init OSS

.dockerignore

@@ -0,0 +1,2 @@
+.git
+.tox

.github/workflows/sdist.yml

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+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

.github/workflows/tox.yml

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+name: tox
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  checks:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11', '3.12']
+
+    steps:
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+
+    - 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
+        python -m pip install tox-gh-actions
+
+    - name: Run tox
+      run: tox

.gitignore

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+*.pyc
+*.swp
+coverage.xml
+*.egg-info
+.coverage
+build/
+dist/
+doc/build
+doc/source/generated
+.tox

.gitmodules

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+[submodule "libsonata"]
+	path = libsonata
+	url = https://github.com/BlueBrain/libsonata.git

.pylintrc

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+[MESSAGES CONTROL]
+disable=fixme,invalid-name,len-as-condition,no-else-return,no-member,empty-docstring
+
+[FORMAT]
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines=^\s*(# )?<?https?://\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 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

.readthedocs.yml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-lts-latest
+  tools:
+    python: "3.11"
+  apt_packages:
+    - graphviz
+
+sphinx:
+  configuration: doc/source/conf.py
+  fail_on_warning: true
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

AUTHORS.txt

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+Maintainer
+----------
+* BBP/NSE
+
+Authors
+-------
+Adrien Christian Fleury
+Eduard Subert
+Eleftherios Zisis
+Genrich Ivaska
+Gianluca Ficarelli
+Ilkan Fabrice Kiliç
+Jaquier Aurélien Tristan
+Joni Herttuainen
+Marek Naskret
+Mike Gevaert

CHANGELOG.rst

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+Changelog
+=========
+
+Version 4.0.0 (2024-07-25)
+--------------------------
+
+Improvements
+~~~~~~~~~~~~
+
+- Open source.

Dockerfile

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+FROM python:3.11-slim
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN ln -sf /usr/share/zoneinfo/Europe/Zurich /etc/localtime
+
+RUN apt-get update && apt-get install -q -y --no-install-recommends curl rsync ssh jq htop
+
+COPY requirements.txt /tmp
+
+RUN apt-get install -q -y --no-install-recommends build-essential && \
+    pip install --no-cache-dir --upgrade setuptools pip && \
+    pip install --no-cache-dir -r /tmp/requirements.txt scikit-learn && \
+    apt-get purge -q -y --auto-remove build-essential
+
+WORKDIR /home/bbp-workflow
+
+COPY logging.cfg ./
+
+ENV HOME=/home/bbp-workflow
+
+COPY dist/* dist/
+RUN pip install --no-cache-dir $(ls -t $PWD/dist/*.* | head -n 1)
+
+ENTRYPOINT ["luigi", "--local-scheduler", "--logging-conf-file", "/home/bbp-workflow/logging.cfg", "--module"]