diff --git a/.gitignore b/.gitignore index d1010bd..12ceede 100644 --- a/.gitignore +++ b/.gitignore @@ -12,3 +12,4 @@ venv .eggs .idea .ipynb_checkpoints +_version.py diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index ab7589d..0000000 --- a/.pylintrc +++ /dev/null @@ -1,50 +0,0 @@ -[MESSAGES CONTROL] -disable=fixme,invalid-name,len-as-condition,no-else-return - -[FORMAT] -# Regexp for a line that is allowed to be longer than the limit. -ignore-long-lines=\bhttps?://\S -# Maximum number of characters on a single line. -max-line-length=100 - -[DESIGN] -# Maximum number of arguments for function / method -max-args=8 -# Argument names that match this expression will be ignored. Default to name -# with leading underscore -ignored-argument-names=_.* -# Maximum number of locals for function / method body -max-locals=15 -# Maximum number of return / yield for function / method body -max-returns=6 -# Maximum number of branch for function / method body -max-branches=12 -# Maximum number of statements in function / method body -max-statements=50 -# Maximum number of parents for a class (see R0901). -max-parents=7 -# Maximum number of attributes for a class (see R0902). -max-attributes=40 -# Minimum number of public methods for a class (see R0903). -min-public-methods=0 -# Maximum number of public methods for a class (see R0904). -max-public-methods=60 - -# Checks for similarities and duplicated code. This computation may be memory / CPU -# intensive, so you should disable it if you experience problems. -[SIMILARITIES] -# Minimum lines number of a similarity. -min-similarity-lines=25 -# Ignore comments when computing similarities. -ignore-comments=yes -# Ignore docstrings when computing similarities. -ignore-docstrings=yes - -[TYPECHECK] -# List of classes names for which member attributes should not be checked -# (useful for classes with attributes dynamically set). - -#as of numpy 1.8.0, name resolution seems to be a problem. Ignore lookups in numpy -ignored-classes=numpy,list - -extension-pkg-whitelist=numpy,lxml diff --git a/AUTHORS.txt b/AUTHORS.txt new file mode 100644 index 0000000..bef05e9 --- /dev/null +++ b/AUTHORS.txt @@ -0,0 +1 @@ +Gianluca Ficarelli diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..ed634aa --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright 2005-2023 Blue Brain Project/EPFL + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.rst b/README.rst index b42f500..73e789e 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,11 @@ +|banner| + +|build_status| |license| |coverage| |docs| |DOI| + blueetl-core ============ -Core transformations for BlueETL +Core transformations for BlueETL. Introduction @@ -9,7 +13,7 @@ Introduction ``BlueETL-core`` automatically registers Pandas accessors using the ``.etl`` namespace, that can be useful to simplify some recurring operations on Pandas DataFrames, Series, and Indexes. -It provides the core transformations used by `BlueETL `__, a package that can help analyse multiple simulations in a Simulation Campaign. +It provides the core transformations used by `BlueETL `__, a package that can help analyse multiple simulations in a Simulation Campaign. Installation @@ -20,8 +24,8 @@ Installation pip install -U blueetl-core -Usage ------ +Examples +-------- To use the Core Transformations provided by the ``.etl`` accessor with any Pandas DataFrame or Series, it's enough to import BlueETL or BlueETL-core, and call the desired methods. @@ -36,12 +40,52 @@ For example: df = pd.DataFrame({"a": [0, 1, 2], "b": [3, 4, 5]}) df = df.etl.q(a=1) -See `this Jupyter notebook `__ for more information and examples. +See `this Jupyter notebook `__ for more information and examples. + + +Contribution Guidelines +----------------------- + +See ``__. + + +Citation +-------- + +When you use this software, we kindly ask you to cite the following DOI: + +.. image:: https://zenodo.org/badge/xxxxxxxx.svg + :target: https://zenodo.org/badge/latestdoi/xxxxxxxx + + +Acknowledgment +-------------- + +The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. + +For license and authors, see ``__ and ``__ respectively. + +Copyright © 2023 Blue Brain Project/EPFL + + +.. |banner| image:: doc/source/_images/BlueETL.jpeg + +.. |build_status| image:: https://github.com/BlueBrain/blueetl-core/actions/workflows/run-tox.yml/badge.svg + :alt: Build Status + +.. |license| image:: https://img.shields.io/pypi/l/blueetl-core + :target: https://github.com/BlueBrain/blueetl-core/blob/main/LICENSE.txt + :alt: License +.. |coverage| image:: https://codecov.io/github/BlueBrain/blueetl-core/coverage.svg?branch=main + :target: https://codecov.io/github/BlueBrain/blueetl-core?branch=main + :alt: codecov.io -Reporting issues ----------------- +.. |docs| image:: https://readthedocs.org/projects/blueetl-core/badge/?version=latest + :target: https://blueetl-core.readthedocs.io/ + :alt: documentation status -``BlueETL-core`` is maintained by the BlueBrain NSE team. +.. |DOI| image:: https://zenodo.org/badge/DOI/xxx/zenodo.yyy.svg + :target: https://doi.org/xxx/zenodo.yyy + :alt: DOI -Should you face any issue with using it, please submit a ticket to our `issue tracker `__. diff --git a/doc/source/_images/BlueETL.jpeg b/doc/source/_images/BlueETL.jpeg new file mode 100644 index 0000000..7885d45 Binary files /dev/null and b/doc/source/_images/BlueETL.jpeg differ diff --git a/pyproject.toml b/pyproject.toml index 5710996..3b9bc41 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,57 @@ +[build-system] +requires = ["setuptools>=64", "setuptools_scm>=8"] +build-backend = "setuptools.build_meta" + +[project] +name = "blueetl-core" +description = "Core transformations for BlueETL" +readme = "README.rst" +requires-python = ">=3.9" +license = { file = "LICENSE.txt" } +authors = [ + { name = "Blue Brain Project, EPFL" }, +] +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Intended Audience :: Education", + "Intended Audience :: Science/Research", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] +dependencies = [ + "numpy>=1.19.4", + "pandas>=1.3.0", + "joblib>=1.3.1", + "packaging>=21.3", +] +dynamic = ["version"] + +[project.optional-dependencies] +docs = [ + "sphinx", + "sphinx-bluebrain-theme", +] + +[project.urls] +Homepage = "https://github.com/BlueBrain/blueetl-core" +Repository = "https://github.com/BlueBrain/blueetl-core.git" +Documentation = "https://blueetl-core.readthedocs.io/" +Tracker = "https://github.com/BlueBrain/blueetl-core/issues" + +[tool.setuptools.packages.find] +where = ["src"] + +[tool.setuptools_scm] +version_file = "src/blueetl_core/_version.py" + [tool.black] line-length = 100 -target-version = ['py39'] -include = 'blueetl_core\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$' +target-version = ["py39"] +include = 'src/blueetl_core\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$' [tool.isort] profile = "black" @@ -39,8 +89,76 @@ source = [ [tool.coverage.run] branch = true parallel = false +omit = [ + "src/blueetl_core/_version.py", +] [tool.coverage.report] show_missing = true precision = 0 fail_under = 80 + +[tool.pydocstyle] +# D413: no blank line after last section +add_ignore = "D413" +convention = "google" + +[tool.pylint.main] +# Files or directories to be skipped. They should be base names, not paths. +ignore = ["CVS", "_version.py"] +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code. +extension-pkg-allow-list = ["numpy", "lxml"] +# List of plugins (as comma separated values of python module names) to load, +# usually to register additional checkers. +load-plugins = [] + +[tool.pylint.design] +# Maximum number of arguments for function / method. +max-args = 8 +# Maximum number of attributes for a class (see R0902). +max-attributes = 40 +# Maximum number of boolean expressions in an if statement (see R0916). +#max-bool-expr = 5 +# Maximum number of branch for function / method body. +max-branches = 12 +# Maximum number of locals for function / method body. +max-locals = 15 +# Maximum number of parents for a class (see R0901). +max-parents = 7 +# Minimum number of public methods for a class (see R0903). +min-public-methods = 0 +# Maximum number of public methods for a class (see R0904). +max-public-methods = 60 +# Maximum number of return / yield for function / method body. +max-returns = 6 +# Maximum number of statements in function / method body. +max-statements = 50 + +[tool.pylint.format] +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines = "\\bhttps?://\\S" +# Maximum number of characters on a single line. +max-line-length = 100 + +[tool.pylint."messages control"] +disable = ["fixme", "invalid-name", "len-as-condition", "no-else-return"] + +[tool.pylint.similarities] +# Comments are removed from the similarity computation +ignore-comments = true +# Docstrings are removed from the similarity computation +ignore-docstrings = true +# Minimum lines number of a similarity. +min-similarity-lines = 25 + +[tool.pylint.typecheck] +# List of class names for which member attributes should not be checked (useful +# for classes with dynamically set attributes). This supports the use of +# qualified names. +ignored-classes = ["numpy", "list"] + +[tool.pylint.variables] +# Argument names that match this expression will be ignored. +ignored-argument-names = "_.*" diff --git a/setup.py b/setup.py index decb8a8..6068493 100644 --- a/setup.py +++ b/setup.py @@ -1,51 +1,3 @@ -#!/usr/bin/env python -import importlib.util -from pathlib import Path +from setuptools import setup -from setuptools import find_namespace_packages, setup - -spec = importlib.util.spec_from_file_location( - "blueetl_core.version", - "src/blueetl_core/version.py", -) -module = importlib.util.module_from_spec(spec) -spec.loader.exec_module(module) -VERSION = module.__version__ - -setup( - name="blueetl-core", - author="bbp-ou-nse", - author_email="bbp-ou-nse@groupes.epfl.ch", - version=VERSION, - description="Core transformations for BlueETL", - long_description=Path("README.rst").read_text(encoding="utf-8"), - long_description_content_type="text/x-rst", - url="https://bbpteam.epfl.ch/documentation/projects/blueetl-core", - project_urls={ - "Tracker": "https://bbpteam.epfl.ch/project/issues/projects/NSETM/issues", - "Source": "https://github.com/BlueBrain/blueetl-core.git", - }, - license="BBP-internal-confidential", - install_requires=[ - "numpy>=1.19.4", - "pandas>=1.3.0", - "joblib>=1.3.1", - "packaging>=21.3", - ], - packages=find_namespace_packages(where="src"), - package_dir={"": "src"}, - include_package_data=True, - python_requires=">=3.9", - extras_require={"docs": ["sphinx", "sphinx-bluebrain-theme"]}, - classifiers=[ - "Development Status :: 2 - Pre-Alpha", - "Intended Audience :: Education", - "Intended Audience :: Science/Research", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Topic :: Scientific/Engineering :: Bio-Informatics", - ], -) +setup() diff --git a/src/blueetl_core/__init__.py b/src/blueetl_core/__init__.py index 52785c5..44e42c7 100644 --- a/src/blueetl_core/__init__.py +++ b/src/blueetl_core/__init__.py @@ -1,6 +1,6 @@ """BlueETL core transformations.""" +from blueetl_core._version import __version__ # noqa from blueetl_core.etl import register_accessors -from blueetl_core.version import __version__ # noqa # registration of Pandas accessors register_accessors() diff --git a/src/blueetl_core/version.py b/src/blueetl_core/version.py deleted file mode 100644 index 4b4c289..0000000 --- a/src/blueetl_core/version.py +++ /dev/null @@ -1,4 +0,0 @@ -"""Package version.""" - -VERSION = "0.1.3" -__version__ = VERSION diff --git a/tox.ini b/tox.ini index 01f8291..ff68f51 100644 --- a/tox.ini +++ b/tox.ini @@ -29,11 +29,6 @@ commands = coverage xml coverage html -[testenv:check-version] -skip_install = true -deps = bbp-nse-ci -commands = do_release.py -p . check-version - [testenv:check-packaging] skip_install = true deps = @@ -51,7 +46,7 @@ allowlist_externals = rm deps = ruff pycodestyle - pydocstyle + pydocstyle[toml] pylint isort black[jupyter] @@ -94,11 +89,6 @@ allowlist_externals = make # E501: line too long (checked with pylint) ignore = E203,E731,W503,W504,E501 -[pydocstyle] -# D413: no blank line after last section -add-ignore = D413 -convention = google - [gh-actions] python = 3.9: py39