Commit graph

16713 commits

Author SHA1 Message Date
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
plamborn
0187807621
libhio: specify use of external json (#15209)
libhio has been building it's own json.  With this change, libhio will rely on the json installed by spack.
2020-02-29 14:25:21 +01:00
Glenn Johnson
94c2e7e7b4
Set http:// in homepage for a few packages (#15275)
This PR adds 'http://' to the homepage setting of a few packages that do
not have it set. Not having that set can cause problems with some wiki
apps when embedding the homepage value into markdown syntax.

- bowtie2
- exuberant-ctags
- perl-want
- samtools
2020-02-29 13:47:56 +01:00
George Hartzell
53f4db938f
Update tree for v1.8.0 (#15272)
- add version info for v1.8.0

- v1.8.0 adds a new source file, `file.c`, which need to be included
  in our hardcoded list of objects to link.

  I discovered this while demonstrating "how easy it is to add a new
  package to Spack", only to scratch my head when it failed `spack
  install` but worked when I ran `make` in the stage dir.  Finally
  looked at tree/package.py and it All Became Clear.

  Perhaps someone should rewrite this to use MakefilePackage, but the
  Makefile starts off with a bunch of twisty turny "uncomment these
  lines to run on this platform", so it might not be worth it.
2020-02-28 17:52:41 -06:00
Anthony Scemama
c10fb2a974
Added package py-versioneer (#15130)
* Added package py-versioneer

* Update python version

* Added python2 to versioneer

* Added python2 to versioneer

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

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

* Cleaning comments

* Removed temporarily @warner as a maintainer, waiting for answer

* Removed line

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-28 15:14:06 -06:00
George Hartzell
d3a2234af9
Add version info for the-silver-searcher@2.2.0 (#15270) 2020-02-28 15:13:05 -06:00
Rémi Lacroix
7ecee48c83
OpenMPI nolegacylaunchers: avoid a fork bomb (#15268)
Due to the use of backquotes, the replacement script for mpirun/mpiexec commands would recursively call itself, effectively causing a fork bomb.
2020-02-28 14:59:49 -06:00
Christoph Junghans
5329308b83
gromacs: add v2019.6 (#15267)
* gromacs: add v2019.6

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

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

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-28 14:58:31 -06:00
iarspider
97e909ef0c
Fix expect on linux (#15230) (#15269)
* Fix expect on linux

* Flake8
2020-02-28 14:57:45 -06:00
Erik Schnetter
38d5d7304d
ssht: Correct recipe (#15217)
- Tell make about the source code path
- Install actual header files, not a wrapper with wrong paths
- Add a patch to prevent compiler warnings
- Improve description
2020-02-28 11:32:41 -06:00
Adam J. Stewart
513f9235c3
Fix detection of redhat enterprise compute node (#15253)
* Fix detection of redhat enterprise compute node

* Add comma

* Remove space
2020-02-28 11:27:15 -06:00
Seth R. Johnson
f2fa4c1e4b
Add new version of libfabric that builds on macOS (#15254)
* Add new version of libfabric that builds on macOS

See https://github.com/ofiwg/libfabric/issues/5339
Fixes https://github.com/spack/spack/issues/15244

Also reduced copy-paste of URLs with `url_for_version`.

* Address reviewer feedback
2020-02-28 11:26:48 -06:00
eugeneswalker
886e072f1d
unifyfs depends on openssl (#15258) 2020-02-28 11:24:53 -06:00
Howard Pritchard
e519bbadc3
UCX: add 1.7.0 (#15266)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2020-02-28 11:22:37 -06:00
Ben Morgan
ec75011a69
Add @drbenmorgan as maintainer for core HEP packages (#15264) 2020-02-28 09:34:07 -06:00
Glenn Johnson
8ee7ee6105
Fixups for jupyter (#15136)
* Fixups for jupyter

This PR fixes a few things for some jupyter related packages.

py-ipython:
- make the python depends_on statements reflect needs of different
  versions
- remove an unneeded conflicts directive

py-ipywidgets:
- add new version
- set version constraints for py-widgetsnbextension

py-jupyter-console
- add new version
- set python dependencies for versions as needed
- set version constraint for py-ipython
- set version constraints for py-prompt-toolkit

py-pyqt5
- build with py-sip

py-qtconsole
- add dependency on py-pyqt5

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

Tweak version ranges.

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

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

Tweak version range.

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

* Make py-pyqt5 a run dependency

Also, make formatting more consistent.

* Fix site_packages_dir

Change reference of site_packages_dir to self.site_packages_dir. Oddly,
this did not show up as a problem until I regenerated the module.

* Restore py-pyqt5 to previous state

* Explicitly set path to site_packages_dir

This change prevents an error when regenerating the py-pyqt5 module
file.

* Fix flake8 errors

* Make sure prefix is in join_path

* Fix flake8 errors

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-27 22:31:46 -06:00
Anwar Koshakji
1616aa7119
Fixed url for SLEPc package (#15257)
* Fixed url for SLEPc package

* Fixed homepage url for SLEPc package
2020-02-27 22:29:29 -06:00
Christoph Junghans
c7d3dee2f7
gsl: build against external cblas (#15261) 2020-02-27 22:29:08 -06:00
Glenn Johnson
f10710d5cd
New package: py-librosa (#15223)
* New package: py-librosa

This PR adds the py-librosa package, along with new dependency packages
and some updates of existing dependency packages.

- new package: py-audioread
- new package: py-resampy
- new package: py-soundfile
- update package: py-numba
- update package: py-llvmlite

py-numba:
- add updated version
- adjust constraints

py-llvmlite:
- add updated version
- adjust constraints
- fix version specifications for llvm
- add environment function to set PIC

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

Ah, yes, I see that `setuptools` is listed in the `install_requires` array. I missed that before.

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

* Fix dependency

- Add dependency of py-soundfile depends on libsndfile
- Add new libsndfile package

* Add py-pytest-runner build dep

* Make numpy a variant for py-soundfile

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-27 22:28:16 -06:00
Seth R. Johnson
09a1f09fd0
Mark GCC7 and newer as conflicting with rhel6 without binutils (#14706)
When building gcc7 and gcc8 on RHEL6 with Spack and installing it as
a spack-available compiler, OpenBLAS will fail to compile because GCC
generates newer instructions than rhel6's `as` assembler knows about
(e.g. "vpermpd").

Building gcc8 with binutils succeeds, and it generates a GCC that can
then successfully build OpenBLAS. This is also expected to work for
gcc7 on RHEL6.
2020-02-27 18:56:48 -08:00
L. Diana Amorim
17fbf78593
Added version 0.12.0 to py-pyfftw (#15252)
* Added version 0.12.0 to fix issue #15218

* Added dependencies specs with compatible versions

* Switched py-scipy dependency to variant (default F)

* Removed variant py-scipy and didn't add py-dask

* Fixed typo: missing '

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

Fixing typos from version ranges in dependencies.

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

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

Removed repeating dependency option.

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

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

Limited version of py-numpy dependency to <2.0.

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

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-27 20:31:34 -06:00
Christoph Junghans
a785e302cc
portage: needs to be linked against lapack:c (#15259) 2020-02-27 20:23:45 -06:00
Jean-Paul Pelteret
7217592c24 Fix Trilinos 12.18.1 build when using Apple Clang 8.0.0 2020-02-27 18:22:09 -08:00
Jean-Paul Pelteret
7fc908e0e1 Update package: Trilinos + Mesquite 2020-02-27 18:22:09 -08:00
Robert Blake
b88c66cb52
Adding an option to build the C api for Umpire. (#15238)
* Adding an option to build the C api for Umpire.

This is useful if you need to link to a C code and you're using
a compiler suite that doesn't support fortran.

* Also updating the versions while I'm here.

* Adding conflict: Fortran requires C.

To ease transition and confusion, default to C-bindings being
present.  This shouldn't hurt anyone who is upgrading an existing
installation.
2020-02-27 20:17:55 -06:00
Glenn Johnson
4d5e75d825
new package: py-auxlib (#15221) 2020-02-27 20:12:32 -06:00
Massimiliano Culpo
7e13c9a6a0 Remove "triage" label from feature request 2020-02-27 16:34:24 -08:00
Massimiliano Culpo
2fbc774c8b Use checkout v2 to avoid issues on retriggering 2020-02-27 16:34:24 -08:00
Massimiliano Culpo
89f4ce964b Improved the feature request template 2020-02-27 16:34:24 -08:00
Massimiliano Culpo
b6531a760b Improved the build error template 2020-02-27 16:34:24 -08:00
Massimiliano Culpo
d36100e429 Improved the bug report template 2020-02-27 16:34:24 -08:00
Mark W. Krentel
fc20b352e7 hpcviewer: add version 2020.02 2020-02-27 15:40:55 -08:00
Roberto Di Remigio
d083c17242
New package: XCFun (#15199) 2020-02-27 15:40:21 -08:00
Michael Kuhn
f580b340f8 Add new timeout fetch_option
This allows packages to override the global connect_timeout.
2020-02-27 10:52:52 -08:00
Michael Kuhn
b7cfd05ef7 Generalize curl_options into fetch_options
This allows us to support higher-level concepts such as 'cookie' and
'timeout' without users having to specify curl options.
2020-02-27 10:52:52 -08:00
Michael Kuhn
7325c20794 config: Add a new option connect_timeout
connect_timeout can be used to increase the time Spack waits for the
server to answer. This can be used to work around slow connections or
servers.

Fixes #14700
2020-02-27 10:52:52 -08:00
Sheng Di
ffb9591dc9
release sz 2.1.8.3 (#15250) 2020-02-27 12:25:06 -06:00
Adam J. Stewart
6153eea2c2
CudaPackage: add support for Tesla K80 and older CUDA (#15031)
* CudaPackage: add support for Tesla K80 and older CUDA

* Flake8 fixes

* Fix cuda_arch when no arch is set

* Fine-tune cuda_arch=37,50 supported CUDA versions

* CUDA 6.5+ supports SM_37

* Add @svenevs as a maintainer
2020-02-27 12:16:20 -06:00
Glenn Johnson
167c75842a
new package: py-cnvkit and py-pomegranate (#15222)
The py-pomegranate package is a dependency of py-cnvkit
2020-02-27 12:06:19 -06:00
Glenn Johnson
c34ed6e6b5
new package: py-pycifrw (#15224) 2020-02-27 11:55:10 -06:00
Glenn Johnson
2d0ae0deb2
new package: py-pycosat (#15225) 2020-02-27 11:53:30 -06:00
Glenn Johnson
130a77f322
New packages: py-pymc3 and py-arviz (#15226)
This PR adds py-pymc3 and py-arviz as a dependency.
2020-02-27 11:51:15 -06:00