adding 2nd bunch of nf-core deps from update/nextflow-tools (#34562)

* adding 2nd bunch of nf-core deps from update/nextflow-tools

* Update var/spack/repos/builtin/packages/py-a2wsgi/package.py

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
This commit is contained in:
Marco De La Pierre 2022-12-17 06:18:49 +08:00 committed by GitHub
parent 1bf87dbb5d
commit e2c5fe4aa3
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# 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 PyA2wsgi(PythonPackage):
"""Convert WSGI app to ASGI app or ASGI app to WSGI app."""
homepage = "https://github.com/abersheeran/a2wsgi"
pypi = "a2wsgi/a2wsgi-1.6.0.tar.gz"
version("1.6.0", sha256="67a9902db6da72c268a24d4e5d01348f736980a577279b7df801c8902aba8554")
depends_on("python@3.6.2:", type=("build", "run"))
depends_on("py-pdm-pep517@1.0.0:", type=("build", "run"))

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# 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 PyApispec(PythonPackage):
"""A pluggable API specification generator."""
homepage = "https://github.com/marshmallow-code/apispec"
pypi = "apispec/apispec-6.0.2.tar.gz"
version("6.0.2", sha256="e76d80b739edef4be213092a6384ad7fd933ba7d64f6d5a0aff8d4da1bef7887")
depends_on("python@3.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-packaging@21.3:", type=("build", "run"))

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# 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 PyBagitProfile(PythonPackage):
"""A simple Python module for validating BagIt profiles."""
homepage = "https://github.com/bagit-profiles/bagit-profiles-validator"
pypi = "bagit-profile/bagit_profile-1.3.1.tar.gz"
version("1.3.1", sha256="57798cdcf98b32a413edb29382d85f4f8c44d3204940d7e12d84998521a98c3f")
depends_on("python@2.7,3.4:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-bagit", type=("build", "run"))
depends_on("py-requests", type=("build", "run"))

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# 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 PyBagit(PythonPackage):
"""bagit is a Python library and command line utility
for working with BagIt style packages.
"""
homepage = "https://libraryofcongress.github.io/bagit-python"
pypi = "bagit/bagit-1.8.1.tar.gz"
version("1.8.1", sha256="37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c")
depends_on("python@2.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-setuptools-scm", type="build")

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# 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 PyBdbag(PythonPackage):
"""The bdbag utilities are a collection of software programs for working
with BagIt packages that conform to the BDBag and Bagit/RO profiles.
"""
homepage = "https://github.com/fair-research/bdbag/"
pypi = "bdbag/bdbag-1.6.3.tar.gz"
version("1.6.3", sha256="1ad2e4956045cb3d43a6276391ad919e42a90a2443727dbc5b1ac6eeb6d6e3c9")
depends_on("python@2.7:2,3.5:3", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-setuptools-scm@:5", type=("build", "run"))
depends_on("py-pytz", type=("build", "run"))
depends_on("py-tzlocal@2.1", type=("build", "run"))
depends_on("py-certifi", type=("build", "run"))
depends_on("py-requests@2.7:", type=("build", "run"))
depends_on("py-bagit@1.8.1", type=("build", "run"))
depends_on("py-bagit-profile@1.3.1", type=("build", "run"))

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# 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 PyBeaker(PythonPackage):
"""Beaker is a web session and general caching library
that includes WSGI middleware for use in web applications.
"""
homepage = "https://beaker.readthedocs.io"
pypi = "Beaker/Beaker-1.12.0.tar.gz"
version("1.12.0", sha256="2d5f427e3b13259c98c934cab0e428fc1c18a4c4b94acbdae930df7e7f51d1ec")
version("1.11.0", sha256="ad5d1c05027ee3be3a482ea39f8cb70339b41e5d6ace0cb861382754076d187e")
depends_on("python@3.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")

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# 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 PyBioblend(PythonPackage):
"""BioBlend is a Python library for interacting with the Galaxy API."""
homepage = "https://bioblend.readthedocs.io"
pypi = "bioblend/bioblend-1.0.0.tar.gz"
version("1.0.0", sha256="3794288bbf891ae6edc1bcdd9618a3ae16b6ed4a04c946505f7e29f2f28898a5")
depends_on("python@3.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-requests@2.20.0:", type=("build", "run"))
depends_on("py-requests-toolbelt@0.5.1:0.8,0.9.1:", type=("build", "run"))
depends_on("py-tuspy", type=("build", "run"))
depends_on("py-typing-extensions", type=("build", "run"))

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# 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 PyCircus(PythonPackage):
"""Circus is a program that will let you run and watch
multiple processes and sockets.
"""
homepage = "https://github.com/circus-tent/circus"
pypi = "circus/circus-0.18.0.tar.gz"
version("0.18.0", sha256="193ce8224e068ced66724cf483106fb6674b51a57583ac1a0e7ed7a7ee8c71ab")
depends_on("python@3.7:", type=("build", "run"))
depends_on("py-flit-core@3.4:3", type="build")
depends_on("py-psutil", type=("build", "run"))
depends_on("py-pyzmq@17.0:", type=("build", "run"))
depends_on("py-tornado@5.0.2:", type=("build", "run"))

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# 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 PyCloudauthz(PythonPackage):
"""Implements means of authorization delegation on cloud-based resource providers."""
homepage = "https://github.com/galaxyproject/cloudauthz"
pypi = "cloudauthz/cloudauthz-0.6.0.tar.gz"
version("0.6.0", sha256="7e62f3ae04b1842540ca484717d40bd9ec17c6764dd842c1f73f6290b9b54ac1")
depends_on("python@3:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-requests@2.18.4:", type=("build", "run"))
depends_on("py-adal@1.0.2:", type=("build", "run"))

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# 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 PyCloudbridge(PythonPackage):
"""A simple layer of abstraction over multiple cloud providers."""
homepage = "http://cloudbridge.cloudve.org"
pypi = "cloudbridge/cloudbridge-3.1.0.tar.gz"
version("3.1.0", sha256="f9d3c1ae36b14a1c953d36c21a35fa2c72d42831cbbfe6117d13b25e9cccb28c")
depends_on("python@3.4:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-nose@1:", type="build")
depends_on("py-six@1.11:", type=("build", "run"))
depends_on("py-tenacity@6.0:", type=("build", "run"))
depends_on("py-deprecation@2.0.7:", type=("build", "run"))
depends_on("py-pyeventsystem@:1", type=("build", "run"))

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# 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 PyCwlUpgrader(PythonPackage):
"""Common Workflow Language standalone document upgrader"""
homepage = "https://github.com/common-workflow-language/cwl-upgrader"
pypi = "cwl-upgrader/cwl-upgrader-1.2.4.tar.gz"
version("1.2.4", sha256="b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec")
depends_on("python@3.6:3", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-ruamel-yaml@0.16.0:0.17.21", when="^python@3.10:", type=("build", "run"))
depends_on("py-ruamel-yaml@0.15.98:0.17.21", when="^python@3.9:", type=("build", "run"))
depends_on("py-ruamel-yaml@0.15.78:0.17.21", when="^python@3.8:", type=("build", "run"))
depends_on("py-ruamel-yaml@0.15.71:0.17.21", type=("build", "run"))
depends_on("py-schema-salad", type=("build", "run"))

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# 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 PyCwlUtils(PythonPackage):
"""Python Utilities and Autogenerated Classes
for loading and parsing CWL v1.0, CWL v1.1, and CWL v1.2 documents.
"""
homepage = "https://github.com/common-workflow-language/cwl-utils"
pypi = "cwl-utils/cwl-utils-0.21.tar.gz"
version("0.21", sha256="583f05010f7572f3a69310325472ccb6efc2db7f43dc6428d03552e0ffcbaaf9")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-cwl-upgrader@1.2.3:", type=("build", "run"))
depends_on("py-packaging", type=("build", "run"))
depends_on("py-rdflib", type=("build", "run"))
depends_on("py-requests", type=("build", "run"))
depends_on("py-cachecontrol", type=("build", "run"))
depends_on("py-schema-salad@8.3.20220825114525:8", type=("build", "run"))

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# 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 PyCwltool(PythonPackage):
"""Common workflow language reference implementation"""
homepage = "https://github.com/common-workflow-language/cwltool"
pypi = "cwltool/cwltool-3.1.20221201130942.tar.gz"
version(
"3.1.20221201130942",
sha256="0152d8cdf6acaf3620f557b442941f577bff2851d9e2e866e6051ea48a37bdbe",
)
version(
"3.1.20221109155812",
sha256="82676ea315ce84fc4057d92c040af15dde3e897527ea4ae70c1033b0eca20c2a",
)
version(
"3.1.20211107152837",
sha256="ae1cd4626b5330457b1a62bcb2580f36f530264a80222f2cc17cf65899ebf04e",
)
depends_on("python@3.6:3", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-requests@2.6.1:", type=("build", "run"))
depends_on("py-ruamel-yaml@0.15:0.17.21", type=("build", "run"))
depends_on("py-rdflib@4.2.2:6.2", type=("build", "run"))
depends_on("py-shellescape@3.4.1:3.8", type=("build", "run"))
depends_on("py-schema-salad@8.2.20211104054942:8", type=("build", "run"))
depends_on("py-prov@1.5.1", type=("build", "run"))
depends_on("py-bagit@1.6.4:", type=("build", "run"))
depends_on("py-mypy-extensions", type=("build", "run"))
depends_on("py-psutil@5.6.6:", type=("build", "run"))
depends_on("py-typing-extensions", type=("build", "run"))
depends_on("py-coloredlogs", type=("build", "run"))
depends_on("py-pydot@1.4.1:", type=("build", "run"))
depends_on("py-argcomplete", type=("build", "run"))
depends_on("py-pyparsing@:3.0.1,3.0.3:", type=("build", "run"))
depends_on("py-cwl-utils@0.19:", type=("build", "run"))

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# 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 PyDictobj(PythonPackage):
"""A set of Python dictionary objects where keys can be accessed as instance attributes."""
homepage = "https://github.com/grimwm/py-dictobj"
pypi = "dictobj/dictobj-0.4.tar.gz"
version("0.4", sha256="15d6ac1c720350dcce3d01c31882cbc8e4a14cb22a8bca290a18ca7b0c0988f1")
depends_on("py-setuptools", type="build")

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# 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 PyPyeventsystem(PythonPackage):
"""An event driven middleware library for Python."""
homepage = "https://github.com/cloudve/pyeventsystem"
pypi = "pyeventsystem/pyeventsystem-0.1.0.tar.gz"
version("0.1.0", sha256="4a3d199759a040d2cd17f8b4293cc1c3f3c2ae50ae531fb5f9f955a895fca8b9")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")

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# 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 PyRdflibJsonld(PythonPackage):
"""rdflib extension adding JSON-LD parser and serializer"""
homepage = "https://github.com/RDFLib/rdflib-jsonld"
pypi = "rdflib-jsonld/rdflib-jsonld-0.6.2.tar.gz"
version("0.6.2", sha256="107cd3019d41354c31687e64af5e3fd3c3e3fa5052ce635f5ce595fd31853a63")
version("0.6.0", sha256="03af8b5540a8e7bb0dae0d9ba1a3bd7f6435abd82cfb4b3ad5e0cdb1bf45a2a6")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-rdflib@5.0.0:", type=("build", "run"))

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# 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 PySchemaSalad(PythonPackage):
"""Schema Annotations for Linked Avro Data (SALAD)"""
homepage = "https://github.com/common-workflow-language/schema_salad"
pypi = "schema-salad/schema-salad-8.3.20221209165047.tar.gz"
version(
"8.3.20221209165047",
sha256="d97cc9a4d7c4255eb8000bcebaa8ac0d1d31801c921fd4113ab3051c1e326c7c",
)
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools@45:", type="build")
depends_on("py-requests@1:", type=("build", "run"))
depends_on("py-ruamel-yaml@0.17.6:0.17.21", type=("build", "run"))
depends_on("py-rdflib@4.2.2:6", type=("build", "run"))
depends_on("py-mistune@2.0.3:2.0", type=("build", "run"))
depends_on("py-cachecontrol@0.11.7:0.12+filecache", type=("build", "run"))
depends_on("py-setuptools-scm@6.2:+toml", type="build")
depends_on("py-mypy@0.991", type="build")
depends_on("py-black@19.10b0:", type="build")
depends_on("py-types-pkg-resources", type="build")
depends_on("py-types-requests", type="build")
depends_on("py-types-dataclasses", type="build")
depends_on("py-types-setuptools", type="build")

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# 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 PyShellescape(PythonPackage):
"""Shell escape a string to safely use it as a token in a shell command"""
homepage = "https://github.com/chrissimpkins/shellescape"
pypi = "shellescape/shellescape-3.8.1.tar.gz"
version("3.8.1", sha256="40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26")
depends_on("py-setuptools", type="build")

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# 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 PyTuspy(PythonPackage):
"""A Python client for the tus resumable upload protocol -> http://tus.io"""
homepage = "http://github.com/tus/tus-py-client/"
pypi = "tuspy/tuspy-1.0.0.tar.gz"
version("1.0.0", sha256="09a81eba7b0ce4da7870961721892c62f1d62570913bcef6727ef5599e3f4181")
depends_on("python@3:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-future@0.16.0:", type=("build", "run"))
depends_on("py-requests@2.18.4:", type=("build", "run"))
depends_on("py-six@1.11.0:", type=("build", "run"))
depends_on("py-tinydb@3.5.0:", type=("build", "run"))
depends_on("py-aiohttp@3.6.2:", type=("build", "run"))

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# 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 PyTypesDataclasses(PythonPackage):
"""Typing stubs for dataclasses"""
homepage = "https://github.com/python/typeshed"
pypi = "types-dataclasses/types-dataclasses-0.6.6.tar.gz"
version("0.6.6", sha256="4b5a2fcf8e568d5a1974cd69010e320e1af8251177ec968de7b9bb49aa49f7b9")
depends_on("py-setuptools", type="build")

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# 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 PyTypesPkgResources(PythonPackage):
"""Typing stubs for pkg_resources"""
homepage = "https://github.com/python/typeshed"
pypi = "types-pkg-resources/types-pkg_resources-0.1.3.tar.gz"
version("0.1.3", sha256="834a9b8d3dbea343562fd99d5d3359a726f6bf9d3733bccd2b4f3096fbab9dae")
depends_on("py-setuptools", type="build")