summaryrefslogtreecommitdiff
AgeCommit message (Collapse)AuthorFilesLines
2019-12-04Bugfix: allow missing modules if they are blacklisted (#13540)Peter Scheibel4-30/+115
`spack module loads` and `spack module find` previously failed if any upstream modules were missing. This prevented it from being used with upstreams (or, really, any spack instance) that blacklisted modules. This PR makes module finding is now more lenient (especially for blacklisted modules). - `spack module find` now does not report an error if the spec is blacklisted - instead, it prints a single warning if any modules will be omitted from the loads file - It comments the missing modules out of the loads file so the user can see what's missing - Debug messages are also printed so users can check this with `spack -d...` - also added tests for new functionality
2019-12-02Speedup environment activation (#13557)Massimiliano Culpo3-4/+21
* Add a transaction around repeated calls to `spec.prefix` in the activation process * cache the computation of home in the python package to speed up setting deps * ensure that module-scope variables are only set *once* per module
2019-12-01bugfix: 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
2019-12-01environments: don't try to modify run-env if a spec is not installed (#13589)Adam J. Stewart1-2/+2
Fixes #13529 Fixes #13509
2019-12-01use semicolons instead of newlines in module/python command (#13904)Greg Becker1-1/+1
2019-12-01verify.py: os.path.exists exception handling (#13656)Daryl W. Grunau1-14/+16
2019-11-17Document use of the maintainers field (#13748)Adam J. Stewart2-0/+19
2019-11-15Bugfix/config caching 13754 (#13759)Greg Becker1-2/+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.
2019-11-15hwloc: added 'master' version pointing at the HEAD of the master branch (#13734)Massimiliano Culpo1-4/+6
2019-11-14Config option to allow gpg warning suppression (#13744)Greg Becker4-3/+17
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.
2019-11-14determine target relative to the link directory rather than the full link ↵Peter Scheibel1-3/+3
path (which includes the file name) (#13727)
2019-11-13Allow binary relocation of strings in relative binaries (#13724)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.
2019-11-05`spack find` now displays variants and other spec constraintsv0.13.1Todd 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.
2019-11-05bugfix: uninstall should find concrete specs by DAG hashTodd 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
2019-11-04environments: make shell modifications partially unconditional (#13523)Greg Becker2-1/+37
* environments: make shell modifications partially unconditional * flake * missing module name * add regression test * flake
2019-11-04binary distribution: relocate text files properly in relative binaries (#13578)Greg Becker3-17/+37
* 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
2019-11-03bugfix: 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`.
2019-11-01version bump: 0.13.1Todd Gamblin1-1/+1
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
2019-11-01Travis CI: Test Python 3.8 (#13347)Adam J. Stewart4-15/+35
* 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
2019-11-01Documentation: 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.
2019-11-01cuda: 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>
2019-11-01cpu: fix clang flags for generic x86_64 (#13491)Greg Becker2-8/+16
* cpu: differentiate flags used for pristine LLVM vs. Apple's version
2019-11-01syaml_int type should use int.__repr__ rather than str.__repr__ (#13487)Peter Scheibel1-1/+1
2019-10-31elpa: prefer 2016.05.004 until sse/avx/avx2 issues are resolved (#13530)eugeneswalker1-1/+1
- configuration fails on newer versions when enabling sse/avx/avx2 - prefer an older version that will build with these features
2019-10-31trilinos: temporarily constrain netcdf@:4.7.1 (#13526)eugeneswalker1-1/+1
remove this when issues are resolved with `trilinos^netcdf@4.7.2`
2019-10-25Add top-level `CHANGELOG.md` with release notes.v0.13.0Todd Gamblin1-0/+262
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).
2019-10-25Add py-twine package (#13449)Adam J. Stewart1-0/+22
2019-10-25Add py-pkginfo package (#13448)Adam J. Stewart1-0/+19
2019-10-25Add latest version of py-tqdm (#13446)Adam J. Stewart1-2/+7
2019-10-25Add latest version of py-requests-toolbelt (#13445)Adam J. Stewart1-2/+3
2019-10-25Add latest version of py-readme-renderer (#13444)Adam J. Stewart1-3/+5
2019-10-25New package: gpu-burn (#13108)Glenn Johnson2-0/+73
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.
2019-10-25py-nbformat package: add version 4.4.0 (#13421)Andreas Baumbach1-0/+1
2019-10-25New package: py-defusedxml (#13419)Andreas Baumbach1-0/+17
2019-10-25New package: OSQP (#13432)Sinan1-0/+22
2019-10-25LIBXSMM package: add version 1.14 (#13436)Hans Pabst1-1/+2
2019-10-25lmdb package: add version 0.9.24 (#13437)Michael Kuhn1-0/+1
2019-10-25sqlite package: add version 3.30.1 (#13438)Michael Kuhn1-0/+1
2019-10-25py-gensim: new package at 3.8.0 (#13136)Justin S1-0/+28
* py-gensim: new package at 3.8.0 * py-gensim: add 3.8.1
2019-10-25completion: add bash completion for `spack spec --json` (#13433)Todd Gamblin1-1/+2
2019-10-25Make error msg of test_api_for_build_and_run_environment more informative ↵Andreas Baumbach1-1/+2
(#13435)