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spack/var/spack/repos/builtin/packages/beast1/package.py

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copyrights: update all files with license headers for 2021 - [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files - [x] update all licensed files to say 2013-2021 using `spack license update-copyright-year` - [x] appease mypy with some additions to package.py that needed for oneapi.py
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# Copyright 2013-2021 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
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
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#
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
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
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from spack import *
class Beast1(Package):
"""BEAST is a cross-platform program for Bayesian
analysis of molecular sequences using MCMC."""
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>
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homepage = "https://beast.community/"
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
2018-03-24 04:19:26 +08:00
beast1 package: add version 1.10.4, use url_for_version (#11009)
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version('1.10.4', sha256='be652c4d55953f7c6c7a9d3eb3de203c77dc380e81ad81cfe0492408990c36a8')
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
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version('1.8.4', sha256='c14e93976008463108aefa34ecc23287ab70703caccf4962e36e295207120d78')
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
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beast1: add libbeagle support (#8525)
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variant('beagle', default=True, description='Build with libbeagle support')
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
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depends_on('java', type='run')
beast1: add libbeagle support (#8525)
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depends_on('libbeagle', type=('build', 'link', 'run'), when="+beagle")
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
2018-03-24 04:19:26 +08:00
beast1 package: add version 1.10.4, use url_for_version (#11009)
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def url_for_version(self, ver):
base = 'https://github.com/beast-dev/beast-mcmc/releases/download'
return '{0}/v{1}/BEASTv{1}.tgz'.format(base, ver.dotted)
Libbeagle fixes (#13463) * Fixes for libbeagle This PR fixes a couple of issues with the libbeagle package. - Use args.append('--with-cuda=%s' % self.spec['cuda'].prefix) - Disable the default of compiling with -march=native as Spack now inserts architecture specific flags - Set BEAST_LIB in the beast1 package not in libbeagle. * Use new setup_run_environment method
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def setup_run_environment(self, env):
env.set('BEAST1', self.prefix)
env.set('BEAST_LIB', self.prefix.lib)
beast1: new package (#7544) * beast1: new package * beast1: taking suggestion
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def install(self, spec, prefix):
install_tree('bin', prefix.bin)
install_tree('examples', prefix.examples)
install_tree('images', prefix.images)
install_tree('lib', prefix.lib)
install_tree('doc', prefix.doc)
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