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(#12513)
mock_archive can now take multiple extension / tar option pairs (default matches old behavior).
url_fetch.test_fetch tests more archive types.
compression.EXTS split into EXTS and NOTAR_EXTS to avoid unwanted, non-meaningful combinatoric extensions such as .tar.tbz2.
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- previously spec parsing didn't allow you to look up missing (but still
known) specs by hash
- This allows you to reference and potentially reinstall
force-uninstalled dependencies
- add testing for force uninstall and for reference by spec
- cmd/install tests now use mutable_database
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* When cleaning the stage root, only remove directories that appear
to be used for staging Spack packages. Previously Spack was clearing
all directories in the stage root, which could remove content not
related to Spack if the user chose a staging root which contains
files/directories not managed by Spack.
* The documentation is updated with warnings about choosing a stage
directory that is only managed by Spack (although generally the
check added in this PR for "spack clean" should avoid removing
content that was not created by Spack)
* The default stage directory (in config.yaml) is now
$tempdir/$user/spack-stage and the logic is updated to omit the
$user portion of this path if $tempdir already contains a $user
directory.
* When creating stage root assign user read/write permissions to all
directories in the path under $user. Previously Spack was assigning
the permissions of the first existing parent directory
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`spec.prefix` reads from Spack's database, and if you do this with
multiple consecutive read transactions, it can take a long time. Or, at
least, you can see the paths get written out one by one.
This uses an outer read transaction to ensure that actual disk locks are
acquired only once for the whole `spack find` operation, and that each
transaction inside `spec.prefix` is an in-memory operation. This speeds
up `spack find -p` a lot.
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- add tests for `spack extensions`
- refactor `test_activations` test to use real extensions.
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Refactor `spack.cmd.display_specs()` and `spack find` so that any options
can be used together with -d. This cleans up the display logic
considerably, as there are no longer multiple "modes".
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- add docs for `spack find --format`
- add docs for `spack find --json`
- update references to Spec.format() docs and add links
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This is another machine-readable version of `spack find`. Supplying the
`--json` argument causes specs to be written out as json records,
easily filered with tools like jq.
e.g.:
$ spack find --json python | jq -C ".[] | { name, version } "
[
{
"name": "python",
"version": "2.7.16"
},
{
"name": "bzip2",
"version": "1.0.8"
}
]
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- spack find --format allows you to supply a format string and have specs
output in a more machine-readable way, without dedcoration
e.g.:
spack find --format "{name}-{version}-{hash}"
autoconf-2.69-icynozk7ti6h4ezzgonqe6jgw5f3ulx4
automake-1.16.1-o5v3tc77kesgonxjbmeqlwfmb5qzj7zy
bzip2-1.0.6-syohzw57v2jfag5du2x4bowziw3m5p67
...
or:
spack find --format "{hash}"
icynozk7ti6h4ezzgonqe6jgw5f3ulx4
o5v3tc77kesgonxjbmeqlwfmb5qzj7zy
syohzw57v2jfag5du2x4bowziw3m5p67
...
This is intended to make it much easier to script with `spack find`
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When Spack installs a package it writes the package.py file and
patches to a separate repository (which reflects the state of the
package at the time it was installed). Previously, Spack only wrote
patches that were used at installation time. This updates the
archiving step to include all patch files that are relevant to the
package (in case that repository is used in another context).
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* Fujitsu compiler: Add flags for c11/c99
* Add unit tests about supported flags
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This commit removes redundant calls to `libtoolize` and `aclocal`.
Some configurations, such as a Spack user using macOS with a
Homebrew-installed `libtool` added to their `packages.yaml`, have
`autoreconf` and GNU libtoolize installed as `glibtoolize`, but not
`libtoolize`. While Spack installations of `libtool` built from source
would install `glibtoolize` and symlink `libtoolize` to `glibtoolize`,
an external installation of GNU libtoolize as `glibtoolize` will not
have such a symlink, and thus the call `m.libtoolize()` will throw an
error because `libtoolize` does not exist at the path referenced by
`m.libtoolize()` (i.e.,
`self.spec['libtool'].prefix.bin.join('libtoolize')).
However, on these same systems, `autoreconf` runs correctly, and calls
`glibtoolize` instead of `libtoolize`, when appropriate. Thus,
removing the call to `libtoolize` should resolve the error mentioned
above.
The redundant call to `aclocal` is also removed in this commit because
the maintainers of GNU Automake state that "`aclocal` is expected to
disappear" and suggest that downstream users never call `aclocal`
directly -- rather, they suggest calling `autoreconf` instead.
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fixes #10246
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Uses code from CMake to detect implicit link paths from compilers
System paths are filtered out of implicit link paths
Implicit link paths added to compiler config and object under `implicit_rpaths`
Implicit link paths added as rpaths to compile line through env/cc wrapper
Authored by: "Ben Boeckel <ben.boeckel@kitware.com>"
Co-authored by: "Peter Scheibel <scheibel1@llnl.gov>"
Co-authored by: "Gregory Becker <becker33@llnl.gov>"
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c9e214f updated template creation by passing **kwargs to package
template classes but the template classes were not updated to accept
them; this adds **kwargs to package template initializers where they
are needed.
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Having a non-directory invisible file causes `spack find` to die. This
fixes the logic to ignore invalid module names but only warn if they're
visible.
```
NotADirectoryError: [Errno 20] Not a directory: '/spack/var/spack/repos/builtin/packages/.DS_Store/package.py'
```
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This adds a special package type to Spack which is used to aggregate
a set of packages that a user might commonly install together; it
does not include any source code itself and does not require a
download URL like other Spack packages. It may include an 'install'
method to generate scripts, and Spack will run post-install hooks
(including module generation).
* Add new BundlePackage type
* Update the Xsdk package to be a BundlePackage and remove the
'install' method (previously it had a noop install method)
* "spack create --template" now takes "bundle" as an option
* Rename cmd_create_repo fixture to "mock_test_repo" and relocate it
to shared pytest fixtures
* Add unit tests for BundlePackage behavior
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This allows "spack spec --yaml" to generate a spec YAML file that can
be used with "spack install -f". Before, this would fail in cases
where the spec had build dependencies.
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* All fetch strategies now accept the Boolean version keyword option `no_cache` in order to allow per-version control of cache-ability.
* New git-specific version keyword option `get_full_repo` (Boolean). When true, disables the default `--depth 1` and `--single-branch` optimizations that are applied if supported by the git version and (in the former case) transport protocol.
* The try / catch blog attempting `--depth 1` and retrying on failure has been removed in favor of more accurately ascertaining when the `--depth` option should work based on git version and protocol choice. Any failure is now treated as a real problem, and the clone is only attempted once.
* Test improvements:
* `mock_git_repository.checks[type_of_test].args['git']` is now specified as the URL (with leading `file://`) in order to avoid complaints when using `--depth`.
* New type_of_test `tag-branch`.
* mock_git_repository now provides `git_exe`.
* Improved the action of the `git_version` fixture, which was previously hard-wired.
* New tests of `--single-branch` and `--depth 1` behavior.
* Add documentation of new options to the packaging guide.
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canonicalized paths vs. Spack config variables like 'tempdir' (#12492)
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(#12491)
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- mkdirp now takes arguments to allow it to properly set permissions on created directories.
- Two arguments (group and mode) set permissions for the leaf directory.
- Intermediate directories can inherit permissions from either the topmost existing directory (the parent) or the leaf.
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On machines where $TMP is owned by a gid with no name, this avoids the
following error when the default spack stage does not exist:
(spackbook):spack$ spack clean
==> Removing all temporary build stages
==> Error: 'getgrgid(): gid not found: 57095'
Spack needs to deal with gids directly unless users pass them in.
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Removes messages accidentally introduced in #12072 .
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Compiler caching was using the `id()` function to refer to configuration dictionary objects. If these objects are garbage-collected, this can produce incorrect results (false positive cache hits). This change replaces `id()` with an object that keeps a reference to the config dictionary so that it is not garbage-collected.
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Fixes #11163
The goal of this work is to simplify stage directory structures by eliminating use of symbolic links. This means, among other things, that` $spack/var/spack/stage` will no longer be the core staging directory. Instead, the first accessible `config:build_stage` path will be used.
Spack will no longer automatically append `spack-stage` (or the like) to configured build stage directories so the onus of distinguishing the directory from other work -- so the other work is not automatically removed with a `spack clean` operation -- falls on the user.
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Skip generating reports for any packages that were found in the binary cache.
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Allow "spack mirror" with no spec arguments to create a mirror for the
active environment (download all concretized specs in the environment)
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Fixes #12062
406c791 addressed "spack module load" for upstream modules but not
the "spack module loads" command. This applies the same fixes from
406c791 to "spack module loads".
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Apparently shlex.split can't deal with unicode encoded characters in
Python2.6. The solution is to convert to str before calling the
function.
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* stack concretization: fix handling of variant names with dashes
* spec_list: bugfix for handling nested matrices
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* Allow Spack to uninstall external extensions without permissions
Raise when self.projections is not empty
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It's no longer possible to set compiler flags under as an entry under
"paths" in compilers.yaml; instead the user must list these under the
"flags" section. This updates the docs accordingly.
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Spack stacks drop invalid dependencies applied to packages by a
spec_list matrix operation
Without this fix, Spack would raise an error if orthogonal dependency
constraints and non-dependency constraints were applied to the same
package by a matrix and the dependency constraint was invalid for
that package. This is an error, fixed by this PR.
An example failing configuration:
spack:
definitions:
- packages: [libelf, hdf5+mpi]
- compilers: ['%gcc']
- mpis: [^openmpi]
specs:
- matrix:
- $packages
- $compilers
- $mpis
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5f74f22 enabled installing compilers for dependencies but not for the root package (and in particular not for DAGs which consist of one package)
this enables bootstrapping compilers for both types of DAGs
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- Add comments to explain that `install_dependency_symlinks` and `flatten_dependencies` are actually used.
- Add a test that exercises the routines.
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- ensure that `$spack` and other variables are substituted into mirror
paths
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* stacks: Fix env.write to properly write references
* stacks: regression test for 12095
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Using "compilers" with the "s" is an invalid config section and throws an error.
Traceback (most recent call last):
File "spack/bin/spack", line 48, in <module>
sys.exit(spack.main.main())
File "/home/omsai/src/libkmap/spack/lib/spack/spack/main.py", line 633, in main
env = ev.find_environment(args)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 263, in find_environment
return Environment(env)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 534, in __init__
self._read_manifest(f)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 561, in _read_manifest
self.yaml = _read_yaml(f)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 402, in _read_yaml
validate(data, filename)
File "/home/omsai/src/libkmap/spack/lib/spack/spack/environment.py", line 395, in validate
e, data, filename, e.instance.lc.line + 1)
spack.config.ConfigFormatError: /home/omsai/src/libkmap/spack.yaml:15: Additional properties are not allowed ('compilers' was unexpected)
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Environment.concretize returns newly-concretized specs rather than
printing them; as a result, the _display argument is removed from
Environment.concretize (originally only used to avoid printing specs
during unit testing). Command logic which invokes
Environment.concretize prints these explicitly.
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