From f92632714c7b97e53047061126c23f92ea96bd00 Mon Sep 17 00:00:00 2001 From: MikeG Date: Wed, 12 Jun 2024 11:04:55 +0200 Subject: [PATCH] OSS (#1) * add SPDX and CONTRIBUTING.md * add LICENSE.txt * update README.md with copyright * add github actions * switch to setuptools_scm using pyproject.yaml --- .github/workflows/sdist.yml | 48 ++++++++ .github/workflows/tox.yml | 38 ++++++ .gitlab-ci.yml | 3 - .pylintrc | 49 -------- CONTRIBUTING.md | 108 +++++++++++++++++ LICENSE.txt | 202 +++++++++++++++++++++++++++++++ README.md | 14 ++- doc/source/conf.py | 6 +- neuroc/__init__.py | 1 + neuroc/axon_shrinker/__init__.py | 1 + neuroc/axon_shrinker/shrink.py | 1 + neuroc/axon_shrinker/viewer.py | 1 + neuroc/cli.py | 1 + neuroc/rat_to_human.py | 1 + neuroc/scale.py | 1 + neuroc/utils/__init__.py | 1 + neuroc/utils/xml.py | 2 +- neuroc/version.py | 3 - pyproject.toml | 119 ++++++++++++++++++ setup.py | 61 +--------- tests/test_cli.py | 1 + tests/test_jitter.py | 1 + tests/test_rat_to_human.py | 2 +- tests/test_shrink.py | 1 + tox.ini | 8 -- 25 files changed, 546 insertions(+), 128 deletions(-) create mode 100644 .github/workflows/sdist.yml create mode 100644 .github/workflows/tox.yml delete mode 100644 .gitlab-ci.yml delete mode 100644 .pylintrc create mode 100644 CONTRIBUTING.md create mode 100644 LICENSE.txt delete mode 100644 neuroc/version.py create mode 100644 pyproject.toml diff --git a/.github/workflows/sdist.yml b/.github/workflows/sdist.yml new file mode 100644 index 0000000..ec2117f --- /dev/null +++ b/.github/workflows/sdist.yml @@ -0,0 +1,48 @@ +name: sdist + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + release: + types: + - published + +jobs: + + build_sdist: + name: Build sdist + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Build SDist + run: pipx run build --sdist + + - name: Check metadata + run: pipx run twine check dist/* + + - uses: actions/upload-artifact@v4 + with: + name: build + path: dist + + upload_sdist: + name: Upload sdist + needs: [build_sdist] + runs-on: ubuntu-latest + permissions: + # IMPORTANT: this permission is mandatory for trusted publishing + id-token: write + if: github.event_name == 'release' && github.event.action == 'published' + + steps: + - uses: actions/download-artifact@v4 + with: + name: build + path: dist + + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/tox.yml b/.github/workflows/tox.yml new file mode 100644 index 0000000..99aae40 --- /dev/null +++ b/.github/workflows/tox.yml @@ -0,0 +1,38 @@ +name: Tox + +on: + workflow_dispatch: + pull_request: + push: + branches: + - main + release: + types: + - published + +jobs: + tox_checks: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.9', '3.10', '3.11', '3.12'] + + steps: + + - uses: actions/checkout@v4 + with: + submodules: true + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: | + python -m pip install --upgrade pip setuptools + pip install tox-gh-actions + + - name: Run tox + run: tox diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml deleted file mode 100644 index 56df1a2..0000000 --- a/.gitlab-ci.yml +++ /dev/null @@ -1,3 +0,0 @@ -include: - - project: nse/ci - file: /ci/pipelines/nse.neuroc.yml \ No newline at end of file diff --git a/.pylintrc b/.pylintrc deleted file mode 100644 index 65b8dee..0000000 --- a/.pylintrc +++ /dev/null @@ -1,49 +0,0 @@ -[MESSAGES CONTROL] -disable=fixme,invalid-name,len-as-condition,no-else-return - -[FORMAT] -# 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 experiments some -# 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/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..24c12d4 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,108 @@ +# Contribution Guide + +We would love for you to contribute to the neuroc project and help make it better than it is today. +As a contributor, here are the guidelines we would like you to follow: + + - [Question or Problem?](#got-a-question) + - [Issues and Bugs](#found-a-bug) + - [Feature Requests](#missing-a-feature) + - [Submissions](#submission-guidelines) + - [Development Guidelines](#development) + - [Release Procedure](#release) + +# Got a Question? + +Please do not hesitate to raise an issue on [github project page][github]. + +# Found a Bug? + +If you find a bug in the source code, you can help us by [submitting an issue](#issues) +to our [GitHub Repository][github]. Even better, you can [submit a Pull Request](#pull-requests) with a fix. + +# Missing a Feature? + +You can *request* a new feature by [submitting an issue](#issues) to our GitHub Repository. +If you would like to *implement* a new feature, please submit an issue with a proposal for your +work first, to be sure that we can use it. + +Please consider what kind of change it is: + +* For a **Major Feature**, first open an issue and outline your proposal so that it can be +discussed. This will also allow us to better coordinate our efforts, prevent duplication of work, +and help you to craft the change so that it is successfully accepted into the project. +* **Small Features** can be crafted and directly [submitted as a Pull Request](#pull-requests). + +# Submission Guidelines + +## Issues + +Before you submit an issue, please search the issue tracker, maybe an issue for your problem +already exists and the discussion might inform you of workarounds readily available. + +We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce +and confirm it. In order to reproduce bugs we will need as much information as possible, and +preferably with an example. + +## Pull Requests + +When you wish to contribute to the code base, please consider the following guidelines: + +* Make a [fork](https://guides.github.com/activities/forking/) of this repository. +* Make your changes in your fork, in a new git branch: + + ```shell + git checkout -b my-fix-branch master + ``` +* Create your patch, **including appropriate Python test cases**. + Please check the coding [conventions](#coding-conventions) for more information. +* Run the full test suite, and ensure that all tests pass. +* Commit your changes using a descriptive commit message. + + ```shell + git commit -a + ``` +* Push your branch to GitHub: + + ```shell + git push origin my-fix-branch + ``` +* In GitHub, send a Pull Request to the `master` branch of the upstream repository of the relevant component. +* If we suggest changes then: + * Make the required updates. + * Re-run the test suites to ensure tests are still passing. + * Rebase your branch and force push to your GitHub repository (this will update your Pull Request): + + ```shell + git rebase master -i + git push -f + ``` + +That’s it! Thank you for your contribution! + +### After your pull request is merged + +After your pull request is merged, you can safely delete your branch and pull the changes from +the main (upstream) repository: + +* Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows: + + ```shell + git push origin --delete my-fix-branch + ``` +* Check out the master branch: + + ```shell + git checkout main -f + ``` +* Delete the local branch: + + ```shell + git branch -D my-fix-branch + ``` +* Update your main with the latest upstream version: + + ```shell + git pull --ff upstream main + ``` + +[github]: https://github.com/BlueBrain/neuroc diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..d645695 --- /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. 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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 [yyyy] [name of copyright owner] + + 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.md b/README.md index b702af2..dbf1904 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ A collections of programs morphology cloning The following packages can be found - axon shrinker: -For each morphology of the FILES_FOLDER, remove the axon splice described by the corresponding annotation (ie. located between the end of the dendritic annotation and the start of the axonal annotation) and replace it by an intermediate vertical segment. For each input morphology, +For each morphology of the FILES\_FOLDER, remove the axon splice described by the corresponding annotation (ie. located between the end of the dendritic annotation and the start of the axonal annotation) and replace it by an intermediate vertical segment. For each input morphology, NSAMPLES output morphologies are generated, each with a different length of the replaced segment. Lengths spans from 0 to the length of initially spliced segment - jitter: @@ -44,7 +44,7 @@ to shrink axons. neuroc scale rat-to-human HUMAN_DIR RAT_DIR MTYPE_MAPPING OUTPUT_DIR ``` -Will scale the rat cells in RAT_DIR to human cells dimensions. +Will scale the rat cells in RAT\_DIR to human cells dimensions. HUMAN\_DIR should be a dir with the following structure: - Must be **only** composed of sub-folders whose filename is a layer name - Each sub folder should be composed of morphology files whose first part of the filename before the '_' is considered as the **mtype** @@ -67,3 +67,13 @@ $ RAT_DIR\L1\AC_cell_name.swc $ RAT_DIR\L1\BTC_cell_name.swc $ ... ``` + +## Acknowledgements + +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. + +This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA). + +For license and authors, see LICENSE.txt. + +Copyright (c) 2013-2024 Blue Brain Project/EPFL diff --git a/doc/source/conf.py b/doc/source/conf.py index 1ad960c..24877fb 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -50,10 +50,10 @@ # built documents. # # The short X.Y version. -from neuroc.version import VERSION -version = VERSION +from neuroc.version import __version__ +version = __version__ # The full version, including alpha/beta/rc tags. -release = VERSION +release = __version__ # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. diff --git a/neuroc/__init__.py b/neuroc/__init__.py index e69de29..9881313 100644 --- a/neuroc/__init__.py +++ b/neuroc/__init__.py @@ -0,0 +1 @@ +# SPDX-License-Identifier: Apache-2.0 diff --git a/neuroc/axon_shrinker/__init__.py b/neuroc/axon_shrinker/__init__.py index e69de29..9881313 100644 --- a/neuroc/axon_shrinker/__init__.py +++ b/neuroc/axon_shrinker/__init__.py @@ -0,0 +1 @@ +# SPDX-License-Identifier: Apache-2.0 diff --git a/neuroc/axon_shrinker/shrink.py b/neuroc/axon_shrinker/shrink.py index a970133..0e7af35 100644 --- a/neuroc/axon_shrinker/shrink.py +++ b/neuroc/axon_shrinker/shrink.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 '''A module to perform axon shrinking ''' import operator import os diff --git a/neuroc/axon_shrinker/viewer.py b/neuroc/axon_shrinker/viewer.py index 0435d25..621a5c4 100644 --- a/neuroc/axon_shrinker/viewer.py +++ b/neuroc/axon_shrinker/viewer.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 '''The morph-tool command line launcher''' import logging import os diff --git a/neuroc/cli.py b/neuroc/cli.py index 7ce8194..dd29295 100644 --- a/neuroc/cli.py +++ b/neuroc/cli.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 '''CLI endpoint''' # pylint: disable=import-outside-toplevel from pathlib import Path diff --git a/neuroc/rat_to_human.py b/neuroc/rat_to_human.py index f446927..87698ea 100644 --- a/neuroc/rat_to_human.py +++ b/neuroc/rat_to_human.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 ''' Module for the scaling of rat cells to human cells dimensions. https://bbpteam.epfl.ch/project/issues/browse/IHNM-6 diff --git a/neuroc/scale.py b/neuroc/scale.py index 18e9557..467191d 100644 --- a/neuroc/scale.py +++ b/neuroc/scale.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 '''Module to produce clones of a morphology by jittering it''' from typing import Optional, Union diff --git a/neuroc/utils/__init__.py b/neuroc/utils/__init__.py index e69de29..9881313 100644 --- a/neuroc/utils/__init__.py +++ b/neuroc/utils/__init__.py @@ -0,0 +1 @@ +# SPDX-License-Identifier: Apache-2.0 diff --git a/neuroc/utils/xml.py b/neuroc/utils/xml.py index a604d44..fd2d70e 100644 --- a/neuroc/utils/xml.py +++ b/neuroc/utils/xml.py @@ -1,6 +1,6 @@ +# SPDX-License-Identifier: Apache-2.0 '''XML utility functions''' - def convert_floats(dict_): '''convert to float where possible diff --git a/neuroc/version.py b/neuroc/version.py deleted file mode 100644 index 2df4079..0000000 --- a/neuroc/version.py +++ /dev/null @@ -1,3 +0,0 @@ -""" Package version. """ -VERSION = "0.2.9" -__version__ = VERSION diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..6a4e57c --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,119 @@ +[build-system] +requires = ["setuptools>=64", "setuptools_scm>=8"] +build-backend = "setuptools.build_meta" + +[project] +name = "neuroc" +description = "NeuroC: a collection of tools for morphology cloning applications" +readme = "README.md" +requires-python = ">=3.9" +license = { text = "Apache-2.0" } +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", + "Topic :: Scientific/Engineering :: Bio-Informatics", +] +dependencies = [ + "attrs>=19.1.0", + "numpy>=1.15.1", + "tqdm>=4.23.4", + "click>=6.7", + "pandas>=1.0.3", + "morphio>=3.0,<4.0", + "morph-tool>=2.9.0,<3.0", + "neurom>=3.0,<4.0", + "scikit-learn>=0.21.3,<1.5", + +] +dynamic = ["version"] + +[project.optional-dependencies] +plotly = [ + "neurom[plotly]>=3.0,<4.0", + "dash>=1.1.1", # The core dash backend + "dash-html-components>=1.0.0", # HTML components + "dash-core-components>=1.1.1", # Supercharged components + "dash-table>=4.1.0", # Interactive DataTable component (new!) +] + +[project.urls] +Homepage = "https://github.com/BlueBrain/neuroc" +Repository = "https://github.com/BlueBrain/neuroc.git" +Documentation = "https://github.com/BlueBrain/neuroc" +Tracker = "https://github.com/BlueBrain/neuroc/issues" + +[project.scripts] +neuroc = "neuroc.cli:cli" + +[tool.setuptools_scm] +version_file = "neuroc/version.py" + +[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", "pydantic"] +# List of plugins (as comma separated values of python module names) to load, +# usually to register additional checkers. +load-plugins = ["pylint_pydantic"] +# List of module names for which member attributes should not be checked. +ignored-modules = ["bluepy"] + +[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 5e01020..0b7e33e 100644 --- a/setup.py +++ b/setup.py @@ -1,59 +1,4 @@ -#!/usr/bin/env python -import importlib.util +# SPDX-License-Identifier: Apache-2.0 +from setuptools import setup -from setuptools import setup, find_packages - -spec = importlib.util.spec_from_file_location( - "neuroc.version", - "neuroc/version.py", -) -module = importlib.util.module_from_spec(spec) -spec.loader.exec_module(module) -VERSION = module.__version__ - -setup( - name="neuroc", - author="BlueBrain NSE", - author_email="bbp-ou-nse@groupes.epfl.ch", - version=VERSION, - description='NeuroC: a collection of tools for morphology cloning applications', - long_description='NeuroC: a collection of tools for morphology cloning applications', - long_description_content_type="text/plain", - url="https://bbpteam.epfl.ch/project/issues/projects/NSETM/issues", - download_url="https://bbpgitlab.epfl.ch/nse/neuroc", - entry_points=''' - [console_scripts] - neuroc=neuroc.cli:cli - ''', - license="BBP-internal-confidential", - python_requires='>=3.7', - install_requires=['attrs>=19.1.0', - 'numpy>=1.15.1', - 'tqdm>=4.23.4', - 'click>=6.7', - 'pandas>=1.0.3', - 'morphio>=3.0,<4.0', - 'morph-tool>=2.9.0,<3.0', - 'neurom>=3.0,<4.0', - 'scikit-learn>=0.21.3', - ], - extras_require={ - 'plotly': [ - 'neurom[plotly]>=3.0,<4.0', - 'dash>=1.1.1', # The core dash backend - 'dash-html-components>=1.0.0', # HTML components - 'dash-core-components>=1.1.1', # Supercharged components - 'dash-table>=4.1.0', # Interactive DataTable component (new!) - ] - }, - packages=find_packages(), - classifiers=[ - 'Development Status :: 2 - Pre-Alpha', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Programming Language :: Python :: 3.10', - ], -) +setup() diff --git a/tests/test_cli.py b/tests/test_cli.py index 586ed34..4aefb44 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 from pathlib import Path import shutil diff --git a/tests/test_jitter.py b/tests/test_jitter.py index e1b00f9..7056367 100644 --- a/tests/test_jitter.py +++ b/tests/test_jitter.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 from pathlib import Path import numpy as np diff --git a/tests/test_rat_to_human.py b/tests/test_rat_to_human.py index edfc09e..2000fc6 100644 --- a/tests/test_rat_to_human.py +++ b/tests/test_rat_to_human.py @@ -1,4 +1,4 @@ -"""Sample nosetest file.""" +# SPDX-License-Identifier: Apache-2.0 import warnings from pathlib import Path from tempfile import TemporaryDirectory diff --git a/tests/test_shrink.py b/tests/test_shrink.py index 6c9ea76..48ea657 100644 --- a/tests/test_shrink.py +++ b/tests/test_shrink.py @@ -1,3 +1,4 @@ +# SPDX-License-Identifier: Apache-2.0 from pathlib import Path from numpy.testing import assert_array_equal diff --git a/tox.ini b/tox.ini index 3079a93..2af0d0e 100644 --- a/tox.ini +++ b/tox.ini @@ -1,7 +1,6 @@ [base] name = neuroc testdeps = - mock pytest [tox] @@ -14,16 +13,9 @@ ignore_basepython_conflict = true [testenv] basepython=python3.10 deps = {[base]testdeps} -setenv = - PIP_INDEX_URL = https://bbpteam.epfl.ch/repository/devpi/simple commands = pytest {posargs} extras = plotly -[testenv:check-version] -skip_install = true -deps = bbp-nse-ci -commands = do_release.py -p . check-version - [testenv:check-packaging] deps = wheel