Commit graph

6378 commits

Author SHA1 Message Date
Hadrien G
c03dcdedb1 FTGL package workarounds (#8812)
* FTGL package workarounds

* Remove blank line

* Only require doxygen at build time
2018-07-26 15:54:46 -05:00
mic84
61aa1831e3 AMReX: update package.py (#8697) 2018-07-26 13:29:03 -05:00
Hadrien G
8b718e7cd6 Templight package (#8782)
* First draft of a templight recipe

* Let's be explicit for now, we can be clever later on

* The clang6 version does not work, drop it

* Reorder FIXMEs more logically

* Add patch for current templight develop branch

* Create an artificial stable release of templight

* Take some additional inspiration from llvm package

* Added the templight supporting tools

* Remove old notes from the no-url branch

* Avoid unnecessary join_path
2018-07-26 11:19:14 -05:00
Simon Flood
80741bc427 hmmer: added version 3.2.1 & updated URL (#8787)
Add HMMER 3.2.1 and updated URL then removed url_for_version function as no longer required - all HMMER downloads available from updated URL.
2018-07-26 10:07:55 -05:00
Michael Kuhn
643a4fbb59 papi: Update to 5.6.0 and fix build with %gcc@8 (#8796) 2018-07-26 10:02:07 -05:00
Mario Melara
cb410b3003 Add package DMTCP (#8808) 2018-07-26 09:47:55 -05:00
Satish Balay
d5957f147b mfem: mfem-3.3-3.4-petsc-3.9.patch is not needed for latest develop version (#8809) 2018-07-26 09:47:28 -05:00
Mark W. Krentel
af60f962cd intel-tbb: Add tm variant to disable transactional memory. (#8799)
* intel-tbb: Add variant `tm` to disable transactional memory.

Some AMD or very old Intel systems don't support transactional memory. This commit adds a variant `tm` that defaults to `True`, but can be switched off to allow running on those systems.
2018-07-25 23:14:17 -07:00
Adam J. Stewart
7902f3eb49 Add docs on new top-level VCS attributes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
5d07042f23 Unit test fixes 2018-07-25 23:10:10 -07:00
Adam J. Stewart
68c2bdfaf6 Further improvements to version parsing 2018-07-25 23:10:10 -07:00
Adam J. Stewart
e948a54d8e All git URLs end in .git 2018-07-25 23:10:10 -07:00
Adam J. Stewart
31417bf66c Replace git=git with explicit branch names 2018-07-25 23:10:10 -07:00
Adam J. Stewart
3f18c04865 Add top-level attributes for git R-Z packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
a1572bb999 Add top-level attributes for git R (Bioconductor) packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
908d2dcd4d Add top-level attributes for git M-P packages 2018-07-25 23:10:10 -07:00
Adam J. Stewart
4c6aca533a Add top-level attributes for hg, svn, and git A-L packages 2018-07-25 23:10:10 -07:00
Todd Gamblin
020c34e136 tests: add checks and tests for consistent version() arguments
- Previously, Spack didn't check the arguments you put in version()
  directives.

- So, you could do something like this, where there are arguments for a
  URL fetcher AND for a git fetcher:

  version('1.0', md5='abc123', git='https://foo.bar', commit='feda2343')

- Now, we check the arguments before constructing a fetcher, to ensure
  that each package has *only* arguments for a single type of fetcher.

- Also added `test_package_version_consistency()` to the `package_sanity`
  test, so that all builtin packages are required to have valid
  `version()` directives.
2018-07-25 23:10:10 -07:00
Todd Gamblin
773cfe088f core: differentiate package-level fetch URLs by args to version()
- packagers can specify two top-level fetch URLs if one is `url`
  - e.g., `url` and `git` or `url` and `svn`

- allow only one VCS fetcher so we can differentiate between URL and VCS.

- also clean up fetcher logic and class structure
2018-07-25 23:10:10 -07:00
Todd Gamblin
498d8cf04b core: fixes and tests for handling of fetcher attributes in packages
- Packages can remove the top-level `url` attribute and still work

- These are now legal:
  - Packages with *only* version-specific URLs (even with gaps)

  - Packages with a top-level git/hg/svn attribute and `version`
    directives for that.

- If a package has both a top-level hg/git/svn attribute AND a top-level
  url attribute, the url attribute takes precedence.
2018-07-25 23:10:10 -07:00
Satish Balay
f59666587b hypre: 'master' is branch - not a tag 2018-07-25 22:17:37 -07:00
sknigh
b0499cf45e Added latest version of charliecloud (#8792) 2018-07-26 06:54:09 +02:00
Todd Gamblin
e2e8108dc4 packages: do not use generic checksum= in version() directives
- This is very old usage -- preparing to deprecate this in favor of being
  explicit about checksums.
2018-07-23 11:57:52 -07:00
Todd Gamblin
bd3ffc7b76 core: use sha256 instead of md5 for spack checksum and spack create
- This changes `get_checksums_for_versions` to generate code that uses an
  explicit `sha256` argument instead if the bare `md5` hash we used to
  generate.

- also use a generic digest parameter for the `version` directive, rather
  than a specific `md5` parameter.
2018-07-23 11:57:52 -07:00
Levi Baber
0cef7b4355 Trinity plugins (#8516)
* trinity: fix plugin installation

* trinity: flake8

* trinity: more specific types for dependencies
2018-07-22 17:17:44 -05:00
Levi Baber
5acdc2e335 beast1: add libbeagle support (#8525) 2018-07-22 17:17:03 -05:00
Levi Baber
8b890db50f libbeagle: add java dependency so jni hooks get built (#8524)
* libbeagle: add java dependency so jni hooks get built

* libbeagle: set BEAST_LIB instead of LD_LIBRARY_PATH

* libbeagle: use BEAST_LIB
2018-07-22 17:16:43 -05:00
Roberto Villegas-Díaz
8a35687d31 Augustus updated to version 3.3.1 (#8588)
* Augustus updated to version 3.3.1

* Augustus - Version-specific URLs replaced by list_url

* Augustus - Adding tool versions back
2018-07-22 17:11:37 -05:00
g-mathias
eecef8d4a7 fix to build libmatheval with guile@2.0: (#8680)
* fix to build libmatheval with guile@2.0:

* fixed formatting issues

* fixed formatting issues2

* fixed check for autoreconf and renaming of configure.in

* fixed force_autoreconf

* now patching configure, which is hopefully more robust

* minimal patches for guile 2.0 and 2.2 (disabeling unit testing for libmatheval)

* minimal patches for guile 2.0 and 2.2 (disabeling unit testing for libmatheval)
2018-07-22 17:07:44 -05:00
Nasr S. Hassanein
2386ce4995 Ncl update (#8747)
* fix ncl url and hash

* adding ncl version 6.5.0

* remove 6.5.0

* using github archive url
2018-07-22 16:54:06 -05:00
Jon Rood
777a0fe5df Make read only source file writeable in perl before patch to avoid failures on lustre filesystem. (#8764) 2018-07-22 16:51:59 -05:00
Lukasz
dcaa675957 add necessary dependence on lapacak, and fix ld_flags for blas (#8776) 2018-07-22 16:32:47 -05:00
Lukasz
a18a642074 add MoFEM packages (#8700)
* add mofem-cephas package

* add mofem fracture module

* add user modules build and fracture modyle

* add minimal surface module

* add slepc variant

* bump mofem core lib version

* bump mofem core lib version

* bump version

* fix bug

* set upper bound to petsc version  and other chanes

* fix indentation

* add minimal med file installation

* chcekc with flake8 and installation with spack packages

* add variants to med package

* upper bound to adol-c and remove obsolete internal package install

* fix basic module install

* module install from external source in extended prefix

* remove obsolte code and reverse to variant doxygen

* fix git adress

* improve packaging for mofem users modules

* fix flake8

* move dependencies after variants

* move  root_cmakelists_dir right before cmake_args

* remove unused variants

* use append for single element

* replace root_cmakelists_dir

* use install_tree instead copy tree

* simplify code

* remove phase and mkdirp

* add run tests

* instal ext modules to ext_users_modules directory

* move version below url

* simplify directory name

* use underscore in variant name

* remove unused variable

* fix link to blas libs

* add missing boost dependence

* fix problem with copying module source code

* change variant name form doxygen to docs

* add expanded description

* make installation consistent with spack

* fix flake8

* make extensions installed

* code comments and minor corrections

* make slepc variant false by default
2018-07-22 15:26:30 -05:00
Christoph Junghans
0e4909cad8 votca: add more deps (#8771)
* votca: add more deps

* Update package.py
2018-07-21 16:45:01 -05:00
Adam J. Stewart
1a136d6db2
Add kealib 1.4.10 (#8769) 2018-07-19 21:21:06 -05:00
lingnanyuan
9653dc2aac r-qorts: Create new package. (#8744)
* r-qorts: Create new package.

* Change dependency to java, change package name.

* Remove some join_path.
2018-07-19 17:58:36 -05:00
sknigh
2a12c3bf07 Packaged iperf2 (#8765) 2018-07-19 17:55:06 -05:00
sknigh
3299d41ef9 Packaged iperf3 (#8762) 2018-07-19 16:02:55 -05:00
Matthias Diener
76b54a214e Py-lark-parser: new package (#8761) 2018-07-19 14:00:19 -05:00
Matthias Diener
9a9998dd2d pycparser: add version 2.18 (#8760) 2018-07-19 12:49:05 -05:00
Levi Baber
b0a0649d2c nwchem: add link type to python dep (#8759) 2018-07-19 12:03:40 -05:00
Christoph Junghans
e0d05d23a1 votca*: update dependencies (#8757) 2018-07-19 11:06:16 -05:00
Hadrien G
f227cf0545 New package: Verrou, a floating point error checker (#8738)
* New package: Verrou, a floating point error checker

* Clean up usage of patch

* Account for future patches in version ranges

* Manual call to autogen is not needed anymore, but extra dependencies are needed

* Use trick from automake to evade shebang length limit

* Use a glob instead of an explicit file list

* Turns out conflict() does not do what I want...

* Suggestions from @citibeth reviews

- Use 'develop' convention for the master branch
- Prefer tarballs over git repositories
- Increase robustness against default configuration

* Drop a couple of older releases with a different patching procedure

* Playing coding style golf

* Various bug squashing

- Missed master -> develop substitution
- Turns out manually calling autogen.sh is needed after all
- Missed + in spec

* More style golfing to fit in 80 columns

* Remove unnecessary mention of the develop branch
2018-07-19 09:57:53 -05:00
Todd Gamblin
d0a808944e style: bring packages in compliance with pep8-naming 2018-07-19 00:41:36 -07:00
Todd Gamblin
20e4038a72 style: make core comply with pep8-naming 2018-07-19 00:41:36 -07:00
Todd Gamblin
264761ccb8 add py-pep8-naming package 2018-07-19 00:41:36 -07:00
Neil Flood
23d911d1a0 py-pytest: Added dependency on py-setuptools-scm, as well as py-setup… (#8750)
* py-pytest: Added dependency on py-setuptools-scm, as well as py-setuptools, to prevent the build from silently installing its own copy of setuptools-scm

* py-pytest: Dependency on setuptools-scm only needs to be 'build'
2018-07-18 22:52:44 -05:00
Neil Flood
186d3669c6 py-snuggs: Added depends_on py-parsing. The build uses setuptools, which would otherwise silently try to install pyparsing itself, presumably into the python home dir (obviously not ideal). (#8748) 2018-07-18 21:42:57 -05:00
Neil Flood
ab262ca916 py-pkgconfig: Made nose dependency type=build,test instead of just type=test, to prevent setuptools from silently installing its own copy of nose (#8749) 2018-07-18 21:42:04 -05:00
Cyrus Harrison
290125f893 openmpi: add c++ exceptions cfg option variant (#8743)
* openmpi: add c++ exceptions cfg option variant

* address review comments
2018-07-18 14:54:12 -05:00