Commit graph

9702 commits

Author SHA1 Message Date
Justin S
c2f45fb4da charmpp: fix build failing from broken hardlink (#13922)
* charmpp: fix build failing from broken hardlink

* charmpp: use setup_dependent_build_environment
2019-12-11 20:20:05 -06:00
Glenn Johnson
fec3a852c7 Fix replacement of embedded 'gcc' in augustus (#14116)
PR #13975 added makefile filtering to replace gcc/g++ with the spack
compiler. This conflicts with other filtering that is done in the package to
add paths for dependencies. The text of the dependency paths might
have 'gcc' in the path name, depending on the install_path_scheme, and
that was being replaced by the new compiler filters. That would mangle
the path to the dependecy resulting in a failed build.

This PR moves the compiler filters to be before the other filters to
make sure that the compiler is set before the dependency paths.
2019-12-11 20:19:27 -06:00
iarspider
695c09a8b7 Add missing dependency on setuptools to py-subprocess32 (#14074)
* Add missing dependency on setuptools to py-subprocess32

* Update package.py

* Update var/spack/repos/builtin/packages/py-subprocess32/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Update package.py
2019-12-11 20:18:39 -06:00
Brian Van Essen
53f73e280a Bugfix for bad hydrogen tags (#14119) 2019-12-11 20:17:10 -06:00
Adam J. Stewart
1f9d37c346
TensorFlow: must specify CUDA compute capabilities (#14118)
* TensorFlow: must specify CUDA compute capabilities

* Correctly restrict cuda_arch version ranges
2019-12-11 20:16:52 -06:00
Adam J. Stewart
7ec1917d9b
Add try-except for Python installation (#14122) 2019-12-11 20:16:33 -06:00
Adam J. Stewart
47615566ea
Fix JDK 8 download URLs (#14120) 2019-12-11 20:16:16 -06:00
iarspider
aac45154fd Fix py-ppft source extension (#14077)
* Fix py-ppft source extension

* PEP-8 fix

* Update package.py

* Apply suggestions from code review

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-11 14:05:14 -06:00
iarspider
d07e988fbc Fix py-pox build recipe (#14078)
* Fix py-pox build recipe

* PEP-8 fix

* Update package.py

* Apply suggestions from code review

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-11 14:04:50 -06:00
iarspider
a254f7011e Fix py-notebook for Python2 (#14079)
* Fix py-notebook for Python2

* PEP-8 fix

* Update package.py

* Update package.py

* Syntax fix

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-11 14:04:33 -06:00
iarspider
34adebc7cf Fix py-hypothesis (#14084)
* Fix py-hypothesis

* Update package.py

* Update package.py

* Update package.py
2019-12-11 14:04:18 -06:00
Dan Lipsa
6f7a58b142 Fix constexpr for llvm 9.0 (#14095) 2019-12-11 14:03:57 -06:00
Adam J. Stewart
69a91b5b6b
Add grass 7.8.2 (#14115) 2019-12-11 14:00:38 -06:00
Brian Van Essen
ee0b9bfa5b Added new versions of hydrogen (#14103) 2019-12-11 12:23:25 -06:00
Michael Kuhn
927f496306 doxygen: Fix libiconv checks (#14106)
PR #10589 introduced a libiconv dependency to doxygen. This causes
problems on Linux systems, since the iconv symbols are included in libc,
which causes CMake to use the external header but not the external
library. Work around this by always using the external libiconv.
2019-12-11 12:22:59 -06:00
Glenn Johnson
f2979da2af Build xed CLI for the intel-xed package (#14114)
The xed CLI is handy, and can be gotten by building the examples in the
intel-xed package. This PR builds the examples and installs the xed CLI.
It would also be possible to install more of the example binaries if
someone thinks they are useful.
2019-12-11 12:13:27 -06:00
Mark Olesen
77482e102a openfoam relocated to https://develop.openfoam.com/Development/openfoam.git (#14101) 2019-12-11 12:12:30 -06:00
noguchi-k
b0a7c8487d diamond: fix narrowing error. (#14064)
* diamond: fix narrowing error

* diamond: fix patch

* diamond: add link to the patch source
2019-12-11 12:07:21 -06:00
iarspider
d4326038b9 Fix py-pkgconfig recipe (#14081)
* Fix py-pkgconfig recipe

* Update package.py

* Proper fix for py-pkgconfig
2019-12-11 12:06:18 -06:00
iarspider
bb3bae4bae Fix py-pathos source file extension (#14080)
* Fix py-pathos source file extension

* PEP-8 fix

* Add version 0.2.3 to spack

* Update package.py
2019-12-11 12:04:45 -06:00
iarspider
ec3d979899 Fix py-llvmlite (#14083)
* Fix py-llvmlite

* Update package.py

* Add llvmlite 0.29

* Update package.py
2019-12-11 12:03:48 -06:00
iarspider
5c2afd0535 Fix py-dill source archive extension (#14085)
* Fix py-dill source archive extension

* Add py-dill 0.2.7, remove extra str()

* Update package.py

* Update package.py

* Update package.py
2019-12-11 12:03:28 -06:00
Howard Pritchard
e7a03d07b6 llvm: fix for building llvm using Cray PE (#12734)
Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-12-11 11:51:44 -06:00
iarspider
3cd6ca02d2 Fix json-c package (#14087)
* Fix json-c package

* Fix PEP-8

* Update package.py

* Update package.py
2019-12-10 17:34:50 -06:00
iarspider
ec060f3d9c Fix libgeotiff dependency of gdal (#14089)
* Fix libgeotiff dependency of gdal

* Update package.py

* Fix typo

* Update package.py
2019-12-10 17:34:35 -06:00
Justin S
2c31776007 openmolcas: new package at 19.11 (#14099)
* openmolcas: new package at 19.11

* openmolcas: fill description

* openmolcas: rewrite using CMakePackage

* openmolcas: add py-six dep

* openmolcas: use setup_build_environment, setup_run_environment

* openmolcas: remove redundant cmake dep

* openmolcas: explicitly cast Executable to str
2019-12-10 17:33:52 -06:00
iarspider
5b3b522861 Alternative locations for tclConfig and tkConfig (#14071)
* Alternative locations for tclConfig and tkConfig

* Fix PEP-8
2019-12-10 15:18:19 -06:00
Eric Berquist
33f603734d Update tmux to 3.0a (#14096)
* Add tmux@2.9 and tmux@3.0a

* Fix checksums
2019-12-10 15:06:21 -06:00
Christoph Junghans
34f0195de8 gromacs-2018.8: fix checksum (#14069) 2019-12-10 12:33:41 -06:00
iarspider
fb6d29adfa ROOT: +http variant doesn't require any external dependency (#14072) 2019-12-10 12:29:11 -06:00
iarspider
f96216cf40 Fix py-pyasn1 version for py-pyasn1-modules (#14076) 2019-12-10 12:26:16 -06:00
iarspider
122264609e Fix for DD4Hep build: can't find boost (#14091) 2019-12-10 11:58:52 -06:00
iarspider
dd67868ef6 More variants for cairo (#14092) 2019-12-10 11:58:37 -06:00
Simo Tuomisto
9e8204d075 openfoam-org: Adding openfoam-org versions 6 and 7. (#12859)
This commit adds openfoam-org versions 6 and 7. It also adding new variant for metis and fixes openfoam-org's old environment modification functions.
2019-12-10 09:42:01 -06:00
Mark W. Krentel
c627e5a6fc intel-tbb: fix and cleanup patch version ranges (#14053)
Recent commit e9ee9eaf (#13989) fixed testing version ranges inside
patch when clauses.  Previously, it was necessary to write all revs
individually for packages with multiple length version numbers (2019
and 2019.1).

This fixes the build for the old 2017.* versions.
2019-12-09 17:11:47 -06:00
Adam J. Stewart
23faffa2d0
TensorFlow: don't override HOME env var (#14054) 2019-12-09 11:22:57 -06:00
Matt Larsen
919a5421b7 fix incorrect gpu arch map for vtk-m package (#14057) 2019-12-09 11:18:51 -06:00
Adam J. Stewart
aa8d5d2e8c
cbtf-krell: fix missing dependencies (#14021) 2019-12-08 15:51:04 -06:00
Adam J. Stewart
2266aab5c5
Add new r-condop package (#14050) 2019-12-08 09:29:51 -06:00
Adam J. Stewart
c72568d01b
Add new r-earth package (#14049) 2019-12-08 09:06:53 -06:00
Adam J. Stewart
bf9661f18a
Add new r-plotmo package (#14048) 2019-12-08 09:06:37 -06:00
Adam J. Stewart
0c1599403d
Add new r-teachingdemos package (#14047) 2019-12-08 09:06:20 -06:00
Adam J. Stewart
cb258daf88
Add new r-graphlayouts package (#14046) 2019-12-08 09:06:04 -06:00
Adam J. Stewart
4593b7b693
Add new r-tidygraph package (#14045) 2019-12-08 09:05:46 -06:00
Adam J. Stewart
3547776921
py-torch: comment out non-existing deps (#14044) 2019-12-08 09:05:21 -06:00
Adam J. Stewart
aca67581e8
Add new py-requests-mock package (#14043) 2019-12-08 09:05:04 -06:00
Adam J. Stewart
99d2bcf64e
py-luigi: fix test dependencies (#14042) 2019-12-08 09:04:45 -06:00
Christoph Junghans
16a61d1422 elpa: port to microarch (#13655)
* elpa: port to microarch

* flake8

* Update package.py

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-08 09:03:59 -06:00
Adam J. Stewart
4e24c4ca5f
Add new py-pytest-mypy package (#14041) 2019-12-08 00:10:46 -06:00
Adam J. Stewart
4fb03f7222
Add new py-sphinxcontrib-issuetracker package (#14040) 2019-12-08 00:10:32 -06:00
Adam J. Stewart
8d21e39f00
py-python-htmlgen -> py-htmlgen (#14039) 2019-12-08 00:10:17 -06:00
Adam J. Stewart
fdc3176920
Add new py-asserts package (#14038) 2019-12-08 00:10:02 -06:00
Adam J. Stewart
4f7c28e9cd
py-brian2: py-nosetests -> py-nose (#14037) 2019-12-07 23:21:27 -06:00
Adam J. Stewart
ab250a2e3a
polymake: fix dependency name (#14034) 2019-12-07 22:14:48 -06:00
Adam J. Stewart
0a1d2a45f4
Add py-jupyter package (#14035) 2019-12-07 22:14:34 -06:00
Adam J. Stewart
db1026cb62
Add new py-wxmplot package (#14036) 2019-12-07 22:14:20 -06:00
Adam J. Stewart
891ccbea3f
Add new py-stestr package (#14029) 2019-12-07 15:40:08 -06:00
Adam J. Stewart
c1826d9d32
Add new py-testrepository package (#14030) 2019-12-07 15:39:53 -06:00
Adam J. Stewart
129e548ac0
Add new py-testresources package (#14031) 2019-12-07 15:39:38 -06:00
Adam J. Stewart
71ec2db3a9
Add new py-testscenarios package (#14032) 2019-12-07 15:39:24 -06:00
Adam J. Stewart
e77a557ca1
Add new py-testtools package (#14033) 2019-12-07 15:39:11 -06:00
Adam J. Stewart
cec03c2db4
Add new py-python-subunit package (#14028) 2019-12-07 15:38:56 -06:00
Quinn
1a662f428e Add New package feh and supporting packages (#14013)
* Adding libid3tag package for supporting feh

* Adding libexif package for supporting feh

* Adding imlib2 package for supporting feh

* Adding the feh package

* Rewording the cleanup function for libid3tag

* Fixing some flake8 issues for imlib2 and libid3tag

* Adding sources for the patches and swapping rm for os.remove

* Flake8 fixes

* swapping md5sums for sha256sums
2019-12-07 15:38:41 -06:00
Adam J. Stewart
a9f6caf863
Add new py-hacking package (#14027) 2019-12-07 14:04:06 -06:00
Adam J. Stewart
c88b95bd28
Add new py-fixtures package (#14026) 2019-12-07 14:03:41 -06:00
Adam J. Stewart
e78865b3ab
Add new py-extras package (#14025) 2019-12-07 14:03:06 -06:00
Adam J. Stewart
b6a6f28482
Add py-tox package (#14024) 2019-12-07 14:02:39 -06:00
Adam J. Stewart
9ece63242a
Add latest version of py-importlib-metadata (#14023) 2019-12-07 14:02:16 -06:00
Adam J. Stewart
31b45d40d9
flann: fix missing dependencies (#14022) 2019-12-07 14:01:39 -06:00
Christoph Junghans
969bc948b5 votca*: add v1.6_rc1 (#14017)
* votca*: add v1.6_rc1

* votca: prefer v1.5.1
2019-12-07 10:04:15 -06:00
Axel Huebl
15bb5da99f openPMD-api: 0.10.1 (#14018)
Add the latest release of openPMD-api.
2019-12-07 10:02:53 -06:00
Axel Huebl
d705e96a63
Spec Header Dirs: Only first include/ (#13991)
* CUDA HeaderList: Unit Test

* Spec Header Dirs: Only first include/

Avoid matching recurringly nested include paths that usually
refer to internally shipped libraries in packages.
Example in CUDA Toolkit, shipping a libc++ fork internally
with libcu++ since 10.2.89:
`<prefix>/include/cuda/some/more/details/include/` or
`<prefix>/include/cuda/std/detail/libcxx/include`

regex: non-greedy first match of include

Co-Authored-By: Massimiliano Culpo <massimiliano.culpo@gmail.com>

* CUDA: Re-Enable 10.2.89 as Default
2019-12-06 23:47:03 -08:00
Mark W. Krentel
9d9737f765 ibm-java: add version 8.0.6.0 (#14003)
* ibm-java: add version 8.0.6.0

Add version 8.0.6.0 and remove 8.0.5.30.  IBM is fairly aggressive
about removing old versions, and 8.0.5.30 is no longer available from
their download site.

* Restore version 8.0.5.30, although it is no longer available for
download from IBM.
2019-12-06 18:11:24 -06:00
Francesco Di Natale
01d35a4f3b Packages/py-maestrowf (#14010)
* Addition of repository branches to maestrowf.

* Addition of 1.1.5dev pre-release.

* Correction of a merge conflict.

* Addition of Maestro release 1.1.5

* Addition of Maestro release 1.1.6 (removal of 1.1.5)

* Sets 1.1.6 to the preferred version.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* Tweak to the url to point to latest.
2019-12-06 18:10:58 -06:00
Adam J. Stewart
66a169e2a5
Add py-parameterized package (#14016) 2019-12-06 18:09:00 -06:00
Adam J. Stewart
350a5422ed
Update py-theano dependencies (#14015) 2019-12-06 18:08:34 -06:00
nicolas le goff
d173ec6a35 mesquite: fix build of the no mpi variant. (#14012)
* mesquite: fix build of the no mpi variant.

* mesquite: added the --without-mpi option to configure.
2019-12-06 18:08:13 -06:00
Teodor Nikolov
65a292fbbf [Package: HPX] Fix Apex and OTF2 support (#13982)
* Fix Apex and OTF2 support

- Comment out apex as a dependncy: it is bundled with HPX.
- Apply a patch to v1.3.0 to correctly build with APEX.
- Add otf2 as a dependency when APEX is enabled.

* Remove depends_on('apex')
2019-12-06 12:41:55 -06:00
t-karatsu
06042ec7ec augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack (#13975)
* augustus: Set compile commands for each compiler and Fix for using 'boost' on Spack

* fix for flake8

* delete 'string' args

* Fix args of filter_file func

* Fix args of other filter_file func
2019-12-06 12:39:23 -06:00
Galen Shipman
5d523dd689 Add patch to fix issue building current llvm develop master on power9 (#13986)
* Add patch to fix issue building current llvm develop master on power9

* Conform to proper block commenting

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-06 12:38:58 -06:00
Tamara Dahlgren
dd26cc4004 Fastmath: Added required version (#13990)
* Fastmath: Added required version

* Changed the version to 'latest' (per balay).
2019-12-06 12:38:29 -06:00
Tamara Dahlgren
5e49b76dd7 Ceed: Added required version (#14006) 2019-12-06 12:38:00 -06:00
t-karatsu
246799d4ce sz: Change optimization flags for Fujitsu compiler (#14007) 2019-12-06 12:05:16 -06:00
Paul
67e45096c8 Specify self for internal setup method (#14008) 2019-12-06 12:04:57 -06:00
Brian Homerding
5e20bd86e4 Convert llvm Spackage to use the monorepo (#11392)
* [WIP] Convert llvm spackage to use the monorepo

* Correcting python dependencies

* Adding develop version for llvm monorepo

* Python 2.6 Fix

* Build Flang fork in a different root_cmakelists_dir

* Formatting Fix

* Including flang package changes

* Removing explicit llvm dependencies variants

* flake8 fix

* Updating patches and llvm+flang logic

* Updating env setup API

* Add top level git

* Conflicting flang variant with other variants
2019-12-06 12:01:30 -06:00
Seth R. Johnson
f069a3feda Add h5sh python package (#14001)
* Add h5sh package

* Fix requirements and update version
2019-12-06 11:58:59 -06:00
Mark W. Krentel
f84ad57fe7 hpcviewer: add version 2019.09 (#14004)
Add version 2019.09.  Adjust the iteration through versions to
eliminate the need for version_list.
2019-12-05 18:59:30 -06:00
Dominik Dold
c3eafde7bf Add new TensorFlow package (#13112)
* add tensorflow

Change-Id: Id778c68d148cc42f0b478a9d10a8f937cb54cdc6

* make bazel and tensorflow build

Change-Id: Iae9005e8f4dcc8f1ed36ea9337d2430aeebb291f

* fix flake8

Change-Id: Ib05529dd796eab4a8855a5d7775cc4efea8e479d

* 2nd flake8 attempt

Change-Id: I46224be3a374b2a65793048b0c5178ea64adbd78

* replace md5 sums with sha256

* add version 1.13.2

* bazel() -> bazel('build',...

* specify versions of bazel dependency

* build with CUDA

* add TODOs

* add more todo"s

* improve enum34 dependency

* py-future is a dependency as of v1.14

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* enable nccl, cuda by default

* explain patches

* add todo

* remove unnecessary copt_flag

* use join

* join argument must be an iterable

* split long line; use same opts for non-cuda build

* without opt flags, configure hangs

* introduce build phases; re-arrange

* undo mistake

* restore unset tmp_path

* as of v1.14, nccl_install_path is parsed correctly, hence change ...prefix.lib to ...prefix

* now, version 1.14 compiles successfully with cuda

* add version 2.1.0

* specify bazel dependency for version 2.1.0-rc0

* account for deprecated bazel opts for v2.1.0-rc0

* disable mkldnn contraction kernel

* Flake8 fixes

* md5 -> sha256

* Fix TF and TF-estimator version deps

* Don't just comment out patch

* Add myself as a maintainer

* Patch py-astor to support newer py-setuptools

* Add more versions and bazel version constraints

* Add a build phase

* Add note about configure interactivity

* dev-build -> build-env

* Disable iOS build

* Use correct optimization flags

* Add variants for all possible features

* nccl isn't always a dependency

* Specify correct dependency versions for each release

* Libs may not be in lib or lib64

* Add py-opt-einsum package

* Add newer version of py-protobuf

* Add newer version of py-wrapt

* Fix Python 2.6 syntax error

* Code review

* Set more env vars for older versions

* Add more env vars, fix bazel versions, add conflicts

* Fix config options

* Specify version that support --config args

* Add py-future dependency for Python 2

* Fix cuda config flag and compute capabilities

* Fix installation on macOS, add unit tests

* Override cuda variant default to True on non-macOS

* Rename tensorflow to py-tensorflow

* Has to extend something

* Fix os.symlink call

* convert cuda_arc values to capabilities

* restore nccl prefix path for v1.13.1

* Revert to v2

* Remove extraneous period

* Add new version of jdk/openjdk

* More stable cuda_arch formatting

* Fix bazel unit tests

* Fix symlinking

* Fix unit tests

* +gcp by default until build error figured out
2019-12-05 18:48:20 -06:00
Chuck Atkins
831133a4c3 paraview: Adjust python version constraints (#13999)
py-matplotlib: No constraint necessary for py3 but py2 has an upper bound
py-numpy: No constraint necessary for py3 but py2 has an upper bound
2019-12-05 12:06:47 -06:00
Paul
9a0b1b6aef Added go 1.13.5 and 1.12.14 (#13997) 2019-12-05 11:29:00 -06:00
Chuck Atkins
fcc9a668bf py-pillow: allow older versions to build with python 3.4 (#14000) 2019-12-05 11:27:33 -06:00
Christoph Junghans
2da2fc8bc5
eospac: fix url (#13998) 2019-12-05 09:30:35 -07:00
Alexander Knieps
dbdc6c4a68 New package: swipl (#13978)
* New package: swipl

* Removed boilerplate, added maintainer

* Fixed python 2 incompatibility

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>

* swipl: Added conflict with intel compiler
2019-12-05 09:51:38 -06:00
Peter Scheibel
e9ee9eaf50 patching: do strict version range checking (#13989)
* apply strict constraint checks for patches, otherwise Spack may incorrectly treat a version range constraint as satisfied when mixing x.y and x.y.z versions
* add mixed version checks to version comparison tests
2019-12-04 22:27:08 -08:00
Adam J. Stewart
ad5d612925
Add py-matplotlib 3.1.2 (#13994) 2019-12-05 00:00:20 -06:00
Axel Huebl
ba156dfcd8 CUDA: Keep 10.1.243 As Preferred (#13983)
Keep CUDA 10.1.243 as the preferred version until the issue
of including implementation details of libcu++ is addressed.
2019-12-04 21:28:10 -06:00
Stephen Hudson
e0e9fb4462 Update libensemble to v0.6.0 (#13987) 2019-12-04 18:01:05 -06:00
Adam J. Stewart
10f4445309
Add latest version of py-scikit-learn (#13979) 2019-12-04 11:47:07 -06:00
Tim Haines
728f5a76f3 Add Elfutils 0.178 (#13976)
* Add elfutils-0.178

* Disable debuginfod server

* Fix flake8
2019-12-04 07:50:44 -06:00
Tim Haines
bb33b6b8e6 Use correct range check for the version (#13977)
Update to #13893
2019-12-04 07:50:05 -06:00