From 6c2df00443a2cd092446c7d84431ae37e64e4296 Mon Sep 17 00:00:00 2001 From: Luke Diorio-Toth Date: Sat, 8 Oct 2022 17:57:45 -0500 Subject: new packages (py-metaphlan, py-hclust2, iqtree2) + updates to others (py-dendropy, py-phylophlan, py-pkgconfig) (#32936) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * added metaphlan v4, cleaned up phylophlan * added iqtree2 * fixed phylophlan, builds now * changed config.yaml to default * fixed style * py-jsonschema: add 4.16.0 and new package py-hatch-fancy-pypi-readme (#32929) * acfl: add v22.1 (#32915) Co-authored-by: Annop Wongwathanarat * Fixup errors introduced by Clingo Pr: (#32905) * re2c depends on cmake on Windows * Winbison properly added to bootstrap package search list * Set CMAKE_HIP_ARCHITECTURES with the value of amdgpu_target (#32901) * libtiff: default to +zlib+jpeg (#32945) * octave: add version 7.2.0 (#32943) * simgrid new releases (#32920) * [rocksdb] Added rtti variant (#32918) * rvs binary path updated for 5.2 rocm release (#32892) * Add checksum for py-pytest-runner 6.0.0 (#32957) * py-einops: add v0.5.0 (#32959) * Replace repo with the NVIDIA one (#32951) * Add checksum for py-tomli 2.0.1 (#32949) * QMCPACK: add @3.15.0 (#32931) * Tidied up configure arguments to use special spack autotools features. (#32930) * casper: old domain fell off, adding github repo (#32928) * unifyfs: pin mercury version; add boost variant (#32911) Mercury has a new version (v2.2) releasing soon that UnifyFS does not build with and hasn't been tested with. This pins UnifyFS to the last version of Mercury used/tested. Add a variant to avoid building/using boost Append -std=gnu99 to cflags if building with gcc@4. Needed for mochi-margo to compile * trilinos: constrain superlu-dist version (#32889) * trilinos: constrain superlu-dist version for 13.x * syntax * FEniCSx: Updates for 0.5.1 (#32665) * Updates for DOLFINx 0.5.1 and associated packages * xtensor needed on anything less than main * Switch back to Python 3.7 minimum. * Might be good to point out in our README how to fix Python version? * Fix basix, xtensor dep * Add numba feature * Fix checksum * Make slepc optional Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * simgrid: add variant and remove flag (#32797) * simgrid: remove std c++11 flag * simgrid: add msg variant * Axom: bring in changes from axom repo (#32643) * bring in changes from axom repo Co-authored-by: white238 Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> * Add checksum for py-pyparsing 3.0.9 (#32952) * rdma-core: fix syntax for external discoverability (#32962) * Add checksum for py-flatbuffers 2.0.7 (#32955) * amrex: add v22.10 (#32966) * Remove CMakePackage.define alias from most packages (#32950) * Bug fix for `ca-certificates-mozilla/package.py` to enable `spack install --source` (#32953) * made suggested changes to iqtree2, py-dendropy, py-metaphlan, and py-pkgconfig. Poetry install still broken * reverted py-pkgconfig deps to poetry-core * made iqtree2 less dedundant, changes to py-dendropy and py-pkgconfig deps Co-authored-by: Manuela Kuhn <36827019+manuelakuhn@users.noreply.github.com> Co-authored-by: Annop Wongwathanarat Co-authored-by: Annop Wongwathanarat Co-authored-by: John W. Parent <45471568+johnwparent@users.noreply.github.com> Co-authored-by: Auriane R <48684432+aurianer@users.noreply.github.com> Co-authored-by: Adam J. Stewart Co-authored-by: Kai Torben Ohlhus Co-authored-by: Vinícius Co-authored-by: Matthieu Dorier Co-authored-by: renjithravindrankannath <94420380+renjithravindrankannath@users.noreply.github.com> Co-authored-by: iarspider Co-authored-by: Paul R. C. Kent Co-authored-by: Brian Van Essen Co-authored-by: snehring <7978778+snehring@users.noreply.github.com> Co-authored-by: Cameron Stanavige Co-authored-by: Cody Balos Co-authored-by: Jack S. Hale Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com> Co-authored-by: Lucas Nesi Co-authored-by: Chris White Co-authored-by: white238 Co-authored-by: Martin Pokorny Co-authored-by: Weiqun Zhang Co-authored-by: Massimiliano Culpo Co-authored-by: Dom Heinzeller --- .../repos/builtin/packages/iqtree2/package.py | 20 +++++++++++ .../repos/builtin/packages/py-dendropy/package.py | 5 +-- .../repos/builtin/packages/py-hclust2/package.py | 23 +++++++++++++ .../repos/builtin/packages/py-metaphlan/package.py | 40 ++++++++++++++++++++++ .../builtin/packages/py-phylophlan/package.py | 31 +++++++++++------ .../repos/builtin/packages/py-pkgconfig/package.py | 4 +-- 6 files changed, 108 insertions(+), 15 deletions(-) create mode 100644 var/spack/repos/builtin/packages/iqtree2/package.py create mode 100644 var/spack/repos/builtin/packages/py-hclust2/package.py create mode 100644 var/spack/repos/builtin/packages/py-metaphlan/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/iqtree2/package.py b/var/spack/repos/builtin/packages/iqtree2/package.py new file mode 100644 index 0000000000..58a35eac72 --- /dev/null +++ b/var/spack/repos/builtin/packages/iqtree2/package.py @@ -0,0 +1,20 @@ +# 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.package import * + + +class Iqtree2(CMakePackage): + """Efficient and versatile phylogenomic software by maximum likelihood""" + + homepage = "http://www.iqtree.org" + url = "https://github.com/iqtree/iqtree2/archive/refs/tags/v2.1.2.tar.gz" + + version("2.1.2", sha256="3aaf5ac7f60d852ac8b733fb82832c049ca48b7203a6a865e99c5af359fcca5a") + + depends_on("boost", type="link") + depends_on("eigen", type="link") + depends_on("zlib", type="link") diff --git a/var/spack/repos/builtin/packages/py-dendropy/package.py b/var/spack/repos/builtin/packages/py-dendropy/package.py index b79a9135dc..48ac925b1a 100644 --- a/var/spack/repos/builtin/packages/py-dendropy/package.py +++ b/var/spack/repos/builtin/packages/py-dendropy/package.py @@ -16,8 +16,9 @@ class PyDendropy(PythonPackage): homepage = "https://www.dendropy.org" pypi = "dendropy/DendroPy-4.3.0.tar.gz" + version("4.5.2", sha256="3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101") version("4.3.0", sha256="bd5b35ce1a1c9253209b7b5f3939ac22beaa70e787f8129149b4f7ffe865d510") version("3.12.0", sha256="38a0f36f2f7aae43ec5599408b0d0a4c80996b749589f025940d955a70fc82d4") - depends_on("python@2.7:,3.4:") - depends_on("py-setuptools", type="build") + depends_on("python@2.7:,3.4:", type=("build", "run")) + depends_on("py-setuptools", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-hclust2/package.py b/var/spack/repos/builtin/packages/py-hclust2/package.py new file mode 100644 index 0000000000..6968f13199 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-hclust2/package.py @@ -0,0 +1,23 @@ +# 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.package import * + + +class PyHclust2(PythonPackage): + """Hclust2 is a handy tool for plotting heat-maps with several useful + options to produce high quality figures that can be used in publication.""" + + homepage = "https://github.com/SegataLab/hclust2/" + pypi = "hclust2/hclust2-1.0.0.tar.gz" + + version("1.0.0", sha256="9667f1d16628940aedd3d1d571b956a6f77795018e3ea4dd83f234419eb0096d") + + depends_on("py-setuptools", type="build") + depends_on("py-numpy", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-pandas", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-metaphlan/package.py b/var/spack/repos/builtin/packages/py-metaphlan/package.py new file mode 100644 index 0000000000..5fcadcc527 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-metaphlan/package.py @@ -0,0 +1,40 @@ +# 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.package import * + + +class PyMetaphlan(PythonPackage): + """MetaPhlAn is a computational tool for profiling the composition of + microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic + shotgun sequencing data (i.e. not 16S) with species-level.""" + + homepage = "https://github.com/biobakery/MetaPhlAn/" + pypi = "MetaPhlAn/MetaPhlAn-4.0.2.tar.gz" + + version("4.0.2", sha256="2549fdf2de97a0024551a7bb8d639613b8a7b612054506c88cdb719353f466ff") + version("3.1.0", sha256="4e7a7a36d07ed6f4f945afc4216db7f691d44a22b059c2404c917a160a687a6b") + + depends_on("python@3.7:", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("py-numpy", type=("build", "run")) + depends_on("py-h5py", type=("build", "run")) + depends_on("py-biom-format", type=("build", "run")) + depends_on("py-biopython", type=("build", "run")) + depends_on("py-pandas", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-hclust2", type=("build", "run"), when="@4.0.2:") + depends_on("py-requests", type=("build", "run")) + depends_on("py-dendropy", type=("build", "run")) + depends_on("py-pysam", type=("build", "run")) + depends_on("py-cmseq", type=("build", "run")) + depends_on("py-phylophlan", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("bowtie2@2.3:", type=("build", "run")) + depends_on("muscle@3.8.1551:", type=("build", "run")) + depends_on("blast-plus@2.6:", type=("build", "run")) + depends_on("raxml@8.2.10:", type=("build", "run")) + depends_on("samtools@1.9:", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-phylophlan/package.py b/var/spack/repos/builtin/packages/py-phylophlan/package.py index 2baf08c8c2..26ea140813 100644 --- a/var/spack/repos/builtin/packages/py-phylophlan/package.py +++ b/var/spack/repos/builtin/packages/py-phylophlan/package.py @@ -3,6 +3,7 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) + from spack.package import * @@ -11,17 +12,25 @@ class PyPhylophlan(PythonPackage): phylogenetic profiling of genomes and metagenomes.""" homepage = "https://github.com/biobakery/phylophlan" - url = "https://github.com/biobakery/phylophlan/archive/refs/tags/3.0.2.tar.gz" + url = "https://github.com/biobakery/phylophlan/archive/refs/tags/3.0.3.tar.gz" + version("3.0.3", sha256="d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054") version("3.0.2", sha256="c342116662bbfbb49f0665291fc7c0be5a0d04a02a7be2da81de0322eb2256b4") - depends_on("python@3:", type=("build", "run")) - depends_on("py-numpy@1.12.1:", type=("build", "run")) - depends_on("py-biopython@1.70:", type=("build", "run")) - depends_on("py-dendropy@4.2.0:", type=("build", "run")) - depends_on("muscle", type=("build", "run")) - depends_on("blast-plus", type=("build", "run")) - depends_on("diamond", type=("build", "run")) - depends_on("py-matplotlib", type=("build", "run")) - depends_on("py-pandas", type=("build", "run")) - depends_on("py-seaborn", type=("build", "run")) + depends_on("python@3.7:", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("py-biopython@1.73:", type=("build", "run")) + depends_on("py-dendropy@4.4.0:", type=("build", "run")) + depends_on("py-matplotlib@3.1.0:", type=("build", "run")) + depends_on("py-numpy@1.15.4:", type=("build", "run")) + depends_on("py-pandas@0.24.2:", type=("build", "run")) + depends_on("py-seaborn@0.9.0:", type=("build", "run")) + depends_on("blast-plus@2.6.0:", type=("build", "run")) + depends_on("diamond@0.9:", type=("build", "run")) + depends_on("trimal@1.4.1:", type=("build", "run")) + depends_on("muscle@3.8.1551:", type=("build", "run")) + depends_on("mafft@7.310:", type=("build", "run")) + depends_on("fasttree@2.1.8:", type=("build", "run")) + depends_on("raxml@8.2.10:", type=("build", "run")) + depends_on("iqtree2", type=("build", "run")) + depends_on("mash", type=("build", "run")) diff --git a/var/spack/repos/builtin/packages/py-pkgconfig/package.py b/var/spack/repos/builtin/packages/py-pkgconfig/package.py index ac1cec73f1..fb1bba14c5 100644 --- a/var/spack/repos/builtin/packages/py-pkgconfig/package.py +++ b/var/spack/repos/builtin/packages/py-pkgconfig/package.py @@ -20,7 +20,7 @@ class PyPkgconfig(PythonPackage): depends_on("python@3.3:", when="@1.5.5:", type=("build", "run")) depends_on("python@2.7,3.3:", when="@1.5:", type=("build", "run")) depends_on("python@2.6:2.7,3.3:", when="@1.4:", type=("build", "run")) - depends_on("py-poetry-core@1:", when="@1.5.5:", type="build") - depends_on("py-poetry-core@0.12:", when="@1.5:", type="build") + depends_on("py-poetry-core@1:", when="@1.5.2:", type="build") + depends_on("py-poetry@0.12:", when="@1.5.0:1.5.1", type="build") depends_on("py-setuptools", when="@:1.4", type="build") depends_on("pkgconfig", type=("build", "run")) -- cgit v1.2.3-70-g09d2