py-pod5: init 0.3.10

spack · May 9, 2024 · 82781c8 · 82781c8
1 parent c7cf5ea
commit 82781c8
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diff --git a/var/spack/repos/builtin/packages/py-lib-pod5/package.py b/var/spack/repos/builtin/packages/py-lib-pod5/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2024 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 *
+import platform
+import sys
+
+arch, os = platform.machine(), sys.platform
+arch64_32, _ = platform.architecture()
+
+class PyLibPod5(PythonPackage):
+    """
+    POD5 is a file format for storing nanopore dna data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format.
+    """
+
+    homepage = "https://github.com/nanoporetech/pod5-file-format"
+    url = "https://files.pythonhosted.org/packages/bd/67/c1720a8e2ccd4442f49320dc238aa5ad5d92266f0aec21e50f5f42d392a6/lib_pod5-0.3.10-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
+
+    maintainers("Pandapip1")
+
+    license("MPL-2.0", checked_by="Pandapip1")
+
+    if (arch == "x86_64" or arch == "x64") and os == "linux":  # Linux on x86_64
+        version(
+            "0.3.10",
+            sha256="6a340e412555855a19b6ffe46409e544e269e89bb4018cd5e0deef2521daddb8",
+            url="https://files.pythonhosted.org/packages/bd/67/c1720a8e2ccd4442f49320dc238aa5ad5d92266f0aec21e50f5f42d392a6/lib_pod5-0.3.10-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl",
+            expand=False
+        )
+    elif arch == "aarch64" and os == "linux":  # Linux on 64-bit ARM
+        version(
+            "0.3.10",
+            sha256="341d27c5d70bfc132906bd8e5231f5bfd0b3963c8025c91e407fceb28c84186c",
+            url="https://files.pythonhosted.org/packages/c5/8b/4ea175749178fa76fd23fbb96d69279bcbcdbaf1c7db0e8d5bbcd44fc422/lib_pod5-0.3.10-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl",
+            expand=False,
+        )
+    elif (arch == "x86_64" or arch == "x64") and os == "darwin":  # MacOS on x86_64
+        version(
+            "0.3.10",
+            sha256="36034e1ffdf35c91e7a4c3c2db878463286417d53ccae0407805f89c6b02f0a9",
+            url="https://files.pythonhosted.org/packages/8a/81/5164a27abafa9db0c725848e7c9a112010e53c5018ef88551bcfc8a0a914/lib_pod5-0.3.10-cp312-cp312-macosx_10_15_universal2.whl",
+            expand=False,
+        )
+    elif not (arch == "x86_64" or arch == "x64") and os == "darwin":  # MacOS on Apple Silicon
+        version(
+            "0.3.10",
+            sha256="438005f335b5ddf7f43a2802e7db2e59e4fe3ec3934bc664a0b53a850e159b3c",
+            url="https://files.pythonhosted.org/packages/c5/a1/e14ac73d099db809b26baff8db0e2dc01e61f13a4d60a516a26affbd3558/lib_pod5-0.3.10-cp312-cp312-macosx_11_0_arm64.whl",
+            expand=False,
+        )
+    elif arch64_32 == "64bit" and os == "win32":  # 64-bit windows
+        version(
+            "0.3.10",
+            sha256="38950890a4555a2b5bb63323090fd0bb4333a536c819d867734f2fe1ff8ce0eb",
+            url="https://files.pythonhosted.org/packages/0c/d1/e8ae7856e7749a57cce33830326dafd41df99756c627e97c18c10ff2a378/lib_pod5-0.3.10-cp312-cp312-win_amd64.whl",
+            expand=False,
+        )
+
+    depends_on("python@3.12", type=("build", "run"), when="@0.3.10:")
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-numpy@1.21.0:", type=("build", "run"))
+
diff --git a/var/spack/repos/builtin/packages/py-pod5/package.py b/var/spack/repos/builtin/packages/py-pod5/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2024 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 PyPod5(PythonPackage):
+    """
+    POD5 is a file format for storing nanopore dna data in an easily accessible way. The format is able to be written in a streaming manner which allows a sequencing instrument to directly write the format.
+    """
+
+    homepage = "https://github.com/nanoporetech/pod5-file-format"
+    url = "https://files.pythonhosted.org/packages/40/7b/5baef5b0627a14d78ec511b9ea5776a0e99ab8c54fb59ff391836de6597e/pod5-0.3.10-py3-none-any.whl"
+
+    maintainers("Pandapip1")
+
+    license("MPL-2.0", checked_by="Pandapip1")
+
+    version("0.3.10", sha256="3ecfce9d4d4b2574242b1effc313f3fd25ef4651c44385beb68ad5ba8f539b11", expand=False)
+
+    depends_on("py-setuptools@61.0:", type="build")
+
+    depends_on("py-lib-pod5@0.3.10", type=("build", "run"))
+    depends_on("py-iso8601", type=("build", "run"))
+    depends_on("py-importlib-metadata", type=("build", "run"))
+    depends_on("py-more-itertools", type=("build", "run"))
+    depends_on("py-numpy@1.21.0:", type=("build", "run"))
+    depends_on("py-typing-extensions", type=("build", "run"))
+    depends_on("py-pyarrow@14.0", type=("build", "run"))
+    depends_on("py-pytz", type=("build", "run"))
+    depends_on("py-packaging", type=("build", "run"))
+    depends_on("py-polars@0.19", type=("build", "run"))
+    depends_on("py-h5py@3.10", type=("build", "run"))
+    depends_on("py-vbz-h5py-plugin", type=("build", "run"))
+    depends_on("py-tqdm", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-polars/package.py b/var/spack/repos/builtin/packages/py-polars/package.py
@@ -15,6 +15,7 @@ class PyPolars(PythonPackage):
     license("MIT")
 
     version("0.20.5", sha256="fa4abc22cee024b5872961ddcd8a13a0a76150df345e21ce4308c2b1a36b47aa")
+    version("0.19.19", sha256="3e904d197aabf36e37fda263470eaf51ec92fb865cdea4f93947713480199303")
 
     # pyproject.toml
     depends_on("py-maturin@1.3.2:", type="build")

diff --git a/var/spack/repos/builtin/packages/py-vbz-h5py-plugin/package.py b/var/spack/repos/builtin/packages/py-vbz-h5py-plugin/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2024 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 PyVbzH5pyPlugin(PythonPackage):
+    """
+    This module provides a plugin to H5Py for the VBZ (de)compression library.
+    """
+
+    homepage = "https://github.com/nanoporetech/vbz_compression"
+    pypi = "vbz_h5py_plugin/vbz_h5py_plugin-1.0.1.tar.gz"
+
+    maintainers("Pandapip1")
+
+    license("MPL-2.0", checked_by="Pandapip1")
+
+    version("1.0.1", sha256="c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341")
+
+    depends_on("py-setuptools@61.0:", type="build")
+
+    depends_on("py-h5py", type=("build", "run"))