new packages (py-metaphlan, py-hclust2, iqtree2) + updates to others (py-dendropy, py-phylophlan, py-pkgconfig) (#32936)

* 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 <annop.wongwathanarat@arm.com>

* 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 <white238@users.noreply.github.com>
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 <annop.wongwathanarat@gmail.com>
Co-authored-by: Annop Wongwathanarat <annop.wongwathanarat@arm.com>
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 <ajstewart426@gmail.com>
Co-authored-by: Kai Torben Ohlhus <k.ohlhus@gmail.com>
Co-authored-by: Vinícius <viniciusvgp@gmail.com>
Co-authored-by: Matthieu Dorier <mdorier@anl.gov>
Co-authored-by: renjithravindrankannath <94420380+renjithravindrankannath@users.noreply.github.com>
Co-authored-by: iarspider <iarspider@gmail.com>
Co-authored-by: Paul R. C. Kent <kentpr@ornl.gov>
Co-authored-by: Brian Van Essen <vanessen1@llnl.gov>
Co-authored-by: snehring <7978778+snehring@users.noreply.github.com>
Co-authored-by: Cameron Stanavige <stanavige1@llnl.gov>
Co-authored-by: Cody Balos <balos1@llnl.gov>
Co-authored-by: Jack S. Hale <mail@jackhale.co.uk>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
Co-authored-by: Lucas Nesi <lucas31nesi@hotmail.com>
Co-authored-by: Chris White <white238@llnl.gov>
Co-authored-by: white238 <white238@users.noreply.github.com>
Co-authored-by: Martin Pokorny <mpokorny@caltech.edu>
Co-authored-by: Weiqun Zhang <WeiqunZhang@lbl.gov>
Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>
Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com>

1 files changed, 40 insertions, 0 deletions

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"))