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
80 lines
3.4 KiB
Python
80 lines
3.4 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 spack.package import *
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class Bowtie2(MakefilePackage):
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"""Bowtie 2 is an ultrafast and memory-efficient tool for aligning
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sequencing reads to long reference sequences"""
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homepage = "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml"
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url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
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version('2.4.2', sha256='4cc555eeeeb8ae2d47aaa1551f3f01b57f567a013e4e0d1f30e90f462865027e')
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version('2.4.1', sha256='566d6fb01a361883747103d797308ee4bdb70f6db7d27bfc72a520587815df22')
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version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
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version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
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version('2.3.4.1', sha256='a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc')
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version('2.3.1', sha256='33bd54f5041a31878e7e450cdcf0afba08345fa1133ce8ac6fd00bf7e521a443')
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version('2.3.0', sha256='f9f841e780e78b1ae24b17981e2469e6d5add90ec22ef563af23ae2dd5ca003c')
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version('2.2.5', sha256='e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0')
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depends_on('tbb', when='@2.3.0:')
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depends_on('readline', when='@2.3.1:')
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depends_on('perl', type='run')
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depends_on('python', type='run')
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depends_on('zlib', when='@2.3.1:')
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depends_on('simde', when='@2.4.0: target=aarch64:', type='link')
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depends_on('simde', when='@2.4.0: target=ppc64le:', type='link')
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patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
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patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
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patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
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# seems to have trouble with 6's -std=gnu++14
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conflicts('%gcc@6:', when='@:2.3.1')
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conflicts('^intel-oneapi-tbb', when='@:2.3.5.1')
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conflicts('@:2.3.5.0', when='target=aarch64:')
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conflicts('@2.4.1', when='target=aarch64:')
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def edit(self, spec, prefix):
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kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
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match = '^#!/usr/bin/env perl'
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perl = spec['perl'].command
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substitute = "#!{perl}".format(perl=perl)
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files = ['bowtie2', ]
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filter_file(match, substitute, *files, **kwargs)
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match = '^#!/usr/bin/env python.*'
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python = spec['python'].command
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substitute = "#!{python}".format(python=python)
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files = ['bowtie2-build', 'bowtie2-inspect']
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filter_file(match, substitute, *files, **kwargs)
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if (self.spec.satisfies('@2.4.0:2.4.2 target=aarch64:') or
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self.spec.satisfies('@2.4.0:2.4.2 target=ppc64le:')):
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match = '-Ithird_party/simde'
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simdepath = spec['simde'].prefix.include
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substitute = "-I{simdepath}".format(simdepath=simdepath)
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files = ['Makefile']
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filter_file(match, substitute, *files, **kwargs)
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@property
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def build_targets(self):
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make_arg = ['PREFIX={0}'.format(self.prefix)]
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if self.spec.satisfies('target=aarch64:'):
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make_arg.append('POPCNT_CAPABILITY=0')
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return make_arg
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@property
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def install_targets(self):
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if self.spec.satisfies('@:2.3.9'):
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return ['prefix={0}'.format(self.prefix), 'install']
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else:
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return ['PREFIX={0}'.format(self.prefix), 'install']
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