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* flang: fixed llvm dep
* add support for llvm-5
* Update package.py
* Update package.py
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Since LLVM 3.9 Clang can use the libc++ library by default using the
CLANG_DEFAULT_CXX_STDLIB cmake configuration variable, without having to
specify the -stdlib=libc++ option on the clang++ command line.
This commit makes clang++ use libc++ by default for LLVM 3.9 and later if the
libcxx variant is on.
Fixes #5942.
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Now one can quickly visually see in the terminal which packages are installed
and where each package begins and ends in the log.
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* Fixes #5754
Previously when RepoPath.repo_for_pkg was invoked with a string,
it did not check if the string included a namespace. Any
namespace-qualified package provided as a string would not be found
(at which point the behavior was to return the highest-precedence
repository).
* handle nested namespaces for packages specified as strings in repo_for_pkg
* add preliminary repository tests
* add test which replicates #5754
* refactor repo tests with fixtures
* define repo_path equivalent at test-level scope for repo tests
* add tests for unknown namespace/package
* rename fixture function (no longer prefixed with 'test_')
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Internally we work against a branch named 'llnl/develop', which
mirrors the public repository's `develop` branch.
It's useful to be able to run flake8 on our changes, using
`llnl/develop` as the base branch instead of `develop`.
Internally the flake8 subcommand generates the list of changes files
using a hardcoded range of `develop...`.
This makes the base of that range a command line option, with a
default of `develop`.
That lets us do this:
```
spack flake8 --base llnl/develop
```
which uses a range of `llnl/develop...`.
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Chasing a performance regression has lead me to this change, going from default optimization gives a significant performance win. The sweet spot for zlib is apparently `-O2`, both `-Ofast` and `-O3` are slightly worse (regression is about 3% compared with `-O2) in my testing.
Happy to share my methodology with people so we can benchmark on a wider variety of systems.
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* Add package for scalpel@0.5.3
Scalpel's a bit of a mess, it expects it's users to just unpack the
tarball, build it in the resulting directory and install that
directory onto their PATH. My install step recapitulates this into
prefix.bin. The alternative was rewiring their scripts (perl), which
use `FindBin` and expect things to be located in the same dir that the
script itself is.
Sigh.
Lightly tested on CentOS 7.
* Flake8 cleanup
* Additional flake8 cleanup
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* perl-bio-perl and dependencies
* minor fixes
* condensing code
* fixing doc error
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* bwa: add 0.7.17
* bwa: add 0.7.13
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* bcftools v1.2 and htslib v1.2
* dependency change - only require dependencies for v1.2
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* Added procedure to edit sbangs of the parallel perl scripts.
* Specify the types of perl dependency
Adding ", type=('build', 'run')" to the dependency declaration to clarify when and how perl is required
* flake8 cleanup
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* adding perl-moose and dependencies
* added missing dependency
* fixed flake8 errors
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Added missing hypre defendency from mfem's hypre-enabled version
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* r-hmisc: Create new package.
* Correct format.
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and added version 0.9.7 (#5848)
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The problem was that the configure script was not using spack's compiler
wrappers. We now pass the proper compiler wrapper using the CC argument
explicitly.
Fixes #5892.
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* amg2013: fix build issues
* amg: add new package
* Update package.py
* amg2013: standardize option name
* amg: standardize option names
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Added Spackage for C version of SW4Lite proxy. Fortran will follow once
race conditions involving .mod files are resolved
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'spack install' can now reinstall a spec even if it has dependents, via
the --overwrite option. This option moves the current installation in a
temporary directory. If the reinstallation is successful the temporary
is removed, otherwise a rollback is performed.
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slepc: add 3.8.0
petsc: no longer prefer 3.7.7
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* r-genomicalignments: created new package
* r-genomicalignments: using git repo source instead
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