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GianlucaFicarelliGianlucaFicarelli
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Setup GitHub CI
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‎.github/workflows/publish-sdist.yml

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name: PyPI
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on:
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workflow_dispatch:
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pull_request:
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push:
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branches:
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- main
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release:
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types:
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- published
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jobs:
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build:
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name: Build distribution
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Build a binary wheel and a source tarball
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run: pipx run build
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- name: Check metadata
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run: pipx run twine check dist/*
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- name: Store the distribution packages
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uses: actions/upload-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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publish-to-pypi:
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name: Publish Python distribution to PyPI
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if: github.event_name == 'release' && github.event.action == 'published'
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needs:
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- build
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runs-on: ubuntu-latest
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environment:
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name: pypi
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url: https://pypi.org/p/connectome-tools
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permissions:
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id-token: write # IMPORTANT: mandatory for trusted publishing
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steps:
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- name: Download all the dists
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uses: actions/download-artifact@v4
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with:
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name: python-package-distributions
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path: dist/
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- name: Publish distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1

‎.github/workflows/run-tox.yml

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name: Run tox
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on:
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pull_request:
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push:
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branches:
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- main
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jobs:
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tests:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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include:
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- python-version: '3.8'
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tox-env: py38
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- python-version: '3.9'
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tox-env: py39
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- python-version: '3.10'
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tox-env: py310
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- python-version: '3.11'
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tox-env: py311
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- python-version: '3.12'
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tox-env: py312
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codecov: codecov
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- python-version: '3.12'
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tox-env: lint
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- python-version: '3.12'
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tox-env: docs
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- python-version: '3.12'
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tox-env: check-packaging
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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python -m pip install --upgrade tox tox-uv
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- name: Run tox
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run: |
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tox run -e ${{ matrix.tox-env }}
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- name: Upload to codecov
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if: ${{ matrix.codecov == 'codecov' }}
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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fail_ci_if_error: false
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files: ./coverage.xml
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flags: pytest
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verbose: true
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name: "${{ github.repository }}-${{ matrix.tox-env }}"

‎.gitlab-ci.yml

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‎connectome_tools/__init__.py

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"""Connectome tools."""
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from connectome_tools.version import __version__
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from connectome_tools._version import __version__ # noqa

‎connectome_tools/version.py

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‎pyproject.toml

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[build-system]
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requires = ["setuptools>=64", "setuptools_scm>=8"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "connectome-tools"
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description = "Connectome statistics; S2F recipe generation"
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readme = "README.rst"
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requires-python = ">=3.8"
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authors = [
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{name = "Blue Brain Project, EPFL", email = "bbp-ou-nse@groupes.epfl.ch"},
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]
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dependencies = [
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"click>=7.0,<9.0",
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"importlib-metadata",
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"importlib-resources",
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"joblib>=1.0.1",
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"jsonschema>=3.2.0,<5.0.0",
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"lxml>=3.3",
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"numpy>=1.9",
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"pandas>=1.0.0",
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"psutil>=5.7.2",
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"pyyaml>=5.3.1",
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"submitit>=1.4,<2.0",
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"bluepysnap<2.0",
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"morphio>=3.0.1,<4.0.0",
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"voxcell>=3.0,<4.0",
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# setuptools needed because of https://github.com/facebookincubator/submitit/issues/1765
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'setuptools;python_version>="3.12"',
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]
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license = {text = "Apache-2.0"}
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classifiers=[
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"Development Status :: 2 - Pre-Alpha",
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"Intended Audience :: Education",
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"Intended Audience :: Science/Research",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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]
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dynamic = ["version"]
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[project.optional-dependencies]
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docs = [
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"sphinx",
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"sphinx-bluebrain-theme",
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]
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[project.urls]
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Homepage = "https://github.com/BlueBrain/connectome-tools"
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Repository = "https://github.com/BlueBrain/connectome-tools.git"
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Documentation = "https://connectome-tools.readthedocs.io"
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Tracker = "https://github.com/BlueBrain/connectome-tools/issues"
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[project.scripts]
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connectome-stats = "connectome_tools.apps.connectome_stats:app"
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s2f-recipe = "connectome_tools.apps.s2f_recipe:app"
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s2f-recipe-merge = "connectome_tools.apps.s2f_recipe_merge:cli"
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[tool.setuptools.packages.find]
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include = ["connectome_tools"]
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[tool.setuptools_scm]
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version_file = "connectome_tools/_version.py"
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[tool.black]
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line-length = 100
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target-version = [
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'py38',
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'py39',
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'py310',
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'py311',
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'py312',
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'py313',
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]
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include = 'connectome_tools\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$'
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‎setup.py

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#!/usr/bin/env python
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# pylint: disable=missing-docstring
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import importlib.util
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from setuptools import setup
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from setuptools import find_packages, setup
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# read the contents of the README file
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with open("README.rst", encoding="utf-8") as f:
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README = f.read()
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spec = importlib.util.spec_from_file_location(
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"connectome_tools.version",
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"connectome_tools/version.py",
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)
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module = importlib.util.module_from_spec(spec)
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spec.loader.exec_module(module)
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VERSION = module.__version__
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setup(
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name="connectome-tools",
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author="BlueBrain NSE",
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author_email="bbp-ou-nse@groupes.epfl.ch",
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version=VERSION,
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description="Connectome statistics; S2F recipe generation",
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long_description=README,
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long_description_content_type="text/x-rst",
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url="https://bbpteam.epfl.ch/documentation/projects/connectome-tools",
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project_urls={
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"Tracker": "https://bbpteam.epfl.ch/project/issues/projects/NSETM/issues",
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"Source": "https://bbpgitlab.epfl.ch/nse/connectome-tools/",
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},
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license="BBP-internal-confidential",
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install_requires=[
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"click>=7.0,<9.0",
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"importlib-metadata",
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"importlib-resources",
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"joblib>=1.0.1",
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"jsonschema>=3.2.0,<5.0.0",
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"lxml>=3.3",
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"numpy>=1.9",
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"pandas>=1.0.0",
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"psutil>=5.7.2",
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"pyyaml>=5.3.1",
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"submitit>=1.4,<2.0",
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"bluepysnap<2.0",
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"morphio>=3.0.1,<4.0.0",
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"voxcell>=3.0,<4.0",
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# setuptools needed because of https://github.com/facebookincubator/submitit/issues/1765
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'setuptools;python_version>="3.12"',
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#"bluepy>=2.3,<3.0",
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],
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packages=find_packages(),
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include_package_data=True,
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python_requires=">=3.8",
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extras_require={"docs": ["sphinx", "sphinx-bluebrain-theme"]},
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classifiers=[
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"Development Status :: 2 - Pre-Alpha",
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"Intended Audience :: Education",
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"Intended Audience :: Science/Research",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.8",
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"Programming Language :: Python :: 3.9",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Topic :: Scientific/Engineering :: Bio-Informatics",
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],
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entry_points={
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"console_scripts": [
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"connectome-stats=connectome_tools.apps.connectome_stats:app",
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"s2f-recipe=connectome_tools.apps.s2f_recipe:app",
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"s2f-recipe-merge=connectome_tools.apps.s2f_recipe_merge:cli",
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],
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},
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)
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setup()

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