Init repo

.github/workflows/changelog.yml

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+name: Changelog
+on:
+  pull_request
+
+jobs:
+  Check-Changelog:
+    name: Check Changelog Action
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: tarides/changelog-check-action@v2
+        with:
+          changelog: CHANGELOG.md
+

.github/workflows/ci.yaml

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+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        description: "Run the build with tmate debugging enabled"
+        required: false
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel previous workflows that are still running
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - name: Checkout latest commit
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0 # fetch all history with version tags
+      - name: Set up python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Set up pip cache
+        uses: actions/cache@v2
+        with:
+          path: ~/.cache/pip
+          key: ${{ matrix.tox-env }}-${{ runner.os }}
+      - name: Set up environment
+        run: |
+          pip install --upgrade pip wheel setuptools
+          pip install bandit[toml]==1.7.4 ruff==0.5.5
+      - name: Linting check
+        run: |
+          bandit -qr -c pyproject.toml src/
+          ruff check src/ tests/
+          ruff format --check src/ tests
+  unit-tests:
+    runs-on: ${{ matrix.os }}
+    services:
+        postgres:
+          image: postgres:latest
+          env:
+            POSTGRES_USER: test
+            POSTGRES_PASSWORD: password
+          options: >-
+            --health-cmd "pg_isready -d postgres://test:password@localhost:5432"
+            --health-interval 10s
+            --health-timeout 5s
+            --health-retries 10
+          ports:
+            - 5432:5432
+    env:
+      PIP_CACHE_DIR: .cache/pip
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.10"]
+    steps:
+      - name: Cancel previous workflows that are still running
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - name: Checkout latest commit
+        uses: actions/checkout@v2
+        with:
+          fetch-depth: 0 # fetch all history with version tags
+      - name: Set up python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Set up pip cache
+        uses: actions/cache@v2
+        with:
+          path: .cache/pip
+          key: ${{ matrix.tox-env }}-${{ matrix.os }}
+      - name: Set up environment
+        run: |
+          pip install --upgrade pip
+          pip install mypy==1.8.0
+          pip install -e ".[dev]"
+      - name: Running mypy and tests
+        run: |
+          mypy src/
+          pytest --color=yes

.github/workflows/docker.yml

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+name: Build and Push Docker Image
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v4
+      with:
+        context: .
+        push: true
+        tags: |
+          bluebrain/neuroagent:${{ github.ref_name }}
+          bluebrain/neuroagent:latest

.github/workflows/docs_buildings.yaml

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+name: GitHub Pages
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  deploy:
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: write
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+
+      - name: Upgrade pip
+        run: |
+          # install pip=>20.1 to use "pip cache dir"
+          python3 -m pip install --upgrade pip
+
+      - name: Get pip cache dir
+        id: pip-cache
+        run: echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+
+      - name: Cache dependencies
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.pip-cache.outputs.dir }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: python3 -m pip install  mkdocs-material mkdocstrings[python]
+
+      - run: mkdocs build
+
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v4
+        if: github.ref == 'refs/heads/main'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site

.github/workflows/release.yml

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+name: Build and Push Python Package
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.10"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url:  https://pypi.org/project/neuroagent/
+    permissions:
+      id-token: write
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

README.md

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+First version of the neuroagent package.

pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+
+[project]
+name = "neuroagent"
+authors = [
+    {name = "Blue Brain Project, EPFL"},
+]
+description = "Search agent for neuroscience."
+readme = "README.md"
+requires-python = ">=3.10"
+dynamic = ["version"]
+dependencies = [
+    ]
+
+[tool.setuptools.dynamic]
+version = {attr = "neuroagent.__version__"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = false

src/neuroagent/__init__.py

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+__version__ = "0.0.0"