Commit graph

8227 commits

Author SHA1 Message Date
Chuck Atkins
a60ffdd5a2 vtk, paraview, catalyst packages: Add maintainers (#11774) 2019-06-19 10:57:19 -07:00
Mark W. Krentel
d29f8d0598 xfd package: use Spack-installed libintl (#11545)
Fixes #11526

The xfd configure script tests for libintl but incorrectly concludes
that no additional library is needed because gettext is provided in
libc. So we add '-lintl' to ldlibs to point to the Spack-installed
gettext. Note that the xfd configure script does not have a
--with-gettext option to do this for us.

Also add version 1.1.3
2019-06-19 10:54:50 -07:00
Daniel Topa
06342923fc eospac package: replace md5 checksums with sha256 (#11757) 2019-06-18 19:20:35 -07:00
Andrey Prokopenko
d1c9367446 New package: ArborX (#11474) 2019-06-18 19:14:05 -07:00
Justin S
2287dd6165 New package: amber (starting at v16) (#11619) 2019-06-18 19:01:03 -07:00
dorier
da800c21bd New package: PRRTE (#11614) 2019-06-18 18:47:24 -07:00
william-dawson
de2e088d43 New Package: ELSI (#11605) 2019-06-18 18:30:57 -07:00
Axel Huebl
e925589fc7 xtensor package: add version 0.20.7 and update dependencies (#11574)
* xtensor-python: add version 0.23.1
* xtensor-python: update xtensor/xtl dependency version constraints
  for 0.23.1
* xtensor-python: remove xtensor/xtl dependency version constraints
  for the develop version to favor the latest (develop) version of
  these dependencies
* xsimd: add version 7.2.3
* xtensor: add tbb variant to enable TBB parallelization
* xtensor: add version 0.20.7
* xtensor: update CMake args enable xsimd/tbb support based on
  variant settings
* xtl: add version 0.6.4
2019-06-18 17:05:47 -07:00
Robert Pavel
2eee507914 Added Cinch Spackage (#11759)
* Added Cinch Spackage and updated Flecsi to Use It

Added spackage for Cinch build system and updated flecsi spackage to use
the external version of cinch

* Flake8 compliance for Cinch and Flecsi

* Fixed Cinch Issue and Requested PR Changes

Swapped cinch back to master branch rather than test branch and style
issues for PR
2019-06-18 16:45:58 -05:00
Adam J. Stewart
d21bec996e Restrict gplates to proj@:5 (#11761)
* Restrict gplates to proj@:5

* Add comment on PROJ dependency
2019-06-18 15:15:14 -04:00
Adam J. Stewart
6d8c69848b Add py-rasterio 1.0.24 (#11738)
* Add py-rasterio 1.0.24

* Python 3 required in the next release
2019-06-18 15:14:27 -04:00
Adam J. Stewart
ff6dfe3c00 Add py-shapely 1.6.4.post2 (#11739) 2019-06-18 14:24:56 -04:00
Adam J. Stewart
ea3e1521fe Add CDO 1.9.7.1 (#11758) 2019-06-18 14:22:22 -04:00
Justin S
d82f8cd405 repeatmasker: perl and HMMER dependency fixes (#11660)
repeatmasker depended on HMMER but was never actually configured to
use it. The package also had many shebangs pointing to random perl
locations, now patched to use Spack's perl installation.
2019-06-18 11:11:00 -07:00
Hadrien G
e35355f040 ACTS package: add versions including 0.10.1 (#11606)
* Also add version 0.10.0
* Add leading '0' to 0.9.x versions (e.g. 0.09.1) and 0.8.x versions
* Don't mention acts-framework, that package isn't in Spack yet
2019-06-18 11:00:02 -07:00
Tamara Dahlgren
2a919c8851 Ensure proper gopath set for rclone (#11755)
Fixes #11745

Set the GOPATH environment variable to the stage path to avoid
creation of a $HOME/go directory.
2019-06-18 10:49:07 -07:00
Gabriel Rockefeller
003f670ef9 r3d: add version 2018-01-07 (#11770) 2019-06-18 09:36:49 -05:00
Adam J. Stewart
7c3137a203 Restrict libspatialite to proj@:5' (#11752) 2019-06-17 23:48:16 -04:00
Adam J. Stewart
7dc6b609d5 r-rgdal does not yet support PROJ.6 (#11766) 2019-06-17 23:47:52 -04:00
Adam J. Stewart
6422130709 Add PROJ.6 (#11730)
* Add PROJ.6

* Add back comment about newer PROJ API
2019-06-17 23:46:42 -04:00
Adam J. Stewart
1891734195 PROJ.6 not yet supported in SAGA-GIS (#11768) 2019-06-17 21:39:05 -04:00
Adam J. Stewart
a239ba33af py-cartopy does not yet support PROJ.6 (#11765) 2019-06-17 21:35:14 -04:00
Adam J. Stewart
a896a33b3b Specify which versions of PROJ work with MapServer (#11764) 2019-06-17 21:34:54 -04:00
Adam J. Stewart
349844a5fd Restrict magics to proj@:5 (#11763) 2019-06-17 21:33:25 -04:00
Adam J. Stewart
3018c64537 GRASS GIS does not yet support PROJ.6 (#11762) 2019-06-17 20:59:12 -04:00
Adam J. Stewart
b0cf2b5855 Add GEOS 3.7.2 (#11734) 2019-06-17 20:58:43 -04:00
Adam J. Stewart
de51be45b9 Add GDAL 3.0.0 (#11733)
* Add GDAL 3.0.0

* Clarify PROJ version requirements
2019-06-17 20:57:48 -04:00
Adam J. Stewart
17f20d0f32 Add py-fiona 1.8.6 (#11736)
* Add py-fiona 1.8.6

* Remove commented code

* Python 3 will be required in the next release
2019-06-17 20:54:58 -04:00
Adam J. Stewart
ee20b4826f Add libgeotiff 1.5.1 (#11731) 2019-06-17 20:46:46 -04:00
Manav Bhatia
0e34cc8a8e Libmesh updates (#11750)
* Updates to libMesh: added v1.3.1 checksum, added vtk variant, bugfix for enabling petsc when slepc variant is specified

* fixed indentation issues identified by Travis CI

* - updates version number
- added master as a version
- added new variant options for perflog, metaphysicl and blocked storage
-- bug-fix for metis

* fixes for spack indentation errors

* renaming develop to master following review comment of PR.
2019-06-17 19:38:19 -05:00
Adam J. Stewart
e23adbd4a9 Add py-pyproj 2.2.0 (#11735)
* Add py-pyproj 2.2.0

* PR review requests

* Make Python requirements more explicit
2019-06-17 20:23:40 -04:00
Adam J. Stewart
10d5008ef5 Restrict pism to proj@:4 (#11754)
* Restrict pism to proj@:5

* PROJ.5 is not yet supported either :(
2019-06-17 18:35:03 -04:00
Paul
93e1336de8 Added newer GoLang versions (#11756) 2019-06-17 17:23:09 -05:00
Adam J. Stewart
a558de117a Restrict ibmisc to proj@:4 (#11753)
* Restrict ibmisc to proj@:5

* Restrict ibmisc to proj@:4
2019-06-17 18:02:09 -04:00
Dan Lipsa
cdf4ba81e5 Remove version from py-mpi4py. (#11587) 2019-06-17 10:59:34 -04:00
Valentin Clement (バレンタイン クレメン)
f4d8b1ee60 Add version 1.2.2 and 1.2.3 to the package (#11748) 2019-06-17 16:03:26 +02:00
Dan Lipsa
83c7959580 Fix condition to enable mpi4py. (#11707)
* Fix condition to enable mpi4py.

* flake8

* Catalyst as paraview for mpi4py.

* Catalyst needs numpy and mpi4py.

* Remove leftover enable python.
2019-06-17 09:30:29 -04:00
Axel Huebl
b57ba6289c
openPMD-api: pybind11>=2.3.0 (#11744)
Update the dependency on pybind11 to the latest version
(constexpr signature support for all C++11 compilers + fixes).
2019-06-16 17:47:55 +02:00
Todd Gamblin
ce3a3507a4
cowsay: new package (#11743)
- A program that generates ASCII pictures of a cow with a message.

- This is used by the ISC19 Singularity tutorial, so we should probably
  have it in Spack.
2019-06-16 17:29:25 +02:00
Adam J. Stewart
3192318f36 Add py-geopandas 0.5.0 (#11737) 2019-06-16 08:57:13 +02:00
Adam J. Stewart
4965e9be53 Add libtiff 4.0.10 (#11732) 2019-06-16 08:52:16 +02:00
Adam J. Stewart
830964c2fb Add nasm 2.14.02 (#11729) 2019-06-16 08:50:05 +02:00
Adam J. Stewart
e259932a1e Add openjpeg 2.3.1 (#11728) 2019-06-16 08:49:36 +02:00
Adam J. Stewart
76490dcdbc Add py-cligj 0.5.0 (#11727) 2019-06-16 08:48:42 +02:00
Adam J. Stewart
69a746e941 Add py-numpy 1.16.4 (#11726) 2019-06-16 08:47:38 +02:00
Adam J. Stewart
7bb44f4620 Add libjpeg-turbo 2.0.2 (#11725) 2019-06-16 08:47:14 +02:00
Adam J. Stewart
92ab46b9ed Update URL for older version of jackcess (#11724) 2019-06-16 08:46:13 +02:00
Adam J. Stewart
53a4ea43c8 Add HDF 4.2.14 (#11723) 2019-06-16 08:45:23 +02:00
Adam J. Stewart
ffb7e83e65 Add new package py-boto3 (#11722) 2019-06-16 08:44:41 +02:00
Adam J. Stewart
0de9d15a49 Add new package py-s3transfer (#11721) 2019-06-16 08:43:41 +02:00
Adam J. Stewart
9a400d13a9 Add new package py-botocore (#11720) 2019-06-16 08:43:06 +02:00
Adam J. Stewart
2a15ab42fe Add new package py-jmespath (#11719) 2019-06-16 08:42:35 +02:00
Adam J. Stewart
07a90b214b Add new package py-freezegun (#11718) 2019-06-16 08:41:27 +02:00
Adam J. Stewart
639cb17322 Rename py-dateutil -> py-python-dateutil (#11717) 2019-06-16 08:40:56 +02:00
Adam J. Stewart
954a36c499 Add py-aenum package (#11716) 2019-06-16 08:39:54 +02:00
Kevin Manalo
91ef079511 intel: add version 19.0.4 (#11741) 2019-06-15 23:19:58 -05:00
Adam J. Stewart
3bad45fedf
Updates to poppler to get pdf2svg working (#11681) 2019-06-15 17:32:39 -05:00
Glenn Johnson
6592b4d46d Fix latest HPL for MKL use (#11712)
The 2.3 version of HPL needs LDFLAGS set for use of MKL libraries.
2019-06-15 15:46:59 -05:00
Axel Huebl
bccfb622e5 pybind11: v2.3.0 (#11713)
Add the latest 2.3.0 release and me as package maintainer.
2019-06-15 10:30:04 -05:00
brietzke
ef55319a9c new package: mutationpp (#11705)
* new package: mutationpp

* Update package.py

* flake8: correct package.py for flake8-python-style

* Update package.py

* modifications as requested by reviewer for #11705
2019-06-15 10:29:36 -05:00
Gabriel Rockefeller
537fa81c5d r3d: add version 2019-04-24 (#11710) 2019-06-15 14:27:03 +02:00
Justin S
9d6f37dc15 montage: new package at 6.0 (#11696) 2019-06-14 16:40:50 -05:00
Matthias Diener
f3eab78b80 scons: add version 3.0.5 (#11709) 2019-06-14 16:39:58 -05:00
Satish Balay
030f0951d4
dtk@develop now requires 'submodules=True' flag (#11694) 2019-06-14 11:04:48 -05:00
Justin M Wozniak
8afae13369 swift-t: New release packages for 1.4.3 (#11684) 2019-06-14 09:49:51 -05:00
Jordan Ogas
e275ddc169 add charliecloud-0.9.10 (#11471)
* add charliecloud-0.9.10; remove obsolete version

* revert older version changes; add version function

* fix space issue

* remove url declaration

* revert url removal

* remove self reference

* fix url; removed preferred tag; use newer package url
2019-06-13 16:50:55 -05:00
Mark W. Krentel
aca1bfdb6a intel-xed and hpcviewer: adapt to new resource placement (#11676)
Change 'destination' to 'placement' in the use of resource() for
intel-xed and hpcviewer.  Recent commits (1842873f and eb584d89)
changed the directory path for a resource and thus broke the build
for these packages.
2019-06-13 09:53:30 +02:00
marvinbernhardt
4f2144a68e added jpeg,png,ffmpeg variants to lammps (#10404) 2019-06-12 21:02:20 -06:00
Tamara Dahlgren
16530f84be Update remaining packages to use Stage.source_path (#11662)
#11528 updated Stage to always store a Package's source in a fixed
directory accessible via `Stage.source_path` This left behind a
number of packages which were expecting to access the source code
via `Stage.path`. This Updates those packages to use
`Stage.source_path` instead.

This also updates the name of the fixed directory: The original name
of the fixed directory was "src", so if an expanded archive created a
"src" directory, then users inspecting the directory structure could
see paths like "src/src" (which wasn't wrong but could be confusing).
Therefore this also updates the name of the fixed directory to
"spack-src".
2019-06-12 17:07:47 -07:00
Dave
fe8297da74 warpx: only allow master branch, and fix build on darwin (#11667)
* warpx: only allow master branch, and fix build on darwin

* warpx: Added CXXFLAGS=-std=c++11 for clang

* warpx: further clean up of openmp and c++11 flags

* warpx: Get around the problem with resources

The update uses placement instead of destination
2019-06-12 23:57:20 +02:00
Robert Pavel
a32382e787 Fixed Flecsi Backend Dependencies (#11679)
Fixed logic behind flecsi backends to not require legion for an mpi
build and to better support required combinations.
Also made graphviz support and tutorial building optional
2019-06-12 15:46:14 -06:00
Sinan
6ae5f38f26 new python package/py-typesentry (#11657)
* new python package/py-typesentry

* add proper version
2019-06-11 14:33:43 -04:00
Dan Lipsa
667e2f20fe Add support for using python3 in new verison of VTK. (#11673)
* Add support for python3 in new versions of VTK.
2019-06-11 12:50:22 -04:00
psakievich
a998fa25b0 Paraview: Add motionfx Intel workaround (#11608)
* Paraview/VTK: Fix failure on intel builds

Paraview@5.6.0 fails to build with intel compilers on certain platforms.
Error messages have been traced to the optional MotionFX lib.
(see https://discourse.paraview.org/t/error-build-5-6-0-rc1/572)
Turning off motionfx allows for succesful builds on these platforms.
2019-06-11 08:15:41 -04:00
Daniel Topa
35b1b81129 Add latest releases for pFUnit (#11642)
* Add latest releases for pFUnit
  - 3.2.10, 3.3.0, 3.3.1, 3.3.2, 3.3.3
  - 3.2.9 now with sha256
  - 4.0.0 is added, but commented out (build fails, see errors)

Verification builds

Darwin x86_64:
dantopa@cn100:pr-pfunit-darwin-general.spack $ spack find pfunit
==> 5 installed packages
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
pfunit@3.2.9  pfunit@3.2.10  pfunit@3.3.0  pfunit@3.3.1  pfunit@3.3.2  pfunit@3.3.3

Darwin Power9:
-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
pfunit@3.2.9  pfunit@3.2.10  pfunit@3.3.0  pfunit@3.3.1  pfunit@3.3.2  pfunit@3.3.3

Darwin ARM:
dantopa@cn805:pr-pfunit-darwin-arm.spack $ spack find pfunit
==> 5 installed packages
-- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------
pfunit@3.2.9  pfunit@3.2.10  pfunit@3.3.0  pfunit@3.3.1  pfunit@3.3.2  pfunit@3.3.3

2019-05-05

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* answer @citibeth comments

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* shortened offending comment to comply with flake8; suppressed error message on entry for v4.0.0

Signed-off-by: Daniel Topa <dantopa@lanl.gov>

* removed tailing space qt 20:55

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-06-10 18:19:52 -04:00
Geoffrey Oxberry
a52ed34fa4 ninja{-fortran}: make pkgs nonvirtual (fix #11628) (#11629) 2019-06-10 12:53:30 -04:00
Dan Lipsa
c98190a6ec ParaView and Catalyst use python3. (#11485)
Use python3 for latest paraview and catalyst versions.
2019-06-10 12:48:49 -04:00
Chuck Atkins
0953cd3a2e
Remove gnutls dependency and disable openssl when appropriate (#11646) 2019-06-10 11:19:26 -04:00
t-karatsu
7178ee3b63 Define LDFLAGS when using fujitsu compiler (#11669) 2019-06-10 11:01:32 -04:00
Quinn
58b797632e dateutils: new package (#11623)
* Adding the dateutils package
* Removing superfluous dependencies
2019-06-08 13:32:57 -07:00
Omar Padron
bdf831469a
fix qt build on gcc8.3 (#11633)
* fix qt build on gcc8.3

* source patches from upstream

* remove old code adding the same patch
2019-06-08 13:09:16 -04:00
Francois Budin
163ff9f1b6 Add ADIOS2 option to Trilinos (#11609)
ADIOS2 is the latest implementation of the ADaptable Input Output System,
ADIOS. This brand new architecture was designed to continue supporting the
performance legacy of ADIOS, and extend its current capabilities to address
current and future input/output (IO) challenges in the scientific data
lifecycle through effective research and development (R&D) activities.

ADIOS2 was recently added as a Third Party Library of Trilinos when it
was integrated to IOSS, a library inside the SEACAS package.
2019-06-08 16:34:34 +02:00
Jeffrey Salmond
9c1c50fb76 add openmp variant to lammps (#11643)
* add openmp variant to lammps

* add conflict for %gcc@9: and +openmp
2019-06-07 06:43:13 -06:00
Gregory Lee
7c8e9ab406 added tix package and python variant for tix (#11599)
* added tix package and python variant for tix

* addressing tix review requests

* python +tix requires +tkinter
2019-06-06 17:19:24 -04:00
Todd Gamblin
89b891d264
bugfix: lua-luafilesystem package should use stage.source_path (#11648) 2019-06-06 14:07:46 -07:00
Justin S
8c173da4b7 nettle: fix broken build (#11611)
* nettle: force C99 build

* nettle: update to use c99_flag

from @alalazo

Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2019-06-05 19:09:01 -05:00
Christoph Junghans
8fd64dfa08 lammps: added v20190605 (#11638) 2019-06-05 19:07:33 -05:00
Patrick Gartung
3c0b746f44
libxpm: revert change made in unrelated PR (#11634) 2019-06-05 15:13:19 -05:00
Gregory Lee
cfcf3996d8
set GUILE env var when building gnutls, fixes issue #11601 (#11607) 2019-06-05 10:14:06 -07:00
Andrew Gaspar
b3379a8890 Add Google Benchmark version 1.5.0 (#11626) 2019-06-04 22:53:07 -05:00
Patrick Gartung
efa45125fb
Revert "Git: patch to make git relocatable with buildcache. (#11596)" (#11625)
This reverts commit 30ec13f375.
2019-06-04 21:09:05 -05:00
Patrick Gartung
964a1d5997
Buildcache relocate.py error fix (#11616)
* Add a trailing / if file --mime does not return a mimetype with a / in it

* Flake8
2019-06-04 14:39:04 -05:00
Justin S
a7776972ad hotspot: new package at 6.0 (#11610) 2019-06-04 09:35:54 +02:00
Chuck Atkins
e4f0726927
mesa: Revert updated meson build and restore autotools build (#11595)
Due to the large number of issues this migration has caused, this rolls back
to the older autotools build.  However, it still keeps the updates wrt
variants and virtual packages.
2019-06-03 10:55:36 -04:00
Patrick Gartung
30ec13f375
Git: patch to make git relocatable with buildcache. (#11596)
* Apply patch to git to make it search for config files from its current location instead of the locations hard coded at install.

* Add provenance info for patch

* Pass needed flags to make

* Environment variables need because of relocation
2019-05-31 15:38:40 -05:00
sameershende
f5a2d7698d Package/tau/tau 2.28.1 update (#11591)
* Updating the TAU package with 2.28 and public repo

* Cleaning up TAU package and fixing binutils to install extras
The extras variant will install the extra ELF headers needed
by the TAU package.  The TAU package has been cleaned up and
extended.

* Adding some comments to the changes in binutils

* Adding correct python support, finding include and lib paths.

* Added PDT 3.25.1.

* Added TAU v2.28.1 with libdwarf and libelf.

* When +libdwarf is activated, +libelf is not automatically activated. It checks separately for libelf.
2019-05-31 10:01:19 -05:00
Justin S
a441fcbe69 alan: new package at 2.1.1 (#11593) 2019-05-30 17:50:14 -05:00
Valentin Reis
0b5ccd22da Adds the aml memory management library. (#11590)
AML is a collection of building blocks for explicit memory management on
complex architectures.

https://xgitlab.cels.anl.gov/argo/aml
https://argo-aml.readthedocs.io/en/latest/
2019-05-30 16:01:28 -05:00
Justin S
f089b9b053 r-randomglm: new package at 1.02-1 (#11589) 2019-05-30 13:35:01 -05:00
Nick Booher
786b59633d Revbayes update (#11559)
* revbayes: new version

* revbayes: pep8
2019-05-30 13:23:32 -04:00