sourmash: new package @4.8.2 (#38571)

* sourmash: new package @4.8.2

* sourmash: new package @4.8.2

* py-bitarray: add 2.7.6, 2.7.4

* Update var/spack/repos/builtin/packages/py-bitstring/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update setuptools dependency

* Adding missing deps

* Update var/spack/repos/builtin/packages/sourmash/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Correcting maturin dep

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/sourmash/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/sourmash/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Update var/spack/repos/builtin/packages/sourmash/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Adding dependency types

* Add `@0.14.17` as the last pre-`@1:` release

* Switch to use `python_platlib`

* Update package.py

* Update var/spack/repos/builtin/packages/py-screed/package.py

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

---------

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

var/spack/repos/builtin/packages/py-bitarray/package.py

@@ -11,8 +11,9 @@ class PyBitarray(PythonPackage):
 
     pypi = "bitarray/bitarray-0.8.1.tar.gz"
 
+    version("2.7.6", sha256="3807f9323c308bc3f9b58cbe5d04dc28f34ac32d852999334da96b42f64b5356")
+    version("2.7.4", sha256="143d4f65e1f45a533e13521be1dc557a782317ecf76520eabd5a903b26ecb187")
     version("2.6.0", sha256="56d3f16dd807b1c56732a244ce071c135ee973d3edc9929418c1b24c5439a0fd")
     version("0.8.1", sha256="7da501356e48a83c61f479393681c1bc4b94e5a34ace7e08cb29e7dd9290ab18")
 
-    depends_on("python")
     depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-bitstring/package.py

@@ -10,9 +10,19 @@ class PyBitstring(PythonPackage):
     """Simple construction, analysis and modification of binary data."""
 
     homepage = "http://pythonhosted.org/bitstring"
-    pypi = "bitstring/bitstring-3.1.5.zip"
+    pypi = "bitstring/bitstring-3.1.6.tar.gz"
 
+    version("4.0.2", sha256="a391db8828ac4485dd5ce72c80b27ebac3e7b989631359959e310cd9729723b2")
     version("3.1.5", sha256="c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa")
 
-    # pip silently replaces distutils with setuptools
+    depends_on("py-setuptools", when="@:4.0.1", type="build")
-    depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools@61:", when="@4.0.2:", type="build")
+    depends_on("py-bitarray@2.7.4", when="@4.1:")
+
+    def url_for_version(self, version):
+        url = "https://pypi.org/packages/source/s/bitstring/bitstring-{}.{}"
+        if version < Version("3.1.6"):
+            suffix = "zip"
+        else:
+            suffix = "tar.gz"
+        return url.format(version, suffix)

var/spack/repos/builtin/packages/py-maturin/package.py

@@ -15,6 +15,7 @@ class PyMaturin(PythonPackage):
     pypi = "maturin/maturin-0.13.7.tar.gz"
 
     version("1.1.0", sha256="4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0")
+    version("0.14.17", sha256="fb4e3311e8ce707843235fbe8748a05a3ae166c3efd6d2aa335b53dfc2bd3b88")
     version("0.13.7", sha256="c0a77aa0c57f945649ca711c806203a1b6888ad49c2b8b85196ffdcf0421db77")
 
     depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-screed/package.py

@@ -0,0 +1,20 @@
+# Copyright 2013-2023 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 PyScreed(PythonPackage):
+    """screed: a Python library for loading FASTA and FASTQ sequences."""
+
+    homepage = "https://screed.readthedocs.io/"
+    pypi = "screed/screed-1.1.2.tar.gz"
+
+    version("1.1.2", sha256="734ffa7a8a645286496d895b736f91d6b2988956e2fd42358123d93ec8519b6a")
+
+    depends_on("py-setuptools@48:", type="build")
+    depends_on("py-setuptools-scm@4:5", type="build")
+    depends_on("py-setuptools-scm-git-archive", type="build")
+    depends_on("py-wheel@0.29.0:", type="build")

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

@@ -0,0 +1,48 @@
+# Copyright 2013-2023 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 Sourmash(PythonPackage):
+    """Sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets with
+    k-mer sketches."""
+
+    homepage = "https://sourmash.bio/"
+    pypi = "sourmash/sourmash-4.8.2.tar.gz"
+
+    version("4.8.2", sha256="e0df78032e53ed88977445933ba3481dd10c7d3bd26d019511a6a4e6d7518475")
+
+    depends_on("python@3.8:", type=("build", "run"))
+    # build-only
+    depends_on("py-maturin@0.14.13:0.14", type="build")
+    depends_on("rust", type="build")
+    # general
+    depends_on("py-screed@1.1.2:1", type=("build", "run"))
+    depends_on("py-cffi@1.14.0:", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-deprecation@2.0.6:", type=("build", "run"))
+    depends_on("py-cachetools@4:5", type=("build", "run"))
+    depends_on("py-bitstring@3.1.9:4", type=("build", "run"))
+    depends_on("py-importlib_metadata@3.6:", when="^python@:3.9", type=("build", "run"))
+
+    def install(self, spec, prefix):
+        # build rust libs
+        cargo = Executable("cargo")
+        cargo("build", "--release")
+        # install python package
+        args = std_pip_args + ["--prefix=" + prefix, "."]
+        pip(*args)
+        # move sourmash.so into expected place
+        site_packages = join_path(python_platlib, "sourmash")
+        lib_ext = "dylib" if spec.platform == "Darwin" else "so"
+        install(
+            join_path("target", "release", "libsourmash.{}".format(lib_ext)),
+            join_path(site_packages, "_lowlevel__lib.so"),
+        )
+        # patch invalid read mode
+        filter_file(r"'(.*)'\), 130\)", r"'\1'))", join_path(site_packages, "_lowlevel.py"))