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Add HMMER 3.2.1 and updated URL then removed url_for_version function as no longer required - all HMMER downloads available from updated URL.
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(#8809)
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* intel-tbb: Add variant `tm` to disable transactional memory.
Some AMD or very old Intel systems don't support transactional memory. This commit adds a variant `tm` that defaults to `True`, but can be switched off to allow running on those systems.
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- Previously, Spack didn't check the arguments you put in version()
directives.
- So, you could do something like this, where there are arguments for a
URL fetcher AND for a git fetcher:
version('1.0', md5='abc123', git='https://foo.bar', commit='feda2343')
- Now, we check the arguments before constructing a fetcher, to ensure
that each package has *only* arguments for a single type of fetcher.
- Also added `test_package_version_consistency()` to the `package_sanity`
test, so that all builtin packages are required to have valid
`version()` directives.
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- this test is checking the package *repository*, not the database.
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- packagers can specify two top-level fetch URLs if one is `url`
- e.g., `url` and `git` or `url` and `svn`
- allow only one VCS fetcher so we can differentiate between URL and VCS.
- also clean up fetcher logic and class structure
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- ensure that packages can't have more than one of git, hg, svn, or url
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- Packages can remove the top-level `url` attribute and still work
- These are now legal:
- Packages with *only* version-specific URLs (even with gaps)
- Packages with a top-level git/hg/svn attribute and `version`
directives for that.
- If a package has both a top-level hg/git/svn attribute AND a top-level
url attribute, the url attribute takes precedence.
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Some packages do not have a `url` and are instead downloaded via `git`,
`hg`, or `svn`. Some packages like `spectrum-mpi` cannot be downloaded at
all, and are placeholder packages for system installations. Previously,
`__init__()` in `PackageBase` crashed if a package did not have a `url`
attribute defined.
I hacked this section of code out, but I have no idea what the
repercussions of that are.
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- This hard-codes the hash lengths rather than computing them on import.
- Also cleans up the code in `spack.util.crypto` to make it easier to
understand.
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Fix this output error:
```
$ spack -m module loads mpileaks
==> Error: `spack module loads -m t -m c -m l ...` has been moved. Try this instead:
$ spack module t loads mpileaks
$ spack module c loads mpileaks
$ spack module l loads mpileaks
```
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In case a deprecated form of the module command is used, the program
will exit non-zero and print an informative error message suggesting
which command should be used instead.
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As requested in the review all the commands meant to manage module
files have been grouped under the `spack module` command.
Unit tests have been refactored to match the new command structure.
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fixes #6321
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fixes #2215
fixes #2570
fixes #6676
fixes #7281
closes #3827
This PR reverts the use of `spack module loads` in favor of
`spack module find` when loading module files via Spack. After this PR
`spack load` will accept a single spec at a time, and will be able
to interpret correctly the `--dependencies` option.
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This reverts commit 732c24f603864ec7dbec425ac4507b47fdb7a641.
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fixes #4400
The feature requested in #4400 was already part of the module file
configuration, but it was neither tested nor documented. This
commit takes care of adding a few lines in the documentation and a
regression test.
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This just because the fixture has been moved one level above the one
it was originally defined. In this more general context there's more
than one configuration file that could be patched for tests.
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Added a subcommand that sets the default module to be loaded, if
multiple installations of the same package are present.
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'spack module' has been split into multiple commands, each one tied to a
specific module type. This permits the specialization of the new
commands with features that are module type specific (e.g. set the
default module file in lmod when multiple versions of the same package
are installed at the same time).
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- repo membership test was broken by the refactor of spack/__init__.py
- refactor singleton so that 'spec in repo' works again for `spack.repo.path`
- fix spec command and add basic tests for `spack spec` and `spack spec --yaml`
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* Test Spack on Python 3.7 as part of Travis CI
* Currently using xenial to pull-in python 3.7
* As xenial is not officially supported yet, Travis tolerates failures on it.
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- This is very old usage -- preparing to deprecate this in favor of being
explicit about checksums.
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- There was a lot of documentation in `PackageBase` dating back to the
very first versions of Spack.
- It was repetitive and out of date, and the docs at spack.readthedocs.io
are better.
- Remove the outdated specifics, and leave the minimal useful set of
developer docs in `package.py`.
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- This changes `get_checksums_for_versions` to generate code that uses an
explicit `sha256` argument instead if the bare `md5` hash we used to
generate.
- also use a generic digest parameter for the `version` directive, rather
than a specific `md5` parameter.
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- Frequently, the documentation build will fail mysteriously in some
spack command.
- The cause is some new bug introduced by the PR, but this is not
apparent because the unit tests haven't run and the doc tests aren't
targeted at code bugs.
- Users end up puzzled by doc failures when they're really code failures.
- Move the doc tests parallel with the code tests, so that we can more
easily see bugs like this.
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* trinity: fix plugin installation
* trinity: flake8
* trinity: more specific types for dependencies
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* libbeagle: add java dependency so jni hooks get built
* libbeagle: set BEAST_LIB instead of LD_LIBRARY_PATH
* libbeagle: use BEAST_LIB
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