Revert "4th chunk of nf-core deps from update/nextflow-tools (#34564)" (#34960)

This reverts commit 4e63d92bc927aeb5380bdc48500abda4cda4b5bd.

19 files changed, 0 insertions, 418 deletions

diff --git a/var/spack/repos/builtin/packages/py-arcp/package.py b/var/spack/repos/builtin/packages/py-arcp/package.py
deleted file mode 100644
index 9764dbd729..0000000000
--- a/var/spack/repos/builtin/packages/py-arcp/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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 PyArcp(PythonPackage):
-    """arcp (Archive and Package) URI parser and generator"""
-
-    homepage = "https://arcp.readthedocs.io"
-    pypi = "arcp/arcp-0.2.1.tar.gz"
-
-    version("0.2.1", sha256="5c17ac7972c9ef82979cc2caf2b3a87c1aefd3fefe9adb8a5dd728ada57715dd")
-
-    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-fabric3/package.py b/var/spack/repos/builtin/packages/py-fabric3/package.py
deleted file mode 100644
index d07b76cd9f..0000000000
--- a/var/spack/repos/builtin/packages/py-fabric3/package.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# 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 PyFabric3(PythonPackage):
-    """Fabric is a simple, Pythonic tool for
-    remote execution and deployment (py2.7/py3.4+ compatible fork).
-    """
-
-    homepage = "https://github.com/mathiasertl/fabric/"
-    pypi = "fabric3/Fabric3-1.14.post1.tar.gz"
-
-    version(
-        "1.14.post1", sha256="647e485ec83f30b587862f92374d6affc217f3d79819d1d7f512e42e7ae51e81"
-    )
-
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-paramiko@2.0:2", type=("build", "run"))
-    depends_on("py-six@1.10.0:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-galaxy2cwl/package.py b/var/spack/repos/builtin/packages/py-galaxy2cwl/package.py
deleted file mode 100644
index 37653eb679..0000000000
--- a/var/spack/repos/builtin/packages/py-galaxy2cwl/package.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# 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 PyGalaxy2cwl(PythonPackage):
-    """Convert a Galaxy workflow to abstract Common Workflow Language (CWL)"""
-
-    homepage = "https://github.com/workflowhub-eu/galaxy2cwl"
-    url = "https://github.com/workflowhub-eu/galaxy2cwl/archive/refs/tags/0.1.4.tar.gz"
-
-    version(
-        "0.1.4",
-        sha256="ceb9024a7bf74c874be216c943cc97343563b1ec78f85fd3ec5b482c64350290",
-    )
-
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-pyyaml@5.3.0:", type=("build", "run"))
-    depends_on("py-gxformat2@0.11.0:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-pycryptodome/package.py b/var/spack/repos/builtin/packages/py-pycryptodome/package.py
deleted file mode 100644
index 1a4b8d4ad2..0000000000
--- a/var/spack/repos/builtin/packages/py-pycryptodome/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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 PyPycryptodome(PythonPackage):
-    """Cryptographic library for Python"""
-
-    homepage = "https://www.pycryptodome.org"
-    pypi = "pycryptodome/pycryptodome-3.16.0.tar.gz"
-
-    version("3.16.0", sha256="0e45d2d852a66ecfb904f090c3f87dc0dfb89a499570abad8590f10d9cffb350")
-
-    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-pylibmagic/package.py b/var/spack/repos/builtin/packages/py-pylibmagic/package.py
deleted file mode 100644
index 1482de4c2e..0000000000
--- a/var/spack/repos/builtin/packages/py-pylibmagic/package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# 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 PyPylibmagic(PythonPackage):
-    """scikit-build project with CMake for compiling libmagic"""
-
-    homepage = "https://github.com/kratsg/pylibmagic"
-    pypi = "pylibmagic/pylibmagic-0.2.2.tar.gz"
-
-    version("0.2.2", sha256="17551b5259db4045c63e595577d42df172e35147e26160a47f4a5ba3933281e7")
-
-    depends_on("python@3.7:", type=("build", "run"))
-    depends_on("py-setuptools@42:", type="build")
-    depends_on("py-setuptools_scm@3.4:+toml", type="build")
-    depends_on("py-scikit-build", type="build")
-    depends_on("cmake", type="build")
-    depends_on("ninja", type="build")
-
-    depends_on("py-importlib-resources", when="^python@:3.8", type=("build", "run"))
-    depends_on("py-typing-extensions@3.7:", when="^python@:3.7", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-python-jose/package.py b/var/spack/repos/builtin/packages/py-python-jose/package.py
deleted file mode 100644
index 2a3905ae54..0000000000
--- a/var/spack/repos/builtin/packages/py-python-jose/package.py
+++ /dev/null
@@ -1,23 +0,0 @@
-# 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 PyPythonJose(PythonPackage):
-    """JOSE implementation in Python"""
-
-    homepage = "http://github.com/mpdavis/python-jose"
-    pypi = "python-jose/python-jose-3.3.0.tar.gz"
-
-    version("3.3.0", sha256="55779b5e6ad599c6336191246e95eb2293a9ddebd555f796a65f838f07e5d78a")
-
-    depends_on("python@3.6:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-rsa", type=("build", "run"))
-    depends_on("py-ecdsa@:0.14.1,0.16.0:", type=("build", "run"))
-    depends_on("py-pyasn1", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-python-multipart/package.py b/var/spack/repos/builtin/packages/py-python-multipart/package.py
deleted file mode 100644
index 6970cbbf89..0000000000
--- a/var/spack/repos/builtin/packages/py-python-multipart/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# 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 PyPythonMultipart(PythonPackage):
-    """A streaming multipart parser for Python"""
-
-    homepage = "https://github.com/andrew-d/python-multipart"
-    pypi = "python-multipart/python-multipart-0.0.5.tar.gz"
-
-    version("0.0.5", sha256="f7bb5f611fc600d15fa47b3974c8aa16e93724513b49b5f95c81e6624c83fa43")
-
-    depends_on("python@:3.6", when="@:0.0.5", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-six@1.4.0:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-python3-openid/package.py b/var/spack/repos/builtin/packages/py-python3-openid/package.py
deleted file mode 100644
index fb4587099a..0000000000
--- a/var/spack/repos/builtin/packages/py-python3-openid/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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 PyPython3Openid(PythonPackage):
-    """OpenID support for modern servers and consumers."""
-
-    homepage = "https://github.com/necaris/python3-openid"
-    pypi = "python3-openid/python3-openid-3.2.0.tar.gz"
-
-    version("3.2.0", sha256="33fbf6928f401e0b790151ed2b5290b02545e8775f982485205a066f874aaeaf")
-
-    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-pyuwsgi/package.py b/var/spack/repos/builtin/packages/py-pyuwsgi/package.py
deleted file mode 100644
index 3e6f8cf7cd..0000000000
--- a/var/spack/repos/builtin/packages/py-pyuwsgi/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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 PyPyuwsgi(PythonPackage):
-    """The uWSGI server"""
-
-    homepage = "https://uwsgi-docs.readthedocs.io"
-    pypi = "pyuwsgi/pyuwsgi-2.0.21.tar.gz"
-
-    version("2.0.21", sha256="211e8877f5191e347ba905232d04ab30e05ce31ba7a6dac4bfcb48de9845bb52")
-
-    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-rocrate/package.py b/var/spack/repos/builtin/packages/py-rocrate/package.py
deleted file mode 100644
index 89c68c21ca..0000000000
--- a/var/spack/repos/builtin/packages/py-rocrate/package.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# 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 PyRocrate(PythonPackage):
-    """RO-Crate metadata generator/parser"""
-
-    homepage = "https://github.com/ResearchObject/ro-crate-py/"
-    pypi = "rocrate/rocrate-0.7.0.tar.gz"
-
-    version("0.7.0", sha256="f7537132f45b724bfa6a212b2ed3daa0aaee1d602a773f0f049b8ca9a14958e1")
-
-    depends_on("python@3.7:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-requests", type=("build", "run"))
-    depends_on("py-arcp@0.2.1", type=("build", "run"))
-    depends_on("py-galaxy2cwl", type=("build", "run"))
-    depends_on("py-jinja2", type=("build", "run"))
-    depends_on("py-python-dateutil", type=("build", "run"))
-    depends_on("py-click", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-routes/package.py b/var/spack/repos/builtin/packages/py-routes/package.py
deleted file mode 100644
index 8dd7de3049..0000000000
--- a/var/spack/repos/builtin/packages/py-routes/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# 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 PyRoutes(PythonPackage):
-    """Routing Recognition and Generation Tools"""
-
-    homepage = "https://routes.readthedocs.io/"
-    pypi = "routes/Routes-2.5.1.tar.gz"
-
-    version("2.5.1", sha256="b6346459a15f0cbab01a45a90c3d25caf980d4733d628b4cc1952b865125d053")
-
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-six", type=("build", "run"))
-    depends_on("py-repoze-lru@0.3:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-social-auth-core/package.py b/var/spack/repos/builtin/packages/py-social-auth-core/package.py
deleted file mode 100644
index 1db319e0e3..0000000000
--- a/var/spack/repos/builtin/packages/py-social-auth-core/package.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# 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 PySocialAuthCore(PythonPackage):
-    """Python social authentication made simple."""
-
-    homepage = "https://github.com/python-social-auth/social-core"
-    pypi = "social-auth-core/social-auth-core-4.3.0.tar.gz"
-
-    version("4.3.0", sha256="4686f0e43cf12954216875a32e944847bb1dc69e7cd9573d16a9003bb05ca477")
-    version("4.0.3", sha256="694eb355825cd72d3346afb816dd899493be1a8ee7405945d2e989cabed10cf2")
-
-    variant("openidconnect", default=False, description="Install requirements for openidconnect")
-
-    depends_on("python@3.6:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-requests@2.9.1:", type=("build", "run"))
-    depends_on("py-oauthlib@1.0.3:", type=("build", "run"))
-    depends_on("py-requests-oauthlib@0.6.1:", type=("build", "run"))
-    depends_on("py-pyjwt@2.0.0:", type=("build", "run"))
-    depends_on("py-cryptography@1.4:", type=("build", "run"))
-    depends_on("py-defusedxml@0.5.0:", type=("build", "run"))
-    depends_on("py-python3-openid@3.0.10:", type=("build", "run"))
-
-    depends_on("py-python-jose@3.0.0:", when="+openidconnect", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy-migrate/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy-migrate/package.py
deleted file mode 100644
index c059d4a56d..0000000000
--- a/var/spack/repos/builtin/packages/py-sqlalchemy-migrate/package.py
+++ /dev/null
@@ -1,25 +0,0 @@
-# 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 PySqlalchemyMigrate(PythonPackage):
-    """Database schema migration for SQLAlchemy"""
-
-    homepage = "http://www.openstack.org/"
-    pypi = "sqlalchemy-migrate/sqlalchemy-migrate-0.13.0.tar.gz"
-
-    version("0.13.0", sha256="0bc02e292a040ade5e35a01d3ea744119e1309cdddb704fdb99bac13236614f8")
-
-    depends_on("py-setuptools", type="build")
-    depends_on("py-pbr@1.8:", type="build")
-
-    depends_on("py-sqlalchemy@0.9.6:", type=("build", "run"))
-    depends_on("py-decorator", type=("build", "run"))
-    depends_on("py-six@1.7.0:", type=("build", "run"))
-    depends_on("py-sqlparse", type=("build", "run"))
-    depends_on("py-tempita@0.4:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-sqlitedict/package.py b/var/spack/repos/builtin/packages/py-sqlitedict/package.py
deleted file mode 100644
index 6d614d1bab..0000000000
--- a/var/spack/repos/builtin/packages/py-sqlitedict/package.py
+++ /dev/null
@@ -1,19 +0,0 @@
-# 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 PySqlitedict(PythonPackage):
-    """Persistent dict in Python, backed up by sqlite3 and pickle, multithread-safe."""
-
-    homepage = "https://github.com/piskvorky/sqlitedict"
-    pypi = "sqlitedict/sqlitedict-2.1.0.tar.gz"
-
-    version("2.1.0", sha256="03d9cfb96d602996f1d4c2db2856f1224b96a9c431bdd16e78032a72940f9e8c")
-
-    depends_on("python@3.7:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-starlette-context/package.py b/var/spack/repos/builtin/packages/py-starlette-context/package.py
deleted file mode 100644
index c63f47538e..0000000000
--- a/var/spack/repos/builtin/packages/py-starlette-context/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# 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 PyStarletteContext(PythonPackage):
-    """Access context in Starlette"""
-
-    homepage = "https://github.com/tomwojcik/starlette-context"
-    pypi = "starlette-context/starlette_context-0.3.5.tar.gz"
-
-    version("0.3.5", sha256="e6b9f905823860e9e36c013dbfcf770562f3b88bec21cb861fef2e0bd0615697")
-
-    depends_on("python@3.7:", type=("build", "run"))
-    depends_on("py-setuptools", type="build")
-
-    depends_on("py-starlette", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-tempita/package.py b/var/spack/repos/builtin/packages/py-tempita/package.py
deleted file mode 100644
index 5df1af2de2..0000000000
--- a/var/spack/repos/builtin/packages/py-tempita/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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 PyTempita(PythonPackage):
-    """A very small text templating language"""
-
-    homepage = "https://pypi.org/project/Tempita"
-    pypi = "tempita/Tempita-0.5.2.tar.gz"
-
-    version("0.5.2", sha256="cacecf0baa674d356641f1d406b8bff1d756d739c46b869a54de515d08e6fc9c")
-
-    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-tuswsgi/package.py b/var/spack/repos/builtin/packages/py-tuswsgi/package.py
deleted file mode 100644
index 4edad8b1c0..0000000000
--- a/var/spack/repos/builtin/packages/py-tuswsgi/package.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# 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 PyTuswsgi(PythonPackage):
-    """python wsgi filter for tus protocol 1.0.0"""
-
-    homepage = "https://github.com/mvdbeek/tusfilter"
-    url = "https://pypi.io/packages/py2.py3/t/tuswsgi/tuswsgi-0.5.4-py2.py3-none-any.whl"
-
-    version(
-        "0.5.4",
-        sha256="f681a386254a161a97301a67c01ee7da77419c007d9bc43dbd48d5a987491a5e",
-        expand=False,
-    )
-
-    depends_on("python@3.6:", type=("build", "run"))
-
-    depends_on("py-webob", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-uvicorn/package.py b/var/spack/repos/builtin/packages/py-uvicorn/package.py
deleted file mode 100644
index a534ce066e..0000000000
--- a/var/spack/repos/builtin/packages/py-uvicorn/package.py
+++ /dev/null
@@ -1,23 +0,0 @@
-# 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 PyUvicorn(PythonPackage):
-    """The lightning-fast ASGI server."""
-
-    homepage = "https://www.uvicorn.org/"
-    pypi = "uvicorn/uvicorn-0.20.0.tar.gz"
-
-    version("0.20.0", sha256="a4e12017b940247f836bc90b72e725d7dfd0c8ed1c51eb365f5ba30d9f5127d8")
-
-    depends_on("python@3.7:", type=("build", "run"))
-    depends_on("py-hatchling", type="build")
-
-    depends_on("py-click@7.0:", type=("build", "run"))
-    depends_on("py-h11@0.8:", type=("build", "run"))
-    depends_on("py-typing-extensions", when="^python@:3.7", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-zipstream-new/package.py b/var/spack/repos/builtin/packages/py-zipstream-new/package.py
deleted file mode 100644
index e93d8d1dc2..0000000000
--- a/var/spack/repos/builtin/packages/py-zipstream-new/package.py
+++ /dev/null
@@ -1,18 +0,0 @@
-# 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 PyZipstreamNew(PythonPackage):
-    """Zipfile generator that takes input files as well as streams"""
-
-    homepage = "https://github.com/arjan-s/python-zipstream"
-    pypi = "zipstream-new/zipstream-new-1.1.8.tar.gz"
-
-    version("1.1.8", sha256="b031fe181b94e51678389d26b174bc76382605a078d7d5d8f5beae083f111c76")
-
-    depends_on("py-setuptools", type="build")