Commit graph

7505 commits

Author SHA1 Message Date
Yifan Zhu
d4906169e0 r-simpleaffy: added versioned dependency on r (#5673) 2017-10-12 16:18:15 -06:00
Satish Balay
59163f9750 petsc: add in maintainers (#5729) 2017-10-12 15:09:47 -06:00
David Hows
8ff8b7476c Add the option for a versioned layout to boost (#5709) 2017-10-12 12:51:39 -06:00
Audrey Thoma
36ed96e7dd kaks-calculator: new package (#5725)
* kaks-calculator: new package

* kaks-calculator: new package

* fixing homepage
2017-10-12 12:47:11 -06:00
Satish Balay
98c2184bd3 petsc: update to latest 3.8 version [and include 3.7.7] (#5723)
Also fix flake8 warning "import os should be before import sys"
2017-10-12 12:46:00 -06:00
Jon Rood
c0b2e7db73 Add OpenFAST package (wind turbine simulation tool). (#5662)
* Add OpenFAST package (wind turbine simulator).
* Adding maintainer to openfast package.
* Fixing copyright date.
2017-10-12 11:42:51 -07:00
Denis Davydov
1b53e82348 various fixes for macOS high sierra (#5647)
* various fixes for macOS high sierra

* add macOS_version() helper function

* flake8 fixes

* update oce and trilinos

* fix bison
2017-10-12 11:41:57 -07:00
David Hows
0dad5b3ee5 Make --trusted default when running spack gpg list (#5678)
* Make --trusted default when running spack gpg list

Currently running `spack gpg list` with no arguments returns nothing. You must supply either the `--trusted` or the `--signing` options. The idea here is to return some initial data to the user when the command is run. The alternative is to return an error, telling the user to select one of the two options.

* Add an extra test case for the empty list command

Fixes the issue with code coverage
2017-10-12 11:14:48 -07:00
Todd Gamblin
65b38764ae Speed up concretization (#5716)
This isn't a rework of the concretizer but it speeds things up a LOT.

The main culprits were:
  1. Variant code, `provider_index`, and `concretize.py` were calling
     `spec.package` when they could use `spec.package_class`
    - `spec.package` looks up a package instance by `Spec`, which requires a
      (fast-ish but not that fast) DAG compare.
    - `spec.package_class` just looks up the package's class by name, and you
        should use this when all you need is metadata (most of the time).
    - not really clear that the current way packages are looked up is
      necessary -- we can consider refactoring that in the future.

  2. `Repository.repo_for_pkg` parses a `str` argument into a `Spec` when
     called with one, via `@_autospec`, but this is not needed.
     - Add some faster code to handle strings directly and avoid parsing

This speeds up concretization 3-9x in my limited tests.  Still not super
fast but much more bearable:

Before:
  - `spack spec xsdk` took 33.6s
  - `spack spec dealii` took 1m39s

After:
  - `spack spec xsdk` takes 6.8s
  - `spack spec dealii` takes 10.8s
2017-10-12 09:52:38 -07:00
Carlos Bederián
db149876a4 samtools: add version 1.6 + some fixes (#5715)
* htslib: add version 1.6

* samtools: add version 1.6, remove zlib dependency

* bcftools: add version 1.6, switch to using standalone htslib
2017-10-12 10:08:31 -06:00
Audrey Thoma
87c65fafa9 minimap2: new package (#5722) 2017-10-12 10:07:42 -06:00
David Hows
90cd075277 Initial version of libpcap (#5710)
Add a package script for libpcap with the current version (1.8.1)
2017-10-12 07:00:21 -06:00
Todd Gamblin
b5e136b729 Better install output (#5714)
* Do not call setup_package for fake installs

- setup package could fail if ``setup_dependent_environment`` or other
  routines expected to use executables from dependencies

- xpetsc and boost try to get python config variables in
  `setup_dependent_package`; this would cause them not to be
  fake-installable

* Remove vestigial deptype_query argument to Spec.traverse()

- The `deptype_query` argument isn't used anymore -- it's only passed
  around and causes confusion when calling traverse.

- Get rid of it and just keep the `deptypes` argument

* Don't print redundant messages when installing dependencies

- `do_install()` was originally depth-first recursive, and printed "<pkg>
  already installed in ..." multiple times for packages as recursive
  calls encountered them.

- For much cleaner output, use spec.traverse(order='post') to install
  dependencies instead
2017-10-12 00:49:59 -07:00
Yifan Zhu
e807397074 r-affy: added versioned dependency on r (#5660) 2017-10-11 19:49:48 -06:00
Yifan Zhu
36eba3bf58 r-affyio: added versioned dependency on r (#5661) 2017-10-11 19:49:28 -06:00
Yifan Zhu
db0fec4d09 r-biocinstaller: added versioned dependency on r (#5663) 2017-10-11 19:49:08 -06:00
Yifan Zhu
4e8ac1d525 r-matrixstats: created new package (#5682) 2017-10-11 19:48:39 -06:00
Yifan Zhu
5e41ad6fed r-biocgenerics: added version 0.22.1 and added versioned dependency on r (#5683) 2017-10-11 19:48:19 -06:00
Yifan Zhu
8d48f07de1 r-genomeinfodbdata: added versioned dependency on r (#5685) 2017-10-11 19:48:00 -06:00
Yifan Zhu
a04e95a492 r-genomeinfodb: created new package (#5695) 2017-10-11 19:47:03 -06:00
Yifan Zhu
dc95dddd61 r-genomicranges: added new package (#5697) 2017-10-11 19:45:03 -06:00
Yifan Zhu
c93ecda872 r-futile-options: created new package (#5699) 2017-10-11 19:43:53 -06:00
Yifan Zhu
4af446d7f4 r-lambda-r: created new package (#5700) 2017-10-11 19:43:33 -06:00
Yifan Zhu
f8db73d567 r-futile-logger: created new package (#5701) 2017-10-11 19:43:15 -06:00
Yifan Zhu
01e104dfcb r-rsamtools: created new package (#5702) 2017-10-11 19:42:55 -06:00
Yifan Zhu
670463e95a r-biocparallel: created new package (#5703) 2017-10-11 19:42:25 -06:00
Yifan Zhu
e08e7af34e r-delayedarray: created new package (#5704) 2017-10-11 19:42:04 -06:00
Yifan Zhu
9a2ef4c4b3 r-biomart: added versioned dependency on r (#5666) 2017-10-11 19:41:08 -06:00
George Hartzell
124bdfb910 Strelka depends on boost 1.56.0 *or newer* (#5690)
Relax/correct the constraint on the version of boost used
by Strelka to match the docs.
2017-10-11 17:21:26 -06:00
Denis Davydov
35a62f715b dealii: minor fixes (#5687)
* dealii: fix minor bug in Assimp config

* dealii: request sundials without pthreads
2017-10-11 15:09:39 -06:00
Christoph Junghans
cfc13dec9f Add a bundle package for the ECP proxy applications suite (#5689)
* Add a bundle package for the ECP proxy applications suite

* Update package.py
2017-10-11 13:39:30 -06:00
健美猫
9e95e8394e Add a package: dmlc/mxnet. (#3579)
* Add dmlc/mxnet packags.

* Build mxnet+cuda+opencv with GCC-4.8.5 and GCC-5.4.0.

* Build mxnet version 0.10.0, 0.10.0.post1 and 0.10.0.post2.

* Add component version constrain for mxnet 0.10.0.x .

* Go through flake8.

* Replace commit hash with commit date as package version.

* Go throught Travis-CI.

* Update submodule version for 0.10.0.post2.

* Add openmp variant for dmlc-core and mxnet.

* Refine variant handling.

* Fix filter_file for dmlc-core.

* Cut long strings into multiple lies due to PEP8 requirements.

* Fix for PEP8.

* Add CUB_INCLUDE.

* Add py-mxnet: Python binding for MXNet.

* Remove distutils.dir_util.

* Add the profiler variant for mxnet.

* Add a shared variant for nnvm.

* Set USE_OPENMP to OFF by default.

* Fix flake8 errors.

* Fix flake8 issues.

* flake8 issues again.
2017-10-10 13:56:26 -07:00
Christoph Junghans
ef822453b9 Adding flang - a llvm based Fortran compiler (#5459)
* flang: initial commit

* flang: added symlink to clang's flang

* add flang wrapper

* flang wrapper: inject rpath as well

* flang wrapper: PATH -> -B
2017-10-10 13:52:31 -07:00
Christoph Junghans
cb7628c9a4 compilers/clang: add flang (#5503)
* compilers/clang: add flang

* Update clang.py
2017-10-10 13:52:10 -07:00
Christoph Junghans
88b515ede8 ninja: add v1.8.2 (#5625) 2017-10-10 12:50:56 -07:00
Massimiliano Culpo
a3bbe066b3 plumed: reworked patching applications, added new version (#5680)
closes #5506

The application of patches to upstream executables has been reworked
according to the suggestions of the main developer in #5506. In
particular we are not maintaining a dictionary that maps plumed
versions to the versions of patchable executables, and we are using a
non-interactive command to patch applications.

All the comments on substituting plumed at run-time do not apply here,
since we use RPATH and we want to maintain a 1:1 relationship between
the DAG hash and the plumed library used.
2017-10-10 12:35:53 -07:00
Audrey Thoma
e3053d7425 snap-korf: new package (#5589) 2017-10-10 11:09:31 -07:00
Jon Rood
f2b49d8f66 Adding openfast variant to nalu. (#5675) 2017-10-09 20:10:47 -06:00
lingnanyuan
35583f48f4 r-adsplit: Create new package and update version for its dependencies. (#5640)
* r-adsplit: Create new package.

* r-rlang: Update version.

* r-s4vectors: Update version.
2017-10-09 17:10:29 -06:00
Audrey Thoma
a8cd92a2e4 switching downloads to git (#5659) 2017-10-09 17:07:13 -06:00
lingnanyuan
196b82f2c7 r-affycompatible: Create new package. (#5664) 2017-10-09 17:05:53 -06:00
lingnanyuan
ef1f71447e r-affydata: Create new package. (#5665) 2017-10-09 17:05:21 -06:00
lingnanyuan
1f05e9ae58 r-affycontam: Create new package. (#5668) 2017-10-09 17:04:51 -06:00
George Hartzell
ab2c7573c1 strelka: new package (#5632)
* Add package for strelka@2.8.2

* Fix flake8 complaints
2017-10-09 17:02:44 -06:00
George Hartzell
0d1c36e559 Add package for aspell and ass't dictionaries (#3890)
* Add package for aspell and ass't dictionaries

Add a package definition for aspell.

Add a handful of dictionaries to convince myself that the support for
a bunch of dictionaries works.

* Flake8 cleanup

* Use six's version of urlparse

`urlparse` is not python3 friendly.  This works around it (stolen from
`.../cmd/md5.py`).

* Fix incorrect trimming regexp

* Clean up dictionary build

- more parsimonious use of `which` (`make()` has already been made)
- use `sh` instead of `bash`

* Use a helper method to generate info for variants

I figured out my issues with static methods.  I *think* that it this
is pythonic.

* Convert aspell to an extendable package

Convert aspell to be extendable and rework the dictionaries to be
extensions.

As it stands, there's a great deal of cut and paste in the
dictionaries, I'll abstract that out next.

The {de,}activate methods copy a great deal of code out of
package.py.  Perhaps there's a better way....

* Create AspellDictPackage and use it for the dictionaries

Reduce the repeated code, pull it into a base class.

I'm confused about why 'from spack import *' wasn't more useful in the
base class.

* Oops, -de & -es should be AspellDictPackages too

* Typo: pakcage -> package

* Address some commentary

* Update copyright dates, 2016->2017
2017-10-09 14:14:19 -07:00
Aaron Fisher
5ccc9c17dc Added mfem v3.3.1-rc1 to the mfem package. (#5644) 2017-10-09 21:48:25 +02:00
Axel Huebl
4ba7359d55 libpng: zlib flags more elegant (#5656) 2017-10-09 21:46:10 +02:00
becker33
5d13f236b4 Fix setup for changes to dirty flag (#5592)
* Pass dirty arg through setup to setup_package
2017-10-09 10:01:55 -07:00
Christoph Junghans
57643ae84e espressopp: added v1.9.5 (#5652) 2017-10-08 18:16:56 -07:00
Piotr Luszczek
1b5410b87b Add PLASMA package (#5540) 2017-10-08 17:59:41 -06:00