Commit graph

12470 commits

Author SHA1 Message Date
xfzhao
c30f9c6833 update bbmap (#12721)
* update bbmap

* remove one extra comment line
2019-09-09 12:55:06 -05:00
Michael Kuhn
62f0286f5e Fix pkgconfig dependencies (#12714)
pkgconfig is the virtual dependency, pkg-config is an implementation.
2019-09-09 12:54:46 -05:00
brietzke
4de32033b1 Update py-bokeh: new version & dependencies" (#12724)
* update py-bokeh: new version & dependencies

* Revert "update py-bokeh: new version & dependencies"

This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.

* update py-bokeh: new version & dependencies

* trigger travis-ci

* adjust python dependency-type to br
2019-09-09 11:59:27 -05:00
brietzke
155a667b7a New package: py-fsspec (#12725)
* update py-bokeh: new version & dependencies

* Revert "update py-bokeh: new version & dependencies"

This reverts commit 5e191a0b20a89f09630b4d223a28b19db715603f.

* new package: py-fsspec: add package.py

* trigger travis-ci

* adjust python dependency-type to br
2019-09-09 11:58:49 -05:00
Dan Lipsa
1a8c572316 Paraview version (#12766)
* Update paraview

* Paraview 5.6.2 provides only .xz (no .gz)

* Add list_url and list_depth
2019-09-09 11:57:53 -05:00
Massimiliano Culpo
bd0fed7090 clang: add another regex for version detection (#12769)
This is similar to #10191. The Ubuntu package for clang 8.0.0 displays
a very unusual version string, and we need this new regex to detect it
as just 8.0.0

Unit test have been complemented by the output that was failing
detection.
2019-09-09 11:37:04 -05:00
viniciusvgp
7849dbb529 binutils: fix undefined symbol libintl_dgettext (#12770) 2019-09-09 11:05:04 -05:00
Axel Huebl
02931a82fd Add CORS for spack.packages.io
Add the HTTP header `Access-Control-Allow-Origin: *` for our NGINX
service that is serving static JSON content on
https://spack.packages.io .
2019-09-08 17:19:37 -07:00
Greg Sjaardema
db1fb16840 CGNS: Add setting of RPATH on Darwin (#9984)
* CGNS: Add setting of RPATH on Darwin

This should go in the CGNS CMakeLists.txt, but it isn't there yet and won't be in previous versions, so best to handle it here.  
If building on darwin/MacOSX, need to set the RPATH so applications can find shared library correctly.

* Restrict MACOSX_RPATH setting

This has now been added to the CGNS distribution, so the setting of `CMAKE_MACOSX_RPATH` should be restricted to current and previous releases and not upcoming releases.
2019-09-08 17:14:56 -05:00
Geoffrey Oxberry
983e6b4a4a fribidi@1.0.5: new package (#12386) 2019-09-08 17:10:39 -05:00
Sinan
4a18d40a66 new package: py-iniparse (#12638)
* new package: py-iniparse

* add git version supporting python3

* redo python dependency
2019-09-08 17:09:24 -05:00
Sinan
d66caf7a66 Package/py configobj (#12639)
* new package: py-configojb

* add version 4.7.2

* improve dependencies

* fix url for versions > 5.0.0

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

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

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

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

* use format to create url strings

* fix typo

* improve style

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

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 17:08:59 -05:00
Owen Solberg
2ad6bed77c for fakeroot support, add "shadow" dependency (#12754)
* adding checksum for singularity 3.4, adding dep for shadow

* make v3.4 a TODO for now -- needs cryptsetup package first
2019-09-08 13:55:15 -05:00
Adam J. Stewart
bff667051b
Fix PyQt installation (#12479)
* Fix PyQt installation

* Switch dependency type

* Replace SIP dependency with resource

* Relax py-pyqt4 Qt dependency
2019-09-08 10:48:50 -05:00
Simo Tuomisto
5a21c781f3 py-gpaw: Fixing missing numpy include path, adding newer version of p… (#12737)
* py-gpaw: Fixing missing numpy include path, adding newer version of py-gpaw and fixing a bug with libxc.c in older py-gpaw

* py-gpaw: Fix Python and ASE version dependencies

- GPAW 19.8.1 requires Python 3.x, add dependency on python@3.5:

- GPAW releases are associated with a corresponding ASE release, add
  matching ASE version dependencies.

* py-gpaw: Enable the scalapack variant by default

GPAW installation instructions say scalapack is optional but "highly
recommended". Thus enable it by default.
2019-09-08 10:46:47 -05:00
Owen Solberg
8fd8b54e97 py-cutadapt: Updated version checksum (#12741)
* add new cutadapt release 2.5, and adjust dependencies conditional on version

* use https, not ssh, for git url

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 10:46:08 -05:00
Owen Solberg
fe26678299 new package: py-bz2file (#12761)
* update py-xopen (add 0.8.2 checksum)

* refine version specific dependencies

add py-bz2file, which needs to be created

* create py-bz2file

* Revert "refine version specific dependencies"

This reverts commit 70649da98851fefb2f936ca99a012fe6bef07b70.

* Revert "update py-xopen (add 0.8.2 checksum)"

This reverts commit 7400f44caa6e98419eb4bc3107704b91e8a2018b.
2019-09-08 10:38:37 -05:00
Owen Solberg
b83fa3909e py-xopen: update release 0.8.2 checksum (#12742)
* update py-xopen (add 0.8.2 checksum)

* refine version specific dependencies

add py-bz2file, which needs to be created

* py-bz2file needed when built with python 2.7

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

* space after comma
2019-09-08 10:38:19 -05:00
Owen Solberg
4468ee2437 py-dnaio: new package need by py-cutadapt (#12743)
* add new package py-dnaio

* provide git url with https, not ssh, protocol

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-08 10:37:49 -05:00
Todd Gamblin
a2220f3150 flake8: make entire repository pass spack flake8 -a
- Fix trailing whitespace missed by the bug described in #12755.

- Fix other style issues that have crept in over time (this can happen
  when flake8 adds new checks with new versions)
2019-09-07 23:59:10 -07:00
Todd Gamblin
0ec80e8f16
flake8: only add E501 exemptions when absolutely necessary (#12755)
E501 (line too long) exemptions are probably our most common ones -- we
add them for directives, URLs, hashes, etc. in packages.  But we
currently add them even when a line *doesn't* need them, which can mask
trailing whitespace errors.

This changes `spack flake8` so that it will only add E501 exemptions if
the line is *actually* too long.

Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-09-07 23:58:12 -07:00
Owen Solberg
48c3c833e8 patch boost version 1.54-1.55 when being built with ANY gcc version after 5.0 (#12718) 2019-09-07 22:45:53 -05:00
Kevin Huck
35221c127e Updating TAU package. Fixing compiler specification for OSX (#12720)
and making Fortran an option that can be disabled.  Also added
support for the POSIX I/O wrapper and OMPT for OpenMP.
2019-09-07 22:44:40 -05:00
Howard Pritchard
1a38285be9 mesa: disable use of libunwind for arm arch (#12735)
There are problems with libunwind for arm and trying to use it with mesa.
See for example:

https://github.com/grate-driver/mesa/issues/6

disabling use of libunwind for arm, allows the package to be built

Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
2019-09-07 22:33:30 -05:00
Jonas Lippuner
c3a2528022 add mpi variant to p4est package to allow turning off MPI (#12739) 2019-09-07 22:29:53 -05:00
Axel Huebl
331e4e32be ncurses: improve build time (#12621)
Apply configure options to skip manpage generation
and test builds for both wide and non-wide builts.
2019-09-07 22:27:07 -05:00
Ruben Di Battista
ac7a17754f luarocks: Use make command instead of install (#12703)
This way luarocks does not attempt to pull stuff from the internet.

Fix #3909
2019-09-07 21:06:52 -05:00
Adam J. Stewart
faa3d6a2a5
Add py-numpy 1.17.2 (#12753) 2019-09-07 20:44:46 -05:00
Piotr Luszczek
bbdb033e5f Add patches to work around CMake versions (#12744)
- Use of symbol testing macro requires explicit include()
- CMake policies are not version-portable and the support has to queried
  based on CMake version
2019-09-07 19:04:20 -05:00
Owen Solberg
c4da66be4c font-util 1.3.2 (#12728) 2019-09-07 18:57:22 -05:00
Adam J. Stewart
a4aa1b5a05
Update docs on module loads command (#12702) 2019-09-07 18:32:02 -05:00
Sinan
754ce972a3 new package: py-pygdal (#12747) 2019-09-07 18:23:38 -05:00
Vanessasaurus
25bbc27716 adding shadow-uidmap (#12750)
Signed-off-by: Vanessa Sochat <vsochat@stanford.edu>
2019-09-07 17:36:45 -05:00
Mathias Jacquelin
696e12da98 upcxx: new package
Adding a UPC++ spack package pointing to the default 2019.3.2 UPC++
version, and allowing to build UPC++ with the experimental CUDA variant.
2019-09-06 16:04:33 -07:00
Toyohisa Kameyama
5def1dd39d openspeedshop: fixed build on arm. (#11861)
* openspeedshop: fixed build on arm.

* remove patch comment.
2019-09-06 13:26:24 -07:00
Geoffrey Oxberry
8fe5405e1b libpeas@1.22.0: new package (#12385)
* libpeas@1.22.0: new package

* libpeas: note more build dependencies

Build and link dependencies were obtained through a combination of
examining the `config.log` file from `configure` and looking at the
pkg-config files of `libpeas`.

* libpeas: add search path for GIR/typelib files
2019-09-06 12:53:12 -05:00
Geoffrey Oxberry
071fb3dd6a iso-codes: new package (#12389) 2019-09-06 12:48:08 -05:00
Greg Becker
3f1c78128e
make env view loading unconditional (#12719) 2019-09-05 18:15:36 -07:00
Toyohisa Kameyama
34647913be fftw: change default value of simd variant for other than x86_64 (#11627)
* Use spec.architecture.target insted of platform.

* remove default in simd variant value.
simd variant change to archtecture independent values.

* Add check simd values.

* rewrite check simd values.

* * flake8
* change aarch64 to arm (neon support only 32 bit arm.)
2019-09-05 11:42:04 -07:00
Matthieu Dorier
1dbf3c208b FIX Catalyst: corrected catalyst package for aarch64 targets (#12707)
* corrected catalyst package for aarch64 targets

* corrected syntax

* corrected undefined variable
2019-09-05 12:44:38 -05:00
Ruben Di Battista
6ef95481ef Add pixz package (#12698) 2019-09-05 09:40:29 -05:00
Jennifer Herting
ca8db06e37 [jemalloc] added version 5.2.1 (#12706) 2019-09-05 09:39:42 -05:00
Hironori-Yamaji
ed6a2f0ef9 textparser: new package (#12713)
* textparser: new package

* textparser: use 'parallel = False'
2019-09-05 09:37:21 -05:00
Michael Kuhn
ad93f47c8f mariadb: Add missing dependencies (#12715)
Found while building mariadb in a minimal build environment.
2019-09-05 09:34:44 -05:00
Janne Blomqvist
30756a643b py-ase: New version 3.18 (#12697)
* py-ase: New version 3.18

Add ASE version 3.18. ASE 3.18 has dropped support for python 2.x,
hence add a dependency on python@3.5: for it.

* Add more ASE dependencies

Address review comments, add dependencies on py-scipy, py-matplotlib,
py-flask, and also add type=('build', 'run') dependency specifiers.
2019-09-05 09:09:37 -05:00
Toyohisa Kameyama
e50dbe6f76 cctools: fixed to build on ARM. (#11862) 2019-09-04 16:45:41 -07:00
Paul Bryant
cb2d18c1e6 Add Go 1.13 2019-09-04 15:04:51 -07:00
t-karatsu
e08f527004 openblas: Add route to f_check for Fujitsu compiler. (#11804) 2019-09-04 15:01:58 -07:00
Chris Green
7f8fe11e4d Improve mock_archive versatility; Remove unwanted ALLOWED_ARCHIVE_TYPES. (#12513)
mock_archive can now take multiple extension / tar option pairs (default matches old behavior).

url_fetch.test_fetch tests more archive types.

compression.EXTS split into EXTS and NOTAR_EXTS to avoid unwanted, non-meaningful combinatoric extensions such as .tar.tbz2.
2019-09-04 13:49:00 -05:00
asmaahassan90
00b02fd234 Add gams recipe (#12700)
* Add gams recipe

* Break down lines to pass lint
2019-09-04 10:13:58 -05:00