Commit graph

31667 commits

Author SHA1 Message Date
pabloaledo
1afbf72037
add bioconductor-ebseq (#38380)
* add buiconductor-ebseq
  Signed-off-by: Pablo <pablo.aledo@seqera.io>

---------

Signed-off-by: Pablo <pablo.aledo@seqera.io>
2023-06-14 12:40:57 -07:00
Rémi Lacroix
407fd80f95
ctffind: Add a patch to fix incorrect return types. (#38085)
Prevent the code from crashing (cf. https://grigoriefflab.umassmed.edu/comment/1696#comment-1696).
2023-06-14 12:29:41 -07:00
Tamara Dahlgren
62525d9076
dsqss: convert to new stand-alone test process (#38372) 2023-06-14 11:54:47 -07:00
Alec Scott
c2371263d1
lastz: add v1.04.22 (#38388)
* lastz: add v1.04.22

* Fix formatting of versions to include extra space
2023-06-14 10:05:45 -07:00
Alec Scott
5a870182ec
ipopt: add v3.14.9 (#38387) 2023-06-14 10:04:54 -07:00
Alec Scott
e33ad83256
imath: add v3.1.9 (#38386) 2023-06-14 10:03:41 -07:00
Alec Scott
0352a1df5d
imagemagick: add v7.1.1-11 (#38385) 2023-06-14 10:02:36 -07:00
Alec Scott
ade44bce62
cgal: add v5.5.2 (#38384) 2023-06-14 10:01:33 -07:00
Mark W. Krentel
ddb29ebc34
intel-xed: add version 2023.06.07 (#38373)
Add version 2023.06.07, update python to 3.7.
2023-06-14 09:46:53 -07:00
Mark W. Krentel
19a62630e5
hpcviewer: add version 2023.05 (#38374) 2023-06-14 09:45:21 -07:00
Alec Scott
5626802aa0
cloc: add v1.96.1 (#38348) 2023-06-14 12:28:08 -04:00
kwryankrattiger
f68063afbc
DaV: Drop propagation of HDF5 to darshan (#38361)
Darshan Runtime does not properly link symols for HDF5 when using shared
libraries.
2023-06-14 11:02:18 -05:00
Alec Scott
8103d019d6
hbase: add v2.5.4 (#38353) 2023-06-14 11:47:53 -04:00
Alec Scott
ce89cdd9d7
fzf: add v0.41.1 (#38351) 2023-06-14 11:38:02 -04:00
Alec Scott
20d9b356f0
hashcat: add v6.2.6 (#38352) 2023-06-14 11:32:56 -04:00
Alec Scott
3401438a3a
hyperfine: add v1.17.0 (#38354) 2023-06-14 11:23:20 -04:00
Alec Scott
dcf1999d22
ftxui: add v4.1.1 (#38350) 2023-06-14 11:16:13 -04:00
snehring
9e3c3ae298
Repeatmodeler 2.0.4 (#38337)
* perl-devel-size: adding new package
* repeatmodeler: adding new version 2.0.4
* perl-devel-size: adding proper description
2023-06-14 11:10:50 -04:00
Tamara Dahlgren
40d6b84b4d
dssp: convert to new stand-alone test process (#38368) 2023-06-14 07:27:49 -07:00
Xavier Delaruelle
2db09f27af
modules: use depends-on to autoload module with Lmod on Tcl (#38347)
Update Tcl modulefile template to use the `depends-on` command to
autoload modules if Lmod is the current module tool.

Autoloading modules with `module load` command in Tcl modulefile does
not work well for Lmod at some extend. An attempt to unload then load
designated module is performed each time such command is encountered. It
may lead to a load storm that may not end correctly with large number of
module dependencies.

`depends-on` command should be used for Lmod instead of `module load`,
as it checks if module is already loaded, and does not attempt to reload
this module.

Lua modulefile template already uses `depends_on` command to autoload
dependencies. Thus it is already considered that to use Lmod with Spack,
it must support `depends_on` command (version 7.6+).

Environment Modules copes well with `module load` command to autoload
dependencies (version 3.2+). `depends-on` command is supported starting
version 5.1 (as an alias of `prereq-all` command) which was relased last
year.

This change introduces a test to determine if current module tool that
evaluates modulefile is Lmod. If so, autoload dependencies are defined
with `depends-on` command. Otherwise `module load` command is used.

Test is based on `LMOD_VERSION_MAJOR` environment variable, which is set
by Lmod starting version 5.1.

Fixes #36764
2023-06-14 15:35:53 +02:00
dependabot[bot]
6979d6a96f
build(deps): bump python-levenshtein in /lib/spack/docs (#38339)
Bumps [python-levenshtein](https://github.com/maxbachmann/python-Levenshtein) from 0.21.0 to 0.21.1.
- [Release notes](https://github.com/maxbachmann/python-Levenshtein/releases)
- [Changelog](https://github.com/maxbachmann/python-Levenshtein/blob/main/HISTORY.md)
- [Commits](https://github.com/maxbachmann/python-Levenshtein/compare/v0.21.0...v0.21.1)

---
updated-dependencies:
- dependency-name: python-levenshtein
  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>
2023-06-14 13:03:15 +02:00
dependabot[bot]
deffd2acc9
build(deps): bump docker/build-push-action from 4.1.0 to 4.1.1 (#38369)
Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 4.1.0 to 4.1.1.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](44ea916f6c...2eb1c1961a)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  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>
2023-06-14 09:48:57 +02:00
dependabot[bot]
988f71f434
build(deps): bump docker/setup-buildx-action from 2.6.0 to 2.7.0 (#38370)
Bumps [docker/setup-buildx-action](https://github.com/docker/setup-buildx-action) from 2.6.0 to 2.7.0.
- [Release notes](https://github.com/docker/setup-buildx-action/releases)
- [Commits](6a58db7e0d...ecf95283f0)

---
updated-dependencies:
- dependency-name: docker/setup-buildx-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2023-06-14 09:36:41 +02:00
kjrstory
4fe76f973a
SU2: add versions up to 7.5.1, update dependencies (#37767)
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2023-06-13 18:33:10 -04:00
Raffaele Solcà
8e4e6ad529
add DLA-Future package (#38224) 2023-06-13 18:03:13 -04:00
Edoardo Aprà
3586a2dbe3
NWChem: fix fftw3 variant + patch (#38250) 2023-06-13 22:43:39 +02:00
Dan Lipsa
4648939043
Windows bugfix: path-to-URL conversion (#37827)
When interpreting local paths as relative URL endpoints, they were
formatted as Windows paths on Windows (i.e. with '\'). URLs should
always be POSIX-style.
2023-06-13 10:08:09 -07:00
Xavier Delaruelle
746eaaf01a
modules: append trailing delimiter to MANPATH when set (#36678)
Update modulefile templates to append a trailing delimiter to MANPATH
environment variable, if the modulefile sets it.

With a trailing delimiter at ends of MANPATH's value, man will search
the system man pages after searching the specific paths set.

Using append-path/append_path to add this element, the module tool
ensures it is appended only once. When modulefile is unloaded, the
number of append attempt is decreased, thus the trailing delimiter is
removed only if this number equals 0.

Disclaimer: no path element should be appended to MANPATH by generated
modulefiles. It should always be prepended to ensure this variable's
value ends with the trailing delimiter.

Fixes #11355.
2023-06-13 10:29:11 +02:00
Alberto Sartori
bd2f78ae9a
justbuild: bump version 1.1.2 (#38320) 2023-06-12 21:34:38 -04:00
Alec Scott
a4ebe01dec
curl: add v8.1.2 (#38332) 2023-06-12 19:34:24 -04:00
Alex Richert
94e9e18558
Update sp package (#38208) 2023-06-12 17:51:57 -04:00
Alec Scott
d2e0ac4d1f
cpp-httplib: add v0.12.5 (#38331) 2023-06-12 14:51:11 -07:00
Alec Scott
36321fef1c
direnv: add v2.32.3 (#38333) 2023-06-12 14:48:06 -07:00
Alec Scott
e879877878
etcd: add v3.5.9 (#38334) 2023-06-12 14:46:43 -07:00
Alec Scott
f0bce3eb25
fastp: add v0.23.4 (#38335) 2023-06-12 14:45:45 -07:00
Wouter Deconinck
316bfd8b7d
opencascade: new variants (#35345)
* opencascade: new variants

OpenCascade has several major modules and not every
application needs all of them. This adds variants for
the various modules.

It also uodatws the 3rdparty dependency treatment.

* [@spackbot] updating style on behalf of wdconinc

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

* opencascade: remove variant foundation_classes (always true)

* [@spackbot] updating style on behalf of wdconinc

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

---------

Co-authored-by: wdconinc <wdconinc@users.noreply.github.com>
2023-06-12 11:56:55 -05:00
Jerome Soumagne
92593fecd5
mercury: add v2.3.0 (#38279)
* fix Boost dependency

* fix testing and move psm2/sockets as unsupported

* fix style to separate maintainers/tags/version
2023-06-12 08:51:22 -07:00
MatthewLieber
8db5fecdf5
mvapich2: add hwloc_graphics variant (#38028)
Co-authored-by: Matthew Lieber <lieber.31@osu.edu>
2023-06-12 17:25:10 +02:00
Niclas Jansson
eee696f320
neko: add v0.6.0 and fixed rocm package recipe (#38024) 2023-06-12 17:17:12 +02:00
willdunklin
8689cf392f
mochi-margo: correct patch versions (#38087) 2023-06-12 17:13:52 +02:00
Bruno Turcksin
15d4cce2eb
Add new Kokkos release (#38049) 2023-06-12 17:08:51 +02:00
Peter Scheibel
45fbb82d1a
pip is a pythonextension not a pythonpackage, and it turns out we werent doing our external surgery on things that inherited pythonextension (#38186) 2023-06-12 17:07:28 +02:00
Adam J. Stewart
2861c89b89
Deprecate R packages for spatial analysis (#38158)
* Deprecate R packages for spatial analysis

* [@spackbot] updating style on behalf of adamjstewart

---------

Co-authored-by: adamjstewart <adamjstewart@users.noreply.github.com>
2023-06-12 15:55:40 +02:00
Alec Scott
135bfeeb27
libtlx: add v0.6.1 (#38134) 2023-06-12 15:54:50 +02:00
Alec Scott
8fa9c66a7d
ccache: add v4.8.1 (#38114) 2023-06-12 15:54:27 +02:00
snehring
5e6174cbe2
cdhit: add missing perl dep, patch shebangs (#38179) 2023-06-12 15:51:59 +02:00
MichaelLaufer
b4ad883b0d
wrf: add v4.5.0 (#37618) 2023-06-12 15:48:54 +02:00
Juan Miguel Carceller
a681111a23
whizard: add tirpc/lib to the link flags (#38050)
Co-authored-by: jmcarcell <jmcarcell@users.noreply.github.com>
2023-06-12 15:24:27 +02:00
Manuela Kuhn
d2436afb66
gdb: fix debuginfod for version 10 (#38058) 2023-06-12 15:20:45 +02:00
Martin Pokorny
e43444cbb6
kokkos: fix c++20 constraint (#37555) 2023-06-12 15:07:03 +02:00