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

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license year bump (#34921) * license bump year * fix black issues of modified files * mypy * fix 2021 -> 2023
2023-01-19 06:30:17 +08:00
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +08:00
# Spack Project Developers. See the top-level COPYRIGHT file for details.
cufflinks: new package (#5158)
2017-08-19 05:02:15 +08:00
#
relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers - remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
2018-10-08 04:52:23 +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 *
cufflinks: new package (#5158)
2017-08-19 05:02:15 +08:00
class Cufflinks(Package):
"""Cufflinks assembles transcripts, estimates their abundances, and tests
for differential expression and regulation in RNA-Seq samples."""
start of work to add spack audit packages-https checker (#25670) This PR will add a new audit, specifically for spack package homepage urls (and eventually other kinds I suspect) to see if there is an http address that can be changed to https. Usage is as follows: ```bash $ spack audit packages-https <package> ``` And in list view: ```bash $ spack audit list generic: Generic checks relying on global variables configs: Sanity checks on compilers.yaml Sanity checks on packages.yaml packages: Sanity checks on specs used in directives packages-https: Sanity checks on https checks of package urls, etc. ``` I think it would be unwise to include with packages, because when run for all, since we do requests it takes a long time. I also like the idea of more well scoped checks - likely there will be other addresses for http/https within a package that we eventually check. For now, there are two error cases - one is when an https url is tried but there is some SSL error (or other error that means we cannot update to https): ```bash $ spack audit packages-https zoltan PKG-HTTPS-DIRECTIVES: 1 issue found 1. Error with attempting https for "zoltan": <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: Hostname mismatch, certificate is not valid for 'www.cs.sandia.gov'. (_ssl.c:1125)> ``` This is either not fixable, or could be fixed with a change to the url or (better) contacting the site owners to ask about some certificate or similar. The second case is when there is an http that needs to be https, which is a huge issue now, but hopefully not after this spack PR. ```bash $ spack audit packages-https xman Package "xman" uses http but has a valid https endpoint. ``` And then when a package is fixed: ```bash $ spack audit packages-https zlib PKG-HTTPS-DIRECTIVES: 0 issues found. ``` And that's mostly it. :) Signed-off-by: vsoch <vsoch@users.noreply.github.com> Co-authored-by: vsoch <vsoch@users.noreply.github.com>
2021-09-02 14:46:27 +08:00
homepage = "https://cole-trapnell-lab.github.io/cufflinks"
Switch http to https where latter exists (#25672) * Switch http to https where latter exists * Hopefully restore original permissions * Add URL updates after include the -L curl option * Manual corrections to select URL format strings
2021-09-14 00:21:35 +08:00
url = "https://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz"
cufflinks: new package (#5158)
2017-08-19 05:02:15 +08:00
checksums: use sha256 checksums everywhere We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
2019-10-11 13:44:41 +08:00
version("2.2.1", sha256="39f812452cae26462e5d2671d38104d9e8ef30aaf9ab6dea8ca57f50f46448e4")
cufflinks: new package (#5158)
2017-08-19 05:02:15 +08:00
def install(self, spec, prefix):
mkdirp(prefix.bin)
install("cuffcompare", prefix.bin)
install("cuffdiff", prefix.bin)
install("cufflinks", prefix.bin)
install("cuffmerge", prefix.bin)
install("cuffnorm", prefix.bin)
install("cuffquant", prefix.bin)
install("gffread", prefix.bin)
install("gtf_to_sam", prefix.bin)
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