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2019-11-30Armor test script against shebang character limit if appropriate. (#12447)Chris Green1-0/+2
2019-11-29Mass conversion of setup_(dependent_)?environment (#13924)Adam J. Stewart3-10/+10
* Mass conversion of setup_(dependent_)?environment * prefix -> self.prefix
2019-11-26use semicolons instead of newlines in module/python command (#13904)Greg Becker1-1/+1
2019-11-26IntelPackage: setup_env -> setup_build_env (#13888)Adam J. Stewart1-47/+24
2019-11-26buildcache list: do not display duplicate specs (#13758)Massimiliano Culpo2-6/+25
fixes #13757
2019-11-26Remove warning from the "Custom Extensions" section of the docs (#13804)Massimiliano Culpo1-6/+0
Extensions have been available for a while and the overall design seems solid enough to be feasible for extensions without losing backward compatibility.
2019-11-25add package cuda@10.2.89 (#13819)René Widera1-3/+10
* add package cuda@10.2.89 add CUDA 10.2 support * CudaPackage: Add 10.2 Conflicts * CUDA: Modernize Run Environment See #11115
2019-11-22cmd/install: remove unused install_status option (#13751)Greg Becker1-1/+1
* cmd/install: remove unused install_status option * update bash completions for spack install
2019-11-21Fixed detection for cascadelake microarchitecture (#13820)Massimiliano Culpo3-1/+23
fixes #13803
2019-11-20mirror bug fixes: symlinks, duplicate patch names, and exception handling ↵Paul Ferrell4-17/+24
(#13789) * Some packages (e.g. mpfr at the time of this patch) can have patches with the same name but different contents (which apply to different versions of the package). This appends part of the patch hash to the cache file name to avoid conflicts. * Some exceptions which occur during fetching are not a subclass of SpackError and therefore do not have a 'message' attribute. This updates the logic for mirroring a single spec (add_single_spec) to produce an appropriate error message in that case (where before it failed with an AttributeError) * In various circumstances, a mirror can contain the universal storage path but not a cosmetic symlink; in this case it would not generate a symlink. Now "spack mirror create" will create a symlink for any package that doesn't have one.
2019-11-20Features/expand microarch for aarch64 (#13780)t-karatsu4-0/+117
* Add process to determine aarch64 microarchitecture * add microarchitectures for thunderx2 and a64fx * Add optimize flags for gcc on aarch64 family processors thunderx2 and a64fx. * Add optimize flags for clang on aarch64 family processors thunderx2 and a64fx * Add testing for thunderx2 and a64fx microarchitectures
2019-11-18binary distribution: relocate text files properly in relative binaries (#13578)Greg Becker2-10/+12
* Make relative binaries relocate text files properly * rb strings aren't valid in python 2 * move perl to new interface for setup_environment family methods
2019-11-15Fix for issue #13754 (#13755)Tim Fuller1-2/+3
* remove reference to `spack.store` in method definition Referencing `spack.store` in method definition will cache the `spack.config.config` singleton variable too early, before we have a chance to add command line and environment scopes.
2019-11-15Document use of the maintainers field (#12270)Adam J. Stewart2-1/+20
* Document use of the maintainers field * Use fake GitHub usernames * GitHub action is not automatic yet
2019-11-14Config option to allow gpg warning suppression (#13743)Greg Becker3-3/+9
Add a configuration option to suppress gpg warnings during binary package verification. This only suppresses warnings: a gpg failure will still fail the install. This allows users who have already explicitly trusted the gpg key they are using to avoid seeing repeated warnings that it is self-signed.
2019-11-13symlink relativization: determine target relative to the link directory (#13710)Peter Scheibel1-3/+3
when making a package relative, relocate links relative to link directory rather than the full link path (which includes the file name) because `os.path.relpath` expects a directory.
2019-11-13Allow binary relocation of strings in relative binaries (#13725)Greg Becker2-15/+25
Binaries with relative RPATHS currently do not relocate strings hard-coded in binaries This PR extends the best-effort relocation of strings hard-coded in binaries to those whose RPATHs have been relativized.
2019-11-13Docs update for deprecated `spack sha256` (#13701)William F Godoy1-2/+2
* Docs update for deprecated `spack sha256` * Added macOS shasum * Update lib/spack/docs/packaging_guide.rst Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com>
2019-11-12docs: use nicer looking code blocks in docs (#13708)Todd Gamblin1-1/+19
- [x] Use higher contrast terminal output font - [x] Use higher contrast code block background color than default - [x] Use a noticeable prompt character See also https://github.com/spack/spack-tutorial/pull/10.
2019-11-11verify.py: os.path.exists exception handling (#13656)Daryl W. Grunau1-14/+16
2019-11-11environments: don't try to modify run-env if a spec is not installed (#13589)Adam J. Stewart1-2/+2
Fixes #13529 Fixes #13509
2019-11-10Improve spack checksum formatting (#13666)Adam J. Stewart2-2/+5
* Improve spack checksum formatting * Add colon * Fix Python 2 bug
2019-11-07bugfix: mirror path works for unknown versions (#13626)Todd Gamblin2-2/+8
`mirror_archive_path` was failing to account for the case where the fetched version isn't known to Spack. - [x] don't require the fetched version to be in `Package.versions` - [x] add regression test for mirror paths when package does not have a version
2019-11-05add depends_on(python) to PythonPackage stub (#13595)Andreas Baumbach1-0/+1
2019-11-05bugfix: uninstall should find concrete specs by DAG hash (#13598)Todd Gamblin1-1/+9
This fixes a regression introduced in #10792. `spack uninstall` in an environment would not match concrete query specs properly after the index hash of enviroments changed. - [x] Search by DAG hash for specs to remove instead of by build hash
2019-11-05`spack find` now displays variants and other spec constraints (#13596)Todd Gamblin3-4/+23
If you do this in a spack environment: spack add hdf5+hl hdf5+hl will be the root added to the `spack.yaml` file, and you should really expect `hdf5+hl` to display as a root in the environment. - [x] Add decoration to roots so that you can see the details about what is required to build. - [x] Add a test.
2019-11-03bugfix: fetch prefers to fetch local mirrors over remote resources (#13545)Omar Padron3-8/+11
- [x] insert at beginning of list so fetch grabs local mirrors before remote resources - [x] update the S3FetchStrategy so that it throws a SpackError if the fetch fails. Before, it was throwing URLError, which was not being caught in stage.py. - [x] move error handling out of S3FetchStrategy and into web_util.read_from_url() - [x] pass string instead of URLError to SpackWebError
2019-11-03environments: only write when necessary (#13546)Greg Becker4-25/+66
This changes Spack environments so that the YAML file associated with the environment is *only* written when necessary (i.e., if it is changed *by spack*). The lockfile is still written out as before. There is a larger question here of which part of Spack should be responsible for setting defaults in config files, and how we can get rid of empty lists and data structures currently cluttering files like `compilers.yaml`. But that probably requires a rework of the default-setting validator in `spack.config`, as well as the code that uses `spack.config`. This will at least help for `spack.yaml`.
2019-11-01spack create: http -> https (#13547)Adam J. Stewart1-2/+2
2019-11-01Bugfix: respect order of mirrors in mirrors.yaml (#13544)Peter Scheibel1-1/+4
Commands like "spack mirror list" were displaying mirrors in a different order than what was listed in the corresponding mirrors.yaml file. This restores commands to iterate over mirrors in the order that they appear in the config file.
2019-11-01environments: make shell modifications partially unconditional (#13523)Greg Becker2-1/+37
* environments: make shell modifications partially unconditional * flake * missing module name * add regression test * flake
2019-11-01allow bootstrap buildcache install of patchelf (#13430)Marc Mengel2-3/+36
* allow bootstrap buildcache install of patchelf * file not path_name on one * style * add test for relocating patchelf * blank lines..
2019-11-01bugfix: spack.util.url.join() now handles absolute paths correctly (#13488)Omar Padron3-2/+379
* fix issue where spack.util.url.join() failed to correctly handle absolute path components * add url util tests
2019-11-01sbang: use utf-8 for encoding when patching (#13490)Gregory Lee1-4/+13
This fixes a UnicodeDecodeError in the sbang patching function.
2019-11-01Specs with quoted flags containing spaces are parsed correctly (#13521)Massimiliano Culpo2-1/+22
2019-11-01targets: print a warning message before downgrading (#13513)Massimiliano Culpo2-25/+57
* Make package preferences a soft failure for targets, instead of a hard failure. * Added unit tests for preferences expressed via packages.yaml
2019-10-31Bugfix: BundlePackage staging/installation (#13524)Peter Scheibel1-0/+3
4af4487 added a mirror_id function to most FetchStrategy implementations that is used to calculate resource locations in mirrors. It left out BundleFetchStrategy which broke all packages making use of BundlePackage (e.g. xsdk). This adds a noop implementation of mirror_id to BundleFetchStrategy so that the download/installation of BundlePackages can proceed as normal.
2019-10-31Docs: unlock requirement versions (#13384)Adam J. Stewart1-3/+3
2019-10-31Travis CI: Test Python 3.8 (#13347)Adam J. Stewart3-4/+20
* Travis CI: Test Python 3.8 * Fix use of deprecated cgi.escape method * Fix version comparison * Fix flake8 F811 change in Python 3.8 * Make flake8 happy * Use Python 3.8 for all test categories
2019-10-30Documentation: Database.query methods share docstrings (#13515)Greg Becker1-41/+53
Currently, query arguments in the Spack core are documented on the Database._query method, where the functionality is defined. For users of the spack python command, this makes the python builtin method help less than ideally useful, as help(spack.store.db.query) and help(spack.store.db.query_local) do not show relevant information. This PR updates the doc attributes for the Database.query and Database.query_local arguments to mirror everything after the first line of the Database._query docstring.
2019-10-30cpu: fix clang flags for generic x86_64 (#13491)Greg Becker2-8/+16
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-10-30cuda: fix conflict statements for x86-64 targets (#13472)Massimiliano Culpo1-4/+6
* cuda: fix conflict statements for x86-64 targets fixes #13462 This build system mixin was not updated after the support for specific targets has been merged. * Updated the version range of cuda that conflicts with gcc@8: * Updated the version range of cuda that conflicts with gcc@8: for ppc64le * Relaxed conflicts for version > 10.1 * Updated versions in conflicts Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>
2019-10-29syaml_int type should use int.__repr__ rather than str.__repr__ (#13487)Peter Scheibel1-1/+1
2019-10-29bugfix: make `spack -d test test_changed_files` work (#13229)Tamara Dahlgren1-1/+1
The `test_changed_files` in `test/cmd/flake8.py` was failing because it calls `ArgumentParser.parse_args()` without arguments. Normally that would just parse `sys.argv` but it seems to fail because of something in either `spack test` or `pytest`. Call it with an empty array so that it doesn't try to touch`sys.argv` at all. - [x] allow `-d` spack option for `test_changed_files`
2019-10-28Update URL parsing regexes and tests (#13411)Adam J. Stewart4-65/+192
* Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
2019-10-28Output directory Spack is looking in for MKL libs (#13465)Adam J. Stewart1-1/+2
2019-10-25version bump: 0.13.0Todd Gamblin1-1/+1
2019-10-25tutorial: move tutorial to standalone site (#13450)Todd Gamblin31-7565/+28
* docs: add a spack environment for building the docs * docs: remove tutorial and link to spack-tutorial.readthedocs.io The tutorial now has its own standalone website, versioned by instances of the tutorial. Link to that instead of versioning it directly with Spack.
2019-10-25`mirror create --all` can mirror everything (#12940)Peter Scheibel11-228/+465
Support mirroring all packages with `spack mirror create --all`. In this mode there is no concretization: * Spack pulls every version of every package into the created mirror. * It also makes multiple attempts for each package/version combination (if there is a temporary connection failure). * Continues if all attempts fail. i.e., this makes its best effort to fetch evrerything, even if all attempts to fetch one package fail. This also changes mirroring logic to prefer storing sources by their hash or by a unique name derived from the source. For example: * Archives with checksums are named by the sha256 sum, i.e., `archive/f6/f6cf3bd233f9ea6147b21c7c02cac24e5363570ce4fd6be11dab9f499ed6a7d8.tar.gz` vs the previous `<package-name>-package-version>.tar.gz` * VCS repositories are stored by a path derived from their URL, e.g. `git/google/leveldb.git/master.tar.gz`. The new mirror layout allows different packages to refer to the same resource or source without duplicating that download in the mirror/cache. This change is not essential to mirroring everything but is expected to save space when mirroring packages that all use the same resource. The new structure of the mirror is: ``` <base directory>/ _source-cache/ <-- the _source-cache directory is new archive/ <-- archives/resources/patches stored by hash 00/ <-- 2-letter sha256 prefix 002748bdd0319d5ab82606cf92dc210fc1c05d0607a2e1d5538f60512b029056.tar.gz 01/ 0154c25c45b5506b6d618ca8e18d0ef093dac47946ac0df464fb21e77b504118.tar.gz 0173a74a515211997a3117a47e7b9ea43594a04b865b69da5a71c0886fa829ea.tar.gz ... git/ OpenFAST/ openfast.git/ master.tar.gz <-- repo by branch name PHASTA/ phasta.git/ 11f431f2d1a53a529dab4b0f079ab8aab7ca1109.tar.gz <-- repo by commit ... svn/ <-- each fetch strategy has its own subdirectory ... openmpi/ <-- the remaining package directories have the old format openmpi-1.10.1.tar.gz <-- human-readable name is symlink to _source-cache ``` In addition to the archive names as described above, `mirror create` now also creates symlinks with the old format to help users understand which package each mirrored archive is associated with, and to allow mirrors to work with old spack versions. The symlinks are relative so the mirror directory can still itself be archived. Other improvements: * `spack mirror create` will not re-download resources that have already been placed in it. * When creating a mirror, the resources downloaded to the mirror will not be cached (things are not stored twice).
2019-10-25bugfix: restore upstream lock safety; update testsPeter Scheibel2-19/+48
Restore upstream lock safety; avoid calling methods directly on upstream DB in test.