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1921 commits

Author SHA1 Message Date
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
becker33
c678a9e3da Merge pull request #1417 from LLNL/features/combined-cray-platform-cleanup 
Removed vestigial cray_xc platform in favor of combined cray platform
 2016-08-01 16:26:20 -07:00
Gregory Becker
0cf1f917d5 fixed architecture test 2016-08-01 16:17:31 -07:00
Mario Melara
0425f5d523 Add import statement 
Add missing import statement for join_path
 2016-08-01 15:59:30 -07:00
Gregory Becker
0ce98d4d65 Removed vestigial cray_xc platform in favor of combined cray platform 2016-08-01 15:43:11 -07:00
becker33
7f43a7d134 Merge pull request #1376 from mpbelhorn/olcf/unified_cray_platform 
Olcf/unified cray platform
 2016-08-01 15:40:11 -07:00
Matt Belhorn
661708b7fa Fixes Flake8 indentation errors. 2016-08-01 17:27:33 -04:00
Matt Belhorn
ae167c09fc Prefers bash over sh. 
Assuming a bash interactive environment will be correctly formed on login, we
should prefer to probe the environment using a shell that reports itself as
`bash` instead of `sh` which may not source files that set the
environment modules in statements like:

```
case "$is" in
bash) test -s /etc/bash.bashrc.local && . /etc/bash.bashrc.local ;;
ksh)  test -s /etc/ksh.kshrc.local   && . /etc/ksh.kshrc.local ;;
zsh)  test -s /etc/zsh.zshrc.local   && . /etc/zsh.zshrc.local ;;
ash)  test -s /etc/ash.ashrc.local   && . /etc/ash.ashrc.local
esac
test -s /etc/sh.shrc.local && . /etc/sh.shrc.local
```
 2016-08-01 17:17:24 -04:00
becker33
14d861a41c Merge pull request #1414 from adamjstewart/fixes/filter_file 
Fix backup=True for filter_file
 2016-08-01 14:10:59 -07:00
Matt Belhorn
e864d27641 Replaces bash-ism source for POSIX-compliant . 
Change is made in order to use `/bin/sh` on systems where `/bin/sh` is not
simply an alias for `/bin/bash --norc`.
 2016-08-01 17:04:09 -04:00
becker33
49e47966a8 Merge pull request #1357 from hartzell/patch-6 
Fix doc for install_tree (cut/paste error)
 2016-08-01 13:45:20 -07:00
becker33
630ff6871d Merge pull request #1346 from glennpj/url_list_fetch 
Url list fetch
 2016-08-01 13:37:57 -07:00
Adam J. Stewart
5b79f0d04a Fix backup=True for filter_file 2016-08-01 15:35:02 -05:00
Glenn Johnson
19578d954f Fix flake8 line length errors 2016-08-01 13:37:42 -05:00
Matt Belhorn
aaa5c9e8a4 Writes default module list to terminal when debugging. 2016-08-01 12:05:29 -04:00
Paul Hopkins
cca240c8f9 Add concretize_preferences tests 2016-08-01 16:18:11 +01:00
Matt Belhorn
dc7e0899a0 Invokes subshell without user init scripts. 2016-07-30 11:38:34 -04:00
Matt Belhorn
5e97eb5ec4 Obtains default modules from a clean subshell. 
The list of default environment modules is obtained by calling

`module list -lt`

from a subshell with a wiped environment. This allows `/etc/profile` and other
init scripts to be fully sourced which should generally include loading the
default modules.

The list of default modules is then parsed for the first acceptable CPU target,
assumed to be the back_end target.
 2016-07-29 15:02:25 -04:00
Paul Hopkins
5eebb2defa Use space characters to separate preferred variants from package name and each other 2016-07-29 13:02:47 +01:00
robertdfrench
eab56b71be PEP8 Goodness 2016-07-27 13:11:24 -04:00
Matt Belhorn
3040381f03 Front-end unification for Cray systems. 
A platform to generically cover all Cray systems is introduced to avoid having
specific platforms for each of XK (XE, XT), XC, and future systems using CrayPE
and CNL.

The platform searches for 'front_end' and 'back_end' targets, in order, from:

  * Environment variables 'SPACK_FRONT_END' and 'SPACK_BACK_END'
  * A spack configuration file 'targets.yaml'
  * Parsing `/etc/bash.bashrc.local` for first loaded CrayPE CPU target.

If a back_end target is not found through one of these methods, an exception is
raised. Otherwise, the back_end is set as the default target. The shell init
script search is based on recommendations in Crayports case #144359.

No automagic way of determining front_end targets has been found (to date) so if
a front_end is not specified through configuration, it is ignored which should
leave a spack instance in a consistant state.
 2016-07-27 11:37:15 -04:00
Matt Belhorn
b1e6c58ff2 Adds __str__ method to CNL operating system class. 2016-07-27 11:25:23 -04:00
Matt Belhorn
4e6fdd12e2 Adds targets config file 2016-07-27 11:25:23 -04:00
alalazo
9c7b98dcc8 modules : handle dashes in environment variables 2016-07-26 09:03:17 +02:00
becker33
e4ced765f1 Merge pull request #1353 from epfl-scitas/qa/minor_cleanup 
qa : minor cleanup
 2016-07-25 10:34:43 -07:00
alalazo
c6a05f4a7d qa : flake8 issues fixes #1109 2016-07-25 18:22:09 +02:00
alalazo
3126ed5f21 modules : permit token expansion in configuration files 2016-07-25 18:10:27 +02:00
George Hartzell
d684b17c06 Fix doc for install_tree (cut/paste error) 
It looks like the docs for copy_tree were cut/paste from copy and still referred to installing a "file".

This fixes that.
 2016-07-25 08:45:44 -07:00
alalazo
5cfaa557d3 qa : flake8 issues 2016-07-25 10:19:58 +02:00