18c2f1a57a
Explicitly import package utilities in all packages, and corresponding fallout.
This includes:
* rename `spack.package` to `spack.package_base`
* rename `spack.pkgkit` to `spack.package`
* update all packages in builtin, builtin_mock and tutorials to include `from spack.package import *`
* update spack style
* ensure packages include the import
* automatically add the new import and remove any/all imports of `spack` and `spack.pkgkit`
from packages when using `--fix`
* add support for type-checking packages with mypy when SPACK_MYPY_CHECK_PACKAGES
is set in the environment
* fix all type checking errors in packages in spack upstream
* update spack create to include the new imports
* update spack repo to inject the new import, injection persists to allow for a deprecation period
Original message below:
As requested @adamjstewart, update all packages to use pkgkit. I ended up using isort to do this,
so repro is easy:
```console
$ isort -a 'from spack.pkgkit import *' --rm 'spack' ./var/spack/repos/builtin/packages/*/package.py
$ spack style --fix
```
There were several line spacing fixups caused either by space manipulation in isort or by packages
that haven't been touched since we added requirements, but there are no functional changes in here.
* [x] add config to isort to make sure this is maintained going forward
54 lines
1.7 KiB
Python
54 lines
1.7 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from os import symlink
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from spack.package import *
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class Recon(MakefilePackage):
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"""RECON: a package for automated de novo identification of repeat families
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from genomic sequences."""
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homepage = "http://eddylab.org/software/recon/"
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url = "http://eddylab.org/software/recon/RECON1.05.tar.gz"
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version('1.05', sha256='4d4f76f439bcffd50380cffc41a80dc15fa4a80f38a04234e24da893ed7c025a')
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variant('repeatmasker', default=False,
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description='Use RepeatMasker developer patches (1.08)')
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patch('repeatmasker_recon.patch', when='+repeatmasker')
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build_directory = 'src'
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depends_on('perl', type='run')
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@property
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def install_targets(self):
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return [
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'install',
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'BINDIR=%s' % self.prefix.bin
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]
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# edit the recon.pl script with the prefix as mentioned in the README
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def edit(self, spec, prefix):
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filter_file('$path = ""', '$path = "%s"' % prefix.bin,
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'scripts/recon.pl', string=True)
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# recon's makefile is very basic -- the target directory must
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# already exist to properly install
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@run_before('install')
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def prepare_bin(self):
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mkdirp(prefix.bin)
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# finally, install the scripts dir as well
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# and link the recon command into bin.
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@run_after('install')
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def finalize(self):
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install_tree('scripts', prefix.scripts)
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symlink(join_path(prefix.scripts, 'recon.pl'),
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join_path(prefix.bin, 'recon'))
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