From 1bf87dbb5d545d0f8b325c2118bfff91bd1cbc1f Mon Sep 17 00:00:00 2001 From: Marco De La Pierre Date: Sat, 17 Dec 2022 05:28:51 +0800 Subject: 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 * Update var/spack/repos/builtin/packages/py-requests-cache/package.py Co-authored-by: Adam J. Stewart * removed nf-core-tools from this branch, will be back at the end Co-authored-by: Adam J. Stewart --- .../repos/builtin/packages/py-attmap/package.py | 20 +++++++++++++++ .../repos/builtin/packages/py-cattrs/package.py | 23 +++++++++++++++++ .../builtin/packages/py-exceptiongroup/package.py | 19 ++++++++++++++ .../repos/builtin/packages/py-filetype/package.py | 21 ++++++++++++++++ .../repos/builtin/packages/py-flit-scm/package.py | 25 +++++++++++++++++++ .../repos/builtin/packages/py-logmuse/package.py | 17 +++++++++++++ .../repos/builtin/packages/py-oyaml/package.py | 20 +++++++++++++++ .../repos/builtin/packages/py-piper/package.py | 27 ++++++++++++++++++++ .../builtin/packages/py-pytest-workflow/package.py | 26 +++++++++++++++++++ .../builtin/packages/py-refgenconf/package.py | 28 +++++++++++++++++++++ .../repos/builtin/packages/py-refgenie/package.py | 25 +++++++++++++++++++ .../builtin/packages/py-requests-cache/package.py | 29 ++++++++++++++++++++++ .../repos/builtin/packages/py-ubiquerg/package.py | 18 ++++++++++++++ .../builtin/packages/py-url-normalize/package.py | 21 ++++++++++++++++ .../repos/builtin/packages/py-yacman/package.py | 25 +++++++++++++++++++ 15 files changed, 344 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-attmap/package.py create mode 100644 var/spack/repos/builtin/packages/py-cattrs/package.py create mode 100644 var/spack/repos/builtin/packages/py-exceptiongroup/package.py create mode 100644 var/spack/repos/builtin/packages/py-filetype/package.py create mode 100644 var/spack/repos/builtin/packages/py-flit-scm/package.py create mode 100644 var/spack/repos/builtin/packages/py-logmuse/package.py create mode 100644 var/spack/repos/builtin/packages/py-oyaml/package.py create mode 100644 var/spack/repos/builtin/packages/py-piper/package.py create mode 100644 var/spack/repos/builtin/packages/py-pytest-workflow/package.py create mode 100644 var/spack/repos/builtin/packages/py-refgenconf/package.py create mode 100644 var/spack/repos/builtin/packages/py-refgenie/package.py create mode 100644 var/spack/repos/builtin/packages/py-requests-cache/package.py create mode 100644 var/spack/repos/builtin/packages/py-ubiquerg/package.py create mode 100644 var/spack/repos/builtin/packages/py-url-normalize/package.py create mode 100644 var/spack/repos/builtin/packages/py-yacman/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-attmap/package.py b/var/spack/repos/builtin/packages/py-attmap/package.py new file mode 100644 index 0000000000..bc0605d991 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-cattrs/package.py b/var/spack/repos/builtin/packages/py-cattrs/package.py new file mode 100644 index 0000000000..74e76d8f33 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-exceptiongroup/package.py b/var/spack/repos/builtin/packages/py-exceptiongroup/package.py new file mode 100644 index 0000000000..3d9fe0eafa --- /dev/null +++ b/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") diff --git a/var/spack/repos/builtin/packages/py-filetype/package.py b/var/spack/repos/builtin/packages/py-filetype/package.py new file mode 100644 index 0000000000..c2f96a9ffb --- /dev/null +++ b/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") diff --git a/var/spack/repos/builtin/packages/py-flit-scm/package.py b/var/spack/repos/builtin/packages/py-flit-scm/package.py new file mode 100644 index 0000000000..d84ced5583 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-logmuse/package.py b/var/spack/repos/builtin/packages/py-logmuse/package.py new file mode 100644 index 0000000000..70b2a2fb7d --- /dev/null +++ b/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") diff --git a/var/spack/repos/builtin/packages/py-oyaml/package.py b/var/spack/repos/builtin/packages/py-oyaml/package.py new file mode 100644 index 0000000000..171338e114 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-piper/package.py b/var/spack/repos/builtin/packages/py-piper/package.py new file mode 100644 index 0000000000..fa3bfc5438 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-pytest-workflow/package.py b/var/spack/repos/builtin/packages/py-pytest-workflow/package.py new file mode 100644 index 0000000000..10aec98c2d --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-refgenconf/package.py b/var/spack/repos/builtin/packages/py-refgenconf/package.py new file mode 100644 index 0000000000..b0cc62e9c7 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-refgenie/package.py b/var/spack/repos/builtin/packages/py-refgenie/package.py new file mode 100644 index 0000000000..d2a5904a96 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-requests-cache/package.py b/var/spack/repos/builtin/packages/py-requests-cache/package.py new file mode 100644 index 0000000000..e930f9126a --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-ubiquerg/package.py b/var/spack/repos/builtin/packages/py-ubiquerg/package.py new file mode 100644 index 0000000000..ef86cceb60 --- /dev/null +++ b/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") diff --git a/var/spack/repos/builtin/packages/py-url-normalize/package.py b/var/spack/repos/builtin/packages/py-url-normalize/package.py new file mode 100644 index 0000000000..361eb5b1f6 --- /dev/null +++ b/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")) diff --git a/var/spack/repos/builtin/packages/py-yacman/package.py b/var/spack/repos/builtin/packages/py-yacman/package.py new file mode 100644 index 0000000000..9ea5ba633d --- /dev/null +++ b/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")) -- cgit v1.2.3-60-g2f50