Adding first bunch of recipes for dependencies of nf-core-tools (#34537)

* nextflow recipe: added latest stable version

* tower-cli recipe: added latest release

* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli

* recipes nf-tower-agent and nf-tower-cli: small fix

* nf-core-tools recipe: added most py- dependencies

* nf-core-tools: recipe without galaxy-tool-util (for testing)

* fixed typos in py-yacman recipe

* fixed typos in py-pytest-workflow recipe

* fixed typo in nf-core-tools recipe

* fixed typos in py-yacman recipe

* fixes in recipes for py-questionary and py-url-normalize

* fixes to py-yacman recipe

* style fixes to py- packages that are dependencies to nf-core-tools

* fix in py-requests-cache recipe

* added missing dep in py-requests-cache recipe

* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper

* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util

* nf-core-tools: new version with extra dependency

* commit to merge packages on focus from update/nextflow-tools

* nf-core: commenting galaxy dep for this pr

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

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

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

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

* removed nf-core-tools from this branch, will be back at the end

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

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

@@ -0,0 +1,20 @@
+# 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 PyAttmap(PythonPackage):
+    """Key-value mapping that supports nested attribute-style access."""
+
+    homepage = "https://github.com/pepkit/attmap/"
+    pypi = "attmap/attmap-0.13.2.tar.gz"
+
+    version("0.13.2", sha256="fdffa45f8671c13428eb8c3a1702bfdd1123badb99f7af14d72ad53cc7e770de")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-ubiquerg@0.2.1:", type=("build", "run"))

var/spack/repos/builtin/packages/py-cattrs/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 PyCattrs(PythonPackage):
+    """An open source Python library for structuring and unstructuring data."""
+
+    homepage = "https://github.com/python-attrs/cattrs"
+    pypi = "cattrs/cattrs-22.2.0.tar.gz"
+
+    version("22.2.0", sha256="f0eed5642399423cf656e7b66ce92cdc5b963ecafd041d1b24d136fdde7acf6d")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-poetry-core@1.1.0:", type="build")
+
+    depends_on("py-attrs@20:", type=("build", "run"))
+    depends_on("py-typing-extensions", when="^python@:3.7", type=("build", "run"))
+    depends_on("py-exceptiongroup", when="^python@:3.10", type=("build", "run"))

var/spack/repos/builtin/packages/py-exceptiongroup/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 PyExceptiongroup(PythonPackage):
+    """A backport of the BaseExceptionGroup and ExceptionGroup classes from Python 3.11."""
+
+    homepage = "https://github.com/agronholm/exceptiongroup"
+    pypi = "exceptiongroup/exceptiongroup-1.0.4.tar.gz"
+
+    version("1.0.4", sha256="bd14967b79cd9bdb54d97323216f8fdf533e278df937aa2a90089e7d6e06e5ec")
+
+    depends_on("python@3.7:", type=("build", "run"))
+    depends_on("py-flit-scm", type="build")

var/spack/repos/builtin/packages/py-filetype/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 PyFiletype(PythonPackage):
+    """Small and dependency free Python package to infer file type and MIME
+    type checking the magic numbers signature of a file or buffer.
+    """
+
+    homepage = "https://github.com/h2non/filetype.py"
+    pypi = "filetype/filetype-1.2.0.tar.gz"
+
+    version("1.2.0", sha256="66b56cd6474bf41d8c54660347d37afcc3f7d1970648de365c102ef77548aadb")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-flit-scm/package.py

@@ -0,0 +1,25 @@
+# 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 PyFlitScm(PythonPackage):
+    """A PEP 518 build backend that uses setuptools_scm
+    to generate a version file from your version control system,
+    then flit to build the package.
+    """
+
+    homepage = "https://gitlab.com/WillDaSilva/flit_scm"
+    pypi = "flit-scm/flit_scm-1.7.0.tar.gz"
+
+    version("1.7.0", sha256="961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2")
+
+    depends_on("python@3.6:", type=("build", "run"))
+
+    depends_on("py-flit-core@3.5:3", type=("build", "run"))
+    depends_on("py-setuptools-scm@6.4:", type=("build", "run"))
+    depends_on("py-tomli", when="^python@:3.10", type=("build", "run"))

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

@@ -0,0 +1,17 @@
+# 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 PyLogmuse(PythonPackage):
+    """A small logging setup package."""
+
+    homepage = "https://github.com/databio/logmuse/"
+    pypi = "logmuse/logmuse-0.2.7.tar.gz"
+
+    version("0.2.7", sha256="a4692c44ddfa912c3cb149ca4c7545f80119aa7485868fd1412e7c647e9a7e7e")
+
+    depends_on("py-setuptools", type="build")

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

@@ -0,0 +1,20 @@
+# 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 PyOyaml(PythonPackage):
+    """Ordered YAML: a drop-in replacement for PyYAML which preserves dict ordering."""
+
+    homepage = "https://github.com/wimglenn/oyaml"
+    pypi = "oyaml/oyaml-1.0.tar.gz"
+
+    version("1.0", sha256="ed8fc096811f4763e1907dce29c35895d6d5936c4d0400fe843a91133d4744ed")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-pyyaml", type=("build", "run"))

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

@@ -0,0 +1,27 @@
+# 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 PyPiper(PythonPackage):
+    """A lightweight python toolkit for gluing together restartable,
+    robust shell pipelines.
+    """
+
+    homepage = "https://github.com/databio/pypiper"
+    pypi = "piper/piper-0.12.3.tar.gz"
+
+    version("0.12.3", sha256="0ec7d4c4fd9cd1142e87193483c4f92022adbe2cd0f4678f2a1ea8227cdcd9fd")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-attmap@0.12.5:", type=("build", "run"))
+    depends_on("py-logmuse@0.2.4:", type=("build", "run"))
+    depends_on("py-psutil", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-ubiquerg@0.4.5:", type=("build", "run"))
+    depends_on("py-yacman", type=("build", "run"))

var/spack/repos/builtin/packages/py-pytest-workflow/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 PyPytestWorkflow(PythonPackage):
+    """A workflow-system agnostic testing framework
+    that aims to make pipeline/workflow testing easy
+    by using YAML files for the test configuration.
+    """
+
+    homepage = "https://github.com/LUMC/pytest-workflow"
+    pypi = "pytest-workflow/pytest-workflow-1.6.0.tar.gz"
+
+    version("1.6.0", sha256="8fb9fb31a6132c783231afbbbb92941297a42713dcd459694b5efe4a13b8cba7")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools@51:", type="build")
+
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-pytest@5.4.0:", type=("build", "run"))
+    depends_on("py-jsonschema", type=("build", "run"))

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

@@ -0,0 +1,28 @@
+# 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 PyRefgenconf(PythonPackage):
+    """A Python object for standardized reference genome assets."""
+
+    homepage = "https://github.com/refgenie/refgenconf"
+    pypi = "refgenconf/refgenconf-0.12.2.tar.gz"
+
+    version("0.12.2", sha256="6c9f9ecd8b91b4f75a535cfbdbdfb136f2dc9e9864142d07aa0352c61cf0cf78")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-future", type=("build", "run"))
+    depends_on("py-jsonschema@3.0.1:", type=("build", "run"))
+    depends_on("py-pyfaidx", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-requests", type=("build", "run"))
+    depends_on("py-rich@9.0.1:", type=("build", "run"))
+    depends_on("py-yacman@0.8.3:", type=("build", "run"))
+    depends_on("py-tqdm", type=("build", "run"))

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

@@ -0,0 +1,25 @@
+# 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 PyRefgenie(PythonPackage):
+    """Refgenie manages storage, access, and transfer of reference genome resources."""
+
+    homepage = "http://refgenie.databio.org"
+    pypi = "refgenie/refgenie-0.12.1.tar.gz"
+
+    version("0.12.1", sha256="cfd007ed0981e00d019deb49aaea896952341096494165cb8378488850eec451")
+
+    depends_on("python@3.5:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-logmuse@0.2.6:", type=("build", "run"))
+    depends_on("py-piper@0.12.1:", type=("build", "run"))
+    depends_on("py-pyfaidx@0.5.5.2:", type=("build", "run"))
+    depends_on("py-refgenconf@0.12.2:", type=("build", "run"))
+    depends_on("py-yacman@0.8.3:", type=("build", "run"))

var/spack/repos/builtin/packages/py-requests-cache/package.py

@@ -0,0 +1,29 @@
+# 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 PyRequestsCache(PythonPackage):
+    """A persistent HTTP cache that provides an easy way
+    to get better performance with the python requests library.
+    """
+
+    homepage = "https://github.com/requests-cache/requests-cache"
+    pypi = "requests-cache/requests_cache-0.9.7.tar.gz"
+
+    version("0.9.7", sha256="b7c26ea98143bac7058fad6e773d56c3442eabc0da9ea7480af5edfc134ff515")
+
+    depends_on("python@3.7:3", type=("build", "run"))
+    depends_on("py-poetry-core@1.0.0:", type="build")
+
+    depends_on("py-requests@2.22:", type=("build", "run"))
+    depends_on("py-urllib3@1.25.5:", type=("build", "run"))
+    depends_on("py-attrs@21.2:", type=("build", "run"))
+    depends_on("py-cattrs@22.2:", type=("build", "run"))
+    # depends_on("py-platformdirs@2.5:", type=("build", "run"))  # will be in future versions
+    depends_on("py-url-normalize@1.4:", type=("build", "run"))
+    depends_on("py-appdirs@1.4.4:", type=("build", "run"))

var/spack/repos/builtin/packages/py-ubiquerg/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 PyUbiquerg(PythonPackage):
+    """Tools for work (erg) everywhere (ubique)."""
+
+    homepage = "https://github.com/pepkit/ubiquerg"
+    pypi = "ubiquerg/ubiquerg-0.6.2.tar.gz"
+
+    version("0.6.2", sha256="a9b1388799d4c366f956e0c912819099ad8f6cd0e5d890923cdde197f80d14cf")
+
+    depends_on("py-setuptools", type="build")

var/spack/repos/builtin/packages/py-url-normalize/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 PyUrlNormalize(PythonPackage):
+    """URL normalization for Python."""
+
+    homepage = "https://github.com/niksite/url-normalize"
+    pypi = "url-normalize/url-normalize-1.4.3.tar.gz"
+
+    version("1.4.3", sha256="d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2")
+
+    depends_on("python@3.6:3", type=("build", "run"))
+    depends_on("py-poetry@0.12:", type="build")
+
+    depends_on("py-six", type=("build", "run"))

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

@@ -0,0 +1,25 @@
+# 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 PyYacman(PythonPackage):
+    """A YAML configuration manager."""
+
+    homepage = "https://github.com/databio/yacman"
+    pypi = "yacman/yacman-0.8.4.tar.gz"
+
+    version("0.8.4", sha256="807972d7f9251f71401fc4ff6c01734ccdad1f92cefd1fd251336a2a094608bd")
+
+    depends_on("python@3.6:", type=("build", "run"))
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-attmap@0.13.0:", type=("build", "run"))
+    depends_on("py-jsonschema@3.2.0:", type=("build", "run"))
+    depends_on("py-oyaml", type=("build", "run"))
+    depends_on("py-pyyaml@3.13:", type=("build", "run"))
+    depends_on("py-ubiquerg@0.6.1:", type=("build", "run"))