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2017-10-04extensions: create install prefixes (#5601)Ben Boeckel3-3/+3
Tests fail locally because the install prefix doesn't exist. Make them exist.
2017-10-04Hotfix: maintain patch order while fixing hashMassimiliano Culpo2-23/+29
fixes #5587 In trying to preserve patch ordering, #5476 made equality inconsistent for the added 'patches' variant. This commit maintains the original weak ordering of patch applications while preserving consistency of comparisons. The ordering DOES NOT enter the hashing mechanism. It's supposed to be a hotfix, while we think of a cleaner and more-permanent solution.
2017-10-04r-tibble: added dependency r-rlang (#5536)Yifan Zhu1-1/+2
* pr-quantities: add version & py-numpy conflict (#5307) * r-tibble: Update version to 1.3.4 * r-tibble: added dependency r-rlang * r-tibble: changed r-lazyeval and r-rlang to be versioned dependencies * Update package.py * Update package.py
2017-10-04tassel: new package (#5583)Audrey Thoma1-0/+45
2017-10-04xerces-c: Fix url (#5597)Michael Kuhn1-1/+1
The main location only carries the latest release, while all previous (and current) ones are available at the archive location.
2017-10-04OpenSSL: Fix Zlib (#5584)Axel Huebl1-0/+2
Fix missing `-lz` on `make` of OpenSSL. Spotted on a system without a system-wide zlib installation.
2017-10-03wrap generator with collection to avoid exhausting it with single iteration ↵scheibelp1-3/+3
(#5586)
2017-10-03r-edger: created new package (#5571)Yifan Zhu1-0/+44
2017-10-03Add package for multitail@6.4.2 (#5567)George Hartzell1-0/+62
* Add package for multitail@6.4.2 Lightly tested on CentOS 7. * Responde to feedback/comments Use `install_targets` to specify PREFIX= and DESTDIR= instead of hacking away at the Makefile. Expand commentary about "Why?". Use `headers.include_flags` and `libs.ld_flags` to avoid explicitly setting `-L` and `-I` when hacking away at the Makefile.
2017-10-03ExaSP2 Spackage (#5570)Robert Pavel1-0/+94
* Added exasp2 spackage Added spackage for exasp2 proxy app * Fixed MPI in ExaSP2 Explicitly disabled MPI when not enabled. Set MPI variant to default as per Spack standards * Generalized BML Passing for ExaSP2 * Modified to follow spack rules on blas Fortunately was able to modify exasp2 build system to support spack model for blas and lapack requirements. No guarantee is made for support of anything other than originally supported libraries * Fixed flake8 error
2017-10-03r-a4base: new package. (#5576)lingnanyuan1-0/+46
2017-10-03r-a4: new package. (#5577)lingnanyuan1-0/+40
2017-10-03fastqvalidator: new package (#5573)Audrey Thoma1-0/+56
* fastqvalidator: new package * adding version-specificity to compiler conflict * quick changes to env vars and build phase * Update package.py * oops. forgot to install executable * Update package.py * updating package.py * turn env into targets
2017-10-03libpng: zlib path (#5581)Axel Huebl1-0/+10
explicitly set the zlib path for libpng configure. fixes: ``` [ ... ] 92 checking for memset... yes 93 checking for pow... no 94 checking for pow in -lm... yes 95 checking for clock_gettime... yes 96 checking for zlibVersion in -lz... no 97 checking for z_zlibVersion in -lz... no >> 98 configure: error: zlib not installed ```
2017-10-03sra-toolkit: new package (#5588)Audrey Thoma1-0/+45
* sra-toolkit: new package * adding description and homepage
2017-10-03Tell configure about gmp (#5585)George Hartzell1-0/+6
This is a partial fix for #5564. This package used to trust that `configure` would discover `gmp` from its environment. It's safer to tell it where to find `gmp` explicitly. This does that by adding a configure_args() that provides a `--with-gmp=...` argument for configure.
2017-10-02patch: add workdir option (#5501)Christoph Junghans3-11/+46
* patch: add working_dir option * added documentation
2017-10-02mrtrix3: new package (#5568)Audrey Thoma1-0/+62
* mrtrix3: new package * specifying conflict dependency ve
2017-10-02r-a4reporting: new package. (#5575)lingnanyuan1-0/+37
2017-10-02r-locfit: created new package (#5572)Yifan Zhu1-0/+37
2017-10-02Added support for BML+mpi variant (#5563)Robert Pavel1-1/+14
* Added support for BML+mpi variant Added support for BML+mpi variant. Currently restricted to master (develop) branch pending release of next bml tag * Update package.py Removing redundant statement * Update package.py Added explicit disabling of MPI when not requested
2017-10-02Added Spackage for YAJL (#5566)Robert Pavel1-0/+35
Added spackage for YAJL
2017-10-02linkphase3: new package (#5493)Audrey Thoma1-0/+41
* linkphase3: new package * adding ifort option * Update package.py
2017-10-02hisat2: new package (#5488)Audrey Thoma1-0/+63
2017-10-02CUDA 9.0.176 (#5562)Axel Huebl1-0/+2
The first stable release of CUDA 9, v9.0.176, is out. This adds its installer and checksum.
2017-09-30Port CTest's log scraping logic to Spack (#5561)Todd Gamblin4-62/+387
- This steals the magic regular expressions that CTest uses to parse log files and addds them to Spack. See here: https://github.com/Kitware/CMake/blob/master/Source/CTest/cmCTestBuildHandler.cxx These are BSD licensed, so the port is in `externa/ctest_log_parser.py` - We currently use these to do better filtering of errors from build output. Plan is to use them to generate good CDash output.
2017-09-30Add testing for spack blame; refactor llnl.util testsTodd Gamblin7-23/+106
2017-09-30Add 'spack blame' command: shows contributors to packagesTodd Gamblin6-25/+280
`spack blame` prints out the contributors to a package. By modification time: ``` $ spack blame --time llvm LAST_COMMIT LINES % AUTHOR EMAIL 3 days ago 2 0.6 Andrey Prokopenko <andrey.prok@gmail.com> 3 weeks ago 125 34.7 Massimiliano Culpo <massimiliano.culpo@epfl.ch> 3 weeks ago 3 0.8 Peter Scheibel <scheibel1@llnl.gov> 2 months ago 21 5.8 Adam J. Stewart <ajstewart426@gmail.com> 2 months ago 1 0.3 Gregory Becker <becker33@llnl.gov> 3 months ago 116 32.2 Todd Gamblin <tgamblin@llnl.gov> 5 months ago 2 0.6 Jimmy Tang <jcftang@gmail.com> 5 months ago 6 1.7 Jean-Paul Pelteret <jppelteret@gmail.com> 7 months ago 65 18.1 Tom Scogland <tscogland@llnl.gov> 11 months ago 13 3.6 Kelly (KT) Thompson <kgt@lanl.gov> a year ago 1 0.3 Scott Pakin <pakin@lanl.gov> a year ago 3 0.8 Erik Schnetter <schnetter@gmail.com> 3 years ago 2 0.6 David Beckingsale <davidbeckingsale@gmail.com> 3 days ago 360 100.0 ``` Or by percent contribution: ``` $ spack blame --percent llvm LAST_COMMIT LINES % AUTHOR EMAIL 3 weeks ago 125 34.7 Massimiliano Culpo <massimiliano.culpo@epfl.ch> 3 months ago 116 32.2 Todd Gamblin <tgamblin@llnl.gov> 7 months ago 65 18.1 Tom Scogland <tscogland@llnl.gov> 2 months ago 21 5.8 Adam J. Stewart <ajstewart426@gmail.com> 11 months ago 13 3.6 Kelly (KT) Thompson <kgt@lanl.gov> 5 months ago 6 1.7 Jean-Paul Pelteret <jppelteret@gmail.com> 3 weeks ago 3 0.8 Peter Scheibel <scheibel1@llnl.gov> a year ago 3 0.8 Erik Schnetter <schnetter@gmail.com> 3 years ago 2 0.6 David Beckingsale <davidbeckingsale@gmail.com> 3 days ago 2 0.6 Andrey Prokopenko <andrey.prok@gmail.com> 5 months ago 2 0.6 Jimmy Tang <jcftang@gmail.com> 2 months ago 1 0.3 Gregory Becker <becker33@llnl.gov> a year ago 1 0.3 Scott Pakin <pakin@lanl.gov> 3 days ago 360 100.0 ```
2017-09-30Typo: file -> directory (#5560)George Hartzell1-1/+1
Mirrors are directories (that use `file://` URLS, not files.
2017-09-30Documentation for dependency patching.Todd Gamblin3-23/+189
2017-09-30Patches are hashed with specs, and can be associated with dependencies.Todd Gamblin26-197/+754
- A package can depend on a special patched version of its dependencies. - The `Spec` YAML (and therefore the hash) now includes the sha256 of the patch in the `Spec` YAML, which changes its hash. - The special patched version will be built separately from a "vanilla" version of the same package. - This allows packages to maintain patches on their dependencies without affecting either the dependency package or its dependents. This could previously be accomplished with special variants, but having to add variants means the hash of the dependency changes frequently when it really doesn't need to. This commit allows the hash to change *just* for dependencies that need patches. - Patching dependencies shouldn't be the common case, but some packages (qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it makes the code structure mirror maintenance responsibilities. - Note that this commit means that adding or changing a patch on a package will change its hash. This is probably what *should* happen, but we haven't done it so far. - Only applies to `patch()` directives; `package.py` files (and their `patch()` functions) are not hashed, but we'd like to do that in the future. - The interface looks like this: `depends_on()` can optionally take a patch directive or a list of them: depends_on(<spec>, patches=patch(..., when=<cond>), when=<cond>) # or depends_on(<spec>, patches=[patch(..., when=<cond>), patch(..., when=<cond>)], when=<cond>) - Previously, the `patch()` directive only took an `md5` parameter. Now it only takes a `sha256` parameter. We restrict this because we want to be consistent about which hash is used in the `Spec`. - A side effect of hashing patches is that *compressed* patches fetched from URLs now need *two* checksums: one for the downloaded archive and one for the content of the patch itself. Patches fetched uncompressed only need a checksum for the patch. Rationale: - we include the content of the *patch* in the spec hash, as that is the checksum we can do consistently for patches included in Spack's source and patches fetched remotely, both compressed and uncompressed. - we *still* need the patch of the downloaded archive, because we want to verify the download *before* handing it off to tar, unzip, or another decompressor. Not doing so is a security risk and leaves users exposed to any arbitrary code execution vulnerabilities in compression tools.
2017-09-30add spack flake8 exception for long checksumsTodd Gamblin1-2/+2
2017-09-30Clean up exceptions and function names in directives.Todd Gamblin1-41/+23
- Functions returned by directives were all called `_execute`, which made reading stack traces hard because you couldn't tell what directive a frame came from. - renamed them all to `_execute_<directive>` - Exceptions in directives were only really used in one or two places -- get rid of the boilerplate init functions and let the callsite specify the message.
2017-09-30Consolidate some web-spidering commands in spack.util.webTodd Gamblin6-116/+118
- move `spack.cmd.checksum.get_checksums` to `spack.util.web.spider_checksums` - move `spack.error.NoNetworkError` to `spack.util.web.NoNetworkError` since it is only used there.
2017-09-30Disable duplicate cross-reference warnings in Sphinx.Todd Gamblin1-0/+14
2017-09-30Refactor Package dependency metadataTodd Gamblin14-123/+217
- Previously, dependencies and dependency_types were stored as separate dicts on Package. - This means a package can only depend on another in one specific way, which is usually but not always true. - Prior code unioned dependency types statically across dependencies on the same package. - New code stores dependency relationships as their own object, with a spec constraint and a set of dependency types per relationship. - Dependency types are now more precise - There is now room to add more information to dependency relationships. - New Dependency class lives in dependency.py, along with deptype definitions that used to live in spack.spec. Move deptype definitions to spack.dependency
2017-09-30Patch.apply() shouldn't affect working directory of caller.Todd Gamblin1-11/+12
2017-09-30Only print "no patches needed" if there were no patches.Todd Gamblin1-1/+5
2017-09-29Add test deptype (#5132)scheibelp10-13/+182
* Add '--test=all' and '--test=root' options to test either the root or the root and all dependencies. * add a test dependency type that is only used when --test is enabled. * test dependencies are not added to the spec, but they are provided in the test environment.
2017-09-29r-limma: added version 3.32.7 (#5558)Yifan Zhu1-0/+2
2017-09-29Masa requires python if +python. (#5547)Jon Rood1-0/+1
2017-09-29r-a4classif: new package. (#5557)lingnanyuan1-0/+43
2017-09-29r-yaml: Correct url (#5550)lingnanyuan1-1/+1
* pr-quantities: add version & py-numpy conflict (#5307) * r-yaml: Correct url.
2017-09-29r-downloader: created new package (#5556)Yifan Zhu1-0/+42
2017-09-29r-mlinterfaces: new package. (#5555)lingnanyuan1-0/+51
* pr-quantities: add version & py-numpy conflict (#5307) * r-mlinterfaces: Create new package.
2017-09-29r-biomart: created new package (#5554)Yifan Zhu1-0/+49
2017-09-29r-threejs: Correct url. (#5553)lingnanyuan1-1/+1
* pr-quantities: add version & py-numpy conflict (#5307) * r-threejs: Correct url.
2017-09-29Adding new Trilinos version and updating Nalu to utilize it. (#5552)Jon Rood2-3/+6
2017-09-29r-hwriter: new package. (#5549)lingnanyuan1-0/+35
* pr-quantities: add version & py-numpy conflict (#5307) * r-hwriter: Create new package.
2017-09-29r-gbm: new package. (#5548)lingnanyuan1-0/+37
* pr-quantities: add version & py-numpy conflict (#5307) * r-gbm: Create new package.
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