Commit graph

9450 commits

Author SHA1 Message Date
Satish Balay
da883f2270 petsc: add version 3.12.2 (#13859) 2019-11-22 20:35:16 -06:00
George Hartzell
48420d0c24 New package: py-wub, with supporting fixes (#13773)
* Add py-wub, with supporting fixes

- add py-wub
- add py-pycmd because py-wub needs it
- update py-statsmodels, which needs at least v0.9.0 to work with
  python3.7 because cython.

* Update based on Adam's comments

* Fix dependency types for py-six in py-wub

* statsmodels tests fail, update comment w/ Issue #

The statsmodels tests weren't run in the previous version of the
package.  If I enable them, the fail.

Update the package comment with the statsmodels issue I opened to
track the problem:
https://github.com/statsmodels/statsmodels/issues/6263

* Update dependency types in py-wub/package.py

* flake8 cleanups

* Make statsmodels tests work

- need to use patsy@0.5.1:
- need to run the tests from within the build/lib* dir
2019-11-22 20:34:43 -06:00
Christoph Junghans
b23d2efd99
votca-*: add v1.5.1 (#13822) 2019-11-21 16:09:03 -07:00
George Hartzell
73038a3f51 Add mg, a gnu-emacs like fork of microemacs (#13812)
* Add mg, a gnu-emacs like fork of microemacs

* Use Package, since not really an Autotools package

Switch from AutotoolsPackage to Package.  Even though mg has a
configure script, it's not really an Autotools package.

* Need to also provide --prefix to configure
2019-11-21 11:40:13 -07:00
Toyohisa Kameyama
bed7e40dcc cbtf-krell: add rpcsvc-proto and libtirpc dependency. (#13800) 2019-11-21 11:38:09 -07:00
Elizabeth Fischer
9a6a19d464 doxygen: added missing dependencies to the package (#10589)
See http://www.doxygen.nl/manual/install.html
2019-11-21 15:30:31 +01:00
t-karatsu
49b9365205 texinfo: fix unescaped braces, and update locale handling (#13815)
* texinfo: Fix unescaped braces for older version.

* texinfo: update locale handling.
2019-11-20 20:54:55 -07:00
Shintaro Iwasaki
71cd91e4c1 update Argobots and BOLT (#13765)
* argobots: update to 1.0rc2

* bolt: update to 1.0rc3

* argobots/bolt: add maintainers

* argobots: use "master" for the master branch
2019-11-20 19:04:46 -07:00
Douglas Duckworth
100fcc2c8e added hmmer v 3.3 (#13793) 2019-11-20 19:04:27 -07:00
Brian Van Essen
2f069b571d Updated versions numbers for Aluminum and Hydrogen. (#13814) 2019-11-20 19:04:01 -07:00
t-karatsu
9cd778f152 ampliconnoise: Change return type of function. (#13766)
* ampliconnoise: Change function type.

* ampliconnoise: updated api call to setup run environment
2019-11-20 16:03:51 -07:00
健美猞猁
1e52aa750a find-circ: a new package. (#13767)
* find-circ: a new package.

* flake8.
2019-11-20 16:02:34 -07:00
健美猞猁
5e9ca0f939 miranda: a new package. (#13768) 2019-11-20 16:01:41 -07:00
Figroc Chen
ace47cecbe tensorflow-serving-client: add new package (#13771) 2019-11-20 16:01:04 -07:00
t-karatsu
af9281b843 bpp-suite: Clarify 'isinf' function's namespace. (#13777) 2019-11-20 15:52:44 -07:00
David Hows
ad4986be94 Fix for overlong shebang in valgrind (#13779)
Fix for some overlong shebangs in valgrind. Borrowed from verrou/package.py
2019-11-20 15:50:14 -07:00
noguchi-k
894267e02e py-numexpr3: fix version (#13781) 2019-11-20 15:49:13 -07:00
Ken Raffenetti
f25cf16b11 mpich: Add 3.3.2 (#13790) 2019-11-20 15:48:11 -07:00
Justin S
63874db562 genrich: new package at 0.6 (#13791) 2019-11-20 15:47:36 -07:00
Justin S
38ae7ab6cd sentieon-genomics: add 201808.07 (#13794) 2019-11-20 15:46:22 -07:00
Adam J. Stewart
4e4e3d192e
Add old version of py-gast (#13806) 2019-11-20 15:21:03 -07:00
Adam J. Stewart
0d1e9c6e06
Add py-google-pasta package (#13807) 2019-11-20 15:20:47 -07:00
Adam J. Stewart
d43364d679
Add new py-grpcio package (#13808) 2019-11-20 15:20:28 -07:00
Adam J. Stewart
d19eb21181
Add c-ares 1.15.0 (#13809) 2019-11-20 15:20:08 -07:00
Adam J. Stewart
33059daff4
Add old versions and missing dependencies to py-protobuf (#13811) 2019-11-20 15:19:47 -07:00
Adam J. Stewart
ea42d67a9a
Add old version of jdk (#13805)
* Add old version of jdk

* setup_environment -> setup_build_environment
2019-11-20 15:19:22 -07:00
Brian Van Essen
66cf530459 Added package for Clara command line parser (#13763)
* Added package for Clara command line parser
2019-11-20 00:12:43 -07:00
albestro
f25a4ab089 add MAX_CPU_COUNT variant to HPX package (#13769)
* add MAX_CPU_COUNT variant to HPX package

* compatibility with python2

* correct variant description

Co-Authored-By: Mikael Simberg <mikael.simberg@iki.fi>

* add maintainers list
2019-11-19 12:49:32 -07:00
George Hartzell
d00be588e3 zlib: use setup_build_environment for build env (#13786)
zlib was using the deprecated setup_environment call.  Now it's using
the current setup_build_environment.

(noticed this in some `spack -d` output)
2019-11-19 12:29:35 -07:00
ktsai7
bb0667ceaf add more legion version and expose more flecsi options (#13741)
* add more legion version and expose more flecsi options

* formatting

* update version pointing to master to master

* fix indentation

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py

* use self.run_tests

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

* Update package.py

* Update package.py

* Update package.py

* Update package.py
2019-11-18 23:51:41 -07:00
Greg Becker
99dfff4475
binary distribution: relocate text files properly in relative binaries (#13578)
* Make relative binaries relocate text files properly
* rb strings aren't valid in python 2
* move perl to new interface for setup_environment family methods
2019-11-18 14:13:42 -07:00
健美猞猁
e433a5dc0b py-rnacocktail: a new package. (#13761)
* py-rnacocktail: a new package.

* flake8.

* Add build-time dependencies.
2019-11-18 14:09:39 -07:00
albestro
e0746a2a07 fix libxml2 url (#13770)
http to https
2019-11-18 10:58:16 -07:00
Xavier Delaruelle
e5b3202352 environment-modules: add version 4.4.0 (#13772) 2019-11-18 10:53:06 -07:00
Massimiliano Culpo
ab62ad463d
py-xattr: fix a package that was pointing to a fork (#13685)
The package now points to the official github repository for master
and to PyPI for release versions.
2019-11-18 12:09:47 +01:00
oracleLee
686e613e94 Update scalpel package.py (#13746)
* Update package.py

Update scalpel version 0.5.4

* Update package.py
2019-11-17 12:45:16 -07:00
Cyrus Harrison
d3c1547dba update to add ascent 0.5.0 release (#13709)
* fix metis src dl url

* update ascent, vtk-h and vtk-m recipes

* update conduit package

* fix vtk-m shas

* mfem conduit fix

* use vtk-h develop

* fix issue with stripped include paths in mfem

* more metis fixes

* simpler fix for mfem conduit include issue

* finish mfem changes

* pin to cmake 3.14, since we hit cuda issues with 3.15

* add rtd theme as dep for ascent

* add vtk-h 0.5.0 release, update ascent to use it

* add ascent 0.5.0 release

* fix cmake pin to allow all vers of 3.14

* fix format string error in mfem pkg

* review fixes for mfem pkg

* review fixes for vtk-h and vtk-m packages

* address review comments for ascent pkg

* changing default off of develop broke downstream use

* revert prefed
2019-11-17 12:36:14 -07:00
Axel Huebl
02f27fc45d openPMD-api: 0.10.0 (#13750)
Add latest release and first to be tagged by number in Spack,
version 0.10.0.
2019-11-17 12:35:40 -07:00
Hector Martinez-Seara
15207bae43 guile package: Handling the threads option. (#13730)
* guile package: Handling the threads option.

Currently guile by default tries to compile its thread variant.
However, the threaded version can only be compiled if bdw-gc is
compiled with some threads support. Currently, the default
compilation of the bdw garbage collector is compiled without any
thread support resulting in a compilation error.

I have changed the the default guile compilation to the non-threaded
version. I have also added the appropiated options for the bdw-gc
compilation in case the user prefers the threaded variant.

* guile package(flake8): fixed identation issues
2019-11-16 14:34:38 -07:00
Nick Booher
c8c8dca5b5 revbayes: add new versions (#13760) 2019-11-16 00:12:38 -07:00
Satish Balay
40c77bf158
xsdk@0.5.0 (#13682)
Update:
 hypre@2.18.2
 mfem@4.0.1-xsdk
 superlu-dist@6.1.1
 trilinos@12.18.1
 - dtk-3.1
 petsc@3.12.1
 dealii@9.1.1
 pflotran@xsdk-0.5.0
 alquimia@xsdk-0.5.0
 sundials@5.0.0
 plasma@19.8.1
 magma@2.5.1
 amrex@19.08
 slepc@3.12.0
 omega-h@9.29.0
 strumpack@3.3.0
 pumi@2.2.1
 tasmanian@7.0
 phist@1.8.0

New:
 ginkgo@1.1.0
 py-libensemble@0.5.2
 precice@1.6.1
 butterflypack@1.1.0

Add variants:
 ginkgo
 libensemble
 precice
 butterflypack
 strumpack
 trilinos

tasmanian:  use ~openmp only on OSX
precice: disable on OSX
enable sundials+superlu-dist
sundials+superlu-dist requires OpenMP 4.5+ (so enable only for gcc@6.1+)
enable mfem+sundials
enable sundials+petsc+superlu_dist
remove hypre~internal-superlu
petsc: build with +batch on cray
precice: use ~petsc on cray
libensemble: add as runtime dependency for PYTHONPATH
2019-11-14 16:36:51 -06:00
t-karatsu
94c9e5f9a0 z3: bugfix about python dependency and fallthrough annotation. (#13713)
* z3:

* Fixed python dependency to always be required.

* bugfix about fallthrough annotation.

* z3: Add patch for before ver.4.4.1.

* Update var/spack/repos/builtin/packages/z3/package.py

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-14 16:28:05 -06:00
Seth R. Johnson
e670476024 Mark conflicts between newer packages and Intel 14 compilers (#13729)
* Mark compiler/version conflict for CMake

Intel 14 lacks some C++11 features needed to compile new versions of
cmake.
```
/tmp/s3j/spack-stage/spack-stage-cmake-3.15.5-46lgp4ybhopy2p4rr66rxnew5iaddvmg/spack-src/Source/
cm_static_string_view.hxx(28): error: expected an operator
   friend static_string_view operator"" _s(const char* data, size_t
                                     ^
```

* Mark compiler/version conflict for icu4c

With Intel 14.0.4 on Linux for icu4c 60.1 and higher:
```
locid.cpp(1156): error #1140: a using-declaration may not name a constructor or destructor
        using KeywordEnumeration::KeywordEnumeration;
```

* Mark compiler/version conflict for nasm

Error installing `nasm@2.14.02%intel@14.0.4`:
```
In file included from nasmlib/crc64.c(35):
./include/nasmlib.h(116): error: expected a ";"
  fatal_func nasm_assert_failed(const char *, int, const char *);
```

* Mark compiler/version conflict for bison

Installing `bison@3.4.2%intel@14.0.4`:
```
In file included from /tmp/s3j/spack-stage/spack-stage-bison-3.4.2-
uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/quotearg.c(33):
/tmp/s3j/spack-stage/spack-stage-bison-3.4.2-uzjszv4owvqsymjpxtxvvegfavc6k5my/spack-src/lib/
xalloc.h(51): warning #303: explicit type is missing ("int" assumed)
  extern _Noreturn void xalloc_die (void);
```

* Mark compiler/version conflict for icu4c

With `icu4c@60.1%intel@16.0.4` and `icu4c@64.1%intel@16.0.4`:

```
In file included from ucurr.cpp(26):
static_unicode_sets.h(130): error #913: invalid multibyte character sequence
      {POUND_SIGN, u'£'},
                     ^
```

* Change conflict comments into messages
2019-11-14 16:27:36 -06:00
George Hartzell
7a6c7f23a0 py-matplotlib only needs backports when ^python@:2 (#13712)
* py-matplotlib only needs backports when ^python@:2

This implements @scheibelp's suggestion in #13711.

py-matplotlib should only depends_on py-backports-functools-lru-cache
when it's using a python that actually *needs* it.

See #13711 for details.

* Don't depend_ons py-enum34 unless python@:3.3

* Tighten up enum34 dependency

@adamjstewart cracked open the setup.py files and suggested a tighter
dependency for py-enum34.  1.4 and 1.5 only require it for pythons
before 3.4, 1.3 requires it unconditionally.  So...., we'll do the
same.

* Remove conflict on python 3.4 from enum34

at @adamjstewart's request see PR notes
2019-11-14 16:26:44 -06:00
Gregory Lee
8490587c76 add boost dependency to stat package (#13735) 2019-11-14 16:26:24 -06:00
xfzhao
2fb5df0284 update to v0.6.4 (#13737) 2019-11-14 16:26:08 -06:00
Emir İşman
46871416b1 Update DMTCP package to v2.6.0 (#13739) 2019-11-14 16:20:44 -06:00
Nicholas Sly
d79d11b6d4 Removed github repository and develop version from dataspaces package as it is no longer present/accessible. (#13740) 2019-11-14 16:20:13 -06:00
xfzhao
11e65661ac update vsearch (#13736) 2019-11-14 16:17:02 -06:00
Massimiliano Culpo
7e84fe966c hwloc: added 'master' version pointing at the HEAD of the master branch (#13731) 2019-11-14 12:06:07 -06:00