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- A package can depend on a special patched version of its dependencies.
- The `Spec` YAML (and therefore the hash) now includes the sha256 of
the patch in the `Spec` YAML, which changes its hash.
- The special patched version will be built separately from a "vanilla"
version of the same package.
- This allows packages to maintain patches on their dependencies
without affecting either the dependency package or its dependents.
This could previously be accomplished with special variants, but
having to add variants means the hash of the dependency changes
frequently when it really doesn't need to. This commit allows the
hash to change *just* for dependencies that need patches.
- Patching dependencies shouldn't be the common case, but some packages
(qmcpack, hpctoolkit, openspeedshop) do this kind of thing and it
makes the code structure mirror maintenance responsibilities.
- Note that this commit means that adding or changing a patch on a
package will change its hash. This is probably what *should* happen,
but we haven't done it so far.
- Only applies to `patch()` directives; `package.py` files (and their
`patch()` functions) are not hashed, but we'd like to do that in the
future.
- The interface looks like this: `depends_on()` can optionally take a
patch directive or a list of them:
depends_on(<spec>,
patches=patch(..., when=<cond>),
when=<cond>)
# or
depends_on(<spec>,
patches=[patch(..., when=<cond>),
patch(..., when=<cond>)],
when=<cond>)
- Previously, the `patch()` directive only took an `md5` parameter. Now
it only takes a `sha256` parameter. We restrict this because we want
to be consistent about which hash is used in the `Spec`.
- A side effect of hashing patches is that *compressed* patches fetched
from URLs now need *two* checksums: one for the downloaded archive and
one for the content of the patch itself. Patches fetched uncompressed
only need a checksum for the patch. Rationale:
- we include the content of the *patch* in the spec hash, as that is
the checksum we can do consistently for patches included in Spack's
source and patches fetched remotely, both compressed and
uncompressed.
- we *still* need the patch of the downloaded archive, because we want
to verify the download *before* handing it off to tar, unzip, or
another decompressor. Not doing so is a security risk and leaves
users exposed to any arbitrary code execution vulnerabilities in
compression tools.
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- Functions returned by directives were all called `_execute`, which made
reading stack traces hard because you couldn't tell what directive a
frame came from.
- renamed them all to `_execute_<directive>`
- Exceptions in directives were only really used in one or two places --
get rid of the boilerplate init functions and let the callsite specify
the message.
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- move `spack.cmd.checksum.get_checksums` to `spack.util.web.spider_checksums`
- move `spack.error.NoNetworkError` to `spack.util.web.NoNetworkError` since
it is only used there.
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- Previously, dependencies and dependency_types were stored as separate
dicts on Package.
- This means a package can only depend on another in one specific way,
which is usually but not always true.
- Prior code unioned dependency types statically across dependencies on
the same package.
- New code stores dependency relationships as their own object, with a
spec constraint and a set of dependency types per relationship.
- Dependency types are now more precise
- There is now room to add more information to dependency relationships.
- New Dependency class lives in dependency.py, along with deptype
definitions that used to live in spack.spec.
Move deptype definitions to spack.dependency
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* Add '--test=all' and '--test=root' options to test either the root or the root and all dependencies.
* add a test dependency type that is only used when --test is enabled.
* test dependencies are not added to the spec, but they are provided in the test environment.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-yaml: Correct url.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-mlinterfaces: Create new package.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-threejs: Correct url.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-hwriter: Create new package.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-gbm: Create new package.
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closes #5473
Prior to this PR we were not exiting early for external packages, which
caused the `configure_options` property of the contexts to fail with
e.g. a key error because the DAG gets truncated for them. More
importantly Spack configure options don't make any sense for externals.
Now we exit early, and leave a message in the module file clarifying
that this package has been installed outside of Spack.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-dbi: Create new package.
* r-dbi: modified according to flake8
* Update package.py
* Update package.py
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* Adding package Metaphysicl.
* Removing list_url from metaphysical package.
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#5428) (#5479)
- latest version requires openmpi+thread_multiple for collated output.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-ggvis: Update version to 0.4.3
* Update package.py
* Update package.py
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-dplyr: Update version to 0.7.3
* Update package.py
* Update package.py
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All ncl scripts hardcode /bin/csh, so fix them up.
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The patches are taken from the Fedora package.
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* r-annaffy: Create New Package.
* r-annaffy: Create new package.
* r-go-db: Create new package.
* r-kegg-db: Create new package.
* r-annaffy: Correct indentation.
* r-go-db: Correct indentation.
* r-kegg-db: Correct format.
* r-kegg-db: Correct format.
* r-go-db: Correct format.
* r-annaffy: Correct format.
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* fastq-screen: new package
* fixing descriptions and previously made packages' old copyright date
* added wrong perl package after change
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-r6: Update version to 2.2.2
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-shiny: Update version to 1.0.5
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-htmltools: Update version to 0.3.6
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-httpuv: Update version to 1.3.5
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-rcpp: Update version to 0.12.13
* r-rcpp: Correct url.
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+ Count, or compute differences of, physical lines of source code in the
given files (may be archives such as compressed tarballs or zip files)
and/or recursively below the given directories.
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* pr-quantities: add version & py-numpy conflict (#5307)
* r-jsonlite: Update version to 1.5
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