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Author SHA1 Message Date
Adam J. Stewart
41e0b069d7
Fix external numpy package support (#13197) 2019-10-12 20:21:03 -05:00
Adam J. Stewart
3df6b05c04
Add py-setuptools 41.4.0 (#13184) 2019-10-12 20:20:41 -05:00
Adam J. Stewart
ebfd06d248
Add py-pytest 5.2.1 (#13181) 2019-10-12 20:18:31 -05:00
Adam J. Stewart
328583decc
Add py-pluggy 0.13.0 (#13176) 2019-10-12 20:14:12 -05:00
Adam J. Stewart
2ced690efb
Add py-pandas 0.25.1 (#13174) 2019-10-12 20:12:41 -05:00
Adam J. Stewart
50e9dc5e2e
Add py-packaging 19.2 (#13173) 2019-10-12 20:12:19 -05:00
Adam J. Stewart
101c287e7b
Add py-numexpr 2.7.0 (#13172) 2019-10-12 20:11:57 -05:00
Adam J. Stewart
db4d06f953
Add py-importlib-metadata 0.23 (#13168) 2019-10-12 20:08:33 -05:00
Adam J. Stewart
1d7eab10ac
Add py-certifi 2019.9.11 (#13165) 2019-10-12 20:05:00 -05:00
Adam J. Stewart
a59e77e374
Add missing test dependency to py-bottleneck (#13164) 2019-10-12 20:04:34 -05:00
Adam J. Stewart
1078dfb6cc
Add py-atomicwrites 1.3.0 (#13162) 2019-10-12 20:03:01 -05:00
Adam J. Stewart
b18e4ad142
Add missing libiconv dependency to wget (#13161) 2019-10-12 20:02:41 -05:00
Adam J. Stewart
7a43817205
Add missing gettext dependency to watch (#13160) 2019-10-12 20:02:24 -05:00
Adam J. Stewart
6beb5da497
Fix valgrind concretization on macOS (#13159) 2019-10-12 20:02:05 -05:00
Adam J. Stewart
22e9aafe5f
Add SCons 3.1.1 (#13157) 2019-10-12 20:00:28 -05:00
Adam J. Stewart
73b2b2a70f
Add LLVM OpenMP 9.0.0 (#13154) 2019-10-12 19:57:36 -05:00
Adam J. Stewart
94d57446c7
Add libjpeg-turbo 2.0.3 (#13152) 2019-10-12 19:55:44 -05:00
Adam J. Stewart
1e2754f0d2
Add help2man 1.47.11 (#13151) 2019-10-12 19:55:14 -05:00
Adam J. Stewart
681c5bcceb
Add graphviz 2.42.2 (#13150) 2019-10-12 19:54:46 -05:00
Adam J. Stewart
0a8be4e311
Add cmake 3.15.4 (#13148) 2019-10-12 19:52:47 -05:00
Adam J. Stewart
18ab375968
Add utf8proc package (#13144) 2019-10-12 19:40:05 -05:00
Nichols A. Romero
ebb5ce4b69 F18 Oct2019 Minor Update (#13192) 
* Minor clean-up of package information.

* Add variants, fix dependencies, and add conflicts for compilers that do not support C++17.

* Correct dependency type for CMake.
 2019-10-12 12:30:43 -05:00
Todd Gamblin
64bdc3251f checksums: enforce that all mainline packages use sha256 checksums 
- Add a test that verifies checksums on all packages

- Also add an attribute to packages that indicates whether they need a
  manual download or not, and add an exception in the tests for these
  packages until we can verify them.
 2019-10-12 07:19:43 -07:00
Todd Gamblin
8cbd349cb4 checksums: fix packages that needed new download locations 
Some packages had incorrect checksums because they needed to be
downloaded from a new place or the package needed tweaking somehow.
These packages to sha256 and the new checksums have been verified by
fetching over https.
 2019-10-12 07:19:43 -07:00
Todd Gamblin
45a9cfcdd7 packages: remove packages that are no longer fetchable 
These packages have either been retired or are no longer retrievable from
any site we can find. They also aren't needed by other packages, so we're
removing them from Spack.

- allinea-reports: is now arm performance reports
- globus-toolkit: retired, globus is now a paid service.
- uberftp: used globus-toolkit, github site is retired.
- mpiblast: site is dead; no longer fetchable.
- py-mxnet: site and github are gone
- soap2, soapindel, soapsnp: site is gone, unfetchable
- arlecore: could not verify md5 securely
 2019-10-12 07:19:43 -07:00
Todd Gamblin
00f91ab22b checksums: Remove or fix up unfetchable or unverifiable md5 versions 
This commit either removes remaining md5 checksums, or it replaces them
with sha256 checksums verified by fetching over https.
 2019-10-12 07:19:43 -07:00
Todd Gamblin
62927654dd checksums: use sha256 checksums everywhere 
We'd like to use a consistent checksum scheme everywhere so that we can:

    a) incorporate archive checksums into our specs and have a
       consistent hashing algorithm across all specs.

    b) index mirrors with a consistent type of checksum, and not one that
       is dependent on how spack packages are written.

- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
 2019-10-12 07:19:43 -07:00
Matthew LeGendre
87fa7c15fc Add adiak package, version 0.1.1 2019-10-11 21:22:33 -07:00
Massimiliano Culpo
fd97f5c491
Fixed constraints in recipes for packages that depends on fftw (#13125) 2019-10-11 07:55:15 +02:00
Nichols A. Romero
884964d551 Fix f18 install method (#13123) 
* Install method is broken and not needed. Built-in install method works fine. Just delete.

* Change version to master.
 2019-10-10 21:52:29 -05:00
Adam J. Stewart
7af8c206ac
Add patches and missing dependency to bash (#13084) 2019-10-10 12:48:49 -05:00
Adam J. Stewart
c131a725af
Add mpfr 4.0.2 (#13091) 2019-10-10 12:48:32 -05:00
Adam J. Stewart
06dffaefed
Add tar 1.32 (#13099) 2019-10-10 12:48:16 -05:00
Jannek Squar
02564ef4ab sublime-text: New version, adapt install process (#13074) 
* Added new version, reworked installation process

* Removed explicit addition to PATH
 2019-10-10 12:13:00 -05:00
Adam J. Stewart
e925dbcefe
Add expat 2.2.9 (#13085) 2019-10-10 12:10:48 -05:00
Adam J. Stewart
f940e8616c
Add gettext 0.20.1 (#13086) 2019-10-10 12:10:19 -05:00
Adam J. Stewart
4d2b300da0
Add isl 0.21 (#13087) 2019-10-10 12:10:03 -05:00
Adam J. Stewart
15d7e2efd5
Add libiconv 1.16 (#13088) 2019-10-10 12:09:46 -05:00
Adam J. Stewart
c570c09cbf
Add libsigsegv 2.12 (#13089) 2019-10-10 12:09:28 -05:00
Adam J. Stewart
db8178d99a
Add latest openssl releases (#13092) 2019-10-10 12:09:02 -05:00
Adam J. Stewart
ace11d857f
Add latest Perl releases (#13093) 2019-10-10 12:08:40 -05:00
Adam J. Stewart
f35c845330
Add pkgconf 1.6.3 (#13094) 2019-10-10 12:08:19 -05:00
Adam J. Stewart
0cf6980437
Add readline 8.0 (#13095) 2019-10-10 12:07:48 -05:00
Adam J. Stewart
4a5bdd1afd
gdbm: https -> http (#13096) 2019-10-10 12:07:24 -05:00
Adam J. Stewart
01b87259e2
ncurses: https -> http (#13097) 2019-10-10 12:07:05 -05:00
Adam J. Stewart
f904e47c4e
Add sqlite 3.30.0 (#13098) 2019-10-10 12:06:44 -05:00
Satish Balay
dd64bdc313 hypre: add compatibility patch for petsc/mfem build failures (#13116) 2019-10-10 09:11:15 -05:00
wspear
a042a7e91e Added new versions to py-tornado (#13080) 
* Added new versions to py-tornado

* Removed all but the latest new version
 2019-10-10 09:06:01 -05:00
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