Commit graph

13210 commits

Author SHA1 Message Date
Scott McMillan
0015dd0bf8
Enable packages to use the NVIDIA HPC SDK (#19452)
* Enable packages to use the NVIDIA HPC SDK

* fix linter and review items

* fix linter issue

Co-authored-by: Scott McMillan <smcmillan@nvidia.com>
2020-10-22 16:42:48 -05:00
Jen Herting
fd3dbb2493
New package: py-torchfile (#19481)
* [py-torchfile] created template

* [py-torchfile] set python versions

* [py-torchfile] depends on py-numpy

* [py-torchfile] fixed url format

* [py-torchfile] added homepage and description. removed fixmes

* [py-torchfile] fixed url format
2020-10-22 16:36:34 -05:00
Jen Herting
d6f19eeed2
[py-pyarrow] cuda and orc support (#19445)
* [py-pyarrow] telling setup.py that we want cuda support

* [py-pyarrow] added orc variant

* [py-pyarrow] passing the orc variant down the line

* [py-pyarrow] added variant description
2020-10-22 15:19:16 -05:00
Jen Herting
0baaeec58d
Arrow: add orc support (#19442)
* [arrow] added orc support variant

* [arrow] depends on orc

* [arrow] added explicit disable of features for variants
2020-10-22 15:18:54 -05:00
daichi-nishi
5407a74f2b
modified:var/spack/repos/builtin/packages/ppopen-appl-amr-fdm/package.py (#19459) 2020-10-22 15:03:09 -05:00
daichi-nishi
680c0ac06d
modified : var/spack/repos/builtin/packages/ppopen-appl-bem/package.py (#19460) 2020-10-22 15:02:41 -05:00
daichi-nishi
fb82810d50
ppopen-appl-dem-util:change download site to github. (#19461)
* modified:var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py

* modified:var/spack/repos/builtin/packages/ppopen-appl-dem-util/package.py:deleted whitespace
2020-10-22 15:02:11 -05:00
lorddavidiii
6a82b2260f
Add opencl-headers and use ocl-icd as OpenCL provider (#19463)
* ocl-icd: fix build problems

* New package: opencl-c-headers

* New package: opencl-clhpp

* New bundled package: opencl-headers

- bundle C and C++ header files

* ocl-icd: Add +headers variant to use this as opencl provider

* ocl-icd: add new upstream release 2.2.13

* ocl-icd: add asciidoc-py3 and xmlto dependency needed for manpage generation

* ocl-icd and opencl-headers provides OpenCL 3.0

- also add more explicit version providing for older ocl-icd versions

* opencl-headers: add maximum of supported opencl versions for all versions

* opencl-headers: there aren't final releases with OpenCL 3.0
2020-10-22 15:00:40 -05:00
daichi-nishi
7c78d15e74
modified:var/spack/repos/builtin/packages/ppopen-appl-fdm-at/package.py (#19464) 2020-10-22 14:57:37 -05:00
dunatotatos
61a7900573
Restrict Python version for Strelka to Python 2. (#19466)
Fix #19465
2020-10-22 14:56:54 -05:00
Jen Herting
32a68fbbd4
New Package: py-fastrlock (#19467)
* [py-fastrlock] created template

* [py-fastrlock] added dependencies and setting --with-cython

* [py-fastrlock] added homepage and description. removed fixmes
2020-10-22 14:55:14 -05:00
Andrew W Elble
e4ce123ddf
hercules (#19434) 2020-10-22 15:20:30 -04:00
darmac
0d46531791
Add new package: py-cantoolz (#18812)
* Add new package: py-cantoolz

* refine depends
2020-10-22 14:11:06 -05:00
Jen Herting
e1e0bbb4cb
New package: orc (#19441)
* [orc] created template

* [orc] depends on maven

* [orc] building with -fPIC

* [orc] fixed name of c flags option

* [orc] depends on openssl

* [orc] added dependencies and disableing installing vendored libs

* [orc] disabling hdfs

* [orc] depending on specific versions of dependencies

* [orc] no building of third party libs

* [orc] helping cmake find the dependencies

* [orc] disabling features that would require static protobuf libraries

* [orc] dependency versions are ranges

* [orc] added homepage and description. removed fixmes

* [orc] flake8

* [orc] switching to compilier indipendent code
2020-10-22 14:05:18 -05:00
Jen Herting
bd0b53f4fb
[treelite] added python and protobuf support (#19444)
* [treelite] added protobuf variant

* [treelite] adding python support

* [treelite] disable protobuf by default

* [treelite] flake8

* [treelite] reordered phases
2020-10-22 14:03:05 -05:00
Justin S
121a8a5cd9
transrate: new package at 1.0.3 (#19295)
* transrate: new package at 1.0.3

* transrate: add macOS binary distribution

* transrate: fix platform switching
2020-10-22 14:01:49 -05:00
Justin S
db167897f4
py-tomlkit: new package at 0.7.0 (#19450)
* py-tomlkit: new package at 0.7.0

* py-tomlkit: add dependencies
2020-10-22 14:01:14 -05:00
Andrew W Elble
f4049a71c2
New package: py-labours (#19433)
* py-labours

* fix dep version constraints
2020-10-22 14:14:57 -04:00
Andrew W Elble
b77279e9cc
py-seriate (#19432) 2020-10-22 12:36:12 -04:00
Andrew W Elble
745875b008
New package: py-or-tools (#19431)
* py-or-tools

* python is, of course, a runtime dep

* more dependency fixes, use extends.

* protobuf is >= 3.12.2
2020-10-22 11:59:48 -04:00
darmac
646af81263
r-sf: fix build error (#19386)
* r-sf: fix build error

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-22 10:57:28 -05:00
iarspider
601636b755
Add herwig3 (#19406)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add herwig3

* Prepare fixes based on MR (needs checking)

* Set all dependencies (except python) as build-type

* OK now

* Move import to the top of the file

* Fix dependency name

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-22 10:56:53 -05:00
Andrew W Elble
019205ec7a
cbc (#19419) 2020-10-22 11:20:19 -04:00
Andrew W Elble
7935ec501f
cgl (#19420) 2020-10-22 10:47:23 -04:00
Andrew W Elble
caab89b9c9
New package: py-lifelines (#19429)
* py-lifelines

* also carry the newer version of lifelines

* 0.25.5 needs python >= 3.6
2020-10-21 22:33:02 -05:00
Andrew W Elble
e800b6029f
clp (#19418) 2020-10-21 22:32:44 -05:00
iarspider
74e93aff41
Add Gosam (#19401)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add gosam

* Flake-8

* Flake-8

* Delete gosam-1.2.4.patch

Remove patch

* Remove patch from recipe

* Changes from MR

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 22:32:29 -05:00
Tom Payerle
94221fa225
new package: py-tinyarray (#19454) 2020-10-21 19:28:34 -05:00
Andrew W Elble
ec068f8070
New package: py-autograd-gamma (#19426)
* py-autograd-gamma

* missing dependencies
2020-10-21 19:19:46 -05:00
iarspider
27211ba90b
Add Njet (#19399)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add NJet

* flake-8

* Flake-8

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 19:16:29 -05:00
iarspider
399ca3b671
Add qgraf (#19404)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add qgraf

* Update package.py

Changes from review

* Changes from MR

* Fix for URLs containing @ symbol

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-21 19:16:11 -05:00
Andrew W Elble
5a0303860d
osi (#19424) 2020-10-21 19:15:34 -05:00
Todd Gamblin
93e7267dcc
unzip: fix build for XCode 12 on macosx (#19453)
- [x] `build_targets` should use `macosx` on macOS, `generic` on other systems
- [x] enable `LARGE_FILE_SUPPORT` by default
2020-10-21 15:31:29 -07:00
iarspider
a1278bfba0
Add Madgraph 2.8.1 (#19400)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Update madgraph to 2.8.1

* Changes from MR

* Changes from MR

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 17:13:00 -05:00
Andrew W Elble
935aa06838
New package: py-fastdtw (#19427)
* py-fastdtw

* cython is buildtime dep
2020-10-21 17:09:41 -05:00
G-Ragghianti
d61c236db4
Lapackpp package update (#19447)
* Updated blaspp package

* Modified lapackpp for newest release

* Formatting

* Updates to lapackpp package for new version

* Added dependency on cblas

* Removed cblas dependency

* updated to lapackpp

* Added new version for blaspp and lapackpp

* Removed debugging output

* Converted version matching logic for for loop
2020-10-21 17:09:25 -05:00
Justin S
05df3c3225
py-drmaa: new package at 0.7.9 (#19451) 2020-10-21 17:09:08 -05:00
Justin S
2b3ead0b72
py-sqlalchemy-utils: new package at 0.36.8 (#19449) 2020-10-21 16:52:37 -05:00
Justin S
bbc9c5533e
py-jsonref: new package at 0.2 (#19448) 2020-10-21 16:51:39 -05:00
Simon Frasch
44a81bf914
spla: Add version 1.2.1 (#19436) 2020-10-21 16:50:44 -05:00
Massimiliano Culpo
c696518efd
Skip malformed spec strings when searching for externals (#19438)
fixes #19266

fzf search method has also been updated

Co-authored-by: Tom Scogland <tom.scogland@gmail.com>
2020-10-21 21:35:02 +02:00
Sajid Ali
2bb775496e
mpich : add python build-only dependency (#19403)
* mpich: yaksa configure fix

	modified:   var/spack/repos/builtin/packages/mpich/package.py

* typo

* python is not needed when building from preconfigured tarballs

* add maintainers
2020-10-21 13:38:09 -05:00
Andrew W Elble
b616dbc56b
New package: py-autograd (#19425)
* py-autograd

* add missing dependencies
2020-10-21 13:37:05 -05:00
Lígia Diana Amorim
947ba7e8bf
Added FFLAGS for apple-clang:11 (#17935)
* Added FFLAGS for apple-clang:11

* Added issue #

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-21 12:34:45 -05:00
Massimiliano Culpo
bd178ead14
gromacs: fix SIMD argument for ppc64le (#19435)
fixes #19414
2020-10-21 11:33:51 -05:00
Chuck Atkins
fdf0cde5b9
veloc: Add missing openssl dependency (#19437) 2020-10-21 12:32:35 -04:00
Andrew W Elble
d4a6efd021
scipoptsuite (#19430) 2020-10-21 10:56:16 -05:00
Andrew W Elble
e9eb9cdc41
py-hdbscan (#19428) 2020-10-21 10:53:43 -05:00
Andrew W Elble
c678f119ba
glog (#19423) 2020-10-21 10:48:07 -05:00
Andrew W Elble
70cfdab372
gflags (#19422) 2020-10-21 10:47:31 -05:00
Andrew W Elble
a26b744b65
coinutils (#19421) 2020-10-21 10:46:50 -05:00
albestro
f006a54db2
Update git to 2.29.0 (#19415) 2020-10-21 11:39:43 -04:00
darmac
f4ecc8bad7
update version to avoid compile error (#19363)
* update version to avoid compile error

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-21 10:39:02 -05:00
Kelly (KT) Thompson
490105ea20
Provide doxygen@1.8.20. (#19412) 2020-10-21 10:38:40 -05:00
darmac
1a57787686
py-cvxopt: refine dependency @1.1.9 and update version to @1.2.5 (#19385)
* refine dependency @1.1.9 and update version to @1.2.5

* refine depends_on() for python
2020-10-21 10:22:26 -05:00
iarspider
640d1a0034
Add FORM (#19397)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add FORM

* Update package.py

Changes from review

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 10:20:26 -05:00
iarspider
cf733b2dd2
Add QD (#19402)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Add QD

* Update package.py

Changes from review

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-21 10:18:15 -05:00
Chris Richardson
f0712bde48
Add Allinea to cray-libsci (#19232) 2020-10-21 10:06:31 -05:00
Toyohisa Kameyama
35ad3bb0fc
quantum-espresso: fix build fail @6.6 and add conflicts a64fx. (#19383)
* quantum-espresso: fix build fail @6.6 and add conflicts a64fx.

* get patch to gitlab.

* Add +patch
2020-10-21 10:03:54 -05:00
Martin Aumüller
0e6b818c52
Add new packages: ispc & embree (#19361)
* Add new package: ispc

* Add new package: embree
2020-10-20 19:00:45 -05:00
iarspider
03611f2e89
Thepeg fix (#19405)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* Fixes for thepeg

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-20 16:33:17 -05:00
Josh Essman
cee5c2e755
mfem: Fix support for SUNDIALS and PETSc features (#19326)
* mfem: specify PETSC_DIR, link correct sundials libraries

* fix: only use PETSC_DIR directly for static builds

* fix: only use sundials nvecmpiplusx for MFEM 4.2+
2020-10-20 16:26:34 -05:00
eugeneswalker
fa9ad0a3da
tau unwind patch: only patch 2.29, not 2.29.1 (#19409) 2020-10-20 16:25:52 -05:00
iarspider
d9bb90d06e
Lhapdf extends python (#19398)
* Add recipe for qgraf

* Revert "Add recipe for qgraf"

This reverts commit 76783f73867a32b4a96e980e31a433ed3c0037fd.

* LHAPDF should extend Python to get env variables correct

Co-authored-by: Ivan Razumov <ivan.razumov@cern.ch>
2020-10-20 14:59:54 -05:00
Jean-Paul Pelteret
3a56248eba
deal.II: Add more conflicts due to symbol clashes between dependencies (#19408) 2020-10-20 14:55:22 -05:00
Massimiliano Culpo
a51702e3a2
py-archspec: added new package at v0.1.1 (#19395) 2020-10-20 18:40:31 +02:00
darmac
53fc4f92b7
axel: fix build error (#19387) 2020-10-20 11:01:26 -05:00
Chuck Atkins
9241cad299
mesa: Restrict llvm to < 11 (#19393) 2020-10-20 11:59:50 -04:00
darmac
0d1002750e
refine setuptools version to avoid spec conflict (#19384) 2020-10-20 10:56:05 -05:00
GaneshPrasadMA
0253f0af29
Adding AOCC compiler to SPACK community (#19345)
* Adding AOCC compiler to SPACK community

The AOCC compiler system offers a high level of advanced optimizations, multi-threading and processor support that includes global optimization, vectorization, inter-procedural analyses, loop transformations, and code generation. AMD also provides highly optimized libraries, which extract the optimal performance from each x86 processor core when utilized. The AOCC Compiler Suite simplifies and accelerates development and tuning for x86 applications.

* Added unit tests for detection and flags for AOCC

* Addressed reviewers comments w.r.t version checks and url,checksum related line lengths

Co-authored-by: Test User <spack@example.com>
2020-10-20 10:50:09 -05:00
ketsubouchi
f68287afe9
boost: fix building old versions with non-system glib and bzip2 (#19389) 2020-10-20 15:39:57 +02:00
Toyohisa Kameyama
9beadc3c14
krims: disable float80 when non x86_64. (#19388) 2020-10-20 15:37:47 +02:00
Roberto Di Remigio
bac1f94046
MRCPP: added new versions up to v1.3.5 (#19257)
Removed all alpha versions too
2020-10-20 14:07:22 +02:00
Seth R. Johnson
18960435af
py-pyqt4: Require older version of PySIP (#19391)
Fixes #19322, thanks sto @Sinan81.
2020-10-20 14:05:11 +02:00
Glenn Johnson
87da91cef6
add updated version of py-dnaio (#19374)
* add updated version of py-dnaio

* Add py-setuptools-scm build dependency

* Fine tune the py-xopen dependency constraint

The needed version of xopen does not become specific until v0.4 of
dnaio.

* Set constraint on py-setuptools-scm

The py-setuptools-scm dependency is needed beginning with v0.4.
2020-10-19 19:53:12 -05:00
Glenn Johnson
bb87c1ff54
updated version of py-cutadapt (#19373)
* updated version of py-cutadapt

* Update dependency specs

* Add py-setuptools-scm build dependency

* More constraint fixes

* Fix version range for py-xopen
2020-10-19 19:52:27 -05:00
Martin Aumüller
b5ff28522a
Add new package: botan (#19362) 2020-10-19 19:51:15 -05:00
Sajid Ali
3fd3676fc0
gdbm patch (#19380)
* gdbm patching

* compiler name fix

* rename patch
2020-10-19 19:49:31 -05:00
Sajid Ali
7052c65031
external find for cpio (#19379)
* external find for cpio

* address reviewer comments
2020-10-19 17:48:27 -05:00
wspear
92bbc2e789
Added tau version 2.29.1 hash (#19329)
* Added tau version 2.29.1 hash

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

Make version name match branch name (master)

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-19 16:25:58 -05:00
Glenn Johnson
449604bfe8
add updated version of py-xopen (#19375)
* add updated version of py-xopen

* Update dependency constraints

* Further refine the python constraints

Also, put them all together.

* Put python constraints at top of list
2020-10-19 16:15:20 -05:00
Sergey Kosukhin
75bfdc7335
netcdf-fortran: support for Cray compiler (#18971) 2020-10-19 16:12:09 -05:00
Glenn Johnson
c31e96dcd7
New package - pulseaudio (#19378)
This PR adds the pulseaudio package and the speexdsp package as a
dependency. In addition, this PR adds a `libs` property to the libtool
package.
2020-10-19 16:11:45 -05:00
Glenn Johnson
95b9875e95
New package - Gate (#19377)
* New package - Gate

This PR adds the Gate package as well as the ITK dependency.

* Fix flake 8 errors

* Be more explicit with CMake options

Make sure Cmake values related to variants are explicitly set to either
ON/OFF.

The ITK_USE_MKL flag will turn on the following:
- USE_FFTWD=ON
- USE_FFTWF=ON
- USE_SYSTEM_FFTW=ON

Since the package depends on fftw-api, those options will always be set.
2020-10-19 16:07:47 -05:00
Glenn Johnson
152144f17a
add updated version of trimgalore (#19376) 2020-10-19 14:53:12 -05:00
Glenn Johnson
302c69eb55
Add updated version of fastqc (#19372) 2020-10-19 13:57:43 -05:00
Dr. Christian Tacke
765b41fd34
util-linux: Add version 2.33.1 (#19370) 2020-10-19 13:27:40 -05:00
Robert Pavel
c3f3cea516
Added thrust@1.8.3 (#19368)
Added version 1.8.3 to thrust
2020-10-19 13:26:58 -05:00
Sebastian Schmitt
aef1ff7ec5
Remove version in extends (#19366)
extends expects the package name only.

Cf. #12480.
2020-10-19 13:26:37 -05:00
Andrew W Elble
0df70e217f
A collection of tensorflow fixes and updates (#19371)
* A collection of tensorflow fixes and updates

* tensorflow 2.3.1 requires the workaround for external protobuf as well
* Update tensorflow-estimator to 2.3.0
* Update tensorboard to 2.3.0
* Update tensorboard-plugin-wit to use actual releases
* Patch that potentially fixes #16073

* add myself to maintainer list
2020-10-19 13:15:49 -05:00
G-Ragghianti
9cd2ab48ab
Slate package: resolves missing header issue (#19032)
* Changed make command to support new slate build variable 'blas='

* Updated to use package's "make install" target

* Added variant 'blas' to support switching blas provider and removed legacy 'mkl' variant.

* Fixed problem caused by systems which use a non-bash /bin/sh

* Removed blas= variant in preference for setting blas provider via spec syntax (e.g., ^openblas).

* Fixed formating

* Changed to MakefilePackage and cleaned up make argument generation

* Implemented "edit" method

* Removed blank line

* Sqitched to using mpi compiler wrapper variables

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-10-19 12:16:10 -05:00
darmac
761b79e34f
r-rgeos: fix build error (#19360) 2020-10-19 10:33:32 -05:00
Amjad Kotobi
432772dbb6
openssh: new version 8.4p1 (#19358) 2020-10-19 10:32:43 -05:00
Amjad Kotobi
cbd100819a
anaconda3: new versions (#19357) 2020-10-19 10:31:58 -05:00
darmac
68b05b43e0
Add new package: py-mido (#19355) 2020-10-19 10:22:08 -05:00
darmac
b4f254df5d
Add new package: py-cekit (#18813)
* Add new package: py-cekit

* refine dependencies
2020-10-19 10:21:08 -05:00
darmac
ced73019de
Add new package: tpm2-tss (#18824)
* Add new package: tpm2-tss

* remove patch(), there's no need to use it
2020-10-19 10:14:51 -05:00
darmac
78986c5575
Add new package: percona-server (#18818) 2020-10-19 10:13:55 -05:00
darmac
d48b186500
py-coapthon3: added new package at v1.0.1 (#18990)
* Add new package: py-coapthon3

* remove mistake version
2020-10-19 11:42:48 +02:00
darmac
3807ceec0b
premake-core: added new package at v5.0.0-alpha15 (#18807) 2020-10-19 10:39:40 +02:00