adding 3rd bunch of nf-core deps from update/nextflow-tools (#34563)

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

* adding 3rd bunch of nf-core deps from update/nextflow-tools

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

* py-gxformat2: added comment

* py-lagom: now using github tarballs

* fix for py-lagom

* adding missing deps to py-fastapi-utils

* another fix to py-lagom

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

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

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

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

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

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

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

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

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

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

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

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

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

17 files changed, 359 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-dnspython/package.py b/var/spack/repos/builtin/packages/py-dnspython/package.py
new file mode 100644
index 0000000000..b35a54c62b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-dnspython/package.py
@@ -0,0 +1,19 @@
+# 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 PyDnspython(PythonPackage):
+    """DNS toolkit"""
+
+    homepage = "https://www.dnspython.org"
+    pypi = "dnspython/dnspython-2.2.1.tar.gz"
+
+    version("2.2.1", sha256="0f7569a4a6ff151958b64304071d370daa3243d15941a7beedf0c9fe5105603e")
+
+    depends_on("python@3.6:3", type=("build", "run"))
+    depends_on("py-poetry-core", type="build")
diff --git a/var/spack/repos/builtin/packages/py-edam-ontology/package.py b/var/spack/repos/builtin/packages/py-edam-ontology/package.py
new file mode 100644
index 0000000000..7ef04599c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-edam-ontology/package.py
@@ -0,0 +1,19 @@
+# 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 PyEdamOntology(PythonPackage):
+    """Versioned, Python packaged EDAM ontology (http://edamontology.org/) data."""
+
+    homepage = "https://github.com/edamontology/edam-ontology.py"
+    pypi = "edam-ontology/edam-ontology-1.25.2.tar.gz"
+
+    version("1.25.2", sha256="608c062ecb1ec260637645f73b4157d5abd47b19058a4ccca3bf292e373b8e06")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-fastapi-utils/package.py b/var/spack/repos/builtin/packages/py-fastapi-utils/package.py
new file mode 100644
index 0000000000..baa533fba4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fastapi-utils/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 PyFastapiUtils(PythonPackage):
+    """Reusable utilities for FastAPI"""
+
+    homepage = "https://fastapi-utils.davidmontague.xyz"
+    pypi = "fastapi-utils/fastapi-utils-0.2.1.tar.gz"
+
+    version("0.2.1", sha256="0e6c7fc1870b80e681494957abf65d4f4f42f4c7f70005918e9181b22f1bd759")
+
+    depends_on("python@3.6:3", type=("build", "run"))
+    depends_on("py-poetry@0.12:", type="build")
+
+    depends_on("py-fastapi", type=("build", "run"))
+    depends_on("py-pydantic@1", type=("build", "run"))
+    depends_on("py-sqlalchemy@1.3.12:1", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-fastapi/package.py b/var/spack/repos/builtin/packages/py-fastapi/package.py
new file mode 100644
index 0000000000..d4f3bc0381
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fastapi/package.py
@@ -0,0 +1,22 @@
+# 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 PyFastapi(PythonPackage):
+    """FastAPI framework, high performance, easy to learn, fast to code, ready for production"""
+
+    homepage = "https://github.com/tiangolo/fastapi"
+    pypi = "fastapi/fastapi-0.88.0.tar.gz"
+
+    version("0.88.0", sha256="915bf304180a0e7c5605ec81097b7d4cd8826ff87a02bb198e336fb9f3b5ff02")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-hatchling", type="build")
+
+    depends_on("py-starlette@0.22.0", type=("build", "run"))
+    depends_on("py-pydantic@1.6.2:1.6,1.7.4:1.7,1.8.2:1", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-galaxy-sequence-utils/package.py b/var/spack/repos/builtin/packages/py-galaxy-sequence-utils/package.py
new file mode 100644
index 0000000000..96bf76c941
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-galaxy-sequence-utils/package.py
@@ -0,0 +1,19 @@
+# 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 PyGalaxySequenceUtils(PythonPackage):
+    """Galaxy utilities for manipulating sequences Galaxy project."""
+
+    homepage = "https://github.com/galaxyproject/sequence_utils"
+    pypi = "galaxy-sequence-utils/galaxy_sequence_utils-1.1.5.tar.gz"
+
+    version("1.1.5", sha256="c32bd91f6ff11ad6e8b62f8de309d695ef5c33a782afbf5122c1db7144ef1162")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-gravity/package.py b/var/spack/repos/builtin/packages/py-gravity/package.py
new file mode 100644
index 0000000000..3c94187a27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gravity/package.py
@@ -0,0 +1,26 @@
+# 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 PyGravity(PythonPackage):
+    """Command-line utilities to assist in managing Galaxy servers"""
+
+    homepage = "https://github.com/galaxyproject/gravity"
+    pypi = "gravity/gravity-0.13.6.tar.gz"
+
+    version("0.13.6", sha256="6fc2377e7c61b7db9406fb5b5c70bf72c571fb777f1313fc98787ef4cd007394")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-click", type=("build", "run"))
+    depends_on("py-supervisor", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-ruamel-yaml", type=("build", "run"))
+    depends_on("py-pydantic", type=("build", "run"))
+    depends_on("py-jsonref", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-gunicorn/package.py b/var/spack/repos/builtin/packages/py-gunicorn/package.py
new file mode 100644
index 0000000000..fc50570b63
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gunicorn/package.py
@@ -0,0 +1,19 @@
+# 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 PyGunicorn(PythonPackage):
+    """WSGI HTTP Server for UNIX"""
+
+    homepage = "https://gunicorn.org"
+    pypi = "gunicorn/gunicorn-20.1.0.tar.gz"
+
+    version("20.1.0", sha256="e0a968b5ba15f8a328fdfd7ab1fcb5af4470c28aaf7e55df02a99bc13138e6e8")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools@3:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-gxformat2/package.py b/var/spack/repos/builtin/packages/py-gxformat2/package.py
new file mode 100644
index 0000000000..6384aa76d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gxformat2/package.py
@@ -0,0 +1,24 @@
+# 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 PyGxformat2(PythonPackage):
+    """Galaxy Workflow Format 2 Descriptions"""
+
+    homepage = "https://github.com/galaxyproject/gxformat2"
+    pypi = "gxformat2/gxformat2-0.16.0.tar.gz"
+    # note that requirements.txt is missing from the tarball. it can be found on github.
+
+    version("0.16.0", sha256="16ff5aae1456e0a65c1ed644537e66626ea047a567c8eda19d2a2eb0b20fb752")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-bioblend", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-schema-salad@8.2:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-isa-rwval/package.py b/var/spack/repos/builtin/packages/py-isa-rwval/package.py
new file mode 100644
index 0000000000..cca4f4bf57
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-isa-rwval/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 PyIsaRwval(PythonPackage):
+    """Metadata tracking tools help to manage an increasingly diverse set
+    of life science, environmental and biomedical experiments
+    """
+
+    homepage = "https://github.com/ISA-tools/isa-rwval"
+    pypi = "isa-rwval/isa-rwval-0.10.10.tar.gz"
+
+    version("0.10.10", sha256="3e9fcf37d5e5ff7e92cf28069ecd95d1e62a4025c2d667519da382e5c2258e51")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-networkx@2.5", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-lagom/package.py b/var/spack/repos/builtin/packages/py-lagom/package.py
new file mode 100644
index 0000000000..851f104860
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lagom/package.py
@@ -0,0 +1,21 @@
+# 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 PyLagom(PythonPackage):
+    """Lagom is a dependency injection container
+    designed to give you 'just enough' help with building your dependencies.
+    """
+
+    homepage = "https://lagom-di.readthedocs.io"
+    url = "https://github.com/meadsteve/lagom/archive/refs/tags/2.2.0.tar.gz"
+    git = "https://github.com/meadsteve/lagom.git"
+
+    version("2.2.0", sha256="69f701a2f81d9ca0ea7c93a5b15f7420bbe03d14175ec128959ad82e2b67460b")
+
+    depends_on("py-setuptools@59.6:", type="build")
+    depends_on("py-mypy@0.971", type="build")
diff --git a/var/spack/repos/builtin/packages/py-parsley/package.py b/var/spack/repos/builtin/packages/py-parsley/package.py
new file mode 100644
index 0000000000..99866bb396
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-parsley/package.py
@@ -0,0 +1,18 @@
+# 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 PyParsley(PythonPackage):
+    """Parsing and pattern matching made easy."""
+
+    homepage = "https://launchpad.net/parsley"
+    pypi = "Parsley/Parsley-1.3.tar.gz"
+
+    version("1.3", sha256="9444278d47161d5f2be76a767809a3cbe6db4db822f46a4fd7481d4057208d41")
+
+    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-paste/package.py b/var/spack/repos/builtin/packages/py-paste/package.py
new file mode 100644
index 0000000000..c4f8ab1d6f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-paste/package.py
@@ -0,0 +1,21 @@
+# 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 PyPaste(PythonPackage):
+    """Tools for using a Web Server Gateway Interface stack"""
+
+    homepage = "https://pythonpaste.readthedocs.io"
+    pypi = "Paste/Paste-3.5.2.tar.gz"
+
+    version("3.5.2", sha256="d5a7340c30bcdf3023dd0106c8a5c430dd8fe84aeb8113bc7b93f8dd729f4af6")
+
+    depends_on("python@3:", type=("build", "run"))
+    depends_on("py-setuptools", type=("build", "run"))
+
+    depends_on("py-six@1.4.0:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-pastedeploy/package.py b/var/spack/repos/builtin/packages/py-pastedeploy/package.py
new file mode 100644
index 0000000000..6d8d4d698a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pastedeploy/package.py
@@ -0,0 +1,21 @@
+# 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 PyPastedeploy(PythonPackage):
+    """Load, configure, and compose WSGI applications and servers"""
+
+    homepage = "https://docs.pylonsproject.org/projects/pastedeploy"
+    pypi = "PasteDeploy/PasteDeploy-3.0.1.tar.gz"
+
+    version("3.0.1", sha256="5f4b4d5fddd39b8947ea727161e366bf55b90efc60a4d1dd7976b9031d0b4e5f")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-setuptools@41:", type="build")
+
+    depends_on("py-importlib-metadata", when="^python@:3.7", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-pebble/package.py b/var/spack/repos/builtin/packages/py-pebble/package.py
new file mode 100644
index 0000000000..8da4139d2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pebble/package.py
@@ -0,0 +1,19 @@
+# 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 PyPebble(PythonPackage):
+    """Threading and multiprocessing eye-candy."""
+
+    homepage = "https://github.com/noxdafox/pebble"
+    pypi = "Pebble/Pebble-5.0.3.tar.gz"
+
+    version("5.0.3", sha256="bdcfd9ea7e0aedb895b204177c19e6d6543d9962f4e3402ebab2175004863da8")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
diff --git a/var/spack/repos/builtin/packages/py-pydantic-tes/package.py b/var/spack/repos/builtin/packages/py-pydantic-tes/package.py
new file mode 100644
index 0000000000..e851b9f688
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pydantic-tes/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 PyPydanticTes(PythonPackage):
+    """Pydantic Models for the GA4GH Task Execution Service"""
+
+    homepage = "https://github.com/jmchilton/pydantic-tes"
+    pypi = "pydantic-tes/pydantic-tes-0.1.5.tar.gz"
+
+    version("0.1.5", sha256="557cc77bdbeae86a6bd155af2d0aeaa5050cd9e3f7d9b17b817f14dd814a7423")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-pydantic", type=("build", "run"))
+    depends_on("py-requests", type=("build", "run"))
+    depends_on("py-typing-extensions", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-starlette/package.py b/var/spack/repos/builtin/packages/py-starlette/package.py
new file mode 100644
index 0000000000..6f877ecb70
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-starlette/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 PyStarlette(PythonPackage):
+    """The little ASGI library that shines."""
+
+    homepage = "https://github.com/encode/starlette"
+    pypi = "starlette/starlette-0.23.1.tar.gz"
+
+    version("0.23.1", sha256="8510e5b3d670326326c5c1d4cb657cc66832193fe5d5b7015a51c7b1e1b1bf42")
+    version("0.22.0", sha256="b092cbc365bea34dd6840b42861bdabb2f507f8671e642e8272d2442e08ea4ff")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-hatchling", type="build")
+
+    depends_on("py-anyio@3.4:4", type=("build", "run"))
+    depends_on("py-typing-extensions@3.10.0:", when="^python@:3.9", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-supervisor/package.py b/var/spack/repos/builtin/packages/py-supervisor/package.py
new file mode 100644
index 0000000000..0cc32512c3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-supervisor/package.py
@@ -0,0 +1,19 @@
+# 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 PySupervisor(PythonPackage):
+    """A system for controlling process state under UNIX"""
+
+    homepage = "http://supervisord.org"
+    pypi = "supervisor/supervisor-4.2.4.tar.gz"
+
+    version("4.2.4", sha256="40dc582ce1eec631c3df79420b187a6da276bbd68a4ec0a8f1f123ea616b97a2")
+
+    depends_on("python@3.4:", type=("build", "run"))
+    depends_on("py-setuptools", type=("build", "run"))