Commit graph

16129 commits

Author SHA1 Message Date
Michael Kuhn
b69cf08cfb python: Add 3.7.6 and 3.7.5 (#14497) 2020-01-15 11:24:48 -06:00
Glenn Johnson
e7add79cba Update the icu4c package (#14450)
* Update the icu4c package

This PR makes several changes to the icu4c package

1. add updated version to 65.1
2. modify the default url as project has moved to github
3. set UTF-8 locale to support building from source files in UTF-8
format

Note that the older versions are not available on github so explicit urls
were used. This PR will close #14399.

* Consolidate the urls

Consolidate the URLs in the `version` directives by using an if test in
`url_for_version`.

* Put version and sha256 on same line

* Put top level url back
2020-01-14 22:05:55 -06:00
Glenn Johnson
9f6ac938b7 Update and fix bcftools package (#14505)
* Update and fix bcftools package

This PR updates bcftools to 1.10.2 and is dependent on PR #14504.

This PR also fixes builds of other versions. Versions 1.2-1.4 did not
use autotools so when the packaeg was converted to use autotools with
version 1.6 those older versions could no longer build. Also, those
versions needed to be patched to use an external htsllib. The method of
finding the external htslib is also different for those older versions.

In addition, this PR adds two variants to bcftools:

- libgsl
- perl-filters

Finally, dependencies for perl and python are added, and an unused
dependency for libzip was removed.

* Do not use '@' in variant description

The '@' character in a variant description will cause a problem with
`spack info`.

```
==> Error: Incomplete color format: '@' in
expressions, for @1.8:
```

* Fix error with python2 processing this package
2020-01-14 22:04:47 -06:00
Erik Schnetter
e78f3ed040 Update armadillo (#14499) 2020-01-14 17:49:49 -06:00
Erik Schnetter
ef68791210 Update HDF5 to 1.10.6 (#14500) 2020-01-14 17:49:21 -06:00
Erik Schnetter
8ffb9605d7 h5cpp: New package (#14501) 2020-01-14 17:48:49 -06:00
Justin S
4b1c356a27 trnascan-se: add and configure infernal dependency (#14502)
* trnascan-se: add and configure infernal dep

* trnascan-se: use patch() for infernal config
2020-01-14 17:47:48 -06:00
Erik Schnetter
ae6afaf8e1 mpich: Correct package name in output (#14503) 2020-01-14 17:46:39 -06:00
Glenn Johnson
ed9ab0668f Update htslib and add libcurl variant (#14504)
* Update htslib and add libcurl variant

This PR updates htslib to version 1.10.2 and adds a libcurl variant. The
libcurl variant defaults to True because, while it is optional, it is
highly recommended by the project developers.

Other things done:

- be consistent with quotes

* Change version in variant description

Apparently, `spack info` does not like the `@` character in a variant
description.

```
==> Error: Incomplete color format: '@' in
@1.3:.
```
2020-01-14 17:39:09 -06:00
Tom Scogland
df8ee438e5 stop word splitting from leaking out of setup-env (#14472)
The pathadd function was using setopt to configure zsh for word
splitting, which leaks out of the function and breaks default
functionality in a number of external zsh plugins and packages.  This
switches to emulate -L, just as the spack function uses, to keep the
setting local to the function.
2020-01-14 15:32:57 -08:00
Justin S
7ddbc9bc87 py-yajl: new package at 0.3.5 (#14278)
* py-yajl: new package at 0.3.5

* py-yajl: use PyPI mirror

* py-yajl: use short PyPI url

* remove py-ujson package

* py-yajl: remove unused imports
2020-01-14 17:23:32 -06:00
Justin S
30694aa501 gapfiller: traverse subdirectories in patch (#14375)
* gapfiller: traverse subdirectories in patch

* gapfiller: revert glob function change

* gapfiller: use more precise glob
2020-01-14 17:22:49 -06:00
Stephanie Brink
a18ab8f765 new package: variorum (#13624) 2020-01-14 12:01:01 -08:00
Rao Garimella
eefccd5d22 Update MSTK to 3.3.1 (#14494) 2020-01-14 13:08:57 -06:00
darmac
a04faa8f6b add new package : rocketmq (#14442)
* add new package : rocketmq

* remove url_for_version()
2020-01-14 11:59:40 -06:00
Adam J. Stewart
240a9e6284
Fix parsing of rocketmq URL (#14490) 2020-01-14 11:59:10 -06:00
darmac
7a88c17d3a add new package : py-ansible (#14436)
* add new package : py-ansible

* update license info

* update py-ansible depends
2020-01-14 11:58:48 -06:00
Kshitij Mehta
5c7a3e2d14 codar-cheetah: Added version 0.5 (#14487)
* codar-cheetah: Added version 0.5

* codar-cheetah: Dropped v0.1 as it was not built as a Python package.
2020-01-14 11:55:15 -06:00
Rob Latham
4c65324084 Sometimes debugging symbols are helpful (#14452) 2020-01-14 11:54:38 -06:00
Nichols A. Romero
6d8ec8890a Flang OpenMP target support for NVidia GPUs. (#14486)
* Flang OpenMP target support for NVidia GPUs.

* explictly disable gpu option with else clause.
2020-01-14 11:54:07 -06:00
eugeneswalker
2e5c9eb2e3 upcxx depends on python 2 >= 2.7.5 (#14462) 2020-01-14 11:53:38 -06:00
Elsa Gonsiorowski, PhD
4366977540 libcircle: add develop version from git master branch (#14420)
* libcircle: add develop version from git master branch

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

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

* libcircle: flake8 fix i think

* libcircle: naming things

* libcircle: 🐑 my sacrifice to the flake8 gods

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-01-13 21:23:56 -06:00
Hadrien G
c51db51bfb verrou: Add support for verrou v2.2.0 (#14480)
* Add support for verrou v2.2.0

* Add myself as a maintainer
2020-01-13 21:23:08 -06:00
t-karatsu
41c40d4ba4 r-mass: Add version '7.3-51.5' and fix checksum. (#14439) 2020-01-13 21:06:44 -06:00
darmac
713d7a3793 add new package : gpdb (#14440)
* add new package : gpdb

* update docstring and license info
2020-01-13 21:04:00 -06:00
darmac
e2e9f02d81 add new package : hive (#14443) 2020-01-13 21:01:27 -06:00
darmac
b33d108c1b add new package : drill (#14444) 2020-01-13 21:00:36 -06:00
darmac
737d2f55a8 Flume (#14445)
* add new package : flume

* add new package : flume
2020-01-13 21:00:06 -06:00
darmac
c41dfb0a75 add new package : flink (#14446) 2020-01-13 20:59:34 -06:00
Gregory Lee
35a696a965 added intel parallel 2020.0 and components (#14451) 2020-01-13 20:51:22 -06:00
Rob Latham
a76ef717bd Support for more libfabric providers (#14453)
Add support for (just about) every provider libfabric knows about
2020-01-13 20:47:48 -06:00
MIchele Martone
fa2e094c81 new package: librsb (#14455)
* new package: librsb

* flake8, be good

* no hardocded FC=gfortran
2020-01-13 20:46:20 -06:00
darmac
6c4c26f538 add new package : keepalived (#14463) 2020-01-13 20:36:16 -06:00
Glenn Johnson
0a666af326 Remove overlapping depends_on statement for py-basemap (#14475)
This PR resolves an overlapping dependency specification for py-basemap.
2020-01-13 20:34:13 -06:00
Rao Garimella
487731e207 Add version 3.3.0 to MSTK spackage (#14476) 2020-01-13 20:33:47 -06:00
Michael Kuhn
8660b0b5b8 python: Fix post-install script without C++ compiler (#14481) 2020-01-13 20:29:02 -06:00
Adam J. Stewart
5b1297378c
Add Python 3.8.1 (#14484) 2020-01-13 20:27:57 -06:00
Adam J. Stewart
d78c52c291
Add GDAL 3.0.3 and 2.4.4 (#14485) 2020-01-13 20:27:41 -06:00
Axel Huebl
0d435630db openPMD-api: Depends on ADIOS 2.5.0 (#14489)
Only ADIOS2 versions we support.
2020-01-13 20:24:00 -06:00
Jonathon Anderson
673a725576 New package: qemu (#14184) 2020-01-13 15:52:18 -06:00
Tamara Dahlgren
eb7a4e1029 Fixes #14402 (#14483)
Check if patchelf is executable, not binary, in case a site is wrapping it.
2020-01-13 13:00:14 -08:00
Paul
5afc407faa Add Go version 1.13.6 and 1.12.15 (#14482) 2020-01-13 16:48:27 +01:00
Simon Pintarelli
465577847d SIRIUS, SpFFT: updated package recipes and versions (#14469) 2020-01-13 14:45:36 +01:00
darmac
6edc7a2558 racon: added v1.4.3, v1.4.2, v1.4.0 and v1.3.3 (#14478) 2020-01-13 14:23:33 +01:00
Sajid Ali
8917d58e7a syned: new package at develop (#14468) 2020-01-13 13:45:47 +01:00
Christoph Junghans
9c4479624c gromacs: add v2020 (#14477) 2020-01-13 09:45:20 +01:00
Nichols A. Romero
d1c708bdf3 LLVM-Flang package (#14389)
* Add 20181226 release of pgmath

* 20190329 release of pgmath requires match for CMPLX macro.

* Add llvm-flang package for Flang fork of LLVM

* Add new and old flang releases.

* Add cmake and python dependencies.

* Update dependencies on llvm-flang and pgmath.

* Fix cmake args and change spec to reflect llvm-flang package.

* change copyright date through 2020.

* Reference Flang package more explicitly.

* More robust support for python executable.

* import os no longer needed, picked up by flake8.

* Use built-in target spec. Variant and targets follow style in main LLVM package.

* Get rid of targets list and only support one target for now.

* Sparc does not appear to be supported in Flang.

* Raise InstallError if architecture not supported.
2020-01-11 16:13:03 -06:00
Adam J. Stewart
257e71d87a
Reformat Bash tab completion script (#14456) 2020-01-10 11:32:50 -06:00
Adam J. Stewart
52df2309cb
Add TensorFlow 2.1.0 (#14429)
* Add TensorFlow 2.1.0

* kafka and ignite are no longer supported
2020-01-09 11:01:51 -06:00
Hadrien G
b982015930 root: Configure ROOT correctly for python3 (#14225)
* Configure ROOT correctly for python3

* Record Python version conflict

* Code editing on a phone sucks
2020-01-09 09:33:10 -06:00