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1949 commits

Author SHA1 Message Date
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
citibeth
2efd7a5e0b Added note on use of 'less -R' for colorized output. 2016-08-23 16:36:02 -04:00
Adam J. Stewart
df623dad15 Suggest setuptools when creating Python package 2016-08-19 14:31:42 -05:00
Nicolas Richart
37faa41b6f stripping the links to remove spaces and '\n' 2016-08-15 21:13:25 +02:00
Todd Gamblin
1e673bfa42 Don't assume spack is in the path when buildign docs. 2016-08-15 10:49:09 -07:00
Adam J. Stewart
c815aed207 Update documentation for spack md5 2016-08-12 10:51:56 -05:00
becker33
ec7f58bf96 Merge pull request #1493 from xjrc/bugfix/nonbool-variants 
Bug Fix : Allow Packages to Have Variants w/ Non-Bool, Non-String Defaults
 2016-08-11 11:33:54 -07:00
Matt Belhorn
568305ddff Corrects Cray compiler name and adds missing version flag. 2016-08-11 13:56:21 -04:00
Mayeul d'Avezac
7769367747 dag_hash stabilised by depending on sorted dict 
Spec.to_node_dict uses OrderedDict

This is to try and ensure that the dag_hash is stable across python
version and processes.
 2016-08-11 16:03:50 +01:00
Todd Gamblin
867121ca68 Move jsonschema files out of config.py to their own package. 2016-08-10 16:33:38 -07:00
Todd Gamblin
bf1072c902 Make Spack core PEP8 compliant. 2016-08-10 16:33:37 -07:00
Todd Gamblin
e7f4fd404d Fix superclass constructor for SpackNamespace objects. 2016-08-10 15:54:13 -07:00
Joseph Ciurej
aa860bf4df Fixed a bug that was making packages with non-bool default variants to crash. 2016-08-10 11:54:33 -07:00
George Hartzell
4bca1c5440 Fix typo 'flexbile' -> 'flexible' 2016-08-09 15:13:08 -07:00
Todd Gamblin
9d4a36a62f Properly re-raise exceptions from lock context handler. 2016-08-09 02:25:09 -07:00
Todd Gamblin
0c75c13cc0 Flake8 fixes 2016-08-09 02:25:07 -07:00
Todd Gamblin
102ac7bcf1 Move provider cache to home directory and refactor Transactions 
Major stuff:

- Created a FileCache for managing user cache files in Spack.  Currently just
  handles virtuals.

- Moved virtual cache from the repository to the home directory so that users do
  not need write access to Spack repositories to use them.

- Refactored `Transaction` class in `database.py` -- moved it to
  `LockTransaction` in `lock.py` and made it reusable by other classes.

Other additions:

- Added tests for file cache and transactions.

- Added a few more tests for database

- Fixed bug in DB where writes could happen even if exceptions were raised
  during a transaction.

- `spack uninstall` now attempts to repair the database when it discovers that a
  prefix doesn't exist but a DB record does.
 2016-08-09 00:24:54 -07:00
Todd Gamblin
2042e9a6d8 Fix bugs with sparse spec printing. 
- Make namespace, arch, and dependnecies show up in spec yaml
  only if they're set.

- Lost some of this functionality with deptypes
 2016-08-08 21:04:23 -07:00
Todd Gamblin
1339714eec Restore text output in verbose mode. 2016-08-08 21:04:23 -07:00
Todd Gamblin
5d690c9270 Make compiler command test last until caching is fixed. 
- global compiler cache breaks tests that come after this one.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
e5743db9b9 Fix issues with import order in tests. 
- modules weren't set properly as attributes in parent modules
 2016-08-08 21:04:23 -07:00
Todd Gamblin
d195576fba WIP 2016-08-08 21:04:23 -07:00
Todd Gamblin
5e5024342f Fix iterator invalidation issues. 2016-08-08 21:04:23 -07:00
Todd Gamblin
4de45c2684 fix scoping issue. 2016-08-08 21:04:23 -07:00
Todd Gamblin
ce6ac93abe rename virtual module to provider_index 2016-08-08 21:04:23 -07:00
Todd Gamblin
1f5a21decf Fix namespace support in Repo.get_pkg_class() 2016-08-08 21:04:23 -07:00
Todd Gamblin
ab049eca41 Faster key in FlagMap._cmp_key 2016-08-08 21:04:23 -07:00
Todd Gamblin
37fc258313 Remove vestigial methods from Package. 2016-08-08 21:04:23 -07:00
Todd Gamblin
faa0a0e4c3 Add a ProviderIndex cache. 
- Spack will check if the index needs updating, and will only parse
  all package files if it does.

- Spack tries to parse as few package files as necessary.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
cf2f902b82 Make ProviderIndexes mergeable, so we can cache them per-repo. 2016-08-08 21:04:23 -07:00
Todd Gamblin
bf028990e7 Make ProviderIndex yaml-izable. 
- allow a provider index to be stored and re-read.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
025609c63f More compact YAML formatting for abstract specs. 
- Don't add empty/absent fields to Spec YAML when they're not there.
 2016-08-08 21:04:23 -07:00
Todd Gamblin
7aaad89ba9 Lazily evaluate all_package_names in repository.py 
- Don't need to list all packages unless we have to.

- Only use the list of all packages for existence checks if we have
  generated it for some other purpose.
 2016-08-08 21:04:23 -07:00
Adam J. Stewart
5d48c108a3 Only strip newline chars, not spaces 2016-08-08 15:02:05 -05:00
Glenn Johnson
20221ee3aa Catch error for version in VCS 
This PR will catch the error where the url can not be determined from a
VCS URL, such as git. It will print a message to the console and move on
because it should not be a fatal error at this point in the process.

This should fix #1459.
 2016-08-05 11:16:43 -05:00
Todd Gamblin
6ab78eb88e sbang filtering now works on non-writable files. (#1445) 
- sbang now changes mode to writable and restores mode if a file is not
  writable.
 2016-08-04 10:46:45 -07:00
becker33
369b2ef01f Merge pull request #1330 from suraia/fix-ascii-graph 
Fix graph command with ASCII output
 2016-08-04 09:37:24 -07:00
Torbjörn Lönnemark
61b3ecb6d2 Fix flake8 issues 2016-08-04 16:28:14 +02:00
Torbjörn Lönnemark
a591e183bc Fix incorrect indentation 2016-08-04 16:09:49 +02:00
Michael Kuhn
2bd1a51193 flake8 fixes 2016-08-04 13:07:33 +02:00
Michael Kuhn
1578a95982 Fix tests. 2016-08-04 13:07:33 +02:00
Michael Kuhn
7affaca321 Fix graph command with ASCII output. 2016-08-04 13:07:33 +02:00
James Riley Wynne III
f0609699ba Added parens to %'s arguments. Fixes #1432 2016-08-03 17:16:04 -04:00
Kelly (KT) Thompson
46e9d85283 Cray: Fix a typo that could cause an infinite recursion when calling /env/cc. 
fixes #1428
 2016-08-03 14:15:44 -06:00
becker33
7ae163d436 Merge pull request #1361 from epfl-scitas/features/module_token_expansion_in_environment 
module : token expansion in environment
 2016-08-03 09:49:28 -07:00
Adam J. Stewart
941acef009 spack create should use setup_py() instead of python() 2016-08-02 12:20:28 -05:00
becker33
326b9838ed Merge pull request #1423 from glennpj/fix_url 
Move archive_version setting to if block
 2016-08-02 10:05:25 -07:00
Glenn Johnson
2929fb0a4d Move archive_version setting to if block 
The archive_version variable should only get set if versions will be
checked and that is only if there is a list_url in the package file. For
VCS repos setting the variable triggers an error from web.py as it
parses the default_fetcher object.

This should fix #1422.
 2016-08-02 11:54:09 -05:00
becker33
21158195fb Merge pull request #1354 from paulhopkins/bugfix/preferred_variants_do_not_recognise_-variant 
Bugfix/preferred variants do not recognise  -variant
 2016-08-02 09:15:06 -07:00
Gregory Becker
679ceabf36 fixed flake8 errors 2016-08-01 17:22:13 -07:00
Gregory Becker
31042e8ed1 further improved error message 2016-08-01 17:16:06 -07:00
Gregory Becker
2705f2c0e3 changed error raised in concretize compiler to provide better error message 2016-08-01 17:11:10 -07:00