Commit graph

7265 commits

Author SHA1 Message Date
Todd Gamblin
527ff860f0 patches: clean up patch.py, directives, and package class properties
- cleanup patch.py:
  - make patch.py constructors more understandable
  - loosen coupling of patch.py with package

- in Package: make package_dir, module, and namespace class properties

  - These were previously instance properties and couldn't be called from
    directives, e.g. in patch.create()

  - make them class properties so that they can be used in class definition

  - also add some instance properties to delegate to class properties so
    that prior usage on Package objects still works
2018-12-30 00:19:08 -08:00
George Hartzell
51cbc278aa Always build glib with iconv (#10219)
* Always build glib with iconv

My early PR, #10165, which added a variant to configure glib to use
libiconv and defaulted to false, seems to be causing more trouble than
the knob is worth.

This changes the glib package to always depend on and use libiconv.

* libiconv depends_on is no longer conditional
2018-12-29 16:01:08 -06:00
Adam J. Stewart
5f957920c4
Add GDAL 2.4.0 (#10215) 2018-12-28 21:20:13 -06:00
Eric
2c76e8feef salmon: Add version 0.12.0 (#10211) 2018-12-28 13:02:36 -06:00
Eric
ada8d5ce5c velvet: Add missing zlib dependency to fix installation errors (#10212) 2018-12-28 13:02:16 -06:00
Eric
722e7058f8 py-testinfra: Add version 1.18.0 (#10210) 2018-12-28 18:24:58 +01:00
Andrew Gaspar
69f1199c55 Add new versions of optional-lite and string-view-lite (#10179) 2018-12-27 17:03:21 +01:00
Justin Stanley
c451733f9a xgboost: new package at 0.81 (#9854) 2018-12-27 07:42:44 +01:00
Lukasz
25129d4a3b fix moab installation for version 5.0.2 removed from ftp (#10201)
* moab install from git repository, fix version 5.0.2 removed from ftp server

* add moab dependencies above verson 5.0.1
2018-12-26 16:18:32 -06:00
StackKorora
39589065b1 Add Stata package (#10189)
* First draft for installing Stata 15

I've tested this works on my systems and gives a successful install of STATA 15.

* Flake8 cleanup

* Another Flake8

* Update license header

* Various improvements

A lot of improvements as suggested by @adamjstewart

* flake8 check
2018-12-26 16:17:42 -06:00
Christoph Junghans
18b128e6c1
pgmath: depend on awk (#10200) 2018-12-26 13:46:52 -07:00
Adam J. Stewart
42de399b18 Fix pkgconf downloads (#10202) 2018-12-26 13:46:30 -07:00
Adam J. Stewart
fc48f65a0f
Fix libxml2+python and libxslt+python import tests (#10196)
* Fix libxml2+python import tests

* Same for libxslt package
2018-12-26 10:36:59 -06:00
Christoph Junghans
58079b13eb mawk: added 1.3.4_p20171017 (#10197) 2018-12-26 08:41:26 -06:00
Satish Balay
0f2f0deee7 slepc: fix homepage URL (#10199) 2018-12-26 08:41:09 -06:00
Denis Davydov
d9da7c98a2 dealii: fix build with some Intel compilers (#10188) 2018-12-24 18:53:53 -06:00
Adam J. Stewart
376ef5f87a
Add latest version of NCCL (#10194) 2018-12-24 17:27:15 -06:00
Adam J. Stewart
9c58dacaec
Add PyTorch 1.0 (#10193) 2018-12-24 17:27:01 -06:00
Eric
791aab8564 manta: Add version 1.5.0 and add missing zlib dependency (#10178) 2018-12-24 21:04:18 +01:00
Satish Balay
908ecf3e74 xsdk-0.4.0: add/update package versions: (#10038)
* xsdk-0.4.0: add/update package versions:
  hypre@2.15.1
  mfem@3.4.0
  superlu-dist@6.1.0
  trilinos@12.14.0-rc1
  petsc@3.10.3
  dealii@9.0.1
  pflotran@xsdk-0.4.0
  alquimia@xsdk-0.4.0
  sundials@3.2.1
  plasma@18.11.1
  magma@2.4.0
  amrex@18.10.1
  slepc@3.10.1
  omega-h@9.19.1
  strumpack@3.1.1
  pumi@2.2.0
  tasmanian@6.0
  phist@1.7.5
  dtk-3.0 [via trilinos features '+dtk+intrepid2+shards']

add option to disable omega-h build [wrt gcc-8 conflict]
  spack install xsdk~omega-h
add option to disable dealii build [wrt cori build error]
  spack install xsdk~dealii

* trilinos: default version should be the prior release
2018-12-23 17:35:03 -08:00
Neil Flood
75b83ef2a7 py-cftime: new package (#10066)
* py-cftime: new package

* Added dependency on py-setuptools, and version range for py-cython, thanks to the ever-vigilant @adamjstewart
2018-12-23 14:56:08 -06:00
Simone Bnà
e7e32cc2d6 openFOAM-paraview-catalyst (#10129)
* paraview: adding variants to use external packages as internal do not compile

* paraview: add latest paraview version

* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5

* catalyst: add latest catalyst version

* catalyst: added ParaView_DIR env variable to catalyst module

* add paraview, catalyst patches

- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436

* - Handle updated library paths for catalyst.

  Versions 5.4 and old places libraries under a paraview subdirectory.
  Eg, "lib/paraview-5.4", they are now placed directly under "lib"

- Minor code style cleanup

* Handle update library and python paths for ParaView-5.5

* catalyst: added ParaView_DIR path to spack_env

* BUG: applied the patch to the extracted catalyst source files

* paraview: added missing self to a member variable

* paraview: added Paraview_DIR to env

* catalyst: added osmesa variant

* of-catalyst: added new package

* add (FOAM,WM)_PROJECT_DIR  also to spack_env environment

* depends on first openfoam release supporting catalyst

* openfoam-com: added missing env variables to module generation

* openfoam: fixed flake8 errors

* of-catalyst: added full variant and openfoam version dependency

* paraview: adding variants to use external packages as internal do not compile

* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5

* catalyst: added ParaView_DIR env variable to catalyst module

* add paraview, catalyst patches

- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436

* - Handle updated library paths for catalyst.

  Versions 5.4 and old places libraries under a paraview subdirectory.
  Eg, "lib/paraview-5.4", they are now placed directly under "lib"

- Minor code style cleanup

* Handle update library and python paths for ParaView-5.5

* catalyst: added ParaView_DIR path to spack_env

* BUG: applied the patch to the extracted catalyst source files

* of-catalyst: added new package

* add (FOAM,WM)_PROJECT_DIR  also to spack_env environment

* depends on first openfoam release supporting catalyst

* paraview: added missing self to a member variable

* openfoam-com: added missing env variables to module generation

* openfoam: fixed flake8 errors

* paraview: added Paraview_DIR to env

* catalyst: added osmesa variant

* of-catalyst: added full variant and openfoam version dependency

* paraview-catalyst: use always external expat and netcdf

* of-catalyst: reformatted package description

* paraview-catalyst: removed duplicated function

* catalyst: fixed flake8 error

* of-catalyst: fixed license header

* of-catalyst: minor changes

* of-catalyst: renamed gitrepo with git

* of-catalyst: removed useless gitrepo parameter
2018-12-23 13:40:25 -06:00
Brian Van Essen
bdc9804078 Feature add breathe and m2r (#10180)
* Added a package for the MDAnalysis toolkit.

* Added python packages for breathe and m2r.  Updated versions and URL
for the sphinx package.

* Fixed flake8 error

* Updated package requirements based on feedback.

* Updated with requirements from the setup.py

* Switched it back to pypi.
2018-12-23 13:39:21 -06:00
Neil Flood
451bfbd1ab py-pynio: new package (#10074)
* py-pynio: new package

* Major re-working to add some of the optional dependencies, and make it conform to the approach described in the pynio setup.py comments. Much of it turned out to be too complicated, and I have added some notes in comments to explain this to future adventurers.

* Added variants for the hdf5 and gdal dependencies, which do seem to be genuinely optional. Also added absolute dependencies for jpeg and zlib, which setup.py says it wants, but were being found as the os-installed versions.

* Added descriptions for the new variants, and moved them to above the dependencies
2018-12-23 09:50:41 -06:00
Jim Galarowicz
93d9139ff6 Add missing module env variable setting causing OSS to fail. (#10182) 2018-12-22 17:24:44 -06:00
Justin Stanley
90dce26db9 r-corhmm: new package at 1.22 (#9859) 2018-12-22 19:09:20 +01:00
Satish Balay
fad4ecc90b
petsc-3.10.3: syncs with superlu-dist-6.1. (#10166) 2018-12-22 10:40:08 -06:00
Levi Baber
ec2c5e5b0d gpgme: new package (#10174) 2018-12-21 12:17:45 -06:00
Jordan Ogas
b1944d4cbf add charliecloud 0.9.6 (#10176) 2018-12-21 12:17:33 -06:00
Matthias Wolf
a3ecdf1f41 py-numba: fix py-llvmlite version (#10175) 2018-12-21 11:34:32 -06:00
George Hartzell
7f095cee48 Add libiconv variant to glib (#10165)
Enable explicitly building glib with or without libiconv.

Heads up: if you build with ~iconv but there is something else in the
spec that includes libiconv then glib will *still* automagically
discover it and the build will fail.
2018-12-21 11:33:28 -06:00
Daryl W. Grunau
36ab7be406 R3D spackage (#10164)
* r3d spackage

* address Adam's review comments

* fix flake8: too many blank lines
2018-12-20 17:23:38 -06:00
Sajid Ali
e57ddda4cc update h5py to 2.9.0 (#10169)
* 	modified:   var/spack/repos/builtin/packages/py-h5py/package.py

* Update package.py

* Update package.py
2018-12-20 17:23:17 -06:00
thelfer
00d84b1978 Update TFEL package (#9995)
* add the tfel package

* fix the tfel package

* fix the tfel package

* fix the tfel package

* Taking Adam J. Steward' remarks into account

* fixes trailing white spaces

* Update description

* Update dependencies following @adamjstewart adices

* Style fixes

* Style fixes

* Add java optional support

* add the maintainers attribute (following @alalazo advice), disable interface not selected (following @adamjstewart advice)

* flake8 fixes

* Fix Cast3M and python-bindings support. Python detection is made compatible with cmake'FindPythonLibs module (at least how it is used in TFEL)

* Style fixes

* Style fixes

* Fix test on python version

* Follow @adamjstewart advices: code is much cleaner and readable

* Small fix

* Small fix

* Add comment

* Small fix in cmake option

* try again (trying to overcome Travis CI unstable build process)
2018-12-20 15:47:24 -06:00
Mark Olesen
7ded7fdbda OpenFOAM-v1812 - new version (#10167) 2018-12-20 13:18:51 -06:00
jthies
9110c727bb packages/phist: add maintainer (#10162) 2018-12-20 13:23:35 +01:00
Greg Sjaardema
93c491f729 CGNS: Allow use of git branch versions (#10156)
* CGNS: Allow use of git branch versions

Add ability to use git `master` and `develop` branches of the CGNS library.  The `seacas` package sometimes needs to use the `master` or `develop` branch due to some new changes to the parallel I/O implementation in CGNS which has not yet been released.

* CGNS: Reorder to put newest version on top

Based on review comments, place newest version (develop) first in list.
2018-12-19 20:02:24 -06:00
Mark W. Krentel
84b33523ec dyninst: patch to build dyninst with older gcc (#10160)
* dyninst: patch to build dyninst with older gcc

Add 'v9.3.2-auto.patch'.  This patch changes some 'auto t: type' usage
to the older but equivalent 'type.begin()'.  This allows building
dyninst 9.3.2 with gcc 4.4 which doesn't support the newer syntax.
This patch is harmless with newer gcc.

* Fix typo in patch.  (My bad for sloppy cut-and-paste.)

* Restrict the patch to gcc 4.7 and earlier.  gcc 4.8 supports the newer
usage and thus doesn't need the patch.
2018-12-19 17:24:43 -08:00
Michael Kuhn
84c547cf6e sqlite: add 3.26.0 (#10138) 2018-12-19 17:07:03 -06:00
Owen Solberg
6b1b9031ea updated checksum for kallisto (#10158) 2018-12-19 17:06:33 -06:00
Michael Kuhn
67ab73d381 fetch_strategy: improve GitFetchStrategy (#10153)
Currently, only the Git repsository's URL shows up in the `spack info`
output, which makes it hard to distinguish different versions:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git
```

This change adds additional information as shown when cloning a Git
repository:
```
Safe versions:
    develop    [git] https://github.com/LLNL/H5Z-ZFP.git on branch master
    0.8.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit af165c4
    0.7.0      [git] https://github.com/LLNL/H5Z-ZFP.git at commit 58ac811
```
2018-12-19 14:33:58 -08:00
jthies
5f3d9a4076 phist tag 1.7.5 was moved (#10155) 2018-12-19 13:36:49 -06:00
sknigh
5adec7e491 Updated Dakota to 6.9 (#10157)
* Updated Dakota to 6.9

* Change comment wording
2018-12-19 13:03:14 -06:00
Adam J. Stewart
adfbe71b1b
Add python bindings to libxslt (#10149) 2018-12-19 11:39:19 -06:00
Adam J. Stewart
654360d2ad
Add missing libiconv dependency to libxml2 (#10148) 2018-12-19 11:38:14 -06:00
Adam J. Stewart
0fcca9f422
Add list_url to docbook-xml (#10146) 2018-12-19 11:37:54 -06:00
Adam J. Stewart
e19e176e67
Add latest version of docbook-xsl (#10147) 2018-12-19 11:37:35 -06:00
Adam J. Stewart
ed0ca18c3c
Restrict patch to oldest version of libbsd (#10145) 2018-12-19 11:37:11 -06:00
Satish Balay
c1e562f333
PETSc: add version 3.10.3 (#10154) 2018-12-19 10:46:02 -06:00
Neil Flood
a6e2f1a96a mapserver: new package (#10067) 2018-12-19 10:04:25 +01:00