Commit graph

26320 commits

Author SHA1 Message Date
dlkuehn
0c4a866c2e
trinotate: add v3.2.2 (#30141)
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
2022-04-19 09:29:30 +02:00
Adam J. Stewart
54e9b6b8fb
py-rtree: add v1.0.0 (#30140) 2022-04-19 09:28:42 +02:00
Harmen Stoppels
a3a61241fc
openmpi: no nvc -fexceptions support (#30044) 2022-04-19 09:21:08 +02:00
snehring
7133838fa5
diamond: add v2.0.14 (#30143) 2022-04-19 09:20:20 +02:00
Sam Grayson
8de726336f
Add music package (#30147) 2022-04-18 20:51:13 -05:00
Peter Brady
3835ac0c41
spdlog: use external fmt (#30051) 2022-04-18 09:41:00 -04:00
range3
a405a6efe3
py-torch: fix cuda dependencies (#30117) 2022-04-16 21:06:43 -06:00
Harmen Stoppels
b0c8affbd9
gcc: avoid excessive stat calls (#30005)
For about a decade GCC has an option `-f[no]-canonical-system-headers`
which basically runs `realpath` on all "system headers", to possibly
reduce the length of paths in diagnostics. [1]

Spack usually installs the "system headers" of GCC in very deeply nested
directories. Calling `realpath` there results in stat calls on every
level, for every header file. On some slow filesystem I have,
`-fno-canonical-system-headers` gives about 5x speedup to compile hello
world in C, meaning that ./configure scripts would be much faster when
using this flag by default.

[1] https://codereview.appspot.com/6495088
2022-04-16 21:12:03 +02:00
marcost2
03a7643816
mpich: Fix @4 build with gcc@10+ (#30084)
* Also set FCFLAGS for gcc@10
* Set FCFLAGS for clang/apple-clang too
2022-04-16 19:53:44 +02:00
Kai Torben Ohlhus
1ada151d80
octave: add version 7.1.0 (#30089)
https://octave.org/news/release/2022/04/06/octave-7.1.0-released.html
2022-04-16 06:28:10 +02:00
John W. Parent
840858c215
CMake package: use Windows SSL implementation (#29943)
Add option to allow using OpenSSL (by default this uses the SSL
implementation that comes with Windows, since that is more likely
to have needed certificates).
2022-04-16 00:38:28 +00:00
John W. Parent
0f80a5a9d5
Remove assert in favor of error message (#29797) 2022-04-15 22:44:44 +00:00
dlkuehn
c8f85ebea3
Update: bamtools to version 2.5.2 (#29021)
Co-authored-by: las_dkuehn <las_dkuehn@gilman-0107-02.las.iastate.edu>
2022-04-15 14:18:47 -07:00
Dom Heinzeller
3b8256ef6a
Backport f2py's define for threading bugfix to numpy versions 1.20.3:1.22.1 (#30065) 2022-04-15 15:47:01 -05:00
Erik Schnetter
33d791bd1c
compose: New package (#30073)
* compose: New package

* compose: Add maintainer

* compose: Remove unused import

* compose: Switch copyright date to 2021
2022-04-15 11:17:50 -07:00
Chris White
374ebe5840
Adiak package: use correct CMake MPI variables (#30086) 2022-04-15 10:33:56 -07:00
Sajid Ali
cf21fd837f
llvm@14: Fix build: Add hwloc include directory for libompd (#29757) 2022-04-15 17:44:22 +02:00
Thomas Madlener
01609b3111
py-awkward: Add latest versions (#29744)
* py-awkward: Add new versions

* py-awkward: Update dependencies

* Make setuptools a runtime dependency as well

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2022-04-15 09:53:27 -05:00
Theofilos Manitaras
fdc9a29a9b
Patch libfabric for the Nvidia compilers (#30090)
* Patch libfabric@1.6.0:1.14.0 for the Nvidia compilers

Signed-off-by: Theofilos Manitaras <manitaras@cscs.ch>
2022-04-15 06:42:26 -06:00
Robert Underwood
0e0c438dd6
Fix R build in containers (#30055)
R needs which as a build dependency, but it may not be provided in a
minimal container.

Co-authored-by: Robert Underwood <runderwood@anl.gov>
2022-04-14 23:06:15 -05:00
Axel Huebl
015046cb97
Add: openPMD-viewer 1.4.0 & validator update (#30083) 2022-04-15 06:03:59 +02:00
Matthieu Dorier
388d5fada3
mochi-thallium: add v0.10.1, update cereal dependency (#30059)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2022-04-14 21:55:35 -06:00
John W. Parent
2d3a613128
NASM package: fix install on Windows (#29905)
* Don't rely on NASM's nmake to export install target. Spack
  now handles NASM installation; the install tree structure
  mimics NASM Windows installer behavior.
* Add dependency on perl
2022-04-14 12:20:41 -07:00
Jen Herting
ce0346abd9
New package: py-nara-wpe (#29451)
* espnet first build with depends

* [py-nara-wpe] fixed copyright

* [py-nara-wpe] fixing up dependencies

Co-authored-by: Sid Pendelberry <sid@rit.edu>
2022-04-14 14:09:03 -05:00
Jen Herting
00313f9e20
New package: py-distance (#29546)
* [py-distance] created template

* [py-distance]

- added homepage
- added description
- removed fixmes

* [py-distance] depends on setuptools
2022-04-14 14:08:09 -05:00
Howard Pritchard
6c03e1efb6
openmpi: main no longer depends on pandoc (#30068)
we switched to an optional sphinx based way of
generating docs, so remove pandoc, which can cause
issues with latex conflicts.

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2022-04-14 12:58:30 -06:00
John W. Parent
b1de8a5680
Windows platform: don't allow MakefilePackage (#29904) 2022-04-14 11:41:12 -07:00
Jason Lee
02a1f6f0f1
New package: SICM (#30066) 2022-04-14 12:30:42 -06:00
Cyrus Harrison
79be21c8e4
add conduit 0.8.3 release (#30067) 2022-04-14 11:42:31 -06:00
Dom Heinzeller
bb70e6ffcd
netcdf-cxx4 Package: updates to build on Mac OS (#29246)
Bug fixes for package netcdf-cxx4 so that it builds on macOS semi
case-sensitive filesystems; this includes additional changes to build
netcdf-cxx4 consistently with netcdf-fortran.

* netcdf-fortran: remove unused config_flags
* netcdf-fortran: avoid building without the optimization flags
* netcdf-cxx4: do not enforce autoreconf. This was a rudiment from the
  times when the package was fetched with git, which broke timestamp
  order of the automatically generated Autoconf files.
* netcdf-cxx4: inject PIC flags for C++ when '+pic'
* netcdf-cxx4: inject C/CXXFLAGS via the wrapper
* netcdf-cxx4: fix the underlinking problem for platforms other than darwin
  (add netcdf-c libs netcdf-cxx4 ldlibs flags)
* netcdf-cxx4: remove redundant extension of CPPFLAGS
* netcdf-cxx4: only need to use MPI compiler wrapper when building C
  (vs both C and C++)
* netcdf-cxx4: remove variant 'static'
  This makes it consistent with other packages from the NetCDF
  constellation: always build the static libraries and additionally
  build the shared ones when '+shared'.
* netcdf-cxx4: do not configure --with/--without-pic.
  This makes it consistent with other packages from the NetCDF
  constellation: build the shared libraries with the PIC flag and
  the static ones without it (the default for Autotools) when
  '~pic', and build the static libraries with PIC when '+pic' (to
  make them injectable into other shared libraries).
* netcdf-cxx4: run the tests serially
* netcdf-cxx4: build the plugins only when the tests are run

Co-authored-by: Sergey Kosukhin <sergey.kosukhin@mpimet.mpg.de>
2022-04-14 10:10:30 -07:00
dlkuehn
b09fb467f1
Package rna-seqc: Change jdk dependency to java (#30049)
Co-authored-by: David Kuehn <las_dkuehn@iastate.edu>
2022-04-14 10:02:06 -07:00
Zack Galbreath
dec3e31e60
spack ci: remove relate-CDash-builds functionality (#29950)
gitlab ci: Remove code for relating CDash builds

Relating CDash builds to their dependencies was a seldom used feature.  Removing
it will make it easier for us to reorganize our CDash projects & build groups in the 
future by eliminating the needs to keep track of CDash build ids in our binary mirrors.
2022-04-14 10:42:30 -06:00
Olivier Cessenat
f5520de4bd
libefence: add package for the Electric Fence library from B. Perens (#29595) 2022-04-14 08:53:52 -07:00
Massimiliano Culpo
be99a72d57 Add CHANGELOG for v0.17.2 2022-04-14 16:19:37 +02:00
Kevin Huck
6f1a5c8fee
apex: add v2.5.0 (#30018) 2022-04-14 11:45:02 +02:00
Valentin Volkl
a482970a35
sherpa: fix build of recola interface (#30000) 2022-04-14 11:43:39 +02:00
dependabot[bot]
bbb3f724af
build(deps): bump actions/setup-python from 3.1.1 to 3.1.2 (#30017)
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3.1.1 to 3.1.2.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](21c0493ecf...98f2ad02fd)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-04-14 10:47:01 +02:00
Peter Scheibel
89f6db21f1
Ad-hoc Git commit versions: support submodules (#30037)
* Allow packages to add a 'submodules' property that determines when ad-hoc Git-commit-based versions should initialize submodules

* add support for ad-hoc git-commit-based versions to instantiate submodules if the associated package has a 'submodules' property and it indicates this should happen for the associated spec

* allow Package-level submodule request to influence all explicitly-defined version() in the Package

* skip test on windows which fails because of long paths
2022-04-13 20:05:14 -07:00
dlkuehn
b28b24ccf8
express: version update to 1.5.3 (#29760)
Co-authored-by: snehring <snehring@iastate.edu>
2022-04-13 20:02:53 -06:00
Chris White
3dfa64edab
BLT package: add version 0.5.1 (#30053) 2022-04-13 20:02:27 -06:00
iarspider
2046ca7722
Add checksum for libisl 0.24 and update URL (#30025) 2022-04-13 17:41:34 -07:00
Mikael Simberg
4f5d5bb2ef
Add hpx-kokkos package (#29766)
Co-authored-by: Mikael Simberg <mikael.simberg@iki.if>
2022-04-14 00:23:33 +00:00
Veselin Dobrev
34d9d58924
New package version: mfem v4.4 (#29658) 2022-04-13 16:27:54 -07:00
Dylan Simon
0804637228
distcc: add 3.3.5 for gcc@10 (#29666) 2022-04-13 16:11:36 -07:00
Matthieu Dorier
a837008ff7
[mochi-thallium] added new version of mochi-thallium (#29791) 2022-04-13 14:51:06 -07:00
Jeremy L Thompson
1ffad2073d
libceed - add v0.9 and 0.10.1 (#29820) 2022-04-13 14:47:11 -07:00
Massimiliano Culpo
c846b5149d
Add support for Python 3.10 (#29581)
* Add support for Python 3.10

* Update unit-tests to use 3.10

* Update Getting started section of the docs

* Update bootstrap action
2022-04-13 14:32:23 -07:00
Seth R. Johnson
4c1250854a
perl: fix mac patch (#30001)
- Apply macosx version workaround to all 5.35 and less
- Delete an obsolete mac patch file that I didn't notice when adding
  #28797
2022-04-13 12:34:48 -06:00
iarspider
fbd94b9ad2
Add checksums for xtensor 0.24.1 and xtl 0.7.4 (#30032) 2022-04-13 11:22:59 -06:00
mcourtois
10a3822728
mumps: install header files as compiled (#29940)
Co-authored-by: Mathieu Courtois <mathieu.courtois@edf.fr>
2022-04-13 09:45:47 -07:00