Commit graph

11222 commits

Author SHA1 Message Date
Adam J. Stewart
4e6285a19b
Ensure that every package has a description (#10896) 2019-03-14 20:49:07 -05:00
Chris Green
9b51fb09f1 Support VISUAL environment variable for editing. (#10898)
If the user has set the environment variable VISUAL, it will be used
in preference to EDITOR for all Spack editing activities. If VISUAL
is not set or fails (perhaps due to a lack of graphical editing
capabilities),EDITOR will be used instead. We fall back to one of
several common editors if neither bears fruit.

This feature has been tailored to:

* Provide identical behavior to the previous implementation in the
  case that VISUAL is not set.
* Not require any change to code utilizing the editor feature.
* Follow usual UNIX behavior concerning VISUAL and EDITOR.
2019-03-14 16:16:26 -05:00
Jordan Ogas
1d73868333 charliecloud: added version 0.9.8 (#10900) 2019-03-14 20:36:53 +01:00
Chris Green
6a9f02c96f cppunit: support cxxstd. (#10888) 2019-03-14 16:17:31 +01:00
Elizabeth Fischer
f15f3076db libxaw: added version 1.0.12 (#10591) 2019-03-14 12:55:56 +01:00
Levi Baber
a71664a42d py-pybigwig: needs curl at link time (#10892) 2019-03-14 11:07:50 +01:00
Cody Balos
4025ec9508 sundials: add new version (4.1.0) (#10890) 2019-03-14 11:00:22 +01:00
Nichols A. Romero
ec5bf38245 QMCPACK More CUDA Fixes (#10864)
* Throw InstallError if more than one GPU architecture is passed to cuda_arch. Previous cuda_arch test was not actually working because comparison with none string was on the cuda_arch list instead of the first entry of the list.

* Removing redundant cuda_arch statement.
2019-03-13 16:03:28 -05:00
Eric Martin
2bca687605 py-treehash: Create new package (#10872) 2019-03-13 16:03:09 -05:00
Levi Baber
39c40ee3fc revbayes: new version (#10873) 2019-03-13 21:36:13 +01:00
Michael Kuhn
d3365e4356 libplist, libusbmuxd: Fix pkgconfig dependency (#10876)
pkgconfig is the correct virtual provider.
2019-03-13 14:55:23 -05:00
Michael Kuhn
db79317eb9 cubelib, cubew: Add missing pkgconfig dependency (#10875) 2019-03-13 20:15:02 +01:00
Michael Kuhn
3019068e0c mpich: Add patch to fix node list parsing (#10870)
mpich@3.3 introduced a new regex-based function for node list parsing
that does not recognize hostnames without a dash properly.
2019-03-13 10:58:05 -07:00
Eric Martin
358226b946 py-biomine: new package (#10868) 2019-03-13 15:17:06 +01:00
Eric Martin
6a87b6215f help2man: Add version 1.47.8 and perl runtime dependency (#10862) 2019-03-13 15:11:45 +01:00
Eric Martin
7d50567423 py-advancedhtmlparser: new package (#10867) 2019-03-13 15:06:01 +01:00
Eric Martin
ffbc4f199e fqtrim: Create new package (#10861) 2019-03-12 21:30:30 -05:00
David Hows
c629a6f780 Fix mysqldb1 (#9978)
* Update package.py

* Add MYSQL Package file

* Fixes for linter
2019-03-12 20:57:29 -05:00
Elizabeth Fischer
82e9c01b5c New package: py-mysql-connector (#10327)
* New package: py-mysql-connector

* Fixed docstring

* 1. Determined that py-setuptools was not needed at all, so removed.
2. Added py-protobuf.  Docs seem to imply that only C protobuf library is required; however, the Python setup.py says differently, and some Python code seems to reference protobuf too.  I don't know why this worked for me, but it looks like including py-protobuf is the right thing to do.

* Applied solution detailed in:

https://github.com/mysql/mysql-connector-python/pull/9

Uncommenting this patch will make `error: option --single-version-externally-managed not recognized`  reappear.

* Clean up / reorder lines

* flake8
2019-03-12 20:52:43 -05:00
Tristan Carel
c3662492de Do not use string module to be compatible with python 3 (#248) (#10667)
`string.find` is not part of Python 3 anymore.
2019-03-12 20:34:47 -05:00
Eric Martin
3d7164c13f varscan: set VARSCAN_HOME variable to jar file location (#10744) 2019-03-12 20:29:48 -05:00
Eric Martin
0ebd81bd15 py-pytables: Add hdf5 1.10.x support for versions above 3.4.0 (#10746) 2019-03-12 20:29:24 -05:00
David Poliakoff
d5c3ce790f Update caliper package (#10750)
* Updating Caliper package with a shared lib option

* Tightened version bounds on Caliper package

* Removed testing. Loosened version constraints

* Add Caliper 2.0.1, cleanup dependency specs
2019-03-12 20:28:13 -05:00
Justin Stanley
2bea940e43 find_versions_of_archive: expand link search (#10758) 2019-03-12 20:19:46 -05:00
Nick Forrington
6bda37f542 Fix clearing EnvironmentModifications with python2 (#10791)
* Fix clearing EnvironmentModifications with python2

* Add EnvironmentModifications::clear unit test

Use re-assignment rather than del to clear array

* Fix flake issues
2019-03-12 20:12:51 -05:00
Rob Latham
da28b592fc "Werror" too strict for recent compilers (#10802)
rapidjson gives warnings with gcc-7.3 and branch fall through
2019-03-12 20:10:51 -05:00
Michael Kuhn
65f37746af qt: Use more system dependencies and fix build with new gcc versions (#10817)
qt currently falls back to bundled versions of sqlite, harfbuzz, pcre,
double-conversion and xcb. This adds the appropriate dependencies and
configure arguments. A new variant adds multibyte support to pcre and
pcre2, which is required by qt.

Additionally, newer versions of gcc (starting with @8.3.0) cause build
failures. This adds a patch to fix the problem.

The changes have been tested with all versions of qt currently available
in Spack. 5.2 and 5.3 do not build for reasons that seem to be unrelated
to these changes, though.
2019-03-12 20:04:11 -05:00
健美猞猁
a79230c832 casacore does not support fftw+mpi . (#10839) 2019-03-12 19:59:48 -05:00
健美猞猁
d32a342fc6 Aoflagger: a new package. (#10840)
* A new package: aoflagger.

* aoflagger does not support boost>1.66.0 .

* Add fftw~mpi dependency.

* flake8.

* Flake8.

* Update package heder.

* md5 -> sha256.
2019-03-12 19:59:24 -05:00
Axel Huebl
fd6d3f6b8c openPMD-api: shared variant (#10847)
Add a variant to control shared/static builds (one at a time) and
make shared the default.
2019-03-12 19:58:44 -05:00
Alberto Chiusole
46fb6ed5b6 Revert to manual flag enabling, due to RegCM bug in configure. (#10863)
The configure of RegCM treats --disable-FEATURE as --enable-FEATURE,
so we cannot use enable_or_disable.
2019-03-12 19:48:45 -05:00
Owen Solberg
dc5b16a8e9 added checksum for 20190222 release of gnu parallel (#10865) 2019-03-12 19:40:29 -05:00
Eric Martin
50193229ea py-llvmlite: Add versions 0.26.0 and 0.27.1 (#10866) 2019-03-12 19:40:01 -05:00
Mark W. Krentel
3ed6e78338 New package: ibm-java (#10777)
* Add binary package of the IBM Java SDK for big and little-endian
  powerpc (power7, 8 and 9).  The jdk and openjdk packages only install
  on x86_64.
* Add ibm-java as a java provider
* The jdk and openjdk packages only install on x86_64. Add conflicts
  for ppc64 and ppc64le to jdk and openjdk.
2019-03-12 18:05:47 -05:00
wspear
e1e5eb29d2 Elfutils package: add m4 dependency and version 0.176 (#10834)
* Elfutils requires m4 to build
* Add version 0.176
2019-03-12 17:35:59 -05:00
Robert Pavel
1450fe72fa New package: Draco (#10844) 2019-03-11 20:57:00 -05:00
Matthias Diener
5e68af5a78 scons package: add missing dependency to py-setuptools (#10856) 2019-03-11 20:30:12 -05:00
Jiawei Zhuang
74b33e9f82 OpenMPI: v4.0.0 + Slurm installation error (#10853)
shmemrun and oshrun do not exist in OpenMPI v4.0.0
(ref: https://www.open-mpi.org/doc/v4.0/)

The Spack OpenMPI package was failing the install by trying to
remove them. This guards the removal of several scripts when
using the Slurm scheduler to handle the case where they don't exist.
2019-03-11 20:18:50 -05:00
Michael Kuhn
1e6b13d335 Fix URLs for VI-HPS projects (#10821)
URLs for the opari2, otf2, and scorep packages have changed (although
the checksums are the same)
2019-03-11 20:12:44 -05:00
Stas Sergienko
9ffd508d7c mpich: add psm2 fabric support (#10814)
psm2 is only supported for versions 2.2 and up, so a conflict is
added for earlier versions
2019-03-11 20:10:02 -05:00
健美猞猁
888bb76758 New package: cotter (#10838) 2019-03-11 19:46:40 -05:00
Eric Martin
1d51cdf824 STAR: Add versions 2.7.0d and 2.7.0e (#10831) 2019-03-11 19:44:54 -05:00
Eric Martin
23b73ca982 py-chardet: Add version 3.0.2 (#10827) 2019-03-11 19:44:30 -05:00
Eric Martin
2e47b45d9f py-urllib3: Add version 1.21.1 (#10826) 2019-03-11 19:44:07 -05:00
Greg Sjaardema
204063e21a cgns package: add version 3.4.0 and update hdf5 dependency (#10803)
* Add version 3.4.0
* Update checksums for older versions to sha256
* Require hdf5~mpi when building with ~mpi
2019-03-11 19:43:16 -05:00
Eric Martin
dc0b6a0613 samtools package: Add version 1.5 and htslib 1.5 dependency (#10825) 2019-03-11 19:29:29 -05:00
Alberto Chiusole
2b591653fa hdf5 package: add version 1.10.5 (#10794) 2019-03-11 15:15:03 -05:00
Justin Stanley
46466381b8 py-crossmap: new package at 0.3.3 (#10854) 2019-03-11 15:13:02 -05:00
Michael Kuhn
9425075a23 flex: Apply 2.6.4 patch regardless of gcc version (#10841)
It seems that this is actually a glibc problem and while 2.6.4 builds
without the patch on newer versions of gcc (@8:), it still sometimes
segfaults (as observed during the doxygen build).
2019-03-11 15:12:28 -05:00
Ce Qin
43525d3445 mpich: remove libpciaccess dependency for MacOS (#10795) 2019-03-11 15:06:49 -05:00