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>

6 files changed, 108 insertions, 15 deletions

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"))