From e73b19024f0d87878faa9d1455cc72fe8ba108c3 Mon Sep 17 00:00:00 2001 From: snehring <7978778+snehring@users.noreply.github.com> Date: Mon, 16 May 2022 03:23:39 -0500 Subject: bpp-suite and deps: urls to GitHub (#30665) * bpp-core: moving url to github. Fixing compilation issue. * bpp-phyl: moving url to github. * bpp-seq: moving url to github * bpp-popgen: new package * bpp-suite: moving url to github, new version. * bpp-popgen: removing unused cmake_args. --- .../packages/bpp-core/global-graph-limits.patch | 21 +++++++++++++++++++++ .../repos/builtin/packages/bpp-core/package.py | 9 +++++++-- .../repos/builtin/packages/bpp-phyl/package.py | 7 +++++-- .../repos/builtin/packages/bpp-popgen/package.py | 19 +++++++++++++++++++ var/spack/repos/builtin/packages/bpp-seq/package.py | 6 ++++-- .../repos/builtin/packages/bpp-suite/package.py | 8 ++++++-- 6 files changed, 62 insertions(+), 8 deletions(-) create mode 100644 var/spack/repos/builtin/packages/bpp-core/global-graph-limits.patch create mode 100644 var/spack/repos/builtin/packages/bpp-popgen/package.py diff --git a/var/spack/repos/builtin/packages/bpp-core/global-graph-limits.patch b/var/spack/repos/builtin/packages/bpp-core/global-graph-limits.patch new file mode 100644 index 0000000000..7d9a950dfe --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-core/global-graph-limits.patch @@ -0,0 +1,21 @@ +diff --git a/src/Bpp/Graph/GlobalGraph.cpp b/src/Bpp/Graph/GlobalGraph.cpp +index ca2d18f..d681314 100644 +--- a/src/Bpp/Graph/GlobalGraph.cpp ++++ b/src/Bpp/Graph/GlobalGraph.cpp +@@ -42,6 +42,7 @@ + #include + #include + #include ++#include + + #include "../Exceptions.h" + #include "../Text/TextTools.h" +@@ -751,7 +752,7 @@ void GlobalGraph::orientate() + // if none, look for node wih minimum number of fathers + if (it == nextNodes.end()) + { +- size_t nbF = numeric_limits::infinity(); ++ size_t nbF = std::numeric_limits::infinity(); + it = nextNodes.begin(); + + for ( ; it != nextNodes.end(); it++) diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py index e2e19f967e..e091b4fc8f 100644 --- a/var/spack/repos/builtin/packages/bpp-core/package.py +++ b/var/spack/repos/builtin/packages/bpp-core/package.py @@ -10,10 +10,12 @@ class BppCore(CMakePackage): """Bio++ core library.""" homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" - url = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz" + url = "https://github.com/BioPP/bpp-core/archive/refs/tags/v2.4.1.tar.gz" + + maintainers = ['snehring'] version('2.4.1', sha256='1150b8ced22cff23dd4770d7c23fad11239070b44007740e77407f0d746c0af6') - version('2.2.0', sha256='aacd4afddd1584ab6bfa1ff6931259408f1d39958a0bdc5f78bf1f9ee4e98b79') + version('2.2.0', sha256='aacd4afddd1584ab6bfa1ff6931259408f1d39958a0bdc5f78bf1f9ee4e98b79', deprecated=True) depends_on('cmake@2.6:', type='build') @@ -21,5 +23,8 @@ class BppCore(CMakePackage): # resolve ambiguous of 'isnan' function. patch('clarify_isnan.patch', when='%fj') + # This is fixed in master, next release should be fine + patch('global-graph-limits.patch', when='@2.4.1') + def cmake_args(self): return ['-DBUILD_TESTING=FALSE'] diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py index 9036681319..0e50ca6091 100644 --- a/var/spack/repos/builtin/packages/bpp-phyl/package.py +++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py @@ -10,9 +10,12 @@ class BppPhyl(CMakePackage): """Bio++ phylogeny library.""" homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" - url = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz" + url = "https://github.com/BioPP/bpp-phyl/archive/refs/tags/v2.4.1.tar.gz" - version('2.2.0', sha256='f346d87bbc7858924f3c99d7d74eb4a1f7a1b926746c68d8c28e07396c64237b') + maintainers = ['snehring'] + + version('2.4.1', sha256='e7bf7d4570f756b7773904ffa600ffcd77c965553ddb5cbc252092d1da962ff2') + version('2.2.0', sha256='f346d87bbc7858924f3c99d7d74eb4a1f7a1b926746c68d8c28e07396c64237b', deprecated=True) depends_on('cmake@2.6:', type='build') depends_on('bpp-core') diff --git a/var/spack/repos/builtin/packages/bpp-popgen/package.py b/var/spack/repos/builtin/packages/bpp-popgen/package.py new file mode 100644 index 0000000000..d22e947d9c --- /dev/null +++ b/var/spack/repos/builtin/packages/bpp-popgen/package.py @@ -0,0 +1,19 @@ +# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class BppPopgen(CMakePackage): + """The Bio++ Population Genetics Library""" + + homepage = "https://https://github.com/BioPP/bpp-popgen" + url = "https://github.com/BioPP/bpp-popgen/archive/refs/tags/v2.4.1.tar.gz" + + maintainers = ['snehring'] + + version('2.4.1', sha256='03b57d71a63c8fa7f11c085e531d0d691fc1d40d4ea541070dabde0ab3baf413') + + depends_on('bpp-seq') diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py index 69851c268c..8f5a7f97f5 100644 --- a/var/spack/repos/builtin/packages/bpp-seq/package.py +++ b/var/spack/repos/builtin/packages/bpp-seq/package.py @@ -10,10 +10,12 @@ class BppSeq(CMakePackage): """Bio++ seq library.""" homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation" - url = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz" + url = "https://github.com/BioPP/bpp-seq/archive/refs/tags/v2.4.1.tar.gz" + + maintainers = ['snehring'] version('2.4.1', sha256='dbfcb04803e4b7f08f9f159da8a947c91906c3ca8b20683ac193f6dc524d4655') - version('2.2.0', sha256='0927d7fb0301c1b99a7353d5876deadb4a3040776cc74e8fe1c366fe920e7b6b') + version('2.2.0', sha256='0927d7fb0301c1b99a7353d5876deadb4a3040776cc74e8fe1c366fe920e7b6b', deprecated=True) depends_on('cmake@2.6:', type='build') depends_on('bpp-core') diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py index f1c2743803..ae24e8c63a 100644 --- a/var/spack/repos/builtin/packages/bpp-suite/package.py +++ b/var/spack/repos/builtin/packages/bpp-suite/package.py @@ -11,15 +11,19 @@ class BppSuite(CMakePackage): sequence analysis.""" homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite" - url = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz" + url = "https://github.com/BioPP/bppsuite/archive/refs/tags/v2.4.1.tar.gz" - version('2.2.0', sha256='761fa5eec794af221d971ae70fd8c43171ad71a6bb5f20549263a1797b43f138') + maintainers = ['snehring'] + + version('2.4.1', sha256='0485adcc17e37439069d27e4fac144e5ae38036ba21f31e6d21f070ce4ea5199') + version('2.2.0', sha256='761fa5eec794af221d971ae70fd8c43171ad71a6bb5f20549263a1797b43f138', deprecated=True) depends_on('cmake@2.6:', type='build') depends_on('texinfo', type='build') depends_on('bpp-core') depends_on('bpp-seq') depends_on('bpp-phyl') + depends_on('bpp-popgen', when='@2.4.1:') # Clarify isinf's namespace, because Fujitsu compiler can't # resolve ambiguous of 'isinf' function. -- cgit v1.2.3-60-g2f50