Commit graph

14654 commits

Author SHA1 Message Date
Massimiliano Culpo
752092f46a
Correct pytest.raises matches to match (#15346) 2020-03-05 11:16:02 +01:00
Massimiliano Culpo
d9626cca50
Bugfix: resolve StopIteration message attribute failure (#15341)
Testing the install StopIteration exception resulted in an attribute error:

AttributeError: 'StopIteration' object has no attribute 'message'

This PR adds a unit test and resolves that error.
2020-03-05 10:26:50 +01:00
Adam J. Stewart
9edf812745
py-matplotlib: add 3.2.0 (#15349) 2020-03-04 21:56:00 -06:00
Peter Scheibel
c5dc4a722e
xgboost: add version 0.90 (#15321) 2020-03-04 18:19:03 -08:00
Axel Huebl
1757ec9eae
New version of simplejson (#15325) 2020-03-04 20:34:06 -05:00
Adam J. Stewart
b813887585
ADIOS2: Cleanup, Development Branch Name (#15334)
* ADIOS2: Version `master`

Rename branch version to supported, real development branch `master`.
The old name is legacy Spack when alternative development branch
names were not yet supported.

* ADIOS: Simplify via spec Variable

use the already defined local variable `spec` to shorten
lines
2020-03-04 19:24:16 -06:00
Adam J. Stewart
136a4897b7
ADIOS2: Testing Depends on Python (#15336)
Add the python dependency and CMake hints when build with tests.
`spack install --tests=root adios2`
2020-03-04 19:23:12 -06:00
Patrick Gartung
e2b3d52999
Add function replace_prefix_nullterm for use on mach-o rpaths. (#15347)
This recovers the old behavior of replace_prefix_bin that was
modified to work with elf binaries by prefixing os.sep to new prefix
until length is the same as old prefix.
2020-03-04 19:21:15 -06:00
Adam J. Stewart
d7f84c738e
Fixed the sha has for 1.3.3. (#15331) 2020-03-04 19:19:16 -06:00
Adam J. Stewart
1973d1c53e
libfabric: default 1.8.1 (#15337)
Since 1.9.0 is broken for Darwin, which impacts many developers, and
the fix is still a RC, let's keep the previous release as default.

This avoids distruption for OSX developers and CI.
2020-03-04 19:11:54 -06:00
Peter Scheibel
cf7dbbf65c
Remove DB conversion of old index.yaml (#15298)
Removed the code that was converting the old index.yaml format into
index.json. Since the change happened in #2189 it should be
considered safe to drop this (untested) code.
2020-03-04 16:39:10 -08:00
Patrick Gartung
3ea0e91533
use os.sep instead of null byte to pad replacement paths in binaries (#15338)
* use os.sep instead of null byte to pad replacement paths in binaries

* Prefix the pading os.sep's
2020-03-04 17:15:09 -06:00
Adam J. Stewart
8eda1db50f
precice: Add version 2.0.1 (#15318) 2020-03-04 13:19:41 -06:00
Adam J. Stewart
60439a5040
pgi-19.10 update version (#15330) 2020-03-04 13:18:46 -06:00
Adam J. Stewart
3be3b2d0e3
gcc: Add 8.4.0 (#15323) 2020-03-04 13:18:02 -06:00
Adam J. Stewart
1ade506f54
Add extra version of py-contextlib2 (#15322) 2020-03-04 13:17:09 -06:00
Adam J. Stewart
5cfd862f47
suite-sparse: fix installation for v5.X (#15326)
fixes #15184

GraphBLAS depends on m4 according to CMake error message
Do not use INSTALL= when compiling the library
2020-03-04 13:16:42 -06:00
Christoph Junghans
32a0f3274f
ecp-proxy-apps: version bump (#14680) 2020-03-04 10:45:23 -07:00
Sergey Kosukhin
b472c13803
Fix FCFLAGS handling for Autotools packages (#14788)
Spack's fflags are meant for both f77 and fc. Therefore, they must
be passed as FFLAGS and FCFLAGS to the configure scripts of
Autotools-based packages.
2020-03-03 13:13:38 -08:00
sknigh
370e7c211d
intel-xed does not support python>3.7 (#15308) 2020-03-03 13:38:55 -06:00
sknigh
cec341594d
Added UQTk package (#14801)
* added UQTk package

* Add missing expat dependency to uqtk
2020-03-03 12:50:20 -06:00
Mark W. Krentel
fddb3f291c
elfutils: increase connect timeout (#15262)
Increase the connect timeout for elfutils to 60 sec.  Elfutils (and
bzip2) tar files are on sourceware.org which is often slow to respond.
2020-03-03 11:27:57 -06:00
Brian Van Essen
f83d98a62d
Protobuf's cmake environment does not properly handle being exported (#15293)
and found when using the RelWithDebInfo build type.  Change protobuf
to only support Release and Debug build types.
2020-03-03 11:27:01 -06:00
Mathias Anselmann
d6b0cf75ed
cherry-picking global ordinal type variant from https://github.com/spack/spack/pull/14215 and setting dealii to GO int, to make it compile again (#15288)
Co-authored-by: Andrey Prokopenko <andrey.prok@gmail.com>
2020-03-03 11:26:20 -06:00
Dr. Christian Tacke
c4237e4a10
fairlogger: add version, other improvements (#15300)
* @develop needs the full git repo to use "git describe"
  properly

* If not specifying the cxxstd variant, let cmake use its
  default

* Improve fmt dependencies: fairlogger < 1.6.2 does not
  work with fmt >= 6.

* Small other stuff
2020-03-03 11:24:37 -06:00
Patrick Schratz
71855707ef
Update package.py (#15299) 2020-03-03 11:02:02 -06:00
Jennifer Herting
a237781c48
Created package glfw (#15296)
* Created stub

* added description and homepage

* added dependencies

* removed extra boilerplae

* switched to the pkgconfig provider
2020-03-03 11:01:29 -06:00
Sergey Kosukhin
2d1592cca7
OpenMPI: patch for NAG. (#15301) 2020-03-03 11:00:27 -06:00
Mathias Anselmann
518d1439c7
Suite sparse compilation fix for 5.7.0 and 5.7.1 (#15289)
Suite-sparse 5.7.0 and 5.7.1 need separate make and make install run to be able to compile, too
2020-03-03 12:06:58 +01:00
George Hartzell
dc4e43682c
Tmux should look for tinfo in -ltinfo (#15282)
Just `depend_on('ncurses')`, pkgconfig seems to cause the right thing
to happen if the package is built +termlib or ~termlib (tested both
ways on a CentOS 7 system).

Additional details in: https://github.com/spack/spack/issues/15281

Tested by building all of the releases of tmux on a CentOS 7 box.
2020-03-03 09:12:06 +01:00
Dr. Christian Tacke
b43812c7c4
boost: Add "container" library (#14878)
"container" is partly a misnomer, as it's realy
the extended allocators part of container.

But every part calls it container, so we do too.
2020-03-02 19:48:07 -06:00
Erik Schnetter
059203b2fd
amrex: New version 20.03 (#15294) 2020-03-02 16:09:50 -06:00
Tamara Dahlgren
73f7301ec4
bugfix: ensure proper dependency handling for package-only installs (#15197)
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not.

- [x] add install status checks for the `--only package` case.
- [x] add initial set of tests
2020-03-02 11:16:20 -08:00
Kai Torben Ohlhus
1db1ae6887
openblas: Add version 0.3.9. (#15287)
[OpenBLAS 0.3.9](https://github.com/xianyi/OpenBLAS/releases/tag/v0.3.9) was released.
2020-03-02 11:58:54 -06:00
Cody Melton
7df761564a
Qmcpack: new variant +afqmc (#14882)
* add preliminary afqmc support in qmcpack

* afqmc updates

* fix spack typos

* edit AFQMC to only allow up 3.7 or above

* added NCCL library support for AFQMC build

* add CMAKE args for BUILD_AFQMC_WITH_NCCL

* update for just AFQMC support. No AFQMC+GPU support

* remove nccl for afqmc

* flake8 whitespace fix
2020-03-02 11:58:33 -06:00
Gregory Lee
8a4f02fb2d
stat: new version 4.0.2 (#15290) 2020-03-02 09:51:28 -08:00
Sergey Kosukhin
e3b357ad87
Update flag_handler for 'netcdf-fortran'. (#14789)
* Update flag_handler for 'netcdf-fortran'.

* Refactoring.

* Enable old versions of netcdf-fortran for NAG.

* Disable parallel 'make check' for versions before 4.5.0.

* Fix shared libraries built with NAG instead of conflicting it.

* Add 'skosukhin' as a maintainer of 'netcdf-fortran'.
2020-03-02 08:40:37 -06:00
noguchi-k
aae59f4866
lastz: set compile commands for each compiler (#15284) 2020-03-02 08:05:31 -06:00
Glenn Johnson
c0032a3660
Update tcsh package (#15283)
This PR adds some fixes for the tcsh package.

- Adds new version
- adds list_url so fetching works for current and old tarballs
- sets ncurses dependency explicitly to `ncurses+termlib`

If `+termlib` is not set then it will link against the system libtinfo.
2020-03-01 22:00:57 -06:00
noguchi-k
27de7a2726
lastz: cast from char to signed char (#15263) 2020-03-01 19:58:27 -06:00
TZ
ac4d0c3af7
Quantum-Espresso: qe-6.5 fails to detect MKL for FFT (#15276)
* Quantum-Espresso: qe-6.5 fails to detect MKL for FFT

qe-6.5 fails to detect MKL for FFT if BLAS_LIBS is set due to
an unfortunate upsteam change in their autoconf/configure:
- qe-6.5/install/m4/x_ac_qe_blas.m4 only sets 'have_blas'
  but no 'have_mkl' if BLAS_LIBS is set (which seems to be o.k.)
- however, qe-6.5/install/m4/x_ac_qe_fft.m4 in 6.5 unfortunately
  relies on x_ac_qe_blas.m4 to detect MKL and set 'have_mkl'
- qe-5.4 up to 6.4.1 had a different logic and worked fine with
  BLAS_LIBS being set
However, MKL is correctly picked up by qe-6.5 for BLAS and FFT if
MKLROOT is set (which SPACK does automatically for ^intel-mkl).
Thus, do not set BLAS_LIBS when compiling qe-6.5 with intel-mkl.

* replace all '^intel-mkl' by '^mkl' to match other packages which also provide MKL

e.g. intel-parallel-studio+mkl as mentioned by @adamjstewart in #15276
2020-03-01 10:08:33 -06:00
George Hartzell
501fdc75b6
Update kallisto (with hackery on std_cmake_args) (#15278)
* Filter problematic flag from std_cmake_args

Including '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' in the cmake args causes
bits of cmake's output to end up in the autoconf-generated configure
script.  See https://github.com/spack/spack/issues/15274 and

* Don't build in parallel (sigh)

* Constrain hackery for newer versions...

... to newer versions.
2020-02-29 22:58:13 -06:00
Sinan
5fc43b3b0e
QGIS: fix typos (#15279)
* fix typos

* minor improvement

* add version 3.4.15
2020-02-29 22:56:41 -06:00
Sinan
7150bd6224
New package: QGIS (#12388)
* [WIP] new package: qgis

* add maintainer

* further improvements

* reflect improvements to qscintilla installation paths

* comment out qtkeychain dependency as the package is created

* uncomment qtkeychaing dependency, since this package is now created

* a comment on webkit

* specify versions of dependencies, add variant

* fix variant description

* fix proj dependency logic

* adjust conflicts and dependencies so that one can compile qgis@2 with qt4, python2.7

* minor improvement

* fix some build errors, improve dependency specs

* qsci python bindings will be build by py-pyqt

* cmake variable QSCINTILLA_LIBRARY should point to library itself not the parent folder

* turn grass off explicitly, fix typo, turn qspatialite off explicitly

* fix typo

* specify more cmake options that doesn"t seem to be set properly, and use spack provided pkg-config

* fix libzip

* fix build issue with sqlite variant, add runtime dependencies

* add more runtime python package dependencies

* reflect variant name change in sqlite

* add maintainer, correct typo

* add TODO's

* add more versions

* improve style

* add latest versions

* netcdf -> netcdf-c

* add variants as shown in cmake config

* add conflict: v3.8.1 won't build if qt@5.13:

* change preferred version to latest long term release, 3.10.3

* add a zillion of build options

* improve style

* add descriptions for variants

* remove and already implemented compilation tip

* add "when" statements for optional dependencies

* make flake8 happy

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

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

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

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

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

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

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

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

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

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

* convert conflicts to depends_on

* undo str conversion for path objects

* fix flake8 E131

* fix flake8 E128, E124

* improve style

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-29 18:52:43 -06:00
Mark W. Krentel
4c506c88f0
hpctoolkit: add version 2020.03.01 (#15277)
Add version 2020.03.01, deprecate Blue Gene to 2019.12.28 and earlier,
tighten a few dependencies.
2020-02-29 18:30:42 -06:00
Richard Berg
d105807a48
Add kraken2 (#15053) 2020-02-29 15:44:42 -06:00
Robert Blake
7562d4e934
Caliper depends on python3. (#15260)
* Caliper depends on python3.

The package needs to be told where to find it.

* More flake8 formatting edits.

* Change explicit python3 to spec['python'].command.path

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

* Removing defunct import for flake8

* Flake8 trailing whitespace warning.

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-29 15:32:51 -06:00
Anthony Scemama
ece5ec8ade
opam: added versions up to v2.0.6 (#15178) 2020-02-29 14:47:44 +01:00
rtohid
ecc7afdad6
HPX: added v1.4.1 and "stable" branch (#15198) 2020-02-29 14:44:09 +01:00
Roberto Di Remigio
4dbeb3563b
MRCPP: New package. (#15201) 2020-02-29 14:41:02 +01:00