Commit graph

8255 commits

Author SHA1 Message Date
Yifan Zhu
7fc654b6a3 r-getopt: new package (#6973) 2018-01-20 19:18:07 +01:00
Geoffrey Oxberry
b83936a1f9 ipopt: add version 3.12.9 (#6982) 2018-01-20 19:11:18 +01:00
Eric
2192644071 perl-list-moreutils: Create new package (#6997) 2018-01-20 19:09:23 +01:00
peetsv
e3b8d6ef08 sniffles: add version 1.0.7 (#7004) 2018-01-20 18:39:29 +01:00
健美猫
0dee143c72 A new package: lumpy-sv. (#7009) 2018-01-20 18:38:31 +01:00
Ondřej Čertík
40ab8fe31f Add Abinit 8.6.3 (#6959) 2018-01-20 10:20:00 -06:00
Bruno Turcksin
62d53b2a5b Add boost 1.66.0 (#7000) 2018-01-20 17:10:25 +01:00
Massimiliano Culpo
621388e5ae
Restore multiprocessing in unit tests (#6949)
* Revert "Travis: use --concurrency=multiprocessing only on build tests (#6872)"

This reverts commit 596d463714.

* Removing 'coverage combine' in test script

According to what was discovered in #6887, one of the problems is
calling 'coverage combine' twice without the '-a' flag. This removes
the first call within our test scripts.
2018-01-20 16:10:25 +01:00
Geoffrey Oxberry
cf736ae911 qt@4 : update corewlan patch for OS X 10.1[23] (#6943)
Update the qt4 CoreWLAN patch to apply to macOS/OS X 10.12 and 10.13,
which both still use the CoreWLAN framework in their SDKs (although
it's apparently deprecated?!). Without this patch update, `spack
install qt@4.8.6` fails on macOS/OS X 10.12 because the linker
cannot find headers from the CoreWLAN framework.
2018-01-20 07:53:50 -06:00
Geoffrey Malcolm Oxberry
7c4c6e72ad vtk@:6.1.0 : disable Obj-C gc for XCode >= 5.1
Apple removed support for Objective-C garbage collection in binaries
in XCode 5.1, but VTK 6.1.0 and earlier set flags for garbage
collection, resulting in a compile-time bug when compiling VTK using
any recent version of XCode (i.e., Apple Clang).

This commit fixes this bug by removing the garbage collection flags
via setting the variable `VTK_REQUIRED_OBJCXX_FLAGS` to the empty
string. This variable has the same value (i.e., the empty string) in
the root-level CMakeLists.txt file for VTK 6.2.0 and later.
2018-01-19 13:44:36 -08:00
Geoffrey Malcolm Oxberry
48ae4c22b2 vtk@:6.1.0 : fix NetCDF C++ bindings detection
VTK 6.1.0 and earlier do not use paths stored in `NETCDF_CXX_ROOT` to
detect the presence of NetCDF C++ headers and libraries. Consequently,
VTK 6.1.0 does not build.

This commit fixes this bug by setting the advanced variables
`NETCDF_CXX_INCLUDE_DIR` and `NETCDF_CXX_LIBRARY` at the command line
to specify the directory containing headers and the full library path
for the NetCDF C++ bindings.
2018-01-19 13:44:36 -08:00
Levi Baber
8d2e340e16 Add --full-path option to module find (#6838) 2018-01-19 20:08:36 +01:00
Christoph Junghans
a102177db7
miniqmc: initial commit (#6991) 2018-01-19 09:38:21 -07:00
Massimiliano Culpo
a389bff949
Added a setter to the Spec.prefix property (#6814)
This commit removes logic from Spec that was there only to be used in
tests, and allows to set a new prefix cleanly in user's code.
2018-01-19 09:31:19 +01:00
becker33
3686c250ed Fix type issues with setting flag handlers (#6960)
The flag_handlers method was being set as a bound method, but when
reset in the package.py file it was being set as an unbound method
(all python2 issues). This gets the underlying function information,
which is the same in either case.

The bug was uncovered for parmetis in #6858. This is a partial fix.
Included are changes to the parmetis package.py file to make use of
flag_handlers.
2018-01-18 17:55:44 -08:00
Howard Pritchard
568db965cf ucx: update for release 1.2.2 (#6990)
Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2018-01-18 13:41:16 -07:00
Massimiliano Culpo
de679abd67
Added flags to unit tests + OSX build done once per day (#6988)
* Adding flags to codecov reports

* OSX builds are triggered once a day
2018-01-18 20:06:26 +01:00
junkudo
9704369f17 ipopt package: set compiler flags in configure (#6714)
This makes use of the new flag_handler logic from 28d8784a to set
compiler flags for ipopt by passing them as arguments to the build
system rather than injecting them into the compiler wrappers. This
avoids conflicts between flags that are chosen by the build system
and flags that are set by the user.
2018-01-18 10:39:08 -08:00
Todd Gamblin
4dd6ee25d6
Fix logo link in README.md to point to the develop branch. (#6969) 2018-01-17 09:06:14 -08:00
Todd Gamblin
84b2cc0823
Final changes for v0.11.0 (#6318) 2018-01-16 22:25:08 -08:00
Massimiliano Culpo
4d7e7f25c4 Fix installing specs from yaml file (#6906)
The feature added in #4611 is currently broken. This commit fixes the
behavior of the command and adds unit tests to ensure the basic semantic
is maintained.

It also changes slightly the behavior of Spec.concretized to avoid
copying caches before the concretization (as this may result in a
wrong hash computation for the DAG).
2018-01-16 08:03:10 -06:00
Todd Gamblin
50ca4979e1
Speed up doc builds with spack list --format=html (#6945)
- Generating the HTML from for >2300 packages from RST in Sphinx seems to
  take forever.

- Add an option to `spack list` to generate straight HTML instead.

- This reduces the doc build time to about a minute (from 5 minutes on a mac laptop).
2018-01-16 00:12:11 -08:00
Massimiliano Culpo
1fb38c9e04
Vendor ordereddict for python2.6 only (#6931)
* Vendor ordereddict for python2.6 only

This commit substitutes the custom module 'ordereddict_backport' with
the more known 'ordereddict' and vendors it only for python 2.6. Other
supported versions of python will use 'collections.OrderedDict'.

* Use absolute imports also for python 2.6

See PEP-328 for more information on the subject

* Added provenance of vendored ordereddict
2018-01-16 07:00:39 +01:00
Adam J. Stewart
498c522a31
Add url_for_version to pango package (#6939) 2018-01-15 14:05:27 -06:00
Geoffrey Oxberry
48b127a225 ipopt: add version 3.12.8, relax metis version requirements (#6936)
* ipopt: add version 3.12.8

* ipopt: allow linking with metis 5
2018-01-15 09:31:50 -06:00
Geoffrey Oxberry
67219a1340 ruby: fix +openssl & +readline variants (#6935)
* ruby: fix +openssl & +readline variants

Fix "unqualified variable spec['openssl']" error in the ruby package
that arises when trying to install the `+openssl` variant by
referencing the `spec` field in the `Ruby` class. A similar error
arises when trying to install the `+readline` variant; this error is
also fixed by this patch.

* ruby: make +openssl variant default to on

Ruby's gem command will fetch gems from HTTPS resources by default
(e.g., gem install bundler). Without openssl, request to fetch gems
bounce back with the error

```
ERROR:  While executing gem ... (Gem::Exception)
    Unable to require openssl, install OpenSSL and rebuild ruby (preferred) or use non-HTTPS sources
```

Without the ability to install gems -- required for some spack
packages -- the ruby installation has limited utility for many users.

* ruby: update rubygems ssl cert to fix ssl errors

The SSL certificate bundled with Ruby 2.2.0 is outdated, so e.g., `gem
install erubis` will fail with an SSL certificate error. This commit
installs the updated SSL certificate to the proper directory so that
gems can be downloaded and installed from RubyGems.
2018-01-15 09:00:07 -06:00
Federico Ficarelli
6093d6df7d Reworked the graphviz package (#6865)
The url in graphviz has been fixed and its version has been 
updated to the latest available (2.40.1). Added variants for 
expat, qt, gtk+ and ghostscript.
2018-01-15 15:26:14 +01:00
Milton Woods
43190a6bf6 Py-fparser: python parser for Fortran code (#6794)
* py-fparser: parser for Fortran 77..2003 code

* py-fparser: guard against external pytest.ini

* py-fparser: define 'develop' version as latest master branch

* py-fparser: fetch tagged versions from git repo

* py-fparser: add latest release 0.0.6

* py-fparser: whitespace adjustments for flake8

* py-fparser: inherit python dependency from PythonPackage

* py-fparser: rely on spack to resolve sub-dependencies

* py-fparser: try type='test' for py-pytest

* py-fparser: fetch release tarballs instead of git commits

* py-fparser: test deptype is available, remove comment

* py-fparser: limit versions that use py-six

* py-fparser: version ranges do not need a lower bound
2018-01-14 15:42:17 -06:00
lingnanyuan
f7db5d9cac r-rappdirs: Create new package. (#6891)
* r-rappdirs: Create new package.

* r-rappdirs: Add version constraints.
2018-01-14 15:41:32 -06:00
Milton Woods
a11765dbdf Qt fixes for RHEL6/7 (#6895)
* qt: move licence acceptance from qt3krell.patch to qt3accept.patch

* qt: ensure that ptrdiff_t is defined for qt@3.3.8b

* qt: disable webglplugin for qt@5.10~opengl

* qt: depend on libxext (for qt@3 and @4)

* qt: avoid X dependencies on darwin platforms

* Revert "qt: avoid X dependencies on darwin platforms"

This reverts commit 05ce08de94be1e02d7e2f2dae0c1ae59baa3f65a.

* qt: limit range of versions depending on libxext
2018-01-14 15:41:17 -06:00
healther
8f6fe9e030 Fix installation of bash-completion (#6911)
* Fix installation of bash-completion

* use run_before decorator instead of overriding install method
2018-01-14 15:40:22 -06:00
healther
e583d789d6 Update py-backports-functools-lru-cache to 1.4 (#6915)
* Update py-backports-functools-lru-cache to 1.4

* fix old url
2018-01-14 15:39:53 -06:00
healther
a03674ebbd make vim python3 compatible (#6925) 2018-01-14 15:39:33 -06:00
David Pérez-Suárez
0adcb610fe Updated catch to newer version (up to 2.1.0) (#6933)
Also updated all the sums from previous versions
2018-01-14 15:39:10 -06:00
healther
d30dc2bf15 Add version 1.81 of cppcheck (#6912) 2018-01-14 08:14:55 -06:00
Simone Bnà
e2908af9b4 Catalyst package (#6834)
* catalyst: added catalyst package

* catalyst: missing libx11 and libxt dependencies

* catalyst: added std cmake args

* catalyst: override paraview git describe cmake variable

* catalyst: fixed flake8 errors
2018-01-13 22:20:39 -06:00
Michael Kuhn
df7876ab54 Do not construct path to perl command manually (#6927)
Instead, use spec['perl'].command.path.
2018-01-13 22:10:42 -06:00
healther
589ea856a5 Add PyNN 0.9.1 (#6926) 2018-01-13 22:10:10 -06:00
healther
b3c96e2e40 Update checksum for version 0.5.3 of yaml-cpp (#6924) 2018-01-13 22:09:36 -06:00
healther
47b554a959 Add py-pyflakes versions up to 1.6.0 (#6923) 2018-01-13 22:09:17 -06:00
healther
b87f9ae5d4 Add py-pycodestyle versions up to 2.3.1 (#6922) 2018-01-13 22:08:51 -06:00
healther
7c4a193b3f Update py-neo to 0.5.2 (#6921) 2018-01-13 22:08:38 -06:00
healther
a2d7939e27 Add py-mccabe versions up to 0.6.1 (#6920) 2018-01-13 22:08:18 -06:00
healther
176814373c add version 1.26 to py-git-review and fix run_env (#6919)
* Update py-git-review to version 1.26.0

* Fix py-git-review package

TypeError: object of type 'Version' has no len()
2018-01-13 22:08:05 -06:00
healther
c6a7979cfd Update py-flake8 to 3.5.0 (#6918) 2018-01-13 22:07:46 -06:00
healther
8c648a73bc py-doxypy conflicts python3 (#6916)
* py-doxypy conflicts python3

* change conflicts to depends_on
2018-01-13 22:07:14 -06:00
healther
25bcabec98 Update py-autopep8 to 1.3.3 (#6914)
* Update py-autopep8 to 1.3.3

* Update package.py
2018-01-13 22:05:44 -06:00
Michael Kuhn
d8b03d1e37 glib: Fix python handling (#6910)
Newer versions of glib require python. Fix up the python sbangs the same
way we already fix up the perl ones.

Fixes #6899
2018-01-13 08:50:06 -06:00
healther
e8df0ddce4 add patch for gccxml with gcc@5: (#6913) 2018-01-13 08:46:00 -06:00
healther
715a173688 Update py-elephant to 0.4.1 (#6917) 2018-01-13 08:44:43 -06:00