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* Fixes #1720: spack reindex fails with invalid ref count.
- Database graph wasn't being built properly; dependencies were set up
incorrectly in the nodes that ended up in the graph on reindex.
- Reworked _add to increment ref count properly and to always build
bottom-up to make the logic simpler to understand.
* Add checks to ensure DB is a valid merkle tree.
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- fix deptype support
- by default, graph command omits build depedencies
- update docs to use deptype args
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- Fixed logic for collapsing backward edges
- Last collapse now depends on whether prior step in left collapse
sequence alrady did the collapse.
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- Distinguish between static (package) and dynamic (spec) graphs.
- static graphs ignore conditions and multiple instances (hashes) and
plot raw dependencies among packages.
- dynamic graphs include information from particular specs (instances of
packages) and can have multiple instances with hashes.
- Allow graphing all packages in the install DB.
- useful for debugging.
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* Perform shebang fix for all files
* Fix sbang for perl scripts
Otherwise perl would look at the #! line and call sbang again, resulting
in an infinite loop.
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* Removed SPACK_DIRTY env var support.
* Finished removing SPACK_DIRTY support.
* Minor changes.
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* Turned <provider>_libs into an iterable
Modifications :
- added class LibraryList + unit tests
- added convenience functions `find_libraries` and `dedupe`
- modifed non Intel blas/lapack providers
- modified packages using blas_shared_libs and similar functions
* atlas : added pthread variant
* intel packages : added lapack_libs and blas_libs
* find_library_path : removed unused function
* PR review : fixed last issues
* LibraryList : added test on __add__ return type
* LibraryList : added __radd__ fixed unit tests
fix : failing unit tests due to missing `self`
* cp2k and dependecies : fixed blas-lapack related statements in package.py
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* Fixed bug propagating --dirty flag to sub-installs.
* Fix syntax error
* Allow --dirty flag to be set with SPACK_DIRTY env var.
* Added dirty flag to `spack diy` and `spack setup`, as is currently in `spack install`
* flake8
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* Set JAVA_HOME on module load and on dependent installs.
* Include environment setup from dependencies in dependee module (#1714)
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Includes :
- treatment of a generic hierarchy (i.e. lapack + mpi + compiler)
- possibility to specify which compilers are to be considered Core
- correct treatment of the 'family' directive
- unit tests for most new features
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When re-using previously downloaded tarballs, spack copies from
`var/spack/stage/PACKAGE-VERSION-HASH/downloaded_file` to
`var/spack/cache/PACKAGE/downloaded_file`. This fails if the source is owned by
a different user (`shutil.copy` tries to retain all meta data including file
ownership). Change to a non-meta-data copy function (`shutil.copyfile`).
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This closes #1308, where fetching a non-expanded resource from a mirror
will cause an error.
This also ensures that when a URL resource is fetched from a mirror,
that it will be named as though it were retrieved from the original
URL. This is particularly useful for non-expanded resources since it
ensures that the resource name is consistent for the installation
(this is less important for expanded resources because the build takes
place inside the expanded resource).
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fixes #1681
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fix a missing include in booststrap.
found on debian 8 with python 2.7
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* pexsi : added package
* cp2k : added pexsi (works for gcc+openmpi with and without plumed)
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- moved ensure_dicts() call from Package.__init__ to
Package.__metaclass__.
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- only output basic lists, dicts, etc.
- spec and database now parse and write specs as ordered data.
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- 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.
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- 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.
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- 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.
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- 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.
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- 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.
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- use a 3-pass algorithm to load the installed package DAG.
- avoid redundant hashing/comparing on load.
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- 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
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