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2020-04-06Docs: fix Spack Environments command (#15891)Adam J. Stewart1-1/+1
2020-04-06Blacklist Lmod variable modifications when sourcing files (#15778)Massimiliano Culpo3-1/+24
fixes #15775 Add all the variables listed here: https://lmod.readthedocs.io/en/latest/090_configuring_lmod.html to the list of those blacklisted when constructing environment modifications by sourcing files.
2020-04-06Source devnull in environment_after_sourcing_files (closes #15775) (#15791)Jonathon Anderson1-1/+2
spack.util.environment_after_sourcing_files compares the local environment against a shell environment after having sourced a file; but this ends up including the default shell profile and rc, which might differ from the local environment. To change this, compare against the default shell environment, expressed here as 'source /dev/null'.
2020-04-05verify `other.exe` attr exists before use in __eq__ (#15882)Stephen McDowell1-1/+1
2020-04-03Add option "--first" for "spack load" (#15622)G-Ragghianti4-7/+34
* Implemented --first option for "spack load" * added test for "spack load --first" Co-authored-by: gragghia <gragghia@localhost.localdomain>
2020-04-03Environments/views: only override spec prefix for non-external packages (#15475)Peter Scheibel2-1/+49
* only override spec prefix for non-external packages * add test that environment shell modifications respect explicitly-specified prefixes for external packages * add clarifying comment
2020-04-02Add commands to facilitate Spack/Python/OS reporting (#15834)Adam J. Stewart4-2/+46
* Add --version arg to spack python command * Add `spack debug report` command
2020-04-01Spelling fixes (#15805)Greg Sjaardema7-13/+13
* Spelling fixes * spelling fixes * spelling fixes * spelling fixes * spelling fix * spelling fix * spelling fix * spelling fixes * spelling fix
2020-03-31packages.yaml: allow virtuals to specify buildable: false (#14934)Greg Becker9-153/+155
Currently, to force Spack to use an external MPI, you have to specify `buildable: False` for every MPI provider in Spack in your packages.yaml file. This is both tedious and fragile, as new MPI providers can be added and break your workflow when you do a git pull. This PR allows you to specify an entire virtual dependency as non-buildable, and specify particular implementations to be built: ``` packages: all: providers: mpi: [mpich] mpi: buildable: false paths: mpich@3.2 %gcc@7.3.0: /usr/packages/mpich-3.2-gcc-7.3.0 ``` will force all Spack builds to use the specified `mpich` install.
2020-03-31Update link for codecov's browser extensions (#15779)Massimiliano Culpo1-2/+2
2020-03-30CUDA 10.1+ supports ICC 19.0 (#15764)Axel Huebl1-2/+2
Fix the CUDA-ICC conflict check. Simplify the XL 17 check.
2020-03-28Buildcache keys command speed up (#15727)Patrick Gartung1-1/+1
* Limit the spidering to depth=0 for keys * depth=0 is default argument
2020-03-25provider index: removed import from + refactored a few parts (#15570)Massimiliano Culpo2-130/+179
Removed provider_index use of 'import from' and refactored a few routines to a further subclassing of _IndexBase for implementing user defined bindings of provider specs.
2020-03-24spack.repo: remove "import from" statements (#15505)Massimiliano Culpo3-39/+71
spack.repo: remove "import from" statements
2020-03-24spack.relocate: add unit test (#15610)Massimiliano Culpo2-67/+130
* relocate: removed import from statements * relocate: renamed *Exception to *Error This aims at consistency in naming with both the standard library (ValueError, AttributeError, etc.) and other errors in 'spack.error'. Improved existing docstrings * relocate: simplified search function by un-nesting conditionals The search function that searches for patchelf has been refactored to remove deeply nested conditionals. Extended docstring. * relocate: removed a condition specific to unit tests * relocate: added test for _patchelf
2020-03-23Bugfix: remove unit tests that install real packages (#15646)Peter Scheibel1-480/+0
Our unit tests run many times. Any unit test which actually installs a package (which involves fetching code on the internet) is a severe bug because it runs an installation many times (i.e. re-downloading the same package for each version of Python that we run unit tests for). This reverts commit 25893f1, which added tests that install real packages.
2020-03-23Vendoring: remove dependency on Setuptools from vendored pytest (#15612)Todd Gamblin3-51/+17
If the Python used by Spack does not include Setuptools, then 'spack test' will fail because Spack's vendored pytest dependency imports and uses Setuptools in some of its functions. It turns out that Spack doesn't use the functionality those methods enable, so this PR removes those functions and thereby allows 'spack test' to run without Setuptools.
2020-03-23Bugfix (config): enable "spack test" when in an active environment (#15618)Todd Gamblin1-4/+9
For any Spack test using Spack's YAML configuration, avoid using real Spack configuration that has been cached by other tests and Spack startup logic. Previously this was only done for tests using 'mutable_config' (i.e. those which expected to *change* the configuration of Spack), but in fact all tests that read Spack config should use it. This was an issue when running tests within an environment, because compiler configuration ends up being queried earlier, and the user's real config "leaks" into the cache. Outside an environment, the cache is never set until tests touch it, so we weren't seeing this issue.
2020-03-22bugfix: TERM may not be in the environment on Cray (#15630)Todd Gamblin1-3/+7
2020-03-22bugfix: spack test should not output [+] for mock installs (#15609)Todd Gamblin1-3/+2
`spack test` has a spurious '[+] ' in the output: ``` lib/spack/spack/test/install.py .........[+] ...... ``` Output is properly suppressed: ``` lib/spack/spack/test/install.py ............... ```
2020-03-21Buildcache: attempt to build and install buildcaches in test environment ↵Patrick Gartung1-0/+480
(#15577) * Put bindist.py on it's own branch * Working on SL7 with python 3.6 * Flake8 * Put back clearing of compiler cache
2020-03-20Merge branch 'releases/v0.14' into developTodd Gamblin1-1/+1
2020-03-20performance: add a verification file to the database (#14693)Andrew W Elble3-3/+52
Reading the database repeatedly can be quite slow. We need a way to speed up Spack when it reads the DB multiple times, but the DB has not been modified between reads (which is nearly all the time). - [x] Add a file containing a unique uuid that is regenerated at database write time. Use this uuid to suppress re-parsing the database contents if we know a previous uuid and the uuid has not changed. - [x] Fix mutable_database fixture so that it resets the last seen verifier when it resets. - [x] Enable not rereading the database immediately after a write. Make the tests reset the last seen verifier in between tests that use the database fixture. - [x] make presence of uuid module optional
2020-03-20Buildcache: add unit tests for normalized path functions in relocate.py (#15607)Patrick Gartung1-5/+57
2020-03-20fix: change typo dependnecies to dependencies (#15602)Ryan Mast2-2/+2
2020-03-20version bump: 0.14.1Todd Gamblin1-1/+1
2020-03-20multiprocessing: allow Spack to run uninterrupted in background (#14682)Greg Becker1-47/+83
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded. This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
2020-03-20multiprocessing: allow Spack to run uninterrupted in background (#14682)Greg Becker1-47/+83
Spack currently cannot run as a background process uninterrupted because some of the logging functions used in the install method (especially to create the dynamic verbosity toggle with the v key) cause the OS to issue a SIGTTOU to Spack when it's backgrounded. This PR puts the necessary gatekeeping in place so that Spack doesn't do anything that will cause a signal to stop the process when operating as a background process.
2020-03-20spack checksum: Use package's fetch_options (#15481)Michael Kuhn2-3/+12
This makes sure that a package's fetch_options are used when fetching new versions to checksum. This allows working around problems with slow servers or those requiring a cookie to be set.
2020-03-20Cray bugfix: TERM missing while reading default target (#15381)Greg Becker1-6/+8
Bug: Spack hangs on some Cray machines Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment. Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
2020-03-20Upstreams: don't write metadata directory to upstream DB (#15526)Kai Germaschewski1-1/+1
When trying to use an upstream Spack repository, as of f2aca86 Spack was attempting to write to the upstream DB based on a new metadata directory added in that commit. Upstream DBs are read-only, so this should not occur. This adds a check to prevent Spack from writing to the upstream DB
2020-03-20Creating versions from urls doesn't modify class attributes (#15452)Massimiliano Culpo3-3/+3
fixes #15449 Before this PR a call to pkg.url_for_version was modifying class attributes determining different results for subsequents calls and an error when the urls was empty.
2020-03-20bugfix: fix install_missing_compilers option bug from v0.14.0 (#15416)Greg Becker1-0/+18
* bugfix: ensure bootstrapped compilers built before packages using the compiler
2020-03-20bugfix: installer.py shouldn't be executable (#15386)Todd Gamblin1-0/+0
This is a minor permission fix on the new installer.py introduced in #13100.
2020-03-20Add function replace_prefix_nullterm for use on mach-o rpaths. (#15347)Patrick Gartung1-3/+34
This recovers the old behavior of replace_prefix_bin that was modified to work with elf binaries by prefixing os.sep to new prefix until length is the same as old prefix.
2020-03-20ArchSpec: fix semantics of satisfies when not concrete and strict is true ↵Massimiliano Culpo2-0/+17
(#15319)
2020-03-20testing: increase installer coverage (#15237)Tamara Dahlgren3-109/+280
2020-03-20bugfix: resolve undefined source_pkg_dir failure (#15339)Tamara Dahlgren2-8/+74
2020-03-20Bugfix: resolve StopIteration message attribute failure (#15341)Massimiliano Culpo2-1/+22
Testing the install StopIteration exception resulted in an attribute error: AttributeError: 'StopIteration' object has no attribute 'message' This PR adds a unit test and resolves that error.
2020-03-20Recover coverage from subprocesses during unit tests (#15354)Tamara Dahlgren4-19/+13
* Recover coverage from subprocesses during unit tests
2020-03-20Correct pytest.raises matches to match (#15346)Massimiliano Culpo3-10/+10
2020-03-20bugfix: Add dependents when initializing spec from yaml (#15220)Tamara Dahlgren2-11/+17
The new build process, introduced in #13100 , relies on a spec's dependents in addition to their dependencies. Loading a spec from a yaml file was not initializing the dependents. - [x] populate dependents when loading from yaml
2020-03-20Uniquify suffixes added to module names (#14920)Seth R. Johnson3-1/+4
2020-03-20bugfix: ensure proper dependency handling for package-only installs (#15197)Tamara Dahlgren3-17/+149
The distributed build PR (#13100) -- did not check the install status of dependencies when using the `--only package` option so would refuse to install a package with the claim that it had uninstalled dependencies whether that was the case or not. - [x] add install status checks for the `--only package` case. - [x] add initial set of tests
2020-03-20Fix for being able to 'spack load' packages that have been renamed. (#14348)Andrew W Elble2-1/+36
* Fix for being able to 'spack load' packages that have been renamed. * tests: add test for 'spack load' of a installed, but renamed/deleted package
2020-03-20modules: store configure args during build (#11084)Michael Kuhn4-11/+41
This change stores packages' configure arguments during build and makes use of them while refreshing module files. This fixes problems such as in #10716.
2020-03-20fetch_strategy: remove vestigial code (#15431)Greg Becker1-18/+0
2020-03-20Show the packaga name for a missing patch sha256 (#15441)Dr. Christian Tacke1-1/+2
When a patches sha256 is missing, also show the packagename, so that analyzing is easier.
2020-03-19Cray bugfix: TERM missing while reading default target (#15381)Greg Becker1-6/+8
Bug: Spack hangs on some Cray machines Reason: The TERM environment variable is necessary to run bash -lc "echo $CRAY_CPU_TARGET", but we run that command within env -i, which wipes the environment. Fix: Manually forward the TERM environment variable to env -i /bin/bash -lc "echo $CRAY_CPU_TARGET"
2020-03-19refactor: `spack.package.possible_dependencies()` handles virtualsTodd Gamblin4-44/+75
- [x] move some logic for handling virtual packages from the `spack dependencies` command into `spack.package.possible_dependencies()` - [x] rework possible dependencies tests so that expected and actual output are on the left/right respectively