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2526 Commits

Author SHA1 Message Date
alalazo
47f6a6d3cf Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases_rebase 
Conflicts:
	lib/spack/spack/build_environment.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/astyle/package.py
	var/spack/repos/builtin/packages/lzo/package.py
	var/spack/repos/builtin/packages/openjpeg/package.py
	var/spack/repos/builtin/packages/swiftsim/package.py
 2016-09-04 10:12:52 +02:00
Axel Huebl
16c5403ab3 spack boostrap: fix missing include (#1657) 
fix a missing include in booststrap.
found on debian 8 with python 2.7
 2016-09-03 09:43:00 -07:00
Massimiliano Culpo
497bbb3ae3 added package : pexsi (#1550) 
* pexsi : added package
* cp2k : added pexsi (works for gcc+openmpi with and without plumed)
 2016-09-03 08:13:47 -07:00
Todd Gamblin
07fa1cd5f8 Attributes for directives need to be set at class construction time. (#1718) 
- moved ensure_dicts() call from Package.__init__ to
  Package.__metaclass__.
 2016-09-02 15:10:30 -07:00
Todd Gamblin
c8b4f978e1 Clean up stable hashing so that specs don't contain !!python/object/apply 
- only output basic lists, dicts, etc.
- spec and database now parse and write specs as ordered data.
 2016-09-02 03:03:47 -07:00
Todd Gamblin
674434b0fc Merge branch 'UCL-RITS-hash_stability' into bugfix/hash-collision 2016-09-02 03:03:25 -07:00
Todd Gamblin
9268b7aa7c Fix hash copying in _dup. 
- Spec._dup() incorrectly copied cached hashes and normal/concrete values
  even when dependency structure was not preserved.

- Now these are only copied when *all* dependencies are copied.
 2016-09-02 01:26:19 -07:00
Todd Gamblin
69d45b49e9 Fix hash handling in directory layout 
- Currently, build dependencies are not currently hashed; we are waiting
  to hash these until we have smarter concretization that can reuse more
  installed specs.  The layout needs to account for this when checking
  whethert things are installed.
 2016-09-02 01:26:01 -07:00
Todd Gamblin
69b68153a1 Fix spack reindex so that it will work if DB is corrupt (duh). 
- Transaction logic had gotten complicated -- DB would not reindex when
  corrupt, rather the error would be reported (ugh).

- DB will now print the error and force a rebuild when errors are
  detected reading the old databse.
 2016-09-01 11:29:32 -07:00
Todd Gamblin
bee5c05568 Update tests to reflect new in-memory hashing vs. coarser dag_hash. 
- Spack currently not hashing build deps (to allow more reuse of packages
  and less frequent re-installing)

- Fast in-memory hash should still hash *all* deptypes, and installed
  specs will only reflect link and run deps.

- We'll revert this when we can concretize more liberally based on what
  is already installed.
 2016-09-01 11:29:32 -07:00
Todd Gamblin
235a045d08 Add option to copy only certain deptypes to Spec.copy() 
- can now pass these to Spec.copy() and Spec._dup():
  - deps=True
  - deps=False
  - deps=(list of deptypes)

- Makes it easy to filter out only part of a spec.
 2016-09-01 11:29:32 -07:00
Todd Gamblin
409e7a2e64 Faster database loading. 
- use a 3-pass algorithm to load the installed package DAG.

- avoid redundant hashing/comparing on load.
 2016-09-01 11:29:32 -07:00
Todd Gamblin
a8aad95d41 Specs now cache result of "fast" in-memory hash. 
- Hash causes major slowdown for reading/setting up large DBs

- New version caches hash for concrete specs, which includes all specs in
  the install DB
 2016-09-01 11:29:32 -07:00
Todd Gamblin
c46a15b574 Fix dependency bug in database. Fixes #1265, #1320. 2016-09-01 11:25:01 -07:00
Todd Gamblin
4a87d4ab8e Make gh-pages redirect to readthedocs.io 2016-08-31 19:40:22 -07:00
Erik Schnetter
efc570afab Expand/clarify description of dependency types 2016-08-31 14:42:32 -04:00
Todd Gamblin
0ff048521b Fix modules.rst doc build warning. 2016-08-30 22:15:13 -07:00
Todd Gamblin
3a9388b43a Move sphinx-apidoc into conf.py, too. 2016-08-30 21:02:34 -07:00
Todd Gamblin
32834dd67d fix sys.path in conf.py 2016-08-30 20:50:14 -07:00
Todd Gamblin
05545a2528 test. 2016-08-30 20:49:56 -07:00
Todd Gamblin
41675e5ed6 sorted command index, better colification. 2016-08-30 20:49:56 -07:00
Todd Gamblin
176a84a828 Don't test sphinx-generated conf.py for flake8 issues. 2016-08-30 20:30:43 -07:00
Todd Gamblin
d9c5191563 Fix issue with path to Spack. 2016-08-30 19:57:33 -07:00
Todd Gamblin
fc748eb3d0 Exclude spack.__all__ from documentation. 
Everything in the __all__ list in the spack module is from some other
module, so only do their documentation in their original location.  This
also avoids issues like the fact that some directive names shadow spack
core module names.
 2016-08-30 16:36:50 -05:00
Adam J. Stewart
1be6267149 Undo changes to trailing triple quotes in docstring 2016-08-30 16:28:55 -05:00
Adam J. Stewart
9b455e9254 Resolve new documentation issues that have cropped up 2016-08-30 15:58:22 -05:00
Adam J. Stewart
ae2a803496 Make subcommands importable, '-' -> '_', fixes #1642 2016-08-30 15:36:33 -05:00
Adam J. Stewart
8d1a753a1b Fix spack --profile, fixes #1639 2016-08-30 15:35:58 -05:00
Adam J. Stewart
6795f4ca12 Use console instead of shell syntax lexer, fixes #1634 2016-08-30 15:35:58 -05:00
Adam J. Stewart
f78134efa5 Fixes #1620, Missing references 2016-08-30 15:32:54 -05:00
Adam J. Stewart
867a92f083 Fixes #1618, Problems with spack package-list 2016-08-30 15:32:54 -05:00
Adam J. Stewart
69e50595bf Fix docstrings for core Spack libraries, fixes #1612 2016-08-30 15:32:54 -05:00
Adam J. Stewart
02239c094e Fix unexpected indentation in .rst files, #1612 2016-08-30 15:29:51 -05:00
Adam J. Stewart
0614bd206f Fix #1608, Include file not found 2016-08-30 15:28:09 -05:00
Adam J. Stewart
2326355497 Fix #1604 and fix #1605, title underline problems 2016-08-30 15:28:08 -05:00
Adam J. Stewart
fda7fcd73d Fix #1594, duplicate explicit target name 2016-08-30 15:21:15 -05:00
Todd Gamblin
dae00fec29 Move all documentation generation into conf.py 
- extra steps in Makefile are ignored by readthedocs
 2016-08-30 00:47:04 -07:00
Massimiliano Culpo
3ecf4ef8c9 resources : added docs fixes #1551 (#1627) 2016-08-29 22:40:50 -07:00
Todd Gamblin
8ab47537c7 Fix exception constructors. (#1663) 2016-08-29 22:34:47 -07:00
Todd Gamblin
f7ee8d001a Merge pull request #1564 from adamjstewart/features/create 
Suggest setuptools when creating Python package
 2016-08-29 09:11:45 -07:00
Tyler Esser
83897af710 Documentation: Fix accidental quotation. version() takes expand as a keyword. (#1640) 2016-08-28 20:16:08 -07:00
Todd Gamblin
2053db4d17 Make clang detection work on AWS Ubuntu14. 2016-08-27 17:04:46 -07:00
Todd Gamblin
7ebb17e459 Remove stale operating_system.py test per discussion in #1631 
- Test has not been registered in `__init__.py` for a while and needs a
  refresh.
 2016-08-25 21:20:34 -07:00
Todd Gamblin
e9bc3a9e32 Merge pull request #663 from citibeth/efischer/160327-DocumentationImprovements 
[RtM] Documentation Improvements
 2016-08-25 02:04:30 -07:00
Todd Gamblin
062ff13da6 Make spack info print deps in sorted order 2016-08-24 14:10:25 -07:00
Elizabeth Fischer
85be3aefa7 Put url_for_version() after versions in example. 2016-08-24 15:26:19 -04:00
Tom Scogland
2b6833cb80 appeasing flake8, also cleaning up header 
The header append lines were too long, so I just converted it into a
multi-line string template so it's all one piece now instead of a bunch
of appends.
 2016-08-24 11:56:33 -07:00
Tom Scogland
73620fe868 avoid specifying --delim unless required 
This increases portability of generated module files to versions of
environment_modules hearkening back to just after the turn of the
millennium.
 2016-08-24 11:00:16 -07:00
citibeth
8a481e7e13 Added CMake-based Development case study to docuemntation. 2016-08-23 16:39:01 -04:00
Elizabeth F
86d39255ec Explained url_for_version() 2016-08-23 16:39:01 -04:00