Commit graph

9953 commits

Author SHA1 Message Date
Matthias Diener
37c1d2d004 cmake: add version 3.16.2 (#14291) 2019-12-24 10:05:54 -06:00
Matthias Diener
ee8bc0df98 scons: add version 3.1.2 (#14290) 2019-12-24 10:05:18 -06:00
健美猞猁
748c552992 Bump nektar to 5.0.0. (#14288) 2019-12-24 10:01:16 -06:00
Gregory Lee
99dee90372 added master branch version to mpip (#14284) 2019-12-23 17:24:19 -06:00
Christoph Junghans
643cc95055 gromacs: add v2019.5 (#14285) 2019-12-23 17:24:03 -06:00
Nicholas Sly
9573fa2299 Added conflict with %pgi in libpciaccess package.py with relevant links in comments. (#14281) 2019-12-23 15:31:59 -06:00
Piotr Luszczek
ae8a72c0da netlib-scalapack: Add int overflow patch (#14276) 2019-12-23 13:06:29 -06:00
Adam J. Stewart
e2ec1c76ce
Add py-boto3 1.10.44 (#14271) 2019-12-22 21:39:25 -06:00
Timo Heister
fa0d710626 add new package : libdap4 (#14267) 2019-12-22 21:36:47 -06:00
Adam J. Stewart
ded5cbec70
Add py-numpy 1.18.0 (#14269) 2019-12-22 21:36:28 -06:00
Adam J. Stewart
0950442ea0
Add awscli 1.16.308 (#14270) 2019-12-22 21:36:14 -06:00
Adam J. Stewart
013ff54731
Add py-botocore 1.13.44 (#14272) 2019-12-22 21:35:39 -06:00
Piotr Luszczek
2a3bf87484 Add new release and remove extraneous patches (#14273) 2019-12-22 18:10:19 -08:00
Glenn Johnson
3690bc44bd Set full xiar path when building cp2k with intel compiler (#14268) 2019-12-22 16:19:12 -06:00
justbennet
b83365c945 Updating preferred OpenMPI version to 3.1.5 (#14266) 2019-12-22 11:59:21 -08:00
Axel Huebl
249c1d9d81 openPMD-api: 0.10.3 (#14265)
Add latest release.
2019-12-22 10:01:28 -06:00
xfzhao
a10253a667 new module beagle (#14257) 2019-12-21 18:22:56 -06:00
Sajid Ali
8fe2c0a4fe Bump py-slepc4py version, update url (#14264)
* version bump

	modified:   var/spack/repos/builtin/packages/py-slepc4py/package.py

* slepc: update URL
slepc4py: add 3.11.0 and update maintainers

Co-authored-by: Satish Balay <balay@mcs.anl.gov>
2019-12-21 18:22:40 -06:00
Sajid Ali
8522d1f0cf build bazel with jdk (#14258)
* build bazel with jdk

* Flake 8

* Fix typo
2019-12-20 19:40:05 -06:00
Adam J. Stewart
87d0ac804e
npm: add Python 3 support (#14255) 2019-12-20 16:38:35 -06:00
Massimiliano Culpo
497fddfcb9 Fetching from URLs falls back to mirrors if they exist (#13881)
Users can now list mirrors of the main url in packages.

- [x] Instead of just a single `url` attribute, users can provide a list (`urls`) in the package, and these will be tried by in order by the fetch strategy.

- [x] To handle one of the most common mirror cases, define a `GNUMirrorPackage` mixin to handle all the standard GNU mirrors.  GNU packages can set `gnu_mirror_path` to define the path within a mirror, and the mixin handles setting up all the requisite GNU mirror URLs.

- [x] update all GNU packages in `builtin` to use the `GNUMirrorPackage` mixin.
2019-12-20 14:32:18 -08:00
Nichols A. Romero
1b93320848 PGMATH library symbols patch (#14254)
* Add symbols patch

* Apply symbols patch to pgmath

* Add github issue number for symbols patch.

* Add naromero77 as a maintainer.

* Patch only applied to March 2019 release and master.
2019-12-20 16:23:38 -06:00
Adam J. Stewart
abf8e09fe5
Add py-pyinstrument package (#14241) 2019-12-20 16:17:22 -06:00
Adam J. Stewart
73dbda8c5a
node-js: add Python 3 support (#14242)
* node-js: add Python 3 support

* Update node-js, fix Python 3 support in v12
2019-12-20 16:17:04 -06:00
Hadrien G
3dd59c569e Latest versions of CMake need a hand for Python detection (#14247) 2019-12-20 14:52:53 -06:00
Hadrien G
3bb9d0feb4 root: Record that old versions of ROOT don't support modern GCC (#14250)
* Record that old versions of ROOT don't support modern GCC

* Well, actually I don't know about 6.07

* Fix typo and follow odd version recommendation from @chissg
2019-12-20 12:55:16 -06:00
Nichols A. Romero
f408535f2d QE Update Dec 2019 (#14238)
* Add QE 6.5

* Support for serial HDF5 case with serial (no mpi) QE is now supported but requires a patch for 6.4.1 and 6.5.

* Add naromero77 as a maintainer.
2019-12-20 12:53:36 -06:00
Hadrien G
97afe560d5 Do not apply the unuran patch to ROOT 6.06/xy, it is not compatible (#14245) 2019-12-20 12:53:20 -06:00
Adam J. Stewart
d01ceabca2
Add py-pyinstrument-cext package (#14240) 2019-12-20 11:59:18 -06:00
Hadrien G
71d10d76dc Adding myself as a ROOT maintainer (#14251) 2019-12-20 11:48:54 -06:00
Andras Wacha
72eef17ff9 Added hwloc dependency to gromacs (#14244) 2019-12-20 08:49:35 -07:00
Patrick Schratz
48fb5b8b17 R: added v3.6.2 (#14248) 2019-12-20 16:25:09 +01:00
Hadrien G
a5cab03d10 ACTS: added v0.13.0 and v0.12.1 (#14246) 2019-12-20 16:05:48 +01:00
Ethan Stam
e89915eacc New package: cinema_lib (#14231)
* Start cinema package

* Remove boilerplate and add description

* Formatting for pep8

* Correct milestone tag

* 'master' instead of 'develop'

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

* Two variants, both with numpy and other small changes

* When +image for scikit

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-19 19:37:22 -06:00
Chris Green
530a67c280 root: Add chissg as maintainer. (#14235) 2019-12-19 17:27:35 -06:00
Adam J. Stewart
01edc28fde
Add py-scipy 1.4.1 (#14230) 2019-12-19 14:33:20 -06:00
Adam J. Stewart
ae52f41448
dmd: setup dependent build environment (#14198)
* dmd: setup dependent build environment

* Fix call signature of setup_dependent_build_environment
2019-12-19 12:47:04 -06:00
Hadrien G
5940ec0d74 Remove python2-ism in root package (#14223) 2019-12-19 12:45:09 -06:00
Todd Gamblin
531f370e0d possible_dependencies() now reports missing dependencies
- Add an optional argument so that `possible_dependencies()` will report
  missing dependencies.
- Add a test to ensure it works.
- Ignore missing dependencies in `possible_dependencies()` by default.
2019-12-18 21:10:31 -08:00
t-karatsu
92c2c47f72 aspell: Rename 'darwin.patch' and apply it to all targets. (#14206) 2019-12-18 17:10:05 -06:00
Greg Sjaardema
8da6fcf324 NETCDF-C: Add latest release 4.7.3 (#14214)
Added checksum for latest NetCDF release 4.7.3
2019-12-18 17:09:50 -06:00
Greg Becker
67603d71bc Add dependencies for hpcrypt (#8067)
* Add dependencies for hpcrypt

* address review comments

* flake

* license-fix

* fix checksums

* Update py-hvace homepage

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

* update py-hvac url

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-18 17:09:26 -06:00
t-karatsu
135cf4835f amrex: Define module directry when compiling with Fujitsu compiler. (#14124) 2019-12-18 13:47:21 -06:00
Michael Kuhn
52894f5c71 Fix pkgconfig dependencies (#14175)
pkgconfig is the virtual provider, pkg-config is an implementation.
2019-12-18 13:46:45 -06:00
Greg Sjaardema
5052ce803d PNETCDF: Update to include latest release 1.12.1 (#14213)
Added checksum for recent 1.12.1 release.
2019-12-18 13:45:19 -06:00
Greg Sjaardema
99a19596c4 SEACAS: Update to include new versions (#14212)
Added checksum and tag name for last two SEACAS releases.
2019-12-18 13:45:03 -06:00
Adam J. Stewart
fa5e8aa876
wireshark: remove non-existing dependencies (#14209) 2019-12-18 12:55:15 -06:00
Adam J. Stewart
09b17ea147
py-scikit-optimize: fix test dependency (#14210) 2019-12-18 12:47:35 -06:00
Marc Mengel
0607579fd3 New package: py-zc-lockfile (#13586)
* package py-zc-lockfile

* package py-zc-lockfile

* autopep8, docutils cleanup

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

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

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

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

* dependency at wrong level

* license bits

* Remove py-zc-buildout dependency
2019-12-18 12:17:39 -06:00
darmac
201a62d957 add new package : filebench (#14158)
* add new package : filebench

* remove alpha version and duplicated autoheader cmd

* refine automake cmd in sh()

* refine filebench url as a stable tarball link
2019-12-18 11:30:10 -06:00
darmac
5a1b6e1cfc add new package : hama (#14159)
* add new package : hama

* mv hama/hama/package.py to hama/package.py
2019-12-18 11:29:48 -06:00
darmac
6e12c49c28 Hbase (#14161)
* add new package : hbase

* add hbase description

* refine hbase version and depends
2019-12-18 11:29:30 -06:00
Chris Green
ae3eac0b19 root: Rationalize and improve version, variant and ROOT option handling. (#14203)
* root: Rationalize and improve version, variant and ROOT option handling.

* Completely re-vamp CMake option handling for readability and maintainability:
  * Three categories of option: control, builtin and feature, alphabetically sorted.
  * Each option is described as a list: an option name followed by an optional value which is either Boolean or a string representing the name of a variant. If the value is omitted, it defaults to the option name.
  * New functions `_process_opts()` and `_process_opt()` (nested) to turn all supplied option/value specifications into CMake arguments.
  * Remove overly-terse per-option comments in favor of (much) more comprehensive notes in README.md.
* Variants and conflicts:
  * Remove `test` variant in favor of pegging ROOT `testing` option to the value of `self.run_tests` since the install is unaffected, per ROOT developer.
  * Remove commented-out and never-functional variants: `asimage`, `avahi`, `kerberos`, `ldap`, `libcxx`, `odbc`, `oracle`, `pythia8`, `xinetd`.
  * New variant `vmc` (default `OFF`) to control the Virtual Monte Carlo interface.
  * Conflict: `+opengl` is incompatible with `~x`.
  * Conflict: `http` is now an unconditional conflict due to dependency issues (see README.md).
* Remove commented-out and non-existent dependencies `avahi`, `kerberos`, `ldap`, `libcxx`, `odbc`, `oracle`, `pythia`, `veccore` (per #13949).
* New and changed options:
  * Option `pch` was inadvertently set to `OFF` due to its dependence on a nonexistent variant `pch`. As it happens its value is ignored in the ROOT configuration handling, so there was no deleterious effect. It has been fixed to `ON` to better reflect actual behavior pending enablement of tuntime C++ modules.
* Add new versions 6.18.0{0,2,4}:
  * Require CMake 3.9 for 6.18.00+.
  * Add conflicts for variants `qt4` and `table` representing ROOT build options for which support was discontinued. Remove redundant conflict on \@master.
  * C++ standard is now specified with `-DCMAKE_CXX_STANDARD=X` rather than `-Dcxx=X`.
* Remove old version 5.34.38 (wrong build system).

See README.md for more details of option-related changes.

* Flake8

* `rpath` option is a control option rather than a feature.
2019-12-18 11:14:47 -06:00
Jimmy Tang
3511245ca4 Add abseil-cpp package (#14208) 2019-12-18 09:33:44 -06:00
Hadrien G
9583bde739 Add new DD4hep release and some forgotten build requirements (#14195)
* Add new DD4hep release and some forgotten build requirements

* PR review suggestions

Use master naming convention for development branch, and put versions in decreasing order.
2019-12-18 09:32:23 -06:00
Sinan
a24b973fa4 package/gdal add v2.4.3 (#14204) 2019-12-17 21:57:39 -06:00
Nathan Pinnow
60a22f1a7a Update and Fix ROSE Package (#14186)
* rose: Update boost dependency for rose

* rose: Updated rose to version 0.9.12.45

* rose: Updated jdk dependency

* rose: Updated rose to version 0.9.13.0

* rose: Fixed formatting

* rose: Added maintainer and switch dependency to java@8
2019-12-17 18:18:24 -06:00
Axel Huebl
5db646d768 openPMD-api: 0.10.2 (#14201)
Add the latest release of openPMD-api, v0.10.2
2019-12-17 18:16:26 -06:00
darmac
07f522bed6 add new package : openresty (#14169)
* add new package : openresty

* remove rc version
2019-12-17 14:30:19 -06:00
darmac
6a0d15a5c9 add new package : nicstat (#14173)
* add new package : nicstat

* refine nicstat edit operation

* refine CMODEL regex expression
2019-12-17 14:29:56 -06:00
Brian Van Essen
dc69256a59 Added package for Half C++ header-only library. (#14189)
* Added package for Half C++ header-only library.

Fixed an checksum for Hydrogen 1.3.2.  Cleaned up the Clara package to
not create an empty bin directory.

* Fixed flake8

* Added maintainer
2019-12-17 14:29:31 -06:00
darmac
a52df46e2c add new package : haproxy (#14160)
* add new package : haproxy

* add url_for_version() and refine haproxy build code
2019-12-17 12:50:10 -06:00
darmac
cd8be44f62 add new package : cosbench (#14171)
* add new package : cosbench

* add cosbench depends and remove unstable version

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

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

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-17 12:48:27 -06:00
Sajid Ali
f657f73e94 tf verbosity to better enable debugging (#14177)
* tf verbosity

* Add more debug flags

	modified:   var/spack/repos/builtin/packages/py-tensorflow/package.py

* Fix later

* More debug/verbose options.

	modified:   var/spack/repos/builtin/packages/py-tensorflow/package.py
2019-12-17 12:46:34 -06:00
Shintaro Iwasaki
1a41380649 sollve: add a version 1.0a2 (#14188) 2019-12-17 12:38:32 -06:00
Yuanqi Wang
8bda848cb9 LAMMPS: Fix USER-REAXC package variant (#14192) 2019-12-17 12:35:06 -06:00
Adam J. Stewart
189eb5b883
Add py-scipy 1.4.0 (#14193) 2019-12-17 10:00:03 -06:00
t-karatsu
d831db37ca adios2: Fix use of builtin __clear_cache (#14123) 2019-12-17 08:08:22 -05:00
Todd Gamblin
a4ff92e42d mrnet: remove nonexisting cti dependency (#14178)
MRNet had an optional dependency on `cti`, which doesn't exist.  Remove
it from the repo, at least until someone adds `cti` back.
2019-12-16 21:03:38 -06:00
Hadrien G
e366d5b559 New ACTS version (#14180) 2019-12-16 10:25:37 -06:00
darmac
9ece934084 add new package : py-s3cmd (#14166)
* add new package : py-s3cmd

* add some depends and move depends behind the version
2019-12-16 10:20:15 -06:00
Peter Scheibel
60580f5871 package hash: gracefully handle @when with non-string args (#14153)
* when constructing package hash, default to including a method in the content hash if we can't determine whether it would be included by examining the AST
* add a test for updated content-hash calculations
* refactor content hash tests to eliminate repeated lines
2019-12-14 14:31:39 -08:00
Mark W. Krentel
410bce91d4 hpctoolkit: update git branch for version 'gpu' (#14155) 2019-12-14 12:37:04 -06:00
Brian Van Essen
34128ca70d Updated Hydrogen version to 1.3.2 (#14156) 2019-12-14 12:36:33 -06:00
darmac
5e9fb6b309 add new package : memcached (#14162) 2019-12-14 12:28:51 -06:00
darmac
986df8c233 add new package : jstorm (#14163) 2019-12-14 12:27:39 -06:00
darmac
0f0e2c4397 add new package : logstash (#14164) 2019-12-14 12:26:43 -06:00
darmac
72390ecd62 add new package : pig (#14165) 2019-12-14 12:26:14 -06:00
darmac
43712b4982 add new package : rabbitmq (#14167) 2019-12-14 12:21:09 -06:00
darmac
2f4521d418 add new package : zookeeper (#14170) 2019-12-14 12:19:40 -06:00
darmac
f40520c6bf add new package : bind9 (#14172) 2019-12-14 12:16:39 -06:00
darmac
33028c8955 add new package : rt-tests (#14174) 2019-12-14 12:12:01 -06:00
Andras Wacha
f757b6f4e5 Patch: explicitly use xbitmaps include dir in the automake package (#14128)
* Patch: explicitly use xbitmaps include dir in the automake package

* Added dependencies required for autoreconf: libtool, autoconf, automake, m4
2019-12-14 10:54:27 -06:00
darmac
7e668b1153 add new package : cassandra (#14144)
* add new package : cassandra

* make stable version as a preferred one
2019-12-13 22:21:18 -06:00
Adam J. Stewart
43e9fe95ea
Add latest version of jq (#14134) 2019-12-13 15:44:09 -06:00
Matthieu Dorier
f589f69a6c FIX: Making berkeley-db package fetch from correct links (#14147)
* making berkeley-db package fetch from oracle website

* removed blank space

* making flake8 happy

* fixing typos and order of versions
2019-12-13 15:19:59 -06:00
Dan Lipsa
0167ceb104 Add shared option to ParaView. (#14131)
* Add shared option to ParaView.

* Use append for one attribute
2019-12-13 15:19:31 -06:00
Adam J. Stewart
83baf35246
Add new aws-parallelcluster package (#14139) 2019-12-13 12:55:15 -06:00
Adam J. Stewart
268914e7a2
Add latest version of py-tabulate (#14138) 2019-12-13 12:54:59 -06:00
Adam J. Stewart
988b377382
Add latest version of py-ipaddress (#14137) 2019-12-13 12:54:42 -06:00
Adam J. Stewart
da501564cb
Add latest version of py-botocore (#14136) 2019-12-13 12:54:23 -06:00
Adam J. Stewart
5db615feca
Add latest version of py-boto3 (#14135) 2019-12-13 12:54:05 -06:00
Adam J. Stewart
2e19a9343b
Add latest version of oniguruma (#14133) 2019-12-13 12:53:44 -06:00
Seth R. Johnson
c659408368 Update CMake to version 3.16 (#14152) 2019-12-13 12:53:19 -06:00
noguchi-k
3e5c926a95 gmodel: fix error (#14140) 2019-12-13 12:53:03 -06:00
darmac
481a920fe8 add new package : activemq (#14142) 2019-12-13 12:51:59 -06:00
darmac
3344bb0a96 add new package : alluxio (#14143) 2019-12-13 12:51:30 -06:00
darmac
03203a86b4 fix libev url (#14066)
* fix libev url

* remove list_url in libev
2019-12-12 22:58:33 -06:00
Sinan
0d7b9de3be compile python with sqlite loadable extensions (#14132) 2019-12-12 22:58:16 -06:00
t-karatsu
ddfca1b2f2 cmake: Fix checksum of 4075.patch (#14125) 2019-12-12 13:57:23 -05:00
iarspider
d98b433a3c Fix py-jupyter-client version ranges (#14126) 2019-12-12 11:31:47 -06:00
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
Sheng Di
ba87a7f53a Release a new version v2.1.8.0 for SZ (#13974)
* Release a new version v2.1.8.0 for SZ

* add maintainer

* add parallel = False to avoid potential compile issue
2019-12-03 22:35:46 -06:00
Rob Latham
92ee0659e2 mpich: update build requirements (#13966)
To build from git, MPICH will need newer autoconf, automake, and libtool than
typically available on many systems.
2019-12-03 17:13:52 -06:00
Rob Latham
c7dbb4f103 argobots: consistently use 'master' (#13965)
Commit 71cd91e4 changed "latest from git" to 'master' from former
'develop'.  Build dependencies still pointed to @develop, though
2019-12-03 12:09:15 -06:00
Cameron Smith
5ddf5e2e7b new package: Simmetrix SimModSuite (#8730)
* package for Simmetrix SimModSuite

* simmodsuite: passes flake8

* simmetrix: add version, set cmake prefix path

A given install will either use the libs built on rhel7 or rhel6.
For now, I'm sticking with the non-spack install convention of
placing the libraries into sub-directories named according to their
build process (os + compiler).

* simmetrix: add older version

* simmetrix: set build env paths

easier to build pumi using CMAKE_PREFIX_PATH

* simmetrix: address review comments

* simmetrix: add new version and remove old one

* simmetrix: flake8 fixes

* simmodsuite: oslib var is in self

* simmodsuite: update version and checksum

* simodsuite: set LD_LIBRARY_PATH for cad kernels

* update license

* update setup_environment calls

* increase indentation for flake8

* python3.8 flake8 fixes

* use spack consistent naming

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

* sha256 required, update versions and hashes
2019-12-03 12:07:27 -06:00
t-karatsu
111dc8f823 kaldi: Change process of version analysis when using Fujitsu compiler. (#13960) 2019-12-03 10:34:05 -06:00
asmaahassan90
fb52f1c7e2 fix_cantera_installation (#13962)
For a successful cantera installation, googletest has to be installed with gmock on, and sundials has to be of version less than 3.2
2019-12-03 10:33:27 -06:00
Phil Carns
88680febc9 bump libfabric to 1.9.0 (#13964) 2019-12-03 10:32:53 -06:00
Yuanqi Wang
a5d872f510 Update MrBayes to 3.2.7a and correct MPI variants (#13929)
* Update MrBayes and correct MPI variant

* Use tarballs and remove autotools dependencies

* MrBayes: remove ISA variants
2019-12-03 10:31:00 -06:00
Jannek Squar
7e2d01b238 Update package libgpg error (#13697)
* Added build dependency on gawk

* Use virtual depdendency

* Added patch to prepare libgpg-error for use with gawk@5

* Added reasoning with link for need for patch
2019-12-03 10:29:15 -06:00
Chris White
cb38725a88 Add missing metis include to superlu-dist (#13956)
* Add missing metis include to superlu-dist

* Fix PEP-8 line length

* Fix PEP-8 indent
2019-12-02 18:30:23 -06:00
Sinan
4f8a2eeca2 add more versions (#13957) 2019-12-02 18:30:08 -06:00
Massimiliano Culpo
bca59f8d83 Speedup environment activation (#13557)
* Add a transaction around repeated calls to `spec.prefix` in the activation process
* cache the computation of home in the python package to speed up setting deps
* ensure that module-scope variables are only set *once* per module
2019-12-02 14:05:02 -08:00
Hector Martinez-Seara
1b624b9d45 amber: Improved package.py and added version 18 (#13945)
* amber: Improved package.py and added version 18

- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()

* dealii: Added 'threads' variant that controls the TBB dependency (#13931)

* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB

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

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

* amber: Improved package.py and added version 18

- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()

* amber: Adding missing flex and bison dependencies

* Removed cray variant; flex and bison now build only

* amber: Improved package.py and added version 18

- Added amber 18 with ambertools 19
- Added all available patches
- Added +update variant to use the self update
- Added +openmp variant to get openmp optomizations
- Added +x11 variant when possible
- Splitted amber 16 and 18 dependencies
- We now detect the copiler type and compile accordingly
- Added cray variant which is a bit special (untested)
- Improved detection of possible cuda versions
- All compilation optimizations +mpi +openmp +cuda are compatible
- Updated to use setup_build_environment(), setup_run_environment()

* amber: Adding missing flex and bison dependencies

* Removed cray variant; flex and bison now build only

* dealii: Fixed flake8 issues

* amber: corrected typo

* amber: Removed unused variant python
2019-12-02 16:01:14 -06:00
Jim Galarowicz
6d127e29de Fix conflict with respect to openssl and qt3 built for openspeedshop. (#13946)
* Fix conflict with respect to openssl and qt3 built for openspeedshop.

* Another fix because the first was incorrect.
2019-12-02 13:13:31 -06:00
Justin M Wozniak
543f37ea51 eq-r: Fix use of Executable.__call__() (#13952) 2019-12-02 13:13:05 -06:00
Alexander Knieps
8e3ff9b39c dealii: Added 'threads' variant that controls the TBB dependency (#13931)
* dealii: Added 'threads' variant that controls the DEAL_II_WITH_THREADS cmake option and the dependency on Intel TBB

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-12-01 13:34:26 -06:00
Sergei Shudler
c7568c9146 Package/sensei: PR request for SENSEI (in situ analysis tool) recipe (#12973)
* Created an initial recipe for Sensei

* Cleanup syntax

* Small fixes for the Sensei recipe

* Cosmetic fixes to comply with PEP8

* More cosmetic fixes before PR

* Added more documentation before PR

* Fixed flake8 errors

* Fixes following PR review

* Fixes to pass Flake8 passes

* Some changes following PR review and support for SENSEI 3

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

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Fixed Flake8 errors
2019-12-01 11:30:14 -06:00
Benjamin Fovet
fdd7a0e236 Add VTK version 8.2.0 (#13941) 2019-11-30 16:32:19 -06:00
jwallior
daaeb412a4 New python packages (#9974)
* New package: add py-jellyfish

* New package: add py-us

* New package: add py-xlwt

* New package: add py-svgpathtools

* New package: add py-svgwrite

* Change checksums to sha256

* Fix Copyright year.

* Add missing dependencies.
2019-11-30 16:32:02 -06:00
Benjamin Fovet
1c8a62aa86 Add package opencascade (#13938)
* Add new package : opencascade

* Remove boilerplate comment

* Fix flake8 errors

* Explicitly disable 3rd parties
2019-11-30 15:08:52 -06:00
Toyohisa Kameyama
c850e80bea cbtf: add rpcsvc-proto and libtirpc dependency. (#13798) 2019-11-30 13:08:24 -06:00
iarspider
aec5874b94 Mark py-argparse dependency everywhere with ^python@:2.6 (#13928)
* Mark py-argparse dependency everywhere with ^python@:2.6

* Update package.py

* Update package.py
2019-11-30 13:07:14 -06:00
darmac
46617b6f12 add new package : lshw (#13933)
* add new package : lshw

* update lshw package

* remove build methord
2019-11-30 01:13:23 -06:00
iarspider
94c8bf0322 Update Geant4 version and recipe (#13840)
* Update Geant4 version and recipe

According to the Geant4 developers, Geant4 supports Qt5 since at least 10.00.

* Update to new API
2019-11-29 16:21:51 -06:00
Adam J. Stewart
ab98ef1765
Mass conversion of setup_(dependent_)?environment (#13924)
* Mass conversion of setup_(dependent_)?environment

* prefix -> self.prefix
2019-11-29 15:00:44 -06:00
Mark W. Krentel
92ca639905 intel-tbb: fix and update patches for latest versions (#13932)
Commit 78724357 added versions 2019.5 to 2019.8 but failed to update
the patches for these versions.

1. gcc_generic-pedantic patch -- include this up through 2019.5.  This
was fixed in the TBB source tree in 2019.6.

2. tbb_cmakeConfig patch -- this needs to be modified (different file)
for 2019.5 and later.

3. tbb_gcc_rtm_key patch -- replace this with filter_file.  This is
simpler and eliminates the need to update the patch whenever the
surrounding context changes.
2019-11-29 13:18:56 -06:00
darmac
0f464b8d9f add new package : pipework (#13934) 2019-11-29 12:19:13 -06:00
darmac
e865856c84 add new package : qperf (#13935) 2019-11-29 12:18:41 -06:00
Peter Scheibel
cacfc3a6e1 Handle external perl (#13903)
* dont add perl bin directory to PATH when setting up env (this is already handled by spack core in a way that omits system dirs); also consolidate repeated logic between build/run env setup.

* the bin/ dir of each dependency is already added to PATH in Spack core, so there is no need to do this in the Perl package
2019-11-29 12:30:40 +01:00
iarspider
4dca63f007 Loosen restriction on setuptools version of py-backports-shutil-get-terminal-size: the bug seems to be fixed at least in setuptools 41.0.0 (#13927) 2019-11-28 11:54:01 -06:00
Tyler Reddy
008fe37941 BLD: enforce C++11 std for boost + xl_r (#13829)
* BLD: enforce C++11 std for boost + xl_r

* the spack `cxxstd` variant is not sufficient to enforce
`-std=c++11` usage in boost compile lines when `xl_r` compiler
spec is in use; while it would be nice if this were fixed
in a boost config file somewhere, for now this patch
allows boost to build on POWER9 with
an %xl_r compiler spec if the user specifies i.e.,:

`spack install boost@1.70.0+mpi cxxstd=11 %xl_r@16.1.1.5`

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-27 23:08:54 -06:00
Glenn Johnson
e974f48be0 Build R without recommended packages (#12015)
The documentation states that Spack builds R without the recommmened
packages, with Spack handling the build of those packages to satisfy
dependencies. From the docs:

> Spack explicitly adds the --without-recommended-packages flag to
> prevent the installation of these packages. Due to the way Spack
> handles package activation (symlinking packages to the R installation
> directory), pre-existing recommended packages will cause conflicts for
> already-existing files. We could either not include these recommended
> packages in Spack and require them to be installed through
> --with-recommended-packages, or we could not install them with R and
> let users choose the version of the package they want to install. We
> chose the latter.

However, this is not what Spack is actually doing. The
`--without-recommended` configure option is not passed to R and
therefore those packages are built. This prevents R extension activation
from working as files in the recommended packages installed with R will
block linking of file from the respective `r-` packages.

This PR adds the `--without-recommended` flag to the configure options
of the R package. This will then have the Spack R build match what is
documented.
2019-11-27 20:58:12 -06:00
Justin S
1b24dfb8ba Replace git-based Bioconductor R packages (#12005)
* Replace git-based Bioconductor R packages

The current collection of bioconductor packages tend to have scattered
dependencies and missing versions. This commit replaces git-based
packages with tool-generated Spack package recipes with correct
dependencies and descriptions in place.

* Fix some broken package names, add periods to title docstrings

* r-clue: new package at 0.3-57

* r-genomeinfodbdata: add 1.2.1

* r-gofuncr: new package at 1.4.0

* r-pfam-db: add 3.8.2

* Add missed package r-genelendatabase

* update r-goseq package

* update r-glimma package

* update r-rots package

* r-org-hs-eg-db: add 3.8.2

* r-vgam: fix incorrect R version

* r-rnaseqmap: new package at 2.42.0

* r-rhdf5lib: new package at 1.6.0

* r-scrime: new package at 1.3.5

* r-delayedmatrixstats: new package at 1.6.0

* r-hdf5array: new package at 1.12.1

* r-biocfilecache: new package at 1.8.0

* r-ctc: add new versions, dependencies

* r-genemeta: new package at 1.56.0

* r-scrime: fix flake8

* r-ensembldb: add missing dependencies

* Added missing dependencies to packages with certain DESCRIPTIONS

* r-mapplots: new package at 1.5.1

* r-beachmat: new package at 2.0.0

* r-beeswarm: new package at 0.2.3

* r-biocneighbors: new package at 1.2.0

* r-biocsingular: new package at 1.0.0

* r-ecp: new package at 3.1.1

* r-enrichplot: new package at 1.4.0

* r-europepmc: new package at 0.3

* r-ggbeeswarm: new package at 0.6.0

* r-ggplotify: new package at 0.0.3

* r-ggraph: new package at 1.0.2

* r-gridgraphics: new package at 0.4-1

* r-rcppannoy: new package at 0.0.12

* r-rcpphnsw: new package at 0.1.0

* r-rsvd: new package at 1.0.1

* r-scater: new package at 1.12.2

* r-singlecellexperiment: new package at 1.6.0

* r-tximport: new package at 1.12.3

* r-upsetr: new package at 1.4.0

* r-vioplot: new package at 0.3.2

* r-readr: add 1.3.1

* r-matrixstats: add 0.54.0

* r-ecp: flake8 fix

* r-biocmanager: new package at 1.30.4

* update bioconductor packages requiring BiocManager, new versions

* r-lambda-r: add 1.2.3

* r-vegan: add 2.5-5

* r-cner, r-rcppannoy, r-reportingtools, r-rsvd: add missing newlines at EOF

* r-chemometrics: flake8 fixes

* r-vgam: flake8 fixes

* CRAN packages: use cloud.r-project.org

* Use DESCRIPTION for R version constraints over bioconductor releases

* Update missed packages ABAData, acde, affydata

* Update remaining missed packages

* bio: Drop 'when' clause from first checksummed versions

* bio: improve package description generation logic

* r-genomeinfodbdata: use explicit sha256 sums

* r-pfam-db: update dependencies, add 3.10.0

* update r-org-hs-eg-db

* r-dirichletmultinomial: re-add gsl

* r-polyclip: new package at 1.10-0

* r-farver: new package at 1.1.0

* r-tweenr: new package at 1.0.1

* r-ggforce: new package at 0.3.1

* r-ggforce: remove redundant dep

* r-ggraph: add missing deps

* r-rcpphnsw: remove redundant depends_on

* r-reportingtools: re-add r-r-utils dep

* r-rhdf5: add gmake dep

* r-rhtslib: add system dependencies

* r-rsamtools: add gmake dep

* r-farver: remove redundant dep

* r-tweenr: remove redundant dep

* r-variantannotation: add gmake dep

* r-rgraphviz: add graphviz dep

* r-vsn: correct r-hexbin constraint

* r-scater: fix obsolete deps

* r-variantannotation: fix gmake dep type

* r-scater: tighten R version constraints

* r-rsamtools: fix gmake dep type

* r-rhtslib: fix gmake dep type

* r-rhtslib: use xz over lzma

* r-rhdf5: fix gmake dep type

* r-farver: replace with newer recipe for 2.0.1

* r-mzr: remove old dependency

* r-reportingtools: remove builtin dependency

* r-mzr: add gmake dep

* r-rhtslib: make system libraries link deps

* r-genomeinfodbdata: fix R version constraints

* r-geoquery: remove old deps from new versions

* r-genomicfeatures: tighten r-rmysql dep

* r-ensembldb: tighten r-annotationhub dep

* r-complexheatmap: fix r-dendextend dep

* r-cner: fix utils dep name

* r-clusterprofiler: fix r-gosemsim version req

* r-biostrings: fix r-iranges version reqs

* r-rhdf5lib: add gmake dep

* r-oligoclasses: fix r-biocinstaller dep range

* r-organismdbi: fix r-biocinstaller dep range

* r-hdf5array: add gmake dep

* r-gtrellis: tighten r-circlize version req

* r-gostats: fix r-graph version req

* r-glimma: fix old dependency ranges

* r-biostrings: syntax fix

* r-organismdbi: syntax fix

* r-dose: fix r-igraph dep

* r-dose: fix r-scales, r-rvcheck deps

* r-affy: fix r-biocinstaller dep

* r-ampliqueso: fix homepage

* r-aneufinder: fix r-biocgenerics dep

* r-beachmat: fix changed deps

* r-biocneighbors: fix old R constraint

* r-biocmanager: rewrite recipe for 1.30.10

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

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

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-27 20:57:15 -06:00
Rene Gassmoeller
0f46c3452f Add version 2.1.0 to 'aspect' package (#13830) 2019-11-27 20:04:00 -06:00
iarspider
6d7250f59c Update cartopy version and fix recipe (#13898)
* Update cartopy version and fix recipe

Cartopy 0.17.0 works fine with proj 6

* Update cartopy version and fix recipe

Cartopy 0.17.0 works fine with proj 6

* Set ACCEPT_USE_OF_DEPRECATED_PROJ_API_H flag when building extension

* Add variants to py-cartopy recipe as suggested

* Fix proj dependency

* Split dependency

* Fix PEP-8; remove extra dependency
2019-11-27 20:01:05 -06:00
Nichols A. Romero
d7db42e201 QMCPACK Update Nov2019 (#13832)
* Bump up QE version number to 6.4.1.

* Fix QMCPACK conflicts.

* HDF5 dependencies where over specified which could cause unnecessary installs of HDF5.

* Update QMCPACK testing option.

* Remove support for serial QE 6.4.1 converter. Add support for parallel QE 6.4.1. converter with serial HDF5.

* Switch to setup_run_environment.

* Fix setup_run_environment call arguements.

* Fix typo.

* switch run_env to env
2019-11-27 16:37:51 -06:00
Ken Raffenetti
85ce22a0b8 mpich: Add ucx dependency (#13921) 2019-11-27 16:34:46 -06:00
Federico Ficarelli
484dab6bac cuda: add polymorphic package versions (#13912) 2019-11-27 15:45:07 -06:00
Marc Mengel
206e7bd5aa scm-git-archive python package (#13915)
* scm-git-archive python package

* flake8

* per comments
2019-11-27 15:43:19 -06:00
Marc Mengel
7125d7eebe New package: py-cheroot (#13583)
* package py-cheroot

* package py-cheroot

* autopep8, docutils cleanup

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

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

* missing deps

* flake8

* license bits

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

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

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

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

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

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

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

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

* python dep

* flake8
2019-11-27 14:02:43 -06:00
Howard Pritchard
399336ae89 openmpi: add 3.1.5 and 3.0.5 (#13918)
Note to spack people: these are expected to be end of line releases for both the 3.1.5 an 3.0.5 releases

Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2019-11-27 14:02:05 -06:00
Adam J. Stewart
3cc8c93883
json-fortran: get unit tests working (#13919) 2019-11-27 13:15:55 -06:00
iarspider
9e397042a7 Fix py-pyarrow recipe (#13914)
Fix name of one dependency
2019-11-27 12:21:01 -06:00
t-karatsu
515f1466c8 accfft: fix narrowing error. (#13909) 2019-11-27 10:15:22 -06:00
健美猞猁
f07131a390 Bump intel compiler suite to 2019u5. (#13835)
* Bump intel compiler suite to 2019u5.

* Remove a duplicate line.
2019-11-27 10:04:48 -06:00
Oliver Breitwieser
d207dceb3a Fix py-line-profiler incompatible decorators (#13911)
`@run_after` and `@when` are incompatible, issue #12736.
2019-11-27 15:30:53 +01:00
Hadrien G
51ee8aa639 ACTS: added version v0.11.1 (#13910) 2019-11-27 15:18:49 +01:00
Tim Haines
c80792fc06 Add version check when building intel-tbb with clang (#13893)
* Add version check when building with clang

* Update for flake8 formatting
2019-11-26 23:15:17 -06:00
Christoph Junghans
07325f5fd0 votca: help concretizer (#13906)
* votca: help concretizer

* flake8
2019-11-26 21:47:42 -06:00