Commit graph

12754 commits

Author SHA1 Message Date
Todd Gamblin
a9b69fa902 ProviderIndex uses json instead of YAML
- indexes should use json, not YAML, to optimize for speed
- only use YAML in human-editable files
- this makes ProviderIndex consistent with other indexes
2018-12-30 00:19:08 -08:00
Todd Gamblin
c1d7adaaac repo: refactor indexes to be more extensible
- virtual provider cache and tags were previously generated by nearly
  identical but separate methods.

- factor out an Indexer interface for updating repository caches, and
  provide implementations for each type of index (TagIndex,
  ProviderIndex) so that more can be added if needed.

- Among other things, this allows all indexes to be updated at once.
  This is an advantage because loading package files is the real
  overhead, and building the indexes once the packages are loaded is
  trivial. We avoid extra bulk read-ins by generating all package indexes
  at once.

- This can be extended for dependents (reverse dependencies) and patches
  later.
2018-12-30 00:19:08 -08:00
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
Todd Gamblin
19b7b15929 coverage: use kcov to get coverage for our cc script 2018-12-29 23:47:29 -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
Todd Gamblin
c92ac70c72
bugfix: add codecov upload back to travis.yml (#10220)
Codecov upload was accidentally removed in #9805
2018-12-29 12:09:42 -08:00
Todd Gamblin
d65c6ba9b2 Use homebrew addon instead of manually invoking brew (#10213) 2018-12-29 06:12:02 +01:00
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
Massimiliano Culpo
28fd1baa86 tests: run 'test_compiler_add' serially in Python 2 (#10127)
* Don't spawn processes during python 2.6/2.7 'test_compiler_add' unit tests
* Travis seems to choke on the excessive parallelism in `compiler find`
2018-12-25 23:47:46 -08:00
Denis Davydov
39b23d277b environment: ignore invalid files names in var/spack/environments (#10198) 2018-12-25 22:22:21 -08:00
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
Todd Gamblin
35dd929651
bugfix: handle unicode properly in spack.util.executable (#10186)
- When returning string output, use text_type and decode utf-8 in Python
  2 instead of using `str`

- This properly handles unicode, whereas before we would pass bad strings
  to colify in `spack blame` when reading git output

- add a test that round-trips some unicode through an Executable object
2018-12-23 23:59:58 -08:00
Omar Padron
fcce8b8dc2 travis: fix pip install for docker stage (#10177) 2018-12-23 17:42:09 -08:00
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
Elsa Gonsiorowski, PhD
74a5d92f07 Remove /nfs/tmp2 from default build_stage locations (#10170)
* Remove /nfs/tmp2 from default configuration
* /nfs/tmp2 is going away from LC... and doesn’t exist for the rest of the world.
* update documentation to remove /nfs/tmp2 as well
2018-12-21 02:03:54 -08:00
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
Omar Padron
60298787e4 Fix docker builds (#9805)
* move docker test logic to share/spack/qa
* update Dockerfile for archlinux
2018-12-20 11:17:46 -08:00
Omar Padron
56cb691fcc fix multiple issues with the docker images (#9718)
- fixed an issue where some undesirable parts of
   the spack source tree were being copied into
   the image context.

 - added a workaround for a tty ioctl warning on
   ubuntu

 - adjusted how the main images are built so that
   `RUN spack ...` works automatically for child
   images that base themselves on them.
2018-12-20 11:11:55 -08:00
Zack Galbreath
b90f619037 Performance improvements for CDash reporter
* Record build output as an array of lines rather than concatenating to a
  single large string.
* Use string.find to avoid running re.search on every line of output.
2018-12-20 09:23:08 -08:00
Zack Galbreath
6355ee208c Include accurate build time in CDash report 2018-12-20 09:23:08 -08:00
Zack Galbreath
8d0872083c Report current git commit of Spack to CDash
When using the CDash reporter, upload a Update.xml file that
indicates the hash of Spack's current git commit.
2018-12-20 09:23:08 -08:00