Fixes#4112
This commit extends the support of the AutotoolsPackage methods
`with_or_without` and `enable_or_disable` to bool-valued variants. It
also defines for those functions a convenience short-cut if the
activation parameter is the prefix of a spec (like in
`--with-{pkg}={prefix}`).
This commit also includes:
* Updates to viennarna and adios accordingly: they have been modified to
use `enable_or_disable` and `with_or_without`
* Improved docstrings in `autotools.py`. Raise `KeyError` if name is
not a variant.
* Added support to query packages by tags.
- The querying commands `spack list`, `spack find` and `spack info` have
been modified to support querying by tags. Tests have been added to
check that the feature is working correctly under what should be the
most frequent use cases.
* Refactored Repo class to make insertion of new file caches easier.
- Added the class FastPackageChecker. This class is a Mapping from
package names to stat info, that gets memoized for faster access.
- Extracted the creation of a ProviderIndex to its own factory function.
* Added a cache file for tags.
- Following what was done for providers, a TagIndex class has been added.
This class can serialize and deserialize objects from json. Repo and
RepoPath have a new method 'packages_with_tags', that uses the TagIndex
to compute a list of package names that have all the tags passed as
arguments.
On Ubuntu 14.04 the effect if the cache reduces the time for spack list
from ~3sec. to ~0.3sec. after the cache has been built.
* Fixed colorization of `spack info`
- Python I/O would not properly interleave (or appear) with output from
subcommands.
- Add a flusing wrapper around sys.stdout and sys.stderr when
redirecting, so that Python output is synchronous with that of
subcommands.
Adds the "buildcache" command to spack. The buildcache command is
used to create gpg signatures for archives of installed spack
packages; the signatures and archives are placed together in a
directory that can be added to a spack mirror. A user can retrieve
the archives from a mirror and verify their integrity using the
buildcache command. It is often the case that the user's Spack
instance is located in a different path compared to the Spack
instance used to generate the package archive and signature, so
this includes logic to relocate the RPATHs generated by Spack.
Fixes#4898
Constraints that were supposed to be conditionally activated for
specified values of a single-valued variant were being activated
unconditionally in the case that the variant was associated with
an implicit dependency. For example if X->Y->Z and Y places a
conditional constraint on Z for a given single-valued variant on
Y, then it would have been applied unconditionally when
concretizing X.
For packages which contain a mix of versions with formats X.Y and
X.Y.Z, if the user entered an X.Y version as a preference in
packages.yaml, Spack would get confused and favor any version A.B.Z
where X=A and Y=B. In the case where there is a mix of these version
types, this commit updates preferences so Spack will favor an exact
match.
Adds SpackCommand class allowing Spack commands to be easily in Python
Example usage:
from spack.main import SpackCommand
info = SpackCommand('info')
out, err = info('mpich')
print(info.returncode)
This allows easier testing of Spack commands.
Also:
* Simplify command tests
* Simplify mocking in command tests.
* Simplify module command test
* Simplify python command test
* Simplify uninstall command test
* Simplify url command test
* SpackCommand uses more compatible output redirection
* During install, remove prior unfinished installs
If a user performs an installation which fails, in some cases the
install prefix is still present, and the stage path may also be
present. With this commit, unless the user specifies
'--keep-prefix', installs are guaranteed to begin with a clean
slate. The database is used to decide whether an install finished,
since a database record is not added until the end of the install
process.
* test updates
* repair_partial uses keep_prefix and keep_stage
* use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not)
* add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
* SV variants are evaluated correctly in `when=` statements fixes#4113
The problem here was tricky:
```python
spec.satisfies(other)
```
changes already the MV variants in others into SV variants (where
necessary) if spec is concrete. If it is not concrete it does
nothing because we may be acting at a pure syntactical level.
When evaluating a `when=` keyword spec is for sure not concrete
as it is in the middle of the concretization process. In this case we
have to trigger manually the substitution in other to not end up
comparing a MV variant "foo=bar" to a SV variant "foo=bar" and having
False in return. Which is wrong.
* sv variants: improved error message for typos in "when=" statements
Modifications:
- added support for multi-valued variants
- refactored code related to variants into variant.py
- added new generic features to AutotoolsPackage that leverage multi-valued variants
- modified openmpi to use new features
- added unit tests for the new semantics
* Properly ignore flake8 F811 redefinition errors
* Add unit tests for flake8 command
* Allow spack flake8 to work on systems with older git
* Skip flake8 unit tests for Python 2.6 and 3.3
* Checksum code wasn't opening binary files as binary.
- Fixes Python 3 issue where files are opened as unicode text by default,
and decoding fails for binary blobs.
* Simplify fetch test parametrization.
* - add tests for URL fetching and checksumming.
- fix coverage on interface functions in FetchStrategy superclass
- add some extra crypto tests.
* Package install remove prior unfinished installs
Depending on how spack is terminated in the middle of building a
package it may leave a partially installed package in the install
prefix. Originally Spack treated the package as being installed if
the prefix was present, in which case the user would have to
manually remove the installation prefix before restarting an
install. This commit adds a more thorough check to ensure that a
package is actually installed. If the installation prefix is present
but Spack determines that the install did not complete, it removes
the installation prefix and starts a new install; if the user has
enabled --keep-prefix, then Spack reverts to its old behavior.
* Added test for partial install handling
* Added test for restoring DB
* Style fixes
* Restoring 2.6 compatibility
* Relocated repair logic to separate function
* If --keep-prefix is set, package installs will continue an install from an existing prefix if one is present
* check metadata consistency when continuing partial install
* Added --force option to make spack reinstall a package (and all dependencies) from scratch
* Updated bash completion; removed '-f' shorthand for '--force' for install command
* dont use multiple write modes for completion file
Previously, this would fail with a NoSuchMethodError:
class Package(object):
# this is the default implementation
def some_method(self):
...
class Foo(Package):
@when('platform=cray')
def some_method(self):
...
@when('platform=linux')
def some_method(self):
...
This fixes the implementation of `@when` so that the superclass method
will be invoked when no subclass method matches.
Adds tests to ensure this works, as well.
- Added a new interface for Specs to pass build information
- Calls forwarded from Spec to Package are now explicit
- Added descriptor within Spec to manage forwarding
- Added state in Spec to maintain query information
- Modified a few packages (the one involved in spack install pexsi) to showcase changes
- This uses an object wrapper to `spec` to implement the `libs` sub-calls.
- wrapper is returned from `__getitem__` only if spec is concrete
- allows packagers to access build information easily
* Spec.satisfies accesses Spec.concrete as property
Fixes#2760
When copying a spec, _concrete is always set to False for each
dependency. "Spec.satisfies" was accessing the member "_concrete"
directly instead of using the property "concrete". This means that
if you copy a spec, the dependencies will be considered equal, but
did not necessarily satisfy one another. Spec.satisfies is a
prerequisite for a package to be considered an extension; as a
consequence, an extension with run-time dependencies that were also
extensions did not activate those extensions. This updates
Spec.satisfies to avoid checking the cached member "_concrete"
directly.
* Added test to check for activation of dependency extension
* Added test to check for transitive satisfiability between a spec and its copy
* PackageMeta: `run_before` is an alias of `precondition`, `run_after` an alias of `sanity_check`
* PackageMeta: removed `precondition` and `sanity_check`
* PackageMeta: decorators are now free-standing
* package: modified/added docstrings. Fixed the semantics of `on_package_attributes`.
* package: added unit test assertion as side effects of install
* build_systems: factored build-time test running into base class
* r: updated decorators in package.py
* docs: updated decorator names
* Rename packages
* Upcasing depends_on() in packages.
* Downcased extends('r')
* Fixed erroneously changed URL that had slipped through.
* Fixed typo
* Fixed link from documentation into package source code.
* Fixed another doc problem.
* Changed underscores to dashes in package names.
* Added test to enforce lowercase, no-underscore naming convention.
* Fix r-xgboost
* Downcase more instances of 'R' in package auto-creation.
* Fix test.
* Converted unit test packages to use dashes not underscores
* Downcase `r` in the docs.
* Update module_file_support.rst
Fix r->R for class R.
* inheritance of directives: using meta-classes to inject attributes coming from directives into packages + lazy directives
* _dep_types -> dependency_types
* using a meta-class to inject directives into packages
* directives are lazy
fixes#2466
* directives.py: allows for multiple inheritance. Added blank lines as suggested by @tgamblin
* directives.py: added a test for simple inheritance of directives
* Minor improvement requested by @tgamblin
CMakePackage: importing names from spack.directives
directives: wrap __new__ to respect pep8
* Refactoring requested by @tgamblin
directives: removed global variables in favor of class variables. Simplified the interface for directives (they return a callable on a package or a list of them).
* Ensure that every package has a license
Also fixes URLs with http://http:// doubled.
This is a continuation of #2656.
* Add license to every file in Spack
* Make sure Todd is the author of all packages
* Fix flake8 tests
* Don't license external Sphinx docs
* Don't display licenses in tutorial example packages
Also fixes typos and converts command-line examples
from tcsh to bash, which is more common
deptypes: allow for different queries
For things like Python modules, they are required for the build and
runtime, but rather than adding a new parameter for what to query across
the dependency DAG, just expose the recursive query parameter.
Package repositories now look like this:
top-level-dir/
repo.yaml
packages/
libelf/
package.py
mpich/
package.py
...
This leaves room at the top level for additional metadata, source,
per-repo configs, indexes, etc., and it makes it easy to see that
something is a spack repo (just look for repo.yaml and packages).
