Commit graph

14341 commits

Author SHA1 Message Date
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
Paul
0d2f8e314b
Added go 1.14 (#15249) 2020-02-27 11:42:48 -06:00
TZ
d6d095a868
Docs: "spack env" is in the meantime called "spack build-env" (#15233) 2020-02-27 09:13:09 +01:00
Kai Torben Ohlhus
b37d7b8ed7
arpack-ng: ILP64 support (#15103)
Details about ILP64 support: `INTERFACE64=1` are described on the [ARPACK-NG GitHub website](https://github.com/opencollab/arpack-ng).
2020-02-27 07:19:24 +01:00
Anthony Scemama
9c194b22dc
f77-zmq: add version 4.3.2 (#15204)
Version 4.3.1 only works with Python3. Version 4.3.2 also works
with Python2. These constraints were not listed before and are added
by this commit.
2020-02-26 19:05:46 -08:00
Andreas Baumbach
f1a12966b0
py-git-review: add version 1.28 (#15203) 2020-02-26 19:02:51 -08:00
Luca Carrogu
350235ba71
AWS ParallelCluster: add version 2.6.0 (#15240) 2020-02-26 19:02:24 -08:00
genric
9a1a346999
h5py: add version 2.10.0 (#15205)
Also add dependency on py-cached-property
2020-02-26 19:01:22 -08:00
Tamara Dahlgren
ed15adbb9e
bugfix: Add dependents when initializing spec from yaml (#15220)
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents.

- [x] populate dependents when loading from yaml
2020-02-26 18:49:29 -08:00
Kevin Huck
ebd248b27e
SQLite shouldn't be enabled by default for TAU package (#15228)
Also Adding conflict for SQLite and ADIOS2 for older TAU releases
2020-02-26 17:14:09 -06:00
Seth R. Johnson
578e8031ce
Default to +termlib for ncurses for LLVM (#15039)
LLVM is the only package that explicitly sets the "termlib" variant
of ncurses and it specifies +termlib. ncurses defaults to ~termlib;
if a package depends on LLVM and ncurses, there is a concretizer bug
that incorrectly detects a constraint conflict (see #267). Setting
+termlib as the default is a stopgap measure to avoid this conflict.

If other packages were to explicitly request ~termlib in the future,
the same issue would come up again (and could not be resolved by
adjusting the default of "termlib").

Setting +termlib on ncurses moves some symbols into a separate
"libtinfo". Not all packages may be able to detect libtinfo properly
so may require an update; vim, samtools, and libedit have been
updated to use ncurses+termlib (in the case of libedit, the only
necessary action was to add a newer version where the build system
was updated to check libtinfo).
2020-02-26 11:27:12 -08:00
Seth R. Johnson
6c445a2c0f
Uniquify suffixes added to module names (#14920) 2020-02-26 18:03:28 +01:00
Anthony Scemama
1c227db7a9
Basis set exchange command-line tool (#15126)
* Flake8 OK

* Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py

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

* Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py

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

* Added missing dependencies proposed by @adamjstewart

* Without py-versioneer

* Added py-versioneer

* Python2 for bse

* Python build error

* Update var/spack/repos/builtin/packages/py-basis-set-exchange/package.py

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

* Removed py-versioneer, according to @adamjstewart

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-02-26 07:27:02 -06:00
Glenn Johnson
a568db00b8
A few edits for the Basic Usage Doc page (#15215)
This PR corrects a few minor things and adds a note about colorized
output.
2020-02-26 10:03:03 +01:00
Patrick Gartung
ae87828520
buildcache cmd: add explicit message with default output dir for buildcaches. (#15090)
* Make -d directory a required option. Print messages about where buildcaches will be written.

* Add mutually exclusive required options

* spack commands --update-completion

* Apply @opadron's patch

* Update share/spack/spack-completion.bash

* Incorporate @opadron's suggestions
2020-02-25 17:49:25 -06:00
Omar Padron
00090f8f97
add --only option to buildcache create cmd (#14921)
* add --only option to buildcache create cmd

replaces the --no-deps option
2020-02-25 17:32:20 -05:00
Omar Padron
8d750db9de
remove catch-all exception handling in buildcache command (#15185)
* remove catch-all exception handling in buildcache command

* fix test
2020-02-25 14:10:50 -06:00
Patrick Gartung
676eb56ab2
Buildcache cmd: add install -o/--otherarch option for installing macOS buildcaches on linux (#15192)
* Buildcache command: add install option -o/--otherarch
This will allow matching specs from other archs, for example
installing macOS buildcaches on linux hosts.

* spack commands --update-completion
2020-02-25 11:01:59 -06:00
Kai Torben Ohlhus
8d8925c725
qrupdate: ILP64 support (#15104)
- When compiling qrupdate with `FFLAGS=-fdefault-integer-8` it can be perfectly used for larger problem dimensions.
- Improved the readability of the file with the added rules.
2020-02-25 10:36:54 +01:00
Kevin Huck
21afb13be6
Adding ADIOS2 and SQLite3 output support to TAU. Also fixing MPI include and library paths. (#15189)
Setup package to use MPI the way Spack recommends, and remove extra iowrapper option from configure
Making flake happy
2020-02-24 22:33:05 -06:00
OliverPerks
5c68caeb1e
Update of OpenFOAM package.py (#15190) 2020-02-24 22:28:13 -06:00
Kai Torben Ohlhus
4a0b7c9d20
suite-sparse: add version 5.7.1 (#15195)
Release notes: https://github.com/DrTimothyAldenDavis/SuiteSparse/releases/tag/v5.7.1

Version 5.7.0 was an incomplete release.
2020-02-24 22:22:00 -06:00
ktsai7
9b3f5f3890
update flecsi and legion package.py (#15159)
* update flecsi and legion package.py

* comment out a conflict

* update to use extend
2020-02-24 13:22:25 -06:00