Commit graph

9048 commits

Author SHA1 Message Date
Matthias Wolf
e69efded32 py-line-profiler: add 2.1.2, re-run cython if needed (#13102)
* py-line-profiler: add 2.1.2, re-run cython if needed

See rkern/line_profiler#166.

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-10 11:34:50 +02:00
Rob Latham
d93cacfa5c libfabric: new upstream release 1.8.1 (#13053) 2019-10-09 22:24:17 -05:00
wspear
c8289fcd90 Added latest versions of SQLAlchemy 1.3.X, 1.2.X and 1.1.X (#13078)
* Added latest versions of SQLAlchemy 1.3.X, 1.2.X and 1.1.X

* Added missing dependencies
2019-10-09 22:23:55 -05:00
wspear
e7e67fdfec Added latest versions to py-traitlets (#13079)
* Added latest versions to py-traitlets

* Added missing dependencies
2019-10-09 22:23:33 -05:00
Francesco Di Natale
4ef64b64d1 Add new versions of py-maestrowf (#13081)
* Addition of 1.1.3 and 1.1.4

* Addition of conditional enum-34 installation.

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

Addition of versioning for pyyaml.

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

* Addition of enum34 back to older versions 1.1.3 and below.
2019-10-09 22:23:19 -05:00
Michael Kuhn
2e2b1a5e02 qt: Add 5.13.1 and missing zlib flags (#13109) 2019-10-09 22:22:52 -05:00
Michael Kuhn
469bef880a mysql: Add missing dependencies (#12717)
This also changes the default for cxxstd from 98 to 14 because (at
least) newer versions of mysql do not compile with 98 (tested with
gcc@9).
2019-10-09 14:45:31 -05:00
Toyohisa Kameyama
b0bf528ab3 perl-perlio-gzip: add zlib dependency. (#13060) 2019-10-08 20:51:39 -05:00
Toyohisa Kameyama
529d0f3e37 psmc: add zlib dependency. (#13061) 2019-10-08 20:51:04 -05:00
Toyohisa Kameyama
f1e1693a6a seqprep: add zlib dependency. (#13062) 2019-10-08 20:50:51 -05:00
Toyohisa Kameyama
fdc91a1705 tabix: add zlib dependency. (#13064) 2019-10-08 20:48:37 -05:00
wspear
2e4bcf223c Added py-certipy package. Dependency of py-jupyterhub. (#13068)
* Added py-certipy package. Dependency of py-jupyterhub.

* Changed url to pypi
2019-10-08 20:48:11 -05:00
Nichols A. Romero
2794e52ddd QMCPACK Oct2019 fix buglets (#13069)
* Support different CMake build types correctly.

* LIBXML2 variables no longer used.

* Fix E501 as part of https://github.com/spack/spack/pull/13069
2019-10-08 20:46:15 -05:00
wspear
8de453af54 Fixed hash of version .0.5 and added latest version (.0.7.1) (#13077) 2019-10-08 20:43:44 -05:00
Mark Olesen
e3f69f8ce6 Build older openfoam (#13071)
* adjust building of OpenFOAM 1806 and earlier

- spack now unpacks into spack-src, but earlier OpenFOAM versions
  still expect particular directory names (eg, OpenFOAM-v1806).

  Resolve by creating a symlink during patching.

* replace openfoam 1806 patch with URL version
2019-10-08 20:42:44 -05:00
wspear
6a99b7e262 Added py-pamela package. Dependency of py-jupyterhub. (#13075) 2019-10-08 20:08:32 -05:00
George Hartzell
4377cc7066 Add headsup note re cryptsetup patch for v2.2.2 (#13076) 2019-10-08 20:07:38 -05:00
Phil Carns
66b9009a07 pmdk: added v 1.7 (#13067) 2019-10-08 09:19:27 +02:00
Oliver Breitwieser
9600eb4f5a py-apipkg: Fix mix up of checksums (#13066)
Change-Id: Ibae329c5a6cf7e3741a879612da523e11e3b0ab9
2019-10-07 20:55:22 -05:00
Adam J. Stewart
c8c795e7db watch: added new package (#13044) 2019-10-07 11:11:17 +02:00
Paul
7d0e7efabb Added go 1.13.1 and 1.12.10 (#12977) 2019-10-06 20:22:05 -05:00
Denis Davydov
79bd6bbd04 gnuplot: add 5.2.7 and fix qt dep (#13058) 2019-10-06 14:28:34 -05:00
Matthias Wolf
3d247d9567 freeimage: new package (#13049)
* freeimage: new package

* Address comments.

* Whitespace
2019-10-06 09:20:29 -05:00
Ruben Di Battista
ba72114ba2 unrar: Add package (#12908) 2019-10-06 09:16:25 -05:00
Oliver Breitwieser
f34162a5b8 Add missing py-contextlib2 (#13056)
Change-Id: I8e0a90d4aa2c9f46230a6fe35ce5f4fa44672faf
2019-10-06 09:15:29 -05:00
Denis Davydov
070a536e49 qt: help pick up dependencies (#11172)
* qt: help pick up dependencies

* qt: add 5.12.5
2019-10-05 21:13:38 -05:00
t-karatsu
c6b8d79ea6 Package/fujitsu mpi (#12807)
* fujitsu-mpi: commit new package

* Add homepage.

* * Modified the MPI commands to a simple form.
* Unnecessary processing has been deleted.

* Add conflict for all compilers except the Fujitsu compiler.

* Fix typo.

* Delete versions.

* Delete conditions for specifying the Fujitsu compiler.
2019-10-05 20:58:43 -05:00
Adam J. Stewart
608f732101
expect: fix darwin install name (#13042)
* expect: fix darwin install name

* Fix expect binary as well
2019-10-05 20:37:44 -05:00
Teodor Nikolov
e78ca66087 New package: cxxopts (#13035)
* New package: cxxopts

* Use +unicode instead of unicode=True

- Make the unicode option more explicit

* [cxxopts] Fix white space warnings
2019-10-05 20:36:59 -05:00
Adam J. Stewart
c45ecafd71 procps: new package (#13043) 2019-10-05 11:39:55 +02:00
Federico Ficarelli
a362cf5ff6 grpc: new package (#13054)
* Add grpc@1.23.1

* Let version in url match actual one
2019-10-04 18:42:09 -05:00
Andreas Baumbach
e366f6ba39 llvm: update link to the document explaining codesign (#13047)
Change-Id: I01242cbb43b0c62a659739a5d7e9d998dd27e794
2019-10-04 13:31:43 -07:00
Robert Maynard
b1cdf8bd57 Update the VTK-m package with better defaults and cuda corrections (#12850) 2019-10-04 15:12:58 -04:00
Cody Balos
3cb4547348 superlu-dist: add openmp variant (#13052) 2019-10-04 13:48:56 -05:00
Toyohisa Kameyama
cb89949018 migrate: add zlib dependency. (#13039)
* migrate: add zlib dependency.

* flake8.

* autotools related tools change to build.
2019-10-04 13:14:09 -05:00
Felix Thaler
437236781d LLVM 9.0.0 (#13050) 2019-10-04 09:56:12 -07:00
Massimiliano Culpo
2cd800306d fftw: simplify the recipe and make use of specific targets (#12889)
* fftw: grouped precisions in a single variant

* fftw: simd options are now based on target features and not on variants

* fftw: simplified computing the selected precisions
2019-10-03 22:32:42 -05:00
t-karatsu
46e319ecd4 boost: Use gcc toolset for bootstrap with Fujitsu compiler. (#12876) 2019-10-03 22:20:55 -05:00
Toyohisa Kameyama
938bae1ab6 graphmap: add zlib dependency. (#13031) 2019-10-03 22:20:13 -05:00
Toyohisa Kameyama
b89fa3e01a fastqvalidator: add zlib dependency and Removes erroneous deletes in Chromosome (#13030) 2019-10-03 22:19:58 -05:00
Toyohisa Kameyama
4046e10b95 hapcut2: add zlib dependency. (#13032) 2019-10-03 22:19:43 -05:00
Toyohisa Kameyama
2233a7b493 liblbxutil: Add zlib dependency. (#13033) 2019-10-03 22:19:22 -05:00
Toyohisa Kameyama
bb1d0ff6fb metabat: Add zlib and ncurses dependency. (#13034) 2019-10-03 22:18:55 -05:00
Toyohisa Kameyama
58a64f69e7 muse: add zlib dependency. (#13040) 2019-10-03 22:18:27 -05:00
Toyohisa Kameyama
c97be22ff5 ngmlr: add zlib dependency. (#13041) 2019-10-03 22:18:12 -05:00
Andreas Baumbach
4e7ea627c8 fix ipykernel dependency, newer versions are python3-only (#13019)
* fix ipykernel dependency, newer versions are python3-only

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

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

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-03 22:17:16 -05:00
George Hartzell
882843974b Update cctools to v7.0.18 (#13037)
- add version/checksum info for v7.0.18
- update checksum for v6.1.1 to use sha256, while I have the editor
  open...
2019-10-03 18:57:20 -05:00
Owen Solberg
bef702d0f3 updated manta checksum (#13038) 2019-10-03 18:23:47 -05:00
Adam J. Stewart
69acb024a5
Add py-flye 2.6 (#13025) 2019-10-03 10:32:00 -05:00
Adam J. Stewart
dac34147c0 Add EasyBuild 4.0.0 (#13024)
* Add EasyBuild 4.0.0

* Update homepage, remove no longer required deps

* Replace version ranges with fixed versions
2019-10-03 16:48:42 +02:00
Chuck Atkins
b973f038fd
Update ECP Data & Vis SDK packages (#13027)
* ecp-io-sdk: Add faodel and sort variants

* ecp-viz-sdk: Re-enable catalyst, sort variants, turn on by default

* ecp-io-sdk and ecp-viz-sdk: Fix dependency variants
2019-10-03 10:05:02 -04:00
Massimiliano Culpo
76b9c56110 Remove support for generating dotkit files (#11986)
Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.

A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.

* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
2019-10-02 22:15:01 -07:00
Miroslav Stoyanov
b11984767b added tasmanian version 7.0 to spack (#13003) 2019-10-02 18:35:49 -05:00
Sinan
b084d095bc New package: mapnik (#12708) 2019-10-02 13:50:57 -07:00
Tiziano Müller
d99b92febd libint + cp2k: 2-stage build with 'tune' and 'fortran' variants (#12475)
* libint: switch to 2-stage build for 2.6.0+

* libint: add tune and fortran variants

* cp2k: add support for libint >= 2.0

* cp2k: use pkg-config for linking libxc
2019-10-02 21:31:19 +02:00
Toyohisa Kameyama
da18ac3a0f cdhit: add zlib dependency. (#13015)
* cdhit: add zlib dependency.

* Add zlib variant.
2019-10-02 12:55:05 -05:00
Toyohisa Kameyama
b85ff04681 denovogear: Add missing zlib depenbdency and fix open handling error. (#13017) 2019-10-02 12:54:50 -05:00
Toyohisa Kameyama
58c01792ef cnpy: add zlib dependency. (#13016) 2019-10-02 12:54:31 -05:00
Dan Lipsa
210dd594a1 Add cuda to paraview build. (#12996) 2019-10-02 12:00:03 -05:00
George Hartzell
21e95e4141 Singularity 3.4.1 still needs the makefile patch (#13008)
* Singularity 3.4.1 still needs the makefile patch

* Constrain build patch to 3.4.0:3.4.1
2019-10-02 11:59:11 -05:00
Sinan
afca223b3d new package: openldap (#12748)
* new package: openldap

* fix mistake

* remove template text

* fix build error involving perl

* flake8

* improvements

* introduce multi valued variant for tls support

* improve tls variant

* overwrite build phase as opposed install

* improve style
2019-10-02 11:58:46 -05:00
Toyohisa Kameyama
1550d5cae6 ants: missing zlib dependency and fix working directory in install. (#13010) 2019-10-02 11:58:25 -05:00
Toyohisa Kameyama
7d9514d3fa breakdancer: missing ncurses dependency. (#13011) 2019-10-02 11:57:05 -05:00
Toyohisa Kameyama
d238b9d394 breseq: fix dependency and limit compiler version. (#13013) 2019-10-02 11:56:37 -05:00
Andreas Baumbach
64ff27626e update py-jupyter-notebook to use the real releases (#13020)
* github releases are not released versions, but from-source
  releases
* they lack the mimification of the JS/CSS components and as
  such require node-js and npm, this conflicts with python@3:
* this commit
  * drops the from-source dependencies on node-js and npm and
  * updates the checksums to the correct sha256 hashes of the
    pypi releases. The pypi-tarballs are different
2019-10-02 11:39:55 -05:00
Axel Huebl
bec2830802
ZFP: CMake Package (#12999)
* ZFP: CMake Package

ZFP is primarily build via CMake, which will have all install logic
and configuration files generated.
The 0.5.0 release did not support this yet, so we toss it.

* Patch ADIOS1: ZFP 0.5.1+ support

* ZFP: Expose all CMake variants
2019-10-01 23:28:36 -07:00
George Hartzell
22e75b77e3 direnv: add info for version 2.20.0 (#13007) 2019-10-01 22:34:14 -05:00
Sinan
d20e3517c2 new package: py-python-ldap (#12599)
* new package: py-python-ldap

* fix dependency types

* improvements

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

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

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

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

* add openldap dependency
2019-10-01 20:59:53 -05:00
Sinan
91488ed8f5 New package: py-python-mapnik (#12786) 2019-10-01 18:37:34 -07:00
codeandkey
5c2b01ebcf picard: add 2.20.8 2019-10-01 18:19:37 -07:00
Daryl W. Grunau
248bc17bb0 go-md2man: disable module-mode (#12985)
* go-md2man: disable module-mode

* Update var/spack/repos/builtin/packages/go-md2man/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01 19:17:10 -05:00
Eduardo Arango
c1ecd037d7 add singularity 3.4.1 (#12995)
* add singularity 3.4.1

Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>

* revert some changes

Signed-off-by: ArangoGutierrez <eduardo@sylabs.io>

* add maintainers list to pkg singularity

Add @alalazo and me to the Singularity maintainers list

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

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

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

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

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-10-01 19:16:20 -05:00
Axel Huebl
436afdd2a8
Dataspaces: Fix Fetch URL, Savanna Spec (#13001) 2019-10-01 14:52:44 -07:00
Peter Scheibel
3575f9b382
GCC package: don't set CC etc. based on bin dir if it doesn't exist (#13000)
7bcb306 updated setup_environment in the GCC package to examine the
bin/ directory to find alternatively-named instances of CC, but this
failed to account for when GCC was being installed and failed when
it attempted to list the not-yet-existing installation prefix. This
commit updates the logic to skip this search if the bin/ directory
doesn't exist.
2019-10-01 14:29:01 -07:00
Massimiliano Culpo
245c1bb208 libaio: fixed a condition that checks whether we are running on OS X (#12976)
* libaio: fixed a condition that checks whether we are running on OS X

* libaio: simplified package by adding an explicit conflict for darwin

* libaio: added information to the docstring

* fio: added version 3.16, added conflict when using libaio, docstring

* lvm2: conflict due to libaio dep, improved docstring, simpler install

* mariadb: conflict due to libaio dep, improved docstring, version 10.4.7

* mariadb: the dependency on libaio is now conditional, removed conflict

* mariadb: fixed a typo in previous commit

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

* libaio: turned into a MakefilePackage
2019-10-01 15:35:50 -05:00
Jimmy Tang
a7e64e5396 Kaldi package: add version 7637de7 and egs (#12911) 2019-10-01 10:24:03 -07:00
Jeffrey Salmond
5868e0f5f2 add new mercurial versions (#12997) 2019-10-01 12:08:28 -05:00
Christopher Edsall
82a3ee0868 Update chapel to current (1.19 -> 1.20) (#12991) 2019-10-01 11:47:57 -05:00
Axel Huebl
10e4d611a5 ADIOS2: 2.5.0 (#12987)
Add the latest ADIOS2 release, v2.5.0 .
2019-10-01 10:49:52 -05:00
Satish Balay
b9a860820a hypre: add version 2.18.0 (#12992) 2019-10-01 10:48:40 -05:00
Mark Olesen
f939697863 add adios2 dependency and configuration for newest OpenFOAM (#12993) 2019-10-01 10:48:14 -05:00
noguchi-k
5b4040ea36 libcerf:add CFLAGS for fujitsu compiler (#12990)
* libcerf:add CFLAGS for fujitsu compiler

* fix for flake8
2019-10-01 08:54:01 -05:00
egreen77
cfc17e9506 Update nano (#12980) 2019-09-30 16:27:29 -05:00
Adam J. Stewart
5b2b0ee9a3
Revert "update neovim (#12965)" (#12978)
This reverts commit 86a85b7eb2.
2019-09-30 13:18:27 -05:00
Satish Balay
c70f9bffe2 petsc, slepc: add new versions - 3.12.0 (#12979) 2019-09-30 13:18:11 -05:00
Seth R. Johnson
7bcb306d4a Fix GCC environment variables for external installations (#12454)
Unlike the compiler binary name search logic, the `setup_environment` in
GCC's package assumes the compiler names are *exactly* `gcc`, `g++`,
etc. In many external installations (Homebrew, Macports) the
installation includes only *suffixed* versions such as `gcc-9`.

This patch uses the GCC compiler search suffixes to actually locate the
correct filenames for the installed compilers, allowing the
Spack-generated module file to have useful definitions of CC, CXX, etc.

It also allows for the possibility that the user's external installation
of GCC is compiled without Fortran support, in which case the `FC`
environment variables are not defined.
2019-09-30 11:02:32 -07:00
t-karatsu
139eaa1306 otf2: add configure args to specify compiler commands. (#12711)
* otf2: add configure args to specify compiler commands.

* Modify the reference of the compile commands.
2019-09-30 08:18:09 -05:00
Glenn Johnson
c56f03a3ba The perl-uri-escape package duplicates perl-uri (#12971)
* The perl-uri-escape package duplicates perl-uri

The Perl URI::Escape module is in the Perl URI package so the Spack
perl-uri-escape package is a duplicate of the perl-uri package. This PR
does the following:

- replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')`
  in packages that dependend on perl-uri-escape
- add the version from perl-uri-escape to perl-uri
- remove the unneeded dependency from perl-uri
- remove the perl-uri-escape package

* Reinstated perl-test-needs dependency

Put the perl-test-needs dependency for perl-uri back in but set it to
type='test'.

* For tests to succeed the type must be ('build', 'test')
2019-09-29 09:27:42 -05:00
Massimiliano Culpo
467261803f raxml: simplified recipe by removing SIMD variants (#12952)
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28 13:45:01 -05:00
t-karatsu
c065c25a4c bowtie: fix for aarch64, and bugfix about c++11-narrowing. (#12953) 2019-09-28 13:44:02 -05:00
Massimiliano Culpo
4cebc68f06 vdt: simplified recipe by removing SIMD variants (#12954)
Now the support for SSE3 or AVX is tested on the selected target
2019-09-28 13:41:57 -05:00
Jaroslav Hron
7e9365036f correct with-xxx-lib= options (#12964) 2019-09-28 13:39:45 -05:00
Patrick Schratz
86a85b7eb2 update neovim (#12965) 2019-09-28 13:28:27 -05:00
Shintaro Iwasaki
3776eccc4b bolt: add a new version, 1.0rc2 (#12966) 2019-09-28 13:27:33 -05:00
Daryl W. Grunau
8db94bcc86 eospac: laws.lanl.gov -> laws-green.lanl.gov (#12970) 2019-09-27 17:28:38 -07:00
Ross Miller
c49c37af9b py-adios package: restrict python dependency to <=3.6.x (#12932)
The adios code (currently) won't compile against the Python 3.7 C API.
This change adds a dependency on 3.6 or less.
2019-09-27 17:19:36 -07:00
Kevin Huck
b4c28182dc Tau package: turn off unsupported variants by default on OSX (#12890) 2019-09-27 17:16:44 -07:00
G-Ragghianti
61d41eea7f New package: libibumad (#12886) 2019-09-27 17:02:34 -07:00
Glenn Johnson
fc99eddb12 New package: maker and dependencies (#12904) 2019-09-27 14:59:58 -07:00
Seth R. Johnson
5201d2615e qt4: fix 'arch' string due to microarchitecture change (#12957)
qt4 fails to build because it's expecting something like 'x86_64' rather 
than 'broadwell'.
2019-09-26 21:15:17 +02:00