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2017-03-21Fix for `find --explicit` #3374 (#3492)George Hartzell1-1/+1
This fixes the problem described in #3374, which describes `spack find` ignore explicit/implicit. I believe that this was broken in #2626. This restores the behavior of implicit/explicit for me. I believe that it does not screw anything else up, but ....
2017-03-20Improve output for compiler commands (#3480)scheibelp2-1/+14
* Order listed compiler sections "spack compiler list" output compiler sections in an arbitrary order. With this commit compiler sections are ordered primarily by compiler name and then by operating system and target. * Compiler search lists config files with compilers If a compiler entry is already defined in a configuration file that the user does not know about, they may be confused when that compiler is not added by "spack compiler find". This commit adds a message at the end of "spack compiler find" to inform the user of the locations of all config files where compilers are defined.
2017-03-20Fix issue with config.guess patching when the overwritten config.guess did ↵Matthew LeGendre1-9/+5
not have write permissions. (#3494)
2017-03-18Use byte-encoded UTF-8 for sourced environment in Python 2 (#3489)Todd Gamblin3-9/+52
- Fixes recurring errors on develop with unicode commit characters. - still Python3-proof: python3 will use str instead of bytestrings.
2017-03-17Don't use @system in packages.yaml (#3472)Adam J. Stewart3-73/+19
2017-03-16Detect when OS updates affect compiler selection (#3410)scheibelp3-21/+77
Fixes #1476 Concretization uses compilers defined in config files and if those are not available defaults to searching typical paths where the detected operating system would have a compiler. If there is an OS update, the detected OS can change; in this case all compilers defined in the config files would no longer match (because they would be associated with the previous OS version). The error message in this case was too vague. This commit adds logic for detecting when it is likely that the OS has been updated (in particular when that affects compiler concretization) and improves the information provided to the user in the error message.
2017-03-16Dont propagate flags between different compilers (#3379)scheibelp2-41/+28
* Dont propagate flags between different compilers Fixes #2786 Previously when a spec had no parents with an equivalent compiler, Spack would default to adding the compiler flags associated with the root of the DAG. This eliminates that default. * added test for compiler flag propagation * simplify compiler flag propagation logic
2017-03-16Dont auto-init compiler conf for 'compiler find' (#3439)scheibelp2-8/+9
Fixes #3428 Users can run 'spack compiler find' to automatically initialize their compilers.yaml configuration file. It also turns out that Spack will implicitly initialize the compilers configuration file as part of detecting compilers if none are found (so if a user were to attempt to concretize a spec without running 'spack compiler find' it would not fail). However, in this case Spack was overlooking its own implicit initialization of the config files and would report that no new compilers were found. This commit removes implicit initialization when the user calls 'spack compiler find'. This did not surface until #2999 because the 'spack compiler' command defaulted to using a scope 'user/platform' that was not accounted for in get_compiler_config (where the implicit initialization logic predates the addition of this new scope); #2999 removed the scope specification when checking through config files, leading to the implicit initialization.
2017-03-14Consistent docs and usage of env mod methods (#3351)Adam J. Stewart2-81/+61
2017-03-14fix automatic mixing of clang with gfortran 6.3.0 on macOS (#3427)Denis Davydov2-14/+5
* fix automatic mixing of clang with gfortran 6.3.0 on macOS * automatically mix any gfortran with any clang on macOS * adjust the unit test
2017-03-14test/file_cache.py: ported to pytest (#3429)Massimiliano Culpo1-44/+36
2017-03-13Fix from_sourcing_files(): decode json input as utf-8 (#3433)Todd Gamblin1-2/+4
2017-03-11Correct inconsistency in comment (#3414)Erik Schnetter1-1/+1
2017-03-11Make multimethods work with inheritance. (#3411)Todd Gamblin2-3/+17
Previously, this would fail with a NoSuchMethodError: class Package(object): # this is the default implementation def some_method(self): ... class Foo(Package): @when('platform=cray') def some_method(self): ... @when('platform=linux') def some_method(self): ... This fixes the implementation of `@when` so that the superclass method will be invoked when no subclass method matches. Adds tests to ensure this works, as well.
2017-03-10Features/compiler config consistency (#2999)scheibelp6-70/+181
* default scope for config command is made consistent with cmd/__init__ default * dont specify a scope when looking for compilers with a matching spec (since compiler concretization is scope-independent) * config edit should default to platform-specific file only for compilers * when duplicate compiler specs are detected, the exception raised now points the user to the files where the duplicates appear * updated error message to emphasize that a spec is duplicated (since multiple specs can reference the same compiler) * 'spack compilers' is now also broken down into sections by os and target * Added tests for new compiler methods
2017-03-09created elf virtual package and updated dependent packages (#3317)Gregory Lee1-0/+13
* created elf virtual package and updated dependent packages * added `hide_files` context manager to handle moving files.
2017-03-07package.py: packages dump build dependencies in prefix (#3373)Massimiliano Culpo1-1/+3
Modifications: - `dump_packages` copies build dependencies into `$prefix/.spack`, as well as the link/run dependencies that we already copied there. - fake installs copy dependency packages into `$prefix/.spack` as well
2017-03-07test/environment.py: ported to pytest, added a test on separators (#3375)Massimiliano Culpo1-171/+235
2017-03-04Allow find_libraries to accept lists or strings (#3363)Adam J. Stewart2-14/+16
* Allow find_libraries to accept lists or strings * Convert one more example from list to string
2017-03-03Fix error raised for multiple virtual packages. (#3306)Joschka Lingemann1-1/+2
2017-03-02New interface for passing build information among specs (#1875)Massimiliano Culpo5-40/+285
- Added a new interface for Specs to pass build information - Calls forwarded from Spec to Package are now explicit - Added descriptor within Spec to manage forwarding - Added state in Spec to maintain query information - Modified a few packages (the one involved in spack install pexsi) to showcase changes - This uses an object wrapper to `spec` to implement the `libs` sub-calls. - wrapper is returned from `__getitem__` only if spec is concrete - allows packagers to access build information easily
2017-03-02test/packages: fixed test suite (#3236)Massimiliano Culpo1-106/+99
It seems the tests in `packages.py` were running just because we had a specific order of execution. This should fix the problem, and make the test_suite more resilient to running order.
2017-02-21Fixing issue wheh overwriting build_args in PythonPackage (#3200)Javier1-1/+1
2017-02-17Fix readline support in `spack python` (#3132)Adam J. Stewart3-0/+87
* Fix readline support in `spack python` * Add documentation on `spack python` * Add unit tests for `spack python`
2017-02-17Set default module type based on modules.yaml (#3173)Adam J. Stewart1-2/+4
2017-02-17More consistent yes/no prompts (#3174)Adam J. Stewart6-54/+51
* More consistent yes/no prompts * Add ==> prefix to yes/no and number prompts
2017-02-17On uninstall, change shortcut flag for --dependents to -R, as per Spack ↵Elizabeth Fischer1-1/+1
convention. (-r = --dependencies, -R = --dependents). (#1917)
2017-02-17Fix missing space in error message output (#3169)Adam J. Stewart1-2/+2
2017-02-17py-git2: New Package (#1971)Elizabeth Fischer1-1/+2
2017-02-17Fix typos in External Packages documentation (#3168)Adam J. Stewart1-2/+2
2017-02-10fix: don't call setup_environment when not needed (#3060)Massimiliano Culpo3-2/+16
* Don't call setup_environment when not needed. fixes #3059 * setup_environment and modules: added unit tests
2017-02-10Make distro more robust to unreadable files (#3110)becker331-7/+12
* Make distro more robust to unreadable files. Will upstream * Comment for clarify
2017-02-09make svn fetch quiet (#3070)Denis Davydov1-1/+1
2017-02-08Revert "db and concretization of packages modified after installation: fixes ↵Todd Gamblin1-1/+0
#2911" (#3078)
2017-02-07db and concretization of modified packages: fixes #2911 (#2920)Massimiliano Culpo1-0/+1
2017-02-03Fix spec hash printing (#2941)becker336-18/+18
- Fix format printing to match command line for hashes and full name formats - Update spack graph to use new format - Changed format string signifier for hashes from `$#` to `$/`
2017-02-03Make module autoload warnings configurable (#2763)George Hartzell1-3/+24
Modules generated by the module creation machinery currently print out a notice that warnts the user that things are being autoloaded. In some situations those warnings are problematic. See #2754 for discussion. This is a first cut at optionally disabling the warning messages: - adds a helper tothe EnvModule base class that encapsulates the config file variable; - adds a method to the base class that provides a default (empty) code fragment for generating a warning message; - passes the warning fragment into the bit that formats the autoload string; - adds specialized autload_warner() methods in the tcl and lmod subclasses;; and finally - touches up the autoload_format strings in the specialized classes.
2017-02-03Blacklist implicit packages for modulefile generation (#2603)George Hartzell2-1/+21
Add the ability to the modules generation process to blacklist packages that were installed implicitly. One can still whitelist modules that were installed implicitly. This changes adds a `blacklist_implicts` boolean as a peer to the `whitelist` and `blacklist` arrays, e.g.: ``` modules: enable:: - lmod lmod: whitelist: - 'lua' - 'py-setuptools' blacklist: - '%gcc@4.8.3' blacklist_implicits: True ``` It adds a small helper in `spec.py` and then touches up the package filtering code in `modules.py`.
2017-01-31Change default fflags for XL compiler to only "-qzerosize" (#2966)serbanmaerean2-14/+2
2017-01-31Add installcheck phase to AutotoolsPackage (#2863)Adam J. Stewart2-0/+33
* Add installcheck phase to AutotoolsPackage * Update installcheck phase with new callbacks API * build_directory has been converted to a property
2017-01-31DOCS: Examplify what file types are automatically extracted (#2955)Henrik Bengtsson1-3/+3
2017-01-31Refactor Spack's URL parsing commands (#2938)Adam J. Stewart7-312/+797
* Replace `spack urls` and `spack url-parse` with `spack url` * Allow spack url list to only list incorrect parsings * Add spack url test reporting * Add unit tests for new URL commands
2017-01-31removed call syntax from property fixes #2944 (#2945)Massimiliano Culpo1-1/+1
2017-01-31Add several new R packages (#2952)Adam J. Stewart1-0/+1
* Add several new R packages * Add a few more R packages * Update more versions * Convert Package to RPackage * Add a few more packages * Add missing dependencies
2017-01-27Fix ambiguous hash message generation. (#2940)becker331-4/+4
* Fix ambiguous hash message generation. Engineering fix
2017-01-26Standardize argparse help messages (#2847)Adam J. Stewart54-252/+252
2017-01-26Packaging docs for MPI (#2838)Todd Gamblin1-283/+447
* Add MPI docs to packaging guide and simplify packaging guide TOC a bit.
2017-01-26AutotoolsPackage: minor improvements (#2859)Massimiliano Culpo4-25/+95
* AutotoolsPackage: added configure_directory to permit build out of source. The configure script executable is now invoked with an absolute path. Modified a few packages accordingly. * build_systems: functions returning directories are now properties * build_systems: fixed issues with tcl and tk * AutotoolsPackage: reworked recipe for autoreconf
2017-01-26Use codecov for coverage instead of coveralls (#2933)Todd Gamblin2-7/+144
* Switch from coveralls to codecov - Add .codecov.yml, simplify .travis.yml - Add codecov badge to README.md * Add tests for spack graph.
2017-01-25Spec.satisfies accesses Spec.concrete as property (#2928)scheibelp4-6/+24
* Spec.satisfies accesses Spec.concrete as property Fixes #2760 When copying a spec, _concrete is always set to False for each dependency. "Spec.satisfies" was accessing the member "_concrete" directly instead of using the property "concrete". This means that if you copy a spec, the dependencies will be considered equal, but did not necessarily satisfy one another. Spec.satisfies is a prerequisite for a package to be considered an extension; as a consequence, an extension with run-time dependencies that were also extensions did not activate those extensions. This updates Spec.satisfies to avoid checking the cached member "_concrete" directly. * Added test to check for activation of dependency extension * Added test to check for transitive satisfiability between a spec and its copy