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
112 lines
4.5 KiB
Python
112 lines
4.5 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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import glob
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import os
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import llnl.util.tty as tty
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from spack.package import *
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from spack.pkg.builtin.boost import Boost
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# This application uses cmake to build, but they wrap it with a
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# configure script that performs dark magic. This package does it
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# their way.
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class Bcl2fastq2(Package):
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"""The bcl2fastq2 Conversion Software converts base
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call (BCL) files from a sequencing run into FASTQ
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files."""
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homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"
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version('2.20.0.422', sha256='8dd3044767d044aa4ce46de0de562b111c44e5b8b7348e04e665eb1b4f101fe3')
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version('2.19.1.403', sha256='cf13580f2c1ebcc3642b4d98a02ad01e41a44e644db7d31730f9767b25521806')
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conflicts('platform=darwin',
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msg='malloc.h/etc requirements break build on macs')
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depends_on('boost@1.54.0:1.55')
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# TODO: replace this with an explicit list of components of Boost,
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# for instance depends_on('boost +filesystem')
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# See https://github.com/spack/spack/pull/22303 for reference
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depends_on(Boost.with_default_variants)
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depends_on('cmake@2.8.9:', type='build')
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depends_on('libxml2@2.7.8')
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depends_on('libxslt@1.1.26~crypto')
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depends_on('libgcrypt')
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depends_on('zlib')
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# Their cmake macros don't set the flag when they find a library
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# that makes them happy.
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patch('cmake-macros.patch')
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# After finding the libxslt bits, cmake still needs to wire in the
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# libexslt bits.
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patch('cxxConfigure-cmake.patch')
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root_cmakelists_dir = 'src'
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# v2.17.1.14 and v2.18.0.12 were available via HTTP.
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# v2.19.1.403 is only available via ftp.
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# who knows what the future will hold.
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def url_for_version(self, version):
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url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
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if version.string == '2.19.1.403':
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return url.format(version.up_to(3).dotted)
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else:
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return url.format(version.up_to(3).dashed)
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# Illumina tucks the source inside a gzipped tarball inside a zip
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# file. We let the normal Spack expansion bit unzip the zip file,
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# then follow it with a function untars the tarball after Spack's
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# done it's bit.
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def do_stage(self, mirror_only=False):
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# wrap (decorate) the standard expand_archive step with a
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# helper, then call the real do_stage().
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self.stage.expand_archive = self.unpack_it(self.stage.expand_archive)
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super(Bcl2fastq2, self).do_stage(mirror_only)
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def unpack_it(self, f):
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def wrap():
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f() # call the original expand_archive()
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# The tarfile should now reside in the well-known source
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# directory (i.e., self.stage.source_path).
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with working_dir(self.stage.path):
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source_subdir = os.path.relpath(self.stage.source_path,
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self.stage.path)
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files = glob.glob(os.path.join(source_subdir,
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'bcl2fastq2*.tar.gz'))
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if len(files) == 1:
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# Rename the tarball so it resides in self.stage.path
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# alongside the original zip file before unpacking it.
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tarball = files[0]
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basename = os.path.basename(tarball)
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os.rename(tarball, basename)
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tty.msg("Unpacking bcl2fastq2 tarball")
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tar = which('tar')
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tar('-xf', basename)
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# Rename the unpacked directory to the well-known
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# source path self.stage.source_path.
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os.rename('bcl2fastq', source_subdir)
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tty.msg("Finished unpacking bcl2fastq2 tarball")
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elif self.stage.expanded:
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# The unpacked files already reside in the "well known"
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# source directory (i.e., self.stage.source_path).
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tty.msg("The tarball has already been unpacked.")
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return wrap
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def install(self, spec, prefix):
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bash = which('bash')
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bash("src/configure", "--prefix={0}".format(prefix),
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"--with-cmake={0}".format(join_path(spec['cmake'].prefix.bin,
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"cmake")))
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make()
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make("install")
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