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2020-07-09Relocation of sbang needs to be done when the spack prefix changes even if ↵Patrick Gartung2-4/+17
the install tree has not changed. (#17455)
2020-07-09aspirin for buildaches (#17437)Harmen Stoppels1-1/+1
2020-07-09clear mpicc and friends before each build (#17450)Sajid Ali1-0/+8
* clear mpi env vars
2020-07-09installation: skip repository metadata for externals (#16954)Greg Becker1-3/+8
When Spack installs a package, it stores repository package.py files for it and all of its dependencies - any package with a Spack metadata directory in its installation prefix. It turns out this was too broad: this ends up including external packages installed by Spack (e.g. installed by another Spack instance). Currently Spack doesn't store the namespace properly for such packages, so even though the package file could be fetched from the external, Spack is unable to locate it. This commit avoids the issue by skipping any attempt to locate and copy from the package repository of externals, regardless of whether they have a Spack repo directory.
2020-07-08Buildcache: bindist test without invoking spack compiler wrappers. (#15687)Patrick Gartung2-0/+472
* Buildcache: * Try mocking an install of quux, corge and garply using prebuilt binaries * Put patchelf install after ccache restore * Add script to install patchelf from source so it can be used on Ubuntu:Trusty which does not have a patchelf pat package. The script will skip building on macOS * Remove mirror at end of bindist test * Add patchelf to Ubuntu build env * Revert mock patchelf package to allow other tests to run. * Remove depends_on('patchelf', type='build') relying instead on * Test fixture to ensure patchelf is available. * Call g++ command to build libraries directly during test build * Flake8 * Install patchelf in before_install stage using apt unless on Trusty where a build is done. * Add some symbolic links between packages * Flake8 * Flake8: * Update mock packages to write their own source files * Create the stage because spec search does not create it any longer * updates after change of list command arguments * cleanup after merge * flake8
2020-07-08spack create: ask how many to download (#17373)Adam J. Stewart2-3/+7
2020-07-08Improve Travis sample in the docs (#17420)Simon Byrne1-3/+4
- printf is better than echo for multiline strings - ** should be && - use line continuation - Use multiline block
2020-07-07Relocate rpaths for all binaries, then do text bin replacement if the rpaths ↵Patrick Gartung1-7/+10
still exist after running patchelf/otool (#17418)
2020-07-07CudaPackage: maintainers are listed in the docstring (#17409)Massimiliano Culpo1-1/+2
fixes #17396 This prevents the class attribute to be inherited and saves current maintainers from becoming the default maintainers of every Cuda package.
2020-07-07releases: document `releases/latest` tag (#17402)Todd Gamblin1-32/+59
We got rid of `master` after #17377, but users still want a way to get the latest stable release without knowing its number. We've added a `releases/latest` tag to replace what was once `master`. Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
2020-07-07Uninstall: tolerate hook failures when force=true (#16513)Peter Scheibel1-2/+32
Fixes #16478 This allows an uninstall to proceed even when encountering pre-uninstall hook failures if the user chooses the --force option for the uninstall. This also prevents post-uninstall hook failures from raising an exception, which would terminate a sequence of uninstalls. This isn't likely essential for #16478, but I think overall it will improve the user experience: if the post-uninstall hook fails, there isn't much point in terminating a sequence of spec uninstalls because at the point where the post-uninstall hook is run, the spec has already been removed from the database (so it will never have another chance to run). Notes: * When doing spack uninstall -a, certain pre/post-uninstall hooks aren't important to run, but this isn't easy to track with the current model. For example: if you are uninstalling a package and its extension, you do not have to do the activation check for the extension. * This doesn't handle the uninstallation of specs that are not in the DB, so it may leave "dangling" specs in the installation prefix
2020-07-06docs: document releases and branches in SpackTodd Gamblin5-6/+384
- [x] Remove references to `master` branch - [x] Document how release branches are structured - [x] Document how to make a major release - [x] Document how to make a point release - [x] Document how to do work in our release projects
2020-07-06Remove references to `master` from CITodd Gamblin1-1/+1
- [x] remove master from github actions - [x] remove master from .travis.yml - [x] make `develop` the default branch for `spack ci`
2020-07-06change master/child to controller/minion in pty docstringsTodd Gamblin2-95/+97
PTY support used the concept of 'master' and 'child' processes. 'master' has been renamed to 'controller' and 'child' to 'minion'.
2020-07-06autotools bugfix: handle missing config.guess (#17356)Michael Kuhn1-2/+2
Spack was attempting to calculate abspath on the located config.guess path even when it was not found (None); this commit skips the abspath calculation when config.guess is not found.
2020-07-03Pipelines doc: fixed two broken links (#17355)Shahzeb Siddiqui1-2/+2
2020-07-02autotools: Fix config.guess detection, take two (#17333)Michael Kuhn1-5/+3
The previous fix from #17149 contained a thinko that produced errors for packages that overwrite configure_directory.
2020-07-01Moved flake8, shell and documentation tests to Github Action (#17328)Massimiliano Culpo1-2/+0
* Move flake8 tests on Github Actions * Move shell test to Github Actions * Moved documentation build to Github Action * Don't run coverage on Python 2.6 Since we get connection errors consistently on Travis when trying to upload coverage results for Python 2.6, avoid computing coverage entirely to speed-up tests.
2020-07-01Fix hashlib function capitalization (#17323)Adam J. Stewart1-1/+1
2020-07-01Documentation update for container example (#17321)Glenn Johnson1-2/+2
This updates the documentation to reflect #17316.
2020-06-30bump version numberGregory Becker3-7/+12
2020-06-30Don't detect "classic" on Cray to avoid a compiler bug (#17314)Massimiliano Culpo4-2/+16
* Don't detect "classic" on Cray to avoid a compiler bug * add tests Co-authored-by: Gregory Becker <becker33@llnl.gov>
2020-06-30Add fish shell support (#9279)Johannes Blaschke5-2/+41
* share/spack/setup-env.fish file to setup environment in fish shell * setup-env.fish testing script * Update share/spack/setup-env.fish Co-Authored-By: Elsa Gonsiorowski, PhD <gonsie@me.com> * Update share/spack/qa/setup-env-test.fish Co-Authored-By: Adam J. Stewart <ajstewart426@gmail.com> * updates completions using `spack commands --update-completion` * added stderr-nocaret warning * added fish shell tests to CI system Co-authored-by: becker33 <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> Co-authored-by: Elsa Gonsiorowski, PhD <gonsie@me.com>
2020-06-30Cray compiler: fix implicit rpaths for classic versions (#17310)Greg Becker4-14/+41
* check link dirs for existence
2020-06-29cray compilers: fix bug with verifying cray compilers (#17303)Greg Becker1-5/+15
* fix bug with verifying cray compilers
2020-06-29remove three commands that have been deprecated since v0.13.0 (#17291)Greg Becker3-150/+0
* remove three commands that have been deprecated since v0.13.0
2020-06-29autotools: Fix config.guess detection (#17149)Michael Kuhn1-2/+4
The config.guess detection used a relative path that did not work in combination with `check_call`. Use an absolute path instead.
2020-06-29Detect FE compilers automatically on Cray (#17267)Massimiliano Culpo2-2/+85
* cray: detect frontend compilers automatically This commit permits to detect frontend compilers automatically, with the exception of cce. Co-authored-by: Gregory Becker <becker33.llnl.gov>
2020-06-29Fix indentation in containerize example (#17228)George Hartzell1-1/+1
[george.hartzell@172-16-193-97 spack-explore-docker]$ spack containerize Running `spack containerize` with the example `spack.yaml` file fails with an error that ends like so: ``` [...] File "/local_scratch/hartzell/tmp/spack-explore-docker/lib/spack/external/ruamel/yaml/scanner.py", line 165, in need_more_tokens self.stale_possible_simple_keys() File "/local_scratch/hartzell/tmp/spack-explore-docker/lib/spack/external/ruamel/yaml/scanner.py", line 309, in stale_possible_simple_keys "could not find expected ':'", self.get_mark()) ruamel.yaml.scanner.ScannerError: while scanning a simple key in "/local_scratch/hartzell/tmp/spack-explore-docker/spack.yaml", line 26, column 1 could not find expected ':' in "/local_scratch/hartzell/tmp/spack-explore-docker/spack.yaml", line 28, column 5 ``` Indenting the block string fixes the problem for me. CentOS 7, ``` $ spack --version 0.14.2-1529-ec58f28c2 ```
2020-06-29Restore compilers.yaml default directory (#17283)Greg Becker1-2/+2
2020-06-27Add support for macOS Big Sur (#17236)Adam J. Stewart1-0/+1
* Add support for macOS Big Sur * Big Sur is actually macOS 11.0
2020-06-26env: no automatic activation (#17258)Greg Becker4-19/+10
* env: no automatic activation * Ensure ci rebuild jobs activate the environment (no longer automagic) Co-authored-by: Scott Wittenburg <scott.wittenburg@kitware.com>
2020-06-26Use json for buildcache index (#15002)Scott Wittenburg12-305/+440
* Start moving toward a json buildcache index * Add spec and database index schemas * Add a schema for buildcache spec.yaml files * Provide a mode for database class to generate buildcache index * Update db and ci tests to validate object w/ new schema * Remove unused temporary upload-s3 command * Use database class to generate buildcache index * Do not generate index with each buildcache creation * Make buildcache index mode into a couple of constructor args to Database class * Use keyword args for _createtarball * Parse new json index when we get specs from buildcache Now that only one index file per mirror needs to be fetched in order to have all the concrete specs for binaries available on the mirror, we can just fetch and refresh the cached specs every time instead of needing to use the '-f' flag to force re-reading.
2020-06-26build_environment: verify compiler executables exist are are accessible (#17260)Greg Becker4-20/+77
* build_environment: verify compiler executables exist and are accessible * fix existing tests * test compiler executable verification
2020-06-26fix sorting issue with ci workarounds (#17277)Omar Padron2-30/+38
2020-06-26First fix for SPACK_DEPENDENCIES problem when doing setup (#10715)cedricchevalier191-9/+2
* First fix for SPACK_DEPENDENCIES problem when doing setup * Get rid of transitive include path in setup. * Export SPACK_INCLUDE_DIRS into spconfig.py
2020-06-26spack ci generate: allow use of --output-file <file> with wo/ preceding path ↵eugeneswalker1-4/+4
(#17275)
2020-06-26add environment-awareness to `buildcache create` (#16580)Jeffrey Salmond2-2/+57
* add buildcache create test * add functionality and test to create buildcache from environment * use env.concretized_user_specs rather than env.roots to get concretized specs, as suggested in review from becker33
2020-06-26Allow `spack remove -f` and `spack uninstall` to work on matrices (#17222)Greg Becker2-10/+55
* Allow `spack remove -f` and `spack uninstall` to work on matrices Allow Environment.remove(force=True) to remove the concrete spec from the environment even when the user spec cannot be removed because it is in a matrix.
2020-06-25Allow detection for "-classic" version of CCE (#17256)Massimiliano Culpo3-6/+21
* cce: detect modules based on the classic backend * cce: tweaked version checks for clang based options * Added unit test for cce flags
2020-06-25add workaround for gitlab ci needs limit (#17219)Omar Padron5-7/+235
* add workaround for gitlab ci needs limit * fix style/address review comments * convert filter obj to list * update command completion * remove dict comprehension * add workaround tests * fix sorting issue between disparate types * add indeces to format
2020-06-25prevent multiple version sigils in the same spec (#17246)Greg Becker3-9/+44
* prevent multiple version sigils in the same spec * fix packages with malformed versions
2020-06-25environment spec lists: improve ability to query architecture in when ↵Greg Becker3-5/+34
clauses (#17056)
2020-06-25Separate Apple Clang from LLVM Clang (#17110)Massimiliano Culpo17-256/+396
* Separate Apple Clang from LLVM Clang Apple Clang is a compiler of its own. All places referring to "-apple" suffix have been updated. * Hack to use a dash in 'apple-clang' To be able to use autodoc from Sphinx we need a valid Python name for the module that contains Apple's Clang code. * Updated packages to account for the existence of apple-clang Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com> * Added unit test for XCode related functions Co-authored-by: Gregory Becker <becker33@llnl.gov> Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
2020-06-25Fix global activation check for upstream extendees (#17231)Peter Scheibel2-0/+34
* short-circuit is_activated check when the extendee is installed upstream * add test for checking activation status of packages with an extendee installed upstream
2020-06-25spack config: new subcommands add/remove (#13920)Greg Becker12-102/+718
spack config add <value>: add nested value value to the configuration scope specified spack config remove/rm: remove specified configuration from the relevant scope
2020-06-24features: Add install failure tracking removal through `spack clean` (#15314)Tamara Dahlgren8-36/+140
* Add ability to force removal of install failure tracking data through spack clean * Add clean failures option to packaging guide
2020-06-24Unset environment variables that are most commonly used by Autotools ↵Sergey Kosukhin2-1/+13
packages. (#8623)
2020-06-23Some minor fixes to set_permissions() in file_permissions.py (#17020)Tom Payerle2-6/+35
* Some minor fixes to set_permissions() in file_permissions.py The set_permissions() routine claims to prevent users from creating world writable suid binaries. However, it seems to only be checking for/preventing group writable suid binaries. This patch modifies the routine to check for both world and group writable suid binaries, and complain appropriately. * permissions.py: Add test to check blocks world writable SUID files The original test_chmod_rejects_group_writable_suid tested that the set_permissions() function in lib/spack/spack/util/file_permissions.py would raise an exception if changed permission on a file with both SUID and SGID plus sticky bits is chmod-ed to g+rwx and o+rwx. I have modified so that more narrowly tests a file with SUID (and no SGID or sticky bit) set is chmod-ed to g+w. I have added a second test test_chmod_rejects_world_writable_suid that checks that exception is raised if an SUID file is chmod-ed to o+w * file_permissions.py: Raise exception when try to make sgid file world writable Updated set_permissions() in file_permissions.py to also raise an exception if try to make an SGID file world writable. And added corresponding unit test as well. * Remove debugging prints from permissions.py
2020-06-23tests: check rpath presence not equality (#17216)Tamara Dahlgren1-1/+2
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