Commit graph

6370 commits

Author SHA1 Message Date
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
Matthias Diener
111512ce7b Cmake: add version 3.12.0 (#8731) 2018-07-17 17:56:04 -05:00
Levi Baber
2ce6299c2b py-pyqi: new package (#8726)
* py-pyqi: new package

* py-pyqi: cleanup
2018-07-17 16:07:38 -05:00
Jon Rood
956faa50cc Confine the xlf_seacas.patch for trilinos to version 12.12.1 (#8725)
* The xlf_seacas.patch fails on the latest trilinos develop branch so confine it up to version 12.12.1.

* Fixing likely mistak in seacas patch version range.
2018-07-17 14:45:39 -05:00
Massimiliano Culpo
373b3d2444 Packages must be added to DB to be considered installed (#8038)
Fixes #8036

Before this PR Package.installed was returning True if the spec prefix
existed, without checking the DB. This is wrong for external packages,
whose prefix exists before being registered into the DB. Now the property
checks for both the prefix and a DB entry.
2018-07-17 11:43:30 -07:00
Christoph Junghans
25062d0bd4
lammps: added v20180629 (#8695) 2018-07-17 11:13:04 -06:00
Christoph Junghans
ab60e2258f fftw: version bump (#8723)
* fftw: version bump

* fftw: add gcc-8 conflict for v3.3.7
2018-07-17 11:11:19 -05:00
Lukasz
9f0f18dad6 fix link to blas libs (#8721) 2018-07-17 08:24:52 -05:00
James Dickson
0a80d94a46 Add fix for bug causing MACSio build failure when hdf5 or typhonio enabled (#8722)
* Add fix for bug causing build failure when hdf5 enabled

* Added correct hdf5 dependency to typhonio
2018-07-17 08:24:16 -05:00