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Author SHA1 Message Date
alalazo
f5433477b9 qa : flake8 issues 2016-08-11 09:08:00 +02:00
alalazo
b4b9ebe7d7 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases 
Conflicts:
	lib/spack/llnl/util/tty/log.py
	lib/spack/spack/__init__.py
	lib/spack/spack/cmd/install.py
	lib/spack/spack/cmd/setup.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/blitz/package.py
	var/spack/repos/builtin/packages/gmp/package.py
	var/spack/repos/builtin/packages/qhull/package.py
	var/spack/repos/builtin/packages/szip/package.py
 2016-08-11 08:55:20 +02:00
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
alalazo
23006d1195 spec : removed dead code 2016-07-25 09:05:50 +02:00
Glenn Johnson
b1e5ec0573 Make sure package has the url attribute. 
In addition to `list_url` make sure the package has the `url` attribute
set before attempting to add urls from a list. This is to cover the case
where there may be a `list_url` specified in tandem with a
`url_for_version`.
 2016-07-24 09:21:11 -05:00
Glenn Johnson
4f09e8c975 Only use list if list_url set 
This commit will make urls from list_url only checked if `list_url` is
set in the package file. This makes more sense as there is no need to
check for those if the attribute is not present. If `url` is present and
`list_url` is not then it would result in the same url. If
`url_for_version` is used then that will not work anyway.
 2016-07-23 22:56:08 -05:00
Glenn Johnson
4181fd79cd Fix flake8 errors related to lines 
Fixed the flake 8 errors that involved too many blank lines or not
enough blank lines. Basically, all of the flake8 errors except line
length errors.
 2016-07-23 19:10:09 -05:00
Glenn Johnson
b51be2bb1b Have fetch use list_url 
This PR allows archive file retrieval from urls derived from the
`list_url` setting in a package file. This allows for continued
retrieval of checksummed archive files even when they are moved to a new
remote location when a package is updated upstream.
 2016-07-23 19:09:58 -05:00
Adam J. Stewart
ebbcebac62 Use example deptypes in newly created packages 2016-07-22 13:55:00 -05:00
alalazo
00d7fd8e21 test_install : removed commented code 2016-07-22 18:14:36 +02:00
Gregory Becker
bcbe9c02da Added cray wrapper names directory to spack_env_paths so the spack compiler wrapper will remove them from the environment (prevents hang) 2016-07-21 14:50:23 -07:00
Gregory Becker
1544f98ee0 fixed flake8 errors 2016-07-21 14:36:10 -07:00
Gregory Becker
f0d5317913 fixed 2016-07-21 14:11:34 -07:00
Gregory Becker
2ae7429b18 Bug fix for cray_xc platform 2016-07-21 14:04:22 -07:00
Todd Gamblin
098af17971 Merge pull request #1208 from paulhopkins/bugfix/github1196-specify-preferred-variants 
Bugfix/github1196 specify preferred variants
 2016-07-21 08:36:19 -07:00
Paul Hopkins
00280936da Flake8 fixes to ensure qa tests pass 2016-07-21 13:12:58 +01:00
Paul Hopkins
480fe9cb9a Re-add documentation for variant preferences 2016-07-21 12:32:00 +01:00
Paul Hopkins
bd91dd9d6d Allow users to supply preferred variants via packages.yaml 2016-07-21 12:32:00 +01:00
Michael Kuhn
4e1f86881a Update documentation for recursive module loading. 2016-07-21 13:15:10 +02:00
Glenn Johnson
16f67b5bb1 Setup environment for Intel Parallel Studio 
Set up the environment for the Intel compilers and tools. This commit
does the following:

- Unset variables that were incorrect from the auto guess prefix
  inspections.
- Add a RemovePath environment_modifications_formats for dotkit.
- Set the module environment variables appropriate for the different
  variants.
- Change the component logic so that the '+all' variant works. It was
  getting split by letter and leaving COMPONENTS empty.
- Added a variant checking function.
- Added NONRPM_DB_DIR to the silent.cfg so that the product database
  goes to the installation directory.
- With the product database in prefix the code to remove the product
  database file from the home directory is no longer needed and was
  removed.
- Reformat the 'tools' variant description.

There are probably more variables needed for the '+tools' for the
'professional' product version but I do not have access to that.
 2016-07-20 19:54:35 -05:00
alalazo
b92deda41b spack setup : work as in documentation for openjpeg 2016-07-20 22:27:01 +02:00
Todd Gamblin
8856a226c7 Merge pull request #1277 from mathstuf/special-deptypes 
deptypes: support special deptypes by string
 2016-07-20 13:15:57 -07:00
Gregory Becker
eda1176ba7 added package as argument to setup_platform_environment 2016-07-20 12:26:31 -07:00
Gregory Becker
6983c1d30d Documented linker default 2016-07-20 12:04:00 -07:00
alalazo
40cb314638 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases 
Conflicts:
	lib/spack/spack/package.py
 2016-07-20 21:02:19 +02:00
Gregory Becker
412618d531 fixed flake errors 2016-07-20 11:52:16 -07:00
Gregory Becker
7db4170062 removed commented-out code 2016-07-20 11:36:47 -07:00
Gregory Becker
f4fb9a0771 Set default link type to dynamic on cray. Includes hooks for platform-based environment changes 2016-07-20 11:35:13 -07:00
Gregory Becker
106147716a fixed flake errors 2016-07-20 11:00:56 -07:00
Gregory Becker
0d18f7249c fixed flake errors 2016-07-20 10:50:18 -07:00
Gregory Becker
26d1ddc176 Improved cray_xc detection bug fix 2016-07-20 10:28:38 -07:00
Gregory Becker
4c506b36c5 Improved cray_xc detection 2016-07-20 10:25:07 -07:00
Todd Gamblin
01a361d637 Merge pull request #1288 from LLNL/features/cray_compiler_names 
Let packages call use_cray_compilers() in install to get , etc set to…
 2016-07-20 09:45:36 -07:00
Todd Gamblin
6501cba5a7 Merge pull request #1309 from LLNL/features/spack-defaults 
Add "default" configuration scope.
 2016-07-19 23:48:12 -07:00
Todd Gamblin
26480f14f9 Add "default" configuration scope. 
- Default scope is versioned with spack and can be overridden by site
  or user config.

- Default scope provides sensible default concretization preferences
  for all of Spack.

- per-platform concretization scope can be added later (to force a
  particular MPI on, e.g., Cray systems)
 2016-07-19 17:10:17 -07:00
Todd Gamblin
dd7bd4f320 Make frontend OS on Cray machines a proper linux distro. 2016-07-19 14:59:04 -07:00
Ben Boeckel
1315753e70 deptypes: support special deptypes by string 2016-07-19 16:26:18 -04:00
alalazo
acfeb5d043 Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh 
Conflicts:
	lib/spack/spack/test/__init__.py
 2016-07-19 09:05:27 +02:00
becker33
013cfafe57 Merge pull request #1229 from suraia/fix-preferred-providers 
Fix preferred providers.
 2016-07-18 16:47:08 -07:00
Gregory Becker
218fc602fa Let packages call use_cray_compilers() in install to get , etc set to cray names 2016-07-18 15:43:21 -07:00
Todd Gamblin
4a276807b1 Merge pull request #1245 from LLNL/features/cray-detection-improvement 
The /cray_home directory is more consistent than the /cray/craype dir…
 2016-07-18 14:36:08 -07:00
Todd Gamblin
51834773b4 Merge pull request #851 from mathstuf/safer-bootstrap 
bootstrap: fall back to the default upstream URL
 2016-07-18 14:25:29 -07:00
Gregory Becker
46ee4a3a53 Using cc -craype-verbose to get cray platform type 2016-07-18 14:25:17 -07:00
Todd Gamblin
653f25d676 Merge pull request #1171 from adamjstewart/features/octave 
Allow spack create to automatically detect octave build system
 2016-07-18 12:32:32 -07:00
Michael Kuhn
19df1ea79d flake8 fix 2016-07-18 17:53:26 +02:00
Paul Hopkins
a46138dea9 More flake8 fixes for package-list 2016-07-18 13:59:58 +01:00
Adam J. Stewart
89c9bec81e Flake8 2016-07-18 07:45:28 -05:00
Adam J. Stewart
262ab40188 Update build_system_guess test with new class name 2016-07-18 07:45:28 -05:00
Adam J. Stewart
199a8af7cc Flake8 2016-07-18 07:45:28 -05:00
Adam J. Stewart
e9f42c1a94 Allow spack create to automatically detect octave build system 2016-07-18 07:45:27 -05:00
alalazo
a96eb7096d Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh 
Conflicts:
	share/spack/setup-env.sh
 2016-07-18 14:12:47 +02:00
Paul Hopkins
cc027148eb Flake8 fixes in cmd/package-list.py file 2016-07-18 12:52:23 +01:00
Paul Hopkins
2b3ba850b3 Fix spack package-list to correctly handle deptypes 2016-07-18 12:51:58 +01:00
Todd Gamblin
b3789a4693 Merge pull request #1269 from davydden/pkg/hypre_trilinos_blas 
Pkg/hypre trilinos blas
 2016-07-18 03:06:37 -07:00
Todd Gamblin
cddaba8add flake8 fixes. 
- package.py
- spec.py
- test/architecture.py
 2016-07-18 02:34:24 -07:00
Todd Gamblin
192369dd2b Fix #1265: Errors in spack reindex 
- Consolidated code to read spec.yaml and database index.yaml into
  one method (`read_yaml_dep_specs()`) in spec.py.

- Code understands old hash format, tuple format, and dicts for dep
  specs, for backward compatibility.

- Spec YAML now uses a dict with keys to represent dep specs (this is
  more future-proof).

- Dep specs no longer contain !!py-tuple entries in YAML (only lists
  properly YAML-ize)

- bump database version.
 2016-07-18 01:19:07 -07:00
Todd Gamblin
73f10c9363 Fix broken spack info command after build dep merge. 
- Added a method to get dependencies of particular types from Package
- Fixed info command.
 2016-07-18 01:19:07 -07:00
Todd Gamblin
cdc2ebee90 Better error messages for spack reindex. 2016-07-18 01:14:47 -07:00
alalazo
6c00a13ed5 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases 
Conflicts:
	var/spack/repos/builtin/packages/swiftsim/package.py
 2016-07-18 08:49:24 +02:00
Todd Gamblin
117743863e Merge pull request #1252 from hartzell/patch-5 
Fix format of explanation of an example & question
 2016-07-17 21:20:02 -07:00
Todd Gamblin
0e8bf79fa4 Merge pull request #1240 from epfl-scitas/truncated_documentation 
doc : fixes #1239
 2016-07-17 20:59:36 -07:00
alalazo
dc671ad037 docs : substituted None with empty cell 2016-07-17 22:17:52 +02:00
Denis Davydov
9ea4f80f15 flake8 fixes 2016-07-16 07:58:51 +02:00
Denis Davydov
992250ddea add to_lib_name() to get library name from a path 2016-07-16 07:24:05 +02:00
Michael Kuhn
d61190c3ff Explicitly request zmpi in module blacklist test. 2016-07-16 00:48:04 +02:00
becker33
63101e9914 Merge pull request #1261 from adamjstewart/features/create-deptype 
Automatically add deptype to newly created packages
 2016-07-15 15:10:10 -07:00
Adam J. Stewart
8c1cc44522 Automatically add deptype to newly created packages 2016-07-15 16:43:25 -05:00
becker33
e822257565 Merge pull request #1251 from hartzell/patch-4 
Minor typo fix
 2016-07-15 13:51:02 -07:00
alalazo
833b0ac282 Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases 
Conflicts:
	lib/spack/spack/__init__.py
	var/spack/repos/builtin/packages/gmp/package.py
	var/spack/repos/builtin/packages/openjpeg/package.py
 2016-07-15 11:03:02 +02:00
alalazo
893a5565fe Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases 
Conflicts:
	lib/spack/spack/__init__.py
	var/spack/repos/builtin/packages/gmp/package.py
	var/spack/repos/builtin/packages/openjpeg/package.py
 2016-07-15 11:02:55 +02:00
alalazo
1f3cb2b93c Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh 
Conflicts:
	lib/spack/spack/cmd/module.py
 2016-07-15 10:37:27 +02:00
Ben Boeckel
5d152edcaf spec: assign namespaces to the full dependency DAG 2016-07-14 16:33:48 -04:00
Ben Boeckel
faa3d43d9c package: mention the package that is no concrete 2016-07-14 16:33:38 -04:00
Ben Boeckel
45c675fe7f spack: introduce dependency types 
deptypes: allow for different queries

For things like Python modules, they are required for the build and
runtime, but rather than adding a new parameter for what to query across
the dependency DAG, just expose the recursive query parameter.
 2016-07-14 16:21:46 -04:00
Ben Boeckel
bae97d17d0 test: use file:// url for git repos 2016-07-14 16:21:45 -04:00
Ben Boeckel
6d2ec9baf7 test/stage: use os.path.realpath on the test paths 
When var/spack/stage is a symlink, the tests fail since realpath is used
on the resulting path, but not the original path, so the string compare
fails. Smarter path testing might be a better option.
 2016-07-14 16:21:45 -04:00
Ben Boeckel
b4682c8ca3 directory_layout: fix error path when specs conflict 2016-07-14 16:21:45 -04:00
Ben Boeckel
e275b567eb typos: fix some typos 2016-07-14 16:21:45 -04:00
George Hartzell
3e718920d1 Remove extraneous letter 'p' 
It got in there by mistake, now it's gone.
 2016-07-14 09:40:47 -07:00
George Hartzell
3051c3d71d Fix format of explanation of an example & question 
This list was not formatted correctly on [the ReadTheDocs site](http://software.llnl.gov/spack/basic_usage.html#specs-dependencies).

I'm not a .rst expert, but I think that it was improperly indented.

The example includes an `arch=...` string but *arch* is not listed in the valid compiler flag specifiers or architecture specifiers.  Should it be, or is it considered an "optional variant specifier?
 2016-07-14 08:31:07 -07:00
George Hartzell
e052aaf44d Minor typo fix 
the packages that depends on => the packages that depend on
 2016-07-14 08:19:32 -07:00
alalazo
b8fccb5f61 CMakePackage : added hook for roo CmakeLists.txt, removed duplicated code from build_environment.py 2016-07-14 12:04:24 +02:00
alalazo
1ecea4c2f1 log : refactored acquire and release semantic to meet the context manager protocol 2016-07-14 09:34:01 +02:00
alalazo
00b8e0b567 package.py : joined and simplified try/except blocks in do_install 2016-07-14 09:11:44 +02:00
Michael Kuhn
5ffc50732b flake8 fixes 2016-07-13 23:05:08 +02:00
alalazo
9d66b85492 log : changed semantic for start / join (now it's explicit) 2016-07-13 22:51:12 +02:00
alalazo
90b131260b log : changed semantic for start / join (now it's explicit) 2016-07-13 22:50:39 +02:00
alalazo
7cedd620f1 package.py : added CMakePackage, changed qhull, ibmisc, openjpeg to work as examples 2016-07-13 17:36:06 +02:00
alalazo
0e2afedb7f doc : fixes #1239 2016-07-13 12:43:48 +02:00
alalazo
ad16830f71 log : added timeout to avoid deadlocks on daemon join 2016-07-13 11:20:23 +02:00
alalazo
468a6431f9 package.py : workaround for a known bug that was not fixed in python 2.6 
https://bugs.python.org/issue1515
 2016-07-13 11:08:19 +02:00
alalazo
5cc59507f7 package.py : hdf5 and lzo have examples of run_tests 2016-07-13 09:27:09 +02:00
alalazo
97c2224cd6 package.py : extra arguments, fixed inheritance issue 
- added attribute to hold extra arguments in PackageBase instances
- fixed registration from within packages
- examples : hdf5, lzo
 2016-07-13 09:27:09 +02:00
alalazo
813cb032c4 package.py : updated logic to log.py rework 
Conflicts:
	lib/spack/spack/package.py
 2016-07-13 09:27:09 +02:00
alalazo
513cdd580e do_install : can stop at an arbitrary phase 
Now uses a StopIteration exception as a signal
 2016-07-13 09:27:09 +02:00
alalazo
9af964a6d6 log_output : moved from os.fork to multiprocessing.Process 2016-07-13 09:27:09 +02:00
alalazo
440e71ff13 build_environment : moved from os.fork to multiprocessing.Process 2016-07-13 09:27:09 +02:00
alalazo
857d7bfe0f do_install : can stop at an arbitrary phase 
The mechanism would be simpler if we could leverage exceptions to raise signals. Unfortunately forking does not permit to do so.
 2016-07-13 09:27:09 +02:00
alalazo
a43c63f149 package : added EditableMakefile 
Modifications :
- added EditableMakefile to PackageBase subclasses
- astyle modified as an example
- preliminary hook to stop at a certain phase of install
 2016-07-13 09:27:09 +02:00
alalazo
8f75d34331 package : added a stub for AutotoolsPackage, examples in szip and swiftsim 2016-07-13 09:27:09 +02:00
alalazo
8ed028e2d6 package : introduced InstallPhase, added decorators for prerequisites and sanity_checks of phases 2016-07-13 09:27:09 +02:00
alalazo
a36f3764af package : added hooks for generic phases 2016-07-13 09:27:09 +02:00
Todd Gamblin
27aa265abd Merge pull request #1211 from hartzell/patch-3 
Typo: verison -> version
 2016-07-12 13:53:52 -07:00
Michael Kuhn
b7d9b58cc5 Fix preferred providers. 2016-07-12 19:57:08 +02:00
Todd Gamblin
283d621b6e Add documentation for fetching submodules. 2016-07-11 13:27:37 -07:00
Todd Gamblin
86b1b28906 Add submodules option for git fetching. 2016-07-11 13:27:35 -07:00
alalazo
5f861e075c Merged develop into branch 2016-07-11 20:57:55 +02:00
Todd Gamblin
7f6541ef02 Merge pull request #1190 from davydden/feature/version_dev 
add special treatment of @develop version
 2016-07-11 11:31:54 -07:00
Denis Davydov
306e601d4e document special treatment of development version 2016-07-11 19:50:33 +02:00
George Hartzell
fbaff33f3f Typo: verison -> version 2016-07-11 09:44:20 -07:00
George Hartzell
1682257b35 Typo: verison -> version 2016-07-11 09:42:49 -07:00
Denis Davydov
b29d5e6032 add special treatment of develop version 2016-07-10 14:21:52 +02:00
Todd Gamblin
b0f4052bd8 Merge pull request #1169 from davydden/feature/install_argument_tests_petsc_fixes 
--run-tests install argument and petsc fixes
 2016-07-09 12:10:16 -07:00
Todd Gamblin
c086ccdab6 Merge pull request #1200 from glennpj/lowpackname 
Have ``spack create`` default to lower case name for package
 2016-07-08 13:29:52 -07:00
Glenn Johnson
33d0660abc Have `spack create` default to lower case name 
This will create package directories with lower case names when using
`spack create`. The documentation was modified to reflect this.
 2016-07-08 15:11:37 -05:00
George Hartzell
1b9e8a0e65 Fix typo 
Comamnds -> Commands
 2016-07-08 11:01:08 -07:00
Todd Gamblin
b9148b1751 Merge pull request #1125 from NERSC/docs/cray 
Update documentation for use on Cray
 2016-07-06 15:06:20 -07:00
Gregory Becker
403a55afb2 Minor bug fix 2016-07-06 14:54:25 -07:00
Gregory Becker
663b30b3e8 Update target autodetection for linux platform 2016-07-06 14:54:22 -07:00
Denis Davydov
081918d71a add --run-tests argument for install() 2016-07-06 22:45:30 +02:00
Todd Gamblin
03fdb2058a Merge pull request #1176 from epfl-scitas/features/version_minor_improvements 
spack.Version : like a duck!
 2016-07-06 09:01:19 -07:00
alalazo
9b926a480f qa : flake8 issues 2016-07-06 17:03:32 +02:00
alalazo
780a57367d version : modified __getitem__ to return either an item or a Version instance + unit tests 2016-07-06 17:00:48 +02:00
alalazo
32e086f44a version : modified __repr__ to return a string representation of the object + unit tests 2016-07-06 15:24:10 +02:00
William Killian
1f64f08cb3 (bugfix) fixed typo of spec --> raw_spec 2016-07-05 13:32:37 -07:00
Todd Gamblin
d687e332ad Fix compile bugs for gcc on Mac OS X with macports. 
- add macports to things that are cleaned out of the environment.
- linker incompatibilities cause issues with packages like OpenSSL.
- also clean up NOQA stuff in OpenSSL
 2016-07-04 22:59:02 -07:00
Todd Gamblin
690937f953 Add --dirty option to spack install. 
- Allow install to be run without cleaning the environment.
 2016-07-04 22:58:01 -07:00
Todd Gamblin
6bac1598f6 Merge branch 'fix-archive' of https://github.com/mwilliammyers/spack into mwilliammyers-fix-archive 2016-07-04 21:35:33 -07:00
Todd Gamblin
890df7153a Merge branch 'efischer/160311-StagedPackage' of https://github.com/citibeth/spack into citibeth-efischer/160311-StagedPackage 2016-07-04 00:27:32 -07:00
alalazo
6d988dde8d qa : fixed flake8 issues 2016-07-02 12:54:36 +02:00
alalazo
3100c5948a module : added unit tests 2016-07-02 12:14:30 +02:00
Glenn Johnson
31e9ded768 Remove more variables from build environment 
Remove the LIBRARY_PATH and CPATH environment variables before building
a package.
 2016-07-01 20:59:14 -05:00
alalazo
d10fceaacc spack commands : refactoring of cli arguments and common utiities. Implemented suggestions on spack module loads 
- Common cli arguments now are in their own module
 - Moved utilities that can be reused by different commands into spack.cmd.__init__.py
 - Modifications to `spack module loads`
 2016-07-01 23:06:07 +02:00
alalazo
f0f7b23c8a module : added rm subcommand, encapsulated logic for constraints in argarse.Action subclass 2016-07-01 14:27:55 +02:00
alalazo
fe4ef286f2 module : added the command 'load-list' 2016-07-01 12:38:04 +02:00
Mario Melara
56adb5d9a5 Change arch spec and fix typo 
Changed old arch specs to new arch specs. Changed intallation to
installation
 2016-06-30 17:03:07 -07:00
Mario Melara
16a4c49f98 Remove Cray examples of config files 
Removed examples of Cray config files and added them under Spack on
Cray. Any users of Cray can just look at the Spack on Cray section to
get an idea of what's used. If they want more information they can click
links to the sections.
 2016-06-30 17:01:18 -07:00
Mario Melara
d784d561fc Add more documentation fix arch spec 
Added more documentation for Spack on Cray. Also fixed the architecture
spec to be linux-debian7-x86_64 since it was reversed in the previous
commit.
 2016-06-30 16:59:36 -07:00
Massimiliano Culpo
6793a54748 --prefix : defaults to empty string 2016-06-30 23:18:32 +02:00
Massimiliano Culpo
ba1ada5424 Merge branch 'develop' of https://github.com/LLNL/spack into features/module_refresh_reworking 
Conflicts:
	lib/spack/spack/cmd/module.py
 2016-06-30 22:19:46 +02:00
alalazo
a770151359 module : minor improvement to output formatting 2016-06-30 16:49:24 +02:00
Elizabeth Fischer
6327877a6f PEP-8 2016-06-30 09:19:57 -04:00
Elizabeth Fischer
50ac98bc04 Merge remote-tracking branch 'upstream/develop' into efischer/160630-StagedPackage 
# Conflicts:
#	lib/spack/docs/packaging_guide.rst
#	lib/spack/spack/package.py

Mostly minor/formatting issues in lib/spack/spack/package.py (the heavyweight merge was already done recently).  Only one serious issue: it looks like the feature branch had accidentally deleted the line `spack.hooks.post_install(self)`.  This got added back in from develop.
 2016-06-30 09:13:24 -04:00
alalazo
ba87937fff module : added detection of file name clashes 2016-06-30 13:44:49 +02:00
alalazo
1b7eedbb7d modules.yaml : added hash_length as a new keyword 
config :
- added `hash_length` under the modules section

EnvModules :
- take into consideration hash_length when constructing `file_name`
- added logic to warn and skip module file writing in case of file name clash
 2016-06-30 12:56:47 +02:00
Todd Gamblin
0e422dec8c Merge pull request #1141 from adamjstewart/fixes/license_docs 
Fix missing code blocks in licensed software documentation
 2016-06-30 02:22:38 -07:00
Todd Gamblin
bc2fa76588 Merge pull request #1146 from scheibelp/features/doc-caching 
added documentation for automatic caching of resources fetched during installs
 2016-06-30 02:13:16 -07:00
Todd Gamblin
30d083c6b7 Merge branch 'efischer/160401-RecursiveModules' of https://github.com/citibeth/spack into citibeth-efischer/160401-RecursiveModules 2016-06-30 02:12:00 -07:00
Peter Scheibel
cfd380d514 added documentation for automatic caching of resources fetched during installs 2016-06-29 18:23:40 -07:00
Ben Boeckel
5f720f9b7c flake8: appease the style checker 2016-06-29 14:49:58 -04:00
Ben Boeckel
e3e94f0ac9 bootstrap: name the current branch the same as the remote 2016-06-29 14:49:19 -04:00
Ben Boeckel
89bf5f4045 bootstrap: allow using alternate remotes 
If you want to bootstrap from a fork, the `--remote` option may be used
to select it.

Also limit the branches to 'develop' and 'master' if the remote is
'origin' since those are the actual integration branches used (other
branches on 'origin' are just PR branches).
 2016-06-29 14:49:19 -04:00
Ben Boeckel
7ec191ce0b bootstrap: use the currently checked out branch 
The `master` branch is not really where Spack development happens, so
default to it, but use the user's current branch if it's there.
 2016-06-29 14:49:19 -04:00
Ben Boeckel
6f69c01915 bootstrap: fall back to the default upstream URL 
Fixes #352.
 2016-06-29 14:49:19 -04:00
Adam J. Stewart
06de8c56af Fix missing code blocks in licensed software documentation 2016-06-29 12:35:38 -05:00
Todd Gamblin
eb388306fd Merge pull request #1112 from adamjstewart/features/dependencies 
Make spack create automatically add dependencies for build system
 2016-06-29 07:57:33 -07:00
Todd Gamblin
c996632113 Add spack purge --cache to purge local archive cache. 2016-06-29 01:41:55 -07:00
Todd Gamblin
bc1320d83a Merge branch 'features/cache-archives' of https://github.com/scheibelp/spack into scheibelp-features/cache-archives 2016-06-29 00:57:26 -07:00
alalazo
b71d430af6 module : can regenerate single module files, homogenized cli options 
spack module :
- refresh accepts a constraint
- find and refresh share common cli options
- ask for confirmation before refreshing
- deleting the module file tree is now optional
 2016-06-28 19:28:18 +02:00
mwilliammyers
0384794912 Fix #1019 - cannot create mirror for git spec 2016-06-27 16:00:38 -06:00
Mario Melara
26325fe812 Add missing link to external packages 
Adding missing _sec-external_packages to link with external packages
page
 2016-06-27 14:35:56 -07:00
Mario Melara
7fb45e4bfd Update documentation for use on Cray 
Updating how to use compilers.yaml on Cray as well as setting up
external packages. Also includes what needs to be set up for usage on
Cray and explains what needs to be done to get Spack properly working.
Also explain the architecture spec and what it does.
 2016-06-27 13:52:48 -07:00
Todd Gamblin
3ea9d1e665 Merge pull request #1122 from LLNL/bugfix/newarch-sys_type 
Bugfix/newarch sys type
 2016-06-27 10:07:03 -07:00
Adam J. Stewart
798dabc8f2 Forgot the unknown key/value pair 2016-06-27 09:01:53 -05:00
Todd Gamblin
0185226042 Merge pull request #1121 from LLNL/bugfix/module-directory-pollution 
Make MockPackagesTest use a different module location.
 2016-06-27 02:25:32 -07:00
Todd Gamblin
99c3ed56fa Add new sys_type method that prints out the *full* arch descriptor. 2016-06-27 02:19:26 -07:00
Todd Gamblin
305d5698df Rename spack.architecture.sys_type() to spack.architecture.platform() 2016-06-27 02:19:08 -07:00
Todd Gamblin
a15aee5d8e Make MockPackagesTest use a different module location. 
- ensures anything tests create is blown away.
 2016-06-27 01:22:03 -07:00
Todd Gamblin
b4c36164b5 Fixes #760: spack test leaves builtin.mock packages in DB 
- install_layout was redirected by the install test, but not the DB.
- redirect the DB now, as well.
 2016-06-27 00:55:16 -07:00
Todd Gamblin
73213ac59d Merge pull request #984 from epfl-scitas/module_file_explicit_load 
module files : explicit load and mnemonic suffixes
 2016-06-26 23:33:48 -07:00
Todd Gamblin
19b69ce3a5 Merge pull request #1097 from citibeth/efischer/160622-DBErrors 
Improved Spack database errors to help users fix them.
 2016-06-26 22:45:44 -07:00
Todd Gamblin
ece72e5337 Merge pull request #1030 from opoplawski/external 
Remove last two remaining from external imports
 2016-06-26 22:41:58 -07:00
Todd Gamblin
8f28df1d14 Merge pull request #1094 from epfl-scitas/documentation/remove_packages_yaml_inconsistencies 
packages.yaml : removed references to a never implemented feature
 2016-06-26 22:37:43 -07:00
Todd Gamblin
30993357d7 Merge pull request #1105 from adamjstewart/fixes/filter_file 
Fix backup logic in filter_file
 2016-06-26 22:33:09 -07:00
Adam J. Stewart
ea88d9cfe9 Make spack create automatically add dependencies for build system 2016-06-24 16:43:31 -05:00
Todd Gamblin
055f7f4ab6 Add package_dir method to package.py. 2016-06-24 12:33:53 -07:00
Adam J. Stewart
71a297f121 Fix backup logic in filter_file 2016-06-23 16:44:41 -05:00
Todd Gamblin
27e9bc6d02 Make sbang handle lua 
- use --! instead of #! for patched lua scripts.
 2016-06-23 00:03:23 -07:00
Elizabeth Fischer
8f846d507d Added --prefix to module command. 2016-06-22 15:36:04 -04:00
Elizabeth Fischer
10810482bc Update database.py 
PEP8
 2016-06-22 14:03:32 -04:00