spack/var/spack/repos/builtin/packages/fastp/package.py

# Copyright Spack Project Developers. See COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)

from spack.package import *


class Fastp(MakefilePackage):
    """A tool designed to provide fast
    all-in-one preprocessing for FastQ files."""

    homepage = "https://github.com/OpenGene/fastp"
    url = "https://github.com/OpenGene/fastp/archive/v0.20.0.tar.gz"

    license("MIT")

    version("0.23.4", sha256="4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5")
    version("0.23.3", sha256="a37ee4b5dcf836a5a19baec645657b71d9dcd69ee843998f41f921e9b67350e3")
    version("0.20.0", sha256="8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22")

    depends_on("cxx", type="build")  # generated

    depends_on("libisal", type=("build", "link"), when="@0.23:")
    depends_on("libdeflate", type=("build", "link"), when="@0.23:")

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        make("install", "PREFIX={0}".format(prefix))
Remove years from license headers (#48352) 2025-01-02 22:40:28 +08:00			`# Copyright Spack Project Developers. See COPYRIGHT file for details.`
A new package: fastp. (#12671) * A new package: fastp. * Flake8. * Flake8. 2019-09-01 13:01:35 +08:00			`#`
			`# SPDX-License-Identifier: (Apache-2.0 OR MIT)`

refactor: packages import `spack.package` explicitly (#30404) 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 2022-05-29 00:55:44 +08:00			`from spack.package import *`
A new package: fastp. (#12671) * A new package: fastp. * Flake8. * Flake8. 2019-09-01 13:01:35 +08:00

			`class Fastp(MakefilePackage):`
			`"""A tool designed to provide fast`
			`all-in-one preprocessing for FastQ files."""`

			`homepage = "https://github.com/OpenGene/fastp"`
black: reformat entire repository with black 2022-07-31 06:19:18 +08:00			`url = "https://github.com/OpenGene/fastp/archive/v0.20.0.tar.gz"`
A new package: fastp. (#12671) * A new package: fastp. * Flake8. * Flake8. 2019-09-01 13:01:35 +08:00
Initial License Checkin This patch adds license information for about 5,300 packages from automated sources. The license information was obtained from Alpine Linux and PyPI and processed using tooling available in https://github.com/boomanaiden154/spack-license-utils. The license field was added in after all other directives in an automated fashion. Note that while this license information is probably fairly accurate, it is not guaranteed to be accurate. In addition some of the license strings from Alpine Linux might not be valid SPDX license strings. Invalid SPDX identifiers can be picked up and fixed once we have validation/parsing infrastructure in place for the solver, and issues can be fixed as they come up. 2023-12-23 03:29:11 +08:00			`license("MIT")`

fastp: add v0.23.4 (#38335) 2023-06-13 05:45:45 +08:00			`version("0.23.4", sha256="4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5")`
fastp: add version 0.23.3, add build dependencies (#37931) Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> 2023-05-26 09:28:13 +08:00			`version("0.23.3", sha256="a37ee4b5dcf836a5a19baec645657b71d9dcd69ee843998f41f921e9b67350e3")`
black: reformat entire repository with black 2022-07-31 06:19:18 +08:00			`version("0.20.0", sha256="8d751d2746db11ff233032fc49e3bcc8b53758dd4596fdcf4b4099a4d702ac22")`
A new package: fastp. (#12671) * A new package: fastp. * Flake8. * Flake8. 2019-09-01 13:01:35 +08:00
Add `depends_on([c,cxx,fortran])` (#45217) Add language dependencies `c`, `cxx`, and `fortran`. These `depends_on` statements are auto-generated based on file extensions found in source tarballs/zipfiles. The `# generated` comment can be removed by package maintainers after validating correctness. 2024-07-17 22:07:43 +08:00			`depends_on("cxx", type="build") # generated`

fastp: add version 0.23.3, add build dependencies (#37931) Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk> 2023-05-26 09:28:13 +08:00			`depends_on("libisal", type=("build", "link"), when="@0.23:")`
			`depends_on("libdeflate", type=("build", "link"), when="@0.23:")`

A new package: fastp. (#12671) * A new package: fastp. * Flake8. * Flake8. 2019-09-01 13:01:35 +08:00			`def install(self, spec, prefix):`
			`mkdirp(prefix.bin)`
black: reformat entire repository with black 2022-07-31 06:19:18 +08:00			`make("install", "PREFIX={0}".format(prefix))`