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- `imp` is deprecated and seems to have started having some weird
issues on certain Linux versions.
- In particular, the file argument to `load_source` is ignored on
arch linux with Python 3.7.
- `imp` is the only way to do imports in 2.6, so we'll keep it around for
now and use it if importlib won't work.
- `importlib` is the new import system, and it allows us to get
lower-level access to the import implementation.
- This consolidates all import logic into `spack.util.imp`, and make it
use `importlib` if it's avialable.
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* added relion 3 beta - WIP
* added relion 3 beta - WIP
* more relion changes - still WIP
* more changes for relion
* more changes
* now correctly handling cuda_arch
* now correctly handling cuda_arch
* fixed flake8 syntax errors
* fixed flake8 syntax errors
* merge
* fixed flake8 errors again
* relion 3 finished
* added print message to cuda_arch exception
* relion - shortened explination
* still need tag=2.0.3 for v 2.0.3 - removed @develop since it no longer exists
* correct cuda versions now used properly
* relion 3 done
* added tags back
* fixed exception message
* relion - added develop back as master
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- foam_add_lib() must be used instead of the undefined foamAddLib()
for adding VTK
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* Fix spack versions behavior when no URL
* Unit test packages without URLs or safe versions
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* add gcc8 patch for python 2.7.14
Change-Id: I48cb5e717577d8158d1f7f1fe270156a01940d8a
* add explaining comment
Change-Id: Ia46168e2269d7de47d7ec8d0bf9e3b7696ea8e31
* remove unnecessary part of the patch
Change-Id: Iee763effe2439f0f160c1547640eca4bb9451a68
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Replace use of `shutil.copytree` with `copy_tree` and `install_tree` functions in `llnl.util.filesystem`.
- `copy_tree` copies without setting permissions. It should be used to copy files around in the build directory.
- `install_tree` copies files and sets permissions. It should be used to copy files into the installation directory.
- `install` and `copy` are analogous single-file functions.
- add more extensive tests for these functions
- update packages to use these functions.
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* zoltan: fix building with Intel compilers
- building with the Intel compilers may require explicit linking
with the Intel Fortran library (libifcore)
* simplify code; get rid of format() for static strings
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- dependency patching test didn't attempt to apply patches; just to see
whether they were on the spec.
- it applies the patch now and verifies that that patch was applied.
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* Change bzip2 download URL
* bzip2.org -> bzip.org
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* r-rots: new package
* r-rots: hash is a commit
* r-rots: dep types
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* r-argparse: new package
* r-argparse: dep types
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* r-genelendatabase: new package
* r-genelendatabase: git not url
* r-genelendatabase: add runtime deps and fix package type
* r-genelendatabase: dep type
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* r-glimma: new package
* r-glimma: git not url
* r-glimma: adding runtime deps
* r-glimma: dep types
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* r-ctc: new package
* r-ctc: fixing package directory name
* r-ctc: git not url
* r-ctc: dep types
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* Add smtools 1.9.
* Add hstlib 1.9.
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* Install sam.h and libbam.a for legacy apps.
* Install bam.h.
* Remove which(mkdir).
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* Add package for fasta
Add a package for the fasta sequence alignment tools.
The build system is novel (fasta is "venerable", so...). The source
tree includes nearly 50 variant Makefiles, the installer is expected
to pick one that's appropriate and then edit the "XDIR" variable to
specify the installation path. I can only test 64 bit darwin and
linux, so that's all I've included. I'm also assuming that every
64bit x86 system we'll see supports the SSE2 extensions. Other
situations can be dealt with when someone has a test case.
* Switch to MakefilePackage and clean up a bit
- Clean up the description
- Switch to MakefilePackage
- generalize the path to the chosen Makefile
- implement separate `edit`, `build`, and `install` phases.
* Fix call to format()
* Fix broken if logic
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* r-bindrcpp: add new version
* r-bindrcpp: version ordering and removing r version restriction
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* r-biasedurn: new package
* r-biasedurn: add list_url
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* r-amap: new package
* r-amap: add list_url
* r-amap: dep type
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* r-fastcluster: new package
* r-fastcluster: add list_url
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* packages/phist: new version 1.6.1
* packages/phist: depends on Python 3.x for generating Fortran and C++ bindings
* packages/phist: new version 1.7.2
* phist: depend on python@3 only for versions later than 1.7
* packages/phist: depend on python@3: rather than 3
* phist: python dependency is type='build', thans @adamjstewart
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* Branch with the meson build-system
* Fix build_environment for dual loads and add create code
* Add documentation
* Fixed option list
* Update build_system_guess for meson
* Fixed documentation errors
* Added meson to build and configure and updated documentation
* fix typos
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* perl6-slurp: new package
* perl-perl6-slurp: changing perl version dependency
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- cc cleanup caused a parsing regression in flag handling
- We added proper quoting to array expansions, but flag variables were
never actually converted to arrays. Old code relied on this.
This commit:
- Adds reads to convert flags to arrays.
- Makes the cc test check for improper space handling to prevent future
regressions.
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* libiberty: new package
The libiberty.a library from GNU binutils. Libiberty provides
demangling and support functions for the GNU toolchain.
This package uses the binutils tarfile but only builds the libiberty
subdirectory. This is useful for other packages that want the
demangling functions without the rest of binutils.
Add variant 'fpic' to compile with -fPIC.
Addresses some issues raised in PR #8806.
* libiberty: change variant name to 'pic'.
Allow libiberty to install the library in lib64 and don't try to copy
it to lib.
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