01:02 -07:00
Glenn Johnson
c2291f7eb3
new packages: r-cmdstanr and cmdstan (#32364) 2022-08-25 11:58:31 -07:00
Glenn Johnson
925a99a043
new package: r-glmgampoi (#32366)
* new package: r-glmgampoi

* Remove duplicate depends_on directive
2022-08-25 11:50:11 -07:00
Glenn Johnson
883b96aeb5
new packages: r-scdblfinder and dependencies (#32367)
- r-bluster
- r-metapod
- r-scran
2022-08-25 11:47:12 -07:00
Matthieu Dorier
9204bd6204
[ycsb] fixes build process and installation of YCSB (#32213)
* [ycsb] fixes build process and installation of YCSB

* [ycsb] fixing style

* [ycsb] removed extra newline
2022-08-25 11:26:08 -07:00
Wileam Y. Phan
b482c71b43
New package: glab (#32251) 2022-08-25 11:23:15 -07:00
robgics
ff2874333d
ddt: Initial commit (#32338)
* ddt: Initial commit

* ddt: Minor change to license date to appease the CI gods

* Get rid of unattractive extra line

* Switch to sha256 instead of md5
2022-08-25 11:03:07 -07:00
Robert Pavel
7214a438dc
Adding e3sm-kernels to Spack (#32341)
* Initial Draft of E3SM-Kernels Spackage

Initial draft of E3SM-Kernels. Currently no support for nested_loops due
to build system limitations

* Style Check and Fixed gfortran Check

Fixed style issues and changed gnu toolchain check to a gfortran check
due to hybrid compilers (e.g. clang+gfortran)

* Fixed Style Issues
2022-08-25 11:01:07 -07:00
Lucas Frérot
06ba4d5c28
lammps: added build dependency to py-setuptools (#32351)
LAMMPS' setup.py uses setuptools as of lammps/lammps@2ed8e5cf02
2022-08-25 10:40:07 -07:00
Mikael Simberg
1c3979dcfa
Add patch for missing template instantiation in pika 0.7.0 on macOS (#32370) 2022-08-25 11:30:00 -06:00
Melven Roehrig-Zoellner
f0925e1823
tixi: new variants (fortran,shared) (#32356)
* tixi: new variants (fortran,shared)

Since some tixi 3 versions, additional CMake flags are needed to build
tixi with shared libraries, respectively with Fortran support.

* tixi: fix style
2022-08-25 10:27:00 -07:00
snehring
ba87413eeb
snap-berkeley: update to version 2.0.1 (#32358) 2022-08-25 10:21:53 -07:00
Tyler Funnell
a4cbdba388
fish: adding v3.5.1 (#32362) 2022-08-25 10:18:39 -07:00
snehring
70388da974
libfabric: adding missing dep for opx fabric (#32377) 2022-08-25 10:10:30 -07:00
Sreenivasa Murthy Kolam
f0df4b653d
Changes for ROCm-5.2.0 changes and new recipe rocwmma (#31667)
* Changes for ROCm-5.2.0 changes and new recipe rocwmma

* modify the maintainers for hipify-clang

* address review comments

* update the rocwmma new recipe as per latest syntax

* fix style errors

* modify the patch file to provide the details about the patch

* fix style errors
2022-08-25 10:00:02 -07:00
Adam J. Stewart
507e06b5d2
Python: add new maintainer (#31755) 2022-08-25 09:46:09 -07:00
H. Joe Lee
c8f8b6957d
libfabric: Match main version. (#32342)
* Match main version.

`develop` no loger exists.

* Change develop to main.
2022-08-25 09:25:43 -07:00
robgics
10ac24874b
cplex: add package.py (#32337)
* cplex: add package.py

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

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

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-08-25 09:11:40 -07:00
Massimiliano Culpo
8654197c56
ASP-based solver: prevent the use of hashes that are not available (#32354)
fixes #32348
2022-08-25 17:55:58 +02:00
Dom Heinzeller
b332c1055c
Update ESMF: bug fix for esmf@8.3.0b09 with PIO (#32360) 2022-08-25 08:52:54 -07:00
Christian Mauch
7e0d8fce89
py-pynn: add version 0.10.0 (#32307) 2022-08-25 08:02:52 -07:00
Robert Cohn
c56abe4247
oneapi e4s: use require: to force gcc build for some packages (#32309) 2022-08-24 16:22:02 -04:00
Graeme A Stewart
ee02623171
whizard: Fix passing of build options, update versions (#32326)
* whizard: Fix passing of build options, update versions

The dependency of whizard on libtirpc is now correctly passed down as
an autotools option.

Update known versions of package with 3.0.2 and 3.0.3.

* Express path to headers via spec object methods
2022-08-24 06:58:48 -07:00
otsukay
6fa6b8a903
fujitsu-fftw: add option for enabling thread support (#31426)
Co-authored-by: Yuichi Otsuka <otsukay@riken.jp>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: otsukay <otsukay@users.noreply.github.com>
2022-08-24 11:36:14 +02:00
Atsushi Hori
14e99a1a5d
process-in-process: overhaul package recipe (#32347) 2022-08-24 11:35:08 +02:00
Massimiliano Culpo
e2468c8928
Allow default requirements in packages.yaml (#32260)
Allow users to express default requirements in packages.yaml. 

These requirements are overridden if more specific requirements
are present for a given package.
2022-08-24 09:33:55 +02:00
Ryan Marcellino
b4df535e8d
New package: py-mkdocs-material-extensions (#32334) 2022-08-23 23:29:56 -06:00
Ryan Marcellino
af4788fdef
New package: py-griffe and new build backend: py-pdm-pep517 (#32335)
* New package: py-griffe and new build backend: py-pdm-pep517

* add pdm to build backend docs
2022-08-23 23:23:23 -05:00