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2017-09-20orthomcl: new package (#5345)Audrey Thoma2-2/+51
Add orthocml package and fix mariadb url
2017-09-20tmhmm: new package (#5335)Audrey Thoma1-0/+56
2017-09-20bbmap: new package (#5396)Audrey Thoma1-0/+39
2017-09-19targetp: new package (#5334)Audrey Thoma1-0/+67
2017-09-19added p7zip package (#5394)sknigh1-0/+41
2017-09-19pr-quantities: add version & py-numpy conflict (#5307)healther1-2/+6
2017-09-19Modulefiles generated with a template engine (#3183)Massimiliano Culpo4-2/+85
* Module files now are generated using a template engine refers #2902 #3173 jinja2 has been hooked into Spack. The python module `modules.py` has been splitted into several modules under the python package `spack/modules`. Unit tests stressing module file generation have been refactored accordingly. The module file generator for Lmod has been extended to multi-providers and deeper hierarchies. * Improved the support for templates in module files. Added an entry in `config.yaml` (`template_dirs`) to list all the directories where Spack could find templates for `jinja2`. Module file generators have a simple override mechanism to override template selection ('modules.yaml' beats 'package.py' beats 'default'). * Added jinja2 and MarkupSafe to vendored packages. * Spec.concretize() sets mutual spec-package references The correct place to set the mutual references between spec and package objects at the end of concretization. After a call to concretize we should now be ensured that spec is the same object as spec.package.spec. Code in `build_environment.py` that was performing the same operation has been turned into an assertion to be defensive on the new behavior. * Improved code and data layout for modules and related tests. Common fixtures related to module file generation have been extracted in `conftest.py`. All the mock configurations for module files have been extracted from python code and have been put into their own yaml file. Added a `context_property` decorator for the template engine, to make it easy to define dictionaries out of properties. The default for `verbose` in `modules.yaml` is now False instead of True. * Extendable module file contexts + short description from docstring The contexts that are used in conjunction with `jinja2` templates to generate module files can now be extended from package.py and modules.yaml. Module files generators now infer the short description from package.py docstring (and as you may expect it's the first paragraph) * 'module refresh' regenerates all modules by default `module refresh` without `--module-type` specified tries to regenerate all known module types. The same holds true for `module rm` Configure options used at build time are extracted and written into the module files where possible. * Fixed python3 compatibility, tests for Lmod and Tcl. Added test for exceptional paths of execution when generating Lmod module files. Fixed a few compatibility issues with python3. Fixed a bug in Tcl with naming_scheme and autoload + unit tests * Updated module file tutorial docs. Fixed a few typos in docstrings. The reference section for module files has been reorganized. The idea is to have only three topics at the highest level: - shell support + spack load/unload use/unuse - module file generation (a.k.a. APIs + modules.yaml) - module file maintenance (spack module refresh/rm) Module file generation will cover the entries in modules.yaml Also: - Licenses have been updated to include NOTICE and extended to 2017 - docstrings have been reformatted according to Google style * Removed redundant arguments to RPackage and WafPackage. All the callbacks in `RPackage` and `WafPackage` that are not build phases have been modified not to accept a `spec` and a `prefix` argument. This permits to leverage the common `configure_args` signature to insert by default the configuration arguments into the generated module files. I think it's preferable to handling those packages differently than `AutotoolsPackage`. Besides only one package seems to override one of these methods. * Fixed broken indentation + improved resiliency of refresh Fixed broken indentation in `spack module refresh` (probably a rebase gone silently wrong?). Filter the writers for blacklisted specs before searching for name clashes. An error with a single writer will not stop regeneration, but instead will print a warning and continue the command.
2017-09-19adios: fixed conditional dependencies on libevpath and dataspaces (#5392)Massimiliano Culpo1-5/+3
fixes #5379
2017-09-18added python version 2.7.14 and 3.6.2 packages (#5389)Gregory Lee1-1/+3
2017-09-18HDF5: Fortran MPI needs Numactl (#5372)Axel Huebl1-0/+1
2017-09-18add variant gmock to googletest (#5278)healther1-1/+8
2017-09-18latte: fix url and add shared variant (#5358)Christoph Junghans1-4/+20
2017-09-18qmd-progress: add shared variant (#5381)Christoph Junghans1-0/+5
2017-09-18bml: add shared variant (#5380)Christoph Junghans1-0/+8
2017-09-18lammps: fix checksum (#5342)Christoph Junghans1-3/+7
2017-09-18Improve scorep package with different compilers and mpi providers (#5386)Pramod S Kumbhar1-3/+17
* Add --with-mpi=spec['mpi'].name at configure step to avoid error when finding 2 MPI implementations * Improve scorep package with different compilers and mpi providers
2017-09-18mesa: merge multiple branches into one (#5170)Milton Woods1-34/+102
Merge work from multiple contributors on the mesa package. This includes the following changes and decisions: * Added in mesa +hwrender support * make +swrender the default selection since this represents a very common usage case (ie, cluster usage) * leave ~llvm as the default, since inadvertently building this package could take a very long time. May need to revisit this assumption in the future since the performance difference can be quite substantial. * build libGLESv1+2 and libGL for all variants * avoid dependence on dri/libdrm when ~hwrender * disable gallium drivers if none are requested
2017-09-17Fix log error parsing bug introduced in c830eda0e (#5387)Todd Gamblin1-0/+49
- '\b' in regular expression needs to be in a raw string (r'\b') - Regression test that would've caught this was unintentionally disabled - This fixes the string and the test
2017-09-17tbb: add 2018 (#5359)Denis Davydov1-1/+2
2017-09-16Open MPI: add Open MPI 3.0.0 (#5360)Howard Pritchard1-1/+2
Open MPI 3.0.0 is released! Add to spack. Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-09-16trilinos: update md5 for 12.10.1 (#5362)Denis Davydov1-1/+1
2017-09-16New Pcakage: numactl (#5371)Axel Huebl1-0/+39
Adds the numactl tools and libnuma.
2017-09-16Feature/methycode (#5374)ynanyam3-0/+123
* methylcode: added package * pyfasta: added package * py-bsddb3: added package * py-bsddb3: added package * Update package.py * Update package.py * Update package.py * removed fixme comments * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
2017-09-16Cntk: fixed dependency on protobuf fixes #5266 (#5267)Pramod S Kumbhar1-1/+1
As protobuf has been converted to CMakePackage, it doesn't have a 'shared' variant anymore.
2017-09-16augustus: url fix (#5311)Audrey Thoma1-2/+3
2017-09-16add Intel 2018 libraries (#5354)Denis Davydov4-0/+8
2017-09-16Bioawk: added new package (#5375)zenln1-0/+51
2017-09-16gromacs: added 2016.4 (#5376)Christoph Junghans1-0/+1
2017-09-15Update hpctoolkit and externals to latest releasePramod S Kumbhar2-8/+8
2017-09-15add new version to package py-pybind11healther1-0/+1
2017-09-15ncl: Fix buffer overflow in ymake-filter (#5357)Michael Kuhn2-0/+35
Fixes a problem in ymake-filter: The line buffer is currently hardcoded to be 2048 bytes large but some Makefiles contain lines longer than that. This caused the Makefiles to sometimes not be generated, consequently failing parts of the build.
2017-09-14Fix checksum of Intel TBB package (#5349)Pramod S Kumbhar1-1/+1
2017-09-14Added Support for NOX Package to Trilinos Spackage (#5366)Robert Pavel1-0/+4
Added support for building NOX package to Trilinis Spackage
2017-09-14ADIOS: Fix Build (Autotools) (#5363)Axel Huebl1-11/+23
This fixes the build of the ADIOS package. The `with_or_without` interface of the Autotools builds seems to have changed, this fixes it.
2017-09-14libsodium: update URLs (#5355)Axel Huebl1-1/+5
* libsodium: update URLs updates the URLs for libsodium releases. Fixes broken builds (404). * libsodium: add new version
2017-09-13Added missing dependencies to nauty package (#5348)Louis Vernon1-0/+2
* Added missing help2man dependency to nauty * Add type=build * Added gmp dependency to nauty package
2017-09-13Boost: 1.65.1 (#5330)Axel Huebl1-0/+2
Add sha of the latest boost bugfix release. http://www.boost.org/users/history/version_1_65_1.html Besides other fixed issues, it adds compatebility for the upcoming CUDA 9 release.
2017-09-12openblas: add ilp64 option (#5289)Denis Davydov1-0/+5
2017-09-11Update libbson and libmongoc to 1.7.0 (#5294)Michael Kuhn2-2/+29
This also introduces the ssl, snappy and zlib variants for libmongoc.
2017-09-11parsplice: initial commit (#5314)Christoph Junghans1-0/+48
2017-09-11dealii: explicitly specify bzip2 libs (#5337)Denis Davydov2-1/+12
* dealii: explicitly specify bzip2 libs * bzip2: add libs() property
2017-09-11'with_or_without' accepts bool variantsMassimiliano Culpo3-73/+51
Fixes #4112 This commit extends the support of the AutotoolsPackage methods `with_or_without` and `enable_or_disable` to bool-valued variants. It also defines for those functions a convenience short-cut if the activation parameter is the prefix of a spec (like in `--with-{pkg}={prefix}`). This commit also includes: * Updates to viennarna and adios accordingly: they have been modified to use `enable_or_disable` and `with_or_without` * Improved docstrings in `autotools.py`. Raise `KeyError` if name is not a variant.
2017-09-11added votca-1.4.1 modules (#5276)Christoph Junghans3-0/+5
2017-09-11elemental: fix broken Config.cmake (#5331)Denis Davydov2-0/+23
2017-09-11berkeley-db: initial commit (#5303)Christoph Junghans1-0/+47
* berkeley-db: initial commit * berkeley-db: added more versions
2017-09-11Added 'ldc' compiler for D language based on LLVM (#5279)Massimiliano Culpo2-0/+150
2017-09-10fix armadillo macro expansions (#5268)Stephen McDowell2-1/+14
* fix armadillo macro expansions - most compilers `#define linux 1` - armadillo does raw pasting of include directories in code - this means macro expansion of `linux-x86_64` -> `1-x86_64` - new version, previous download url seems broken - lib64 instead of lib? - needs verification, was required for intel, works for others * flake8: two spaces is modules, one for classes * add some explanation of how the patch works * use p1 patch file with -U0 to prepend undef linux * armadillo v8.100.1
2017-09-10Missing opencv dependencies (#5285)Eloy Gil1-1/+1
There are some opencv dependencies missing such as "core" that are mandatory in order to complete the caffe build.
2017-09-10add package py-line-profiler (#5291)healther1-0/+39
2017-09-10Change glog from Autotools to CMakePackage (#5323)Pramod S Kumbhar1-1/+4