diff --git a/.github/workflows/annotationengine.yml b/.github/workflows/annotationengine.yml index 3d738f3..8fd1ef0 100644 --- a/.github/workflows/annotationengine.yml +++ b/.github/workflows/annotationengine.yml @@ -33,43 +33,32 @@ jobs: - 5432:5432 options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - name: Set up Python 3.9 - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: 3.9 - - uses: actions/cache@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-${{ hashFiles('**/test_requirements.txt') }} - restore-keys: | - ${{ runner.os }}-pip- - - uses: conda-incubator/setup-miniconda@v2 - with: - auto-update-conda: true - auto-activate-base: true - python-version: 3.9 - - name: Install dependencies - shell: bash -l {0} + version: "latest" + enable-cache: true + - name: Validate lockfile run: | - pip install flake8 pytest - pip install -r requirements.txt - if [ -f test_requirements.txt ]; then pip install -r test_requirements.txt; fi + uv lock --check - name: Lint with flake8 - shell: bash -l {0} run: | # stop the build if there are Python syntax errors or undefined names # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + uv run --frozen --with flake8 flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Test with pytest - shell: bash -l {0} env: AUTH_DISABLED: true run: | - python -c "import os; print('AUTH_DISABLED:', os.getenv('AUTH_DISABLED'), type(os.getenv('AUTH_DISABLED')))" - pytest --cov annotationengine + uv run --frozen python -c "import os; print('AUTH_DISABLED:', os.getenv('AUTH_DISABLED'), type(os.getenv('AUTH_DISABLED')))" + uv run --frozen pytest --cov annotationengine - name: Upload coverage to codecov uses: codecov/codecov-action@v5 with: diff --git a/Dockerfile b/Dockerfile index a473b37..27ebe80 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,10 +1,32 @@ FROM tiangolo/uwsgi-nginx-flask:python3.9 -RUN git config --global http.sslVerify false && \ - mkdir -p /home/nginx/.cloudvolume/secrets && chown -R nginx /home/nginx && usermod -d /home/nginx -s /bin/bash nginx +RUN apt-get update && apt-get install -y gcc curl ca-certificates \ + && rm -rf /var/lib/apt/lists/* + +RUN pip install uv + +# Enable bytecode compilation and avoid hardlinks in mounted cache volumes. +ENV UV_COMPILE_BYTECODE=1 +ENV UV_LINK_MODE=copy +ENV UV_PYTHON_DOWNLOADS=0 + +RUN git config --global http.sslVerify false && \ + mkdir -p /home/nginx/.cloudvolume/secrets && \ + chown -R nginx /home/nginx && \ + usermod -d /home/nginx -s /bin/bash nginx + +WORKDIR /app + +# Install runtime dependencies from the lockfile before copying source. +COPY uv.lock pyproject.toml ./ +ENV UV_PROJECT_ENVIRONMENT="/usr/local/" +RUN --mount=type=cache,target=/root/.cache/uv \ + UV_VENV_ARGS="--system-site-packages" uv sync --frozen --no-install-project --no-default-groups + +ENV UWSGI_INI /app/uwsgi.ini +ENV PATH /app/.venv/bin:/home/nginx/google-cloud-sdk/bin:/root/google-cloud-sdk/bin:$PATH +ENV PYTHONNOUSERSITE=1 -COPY requirements.txt /app/. -RUN pip install -r requirements.txt COPY timeout.conf /etc/nginx/conf.d/ COPY . /app \ No newline at end of file diff --git a/annotationengine/anno_database.py b/annotationengine/anno_database.py index 0dc91bf..312fc0f 100644 --- a/annotationengine/anno_database.py +++ b/annotationengine/anno_database.py @@ -13,6 +13,30 @@ def get_db(aligned_volume) -> DynamicAnnotationInterface: return cache[aligned_volume] +def clear_db_cache(): + for interface in cache.values(): + for database in ( + getattr(interface, "_database", None), + getattr(getattr(interface, "_annotation", None), "db", None), + getattr(getattr(interface, "_segmentation", None), "db", None), + ): + if database is None: + continue + try: + database.close_session() + except Exception: + pass + try: + database.session.remove() + except Exception: + pass + try: + database.engine.dispose() + except Exception: + pass + cache.clear() + + def check_write_permission(db, table_name): metadata = db.database.get_table_metadata(table_name) if metadata["user_id"] != str(g.auth_user["id"]): diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..a6b1927 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,64 @@ +[build-system] +requires = ["hatchling>=1.26.1"] +build-backend = "hatchling.build" + +[project] +name = "annotationengine" +dynamic = ["version"] +description = "A service for storing arbitrary annotation data on EM volumes stored in a cloud volume" +readme = "README.md" +requires-python = ">=3.9,<3.10" +authors = [ + { name = "Forrest Collman", email = "forrestc@alleninstitute.org" } +] +classifiers = [ + "License :: OSI Approved :: MIT License", +] +dependencies = [ + "Flask<2.0", + "MarkupSafe<2.1", + "emannotationschemas>=5.26.3", + "dynamicannotationdb>=5.15.0", + "caveclient>=4.20.2", + "multiwrapper", + "jsonschema<4.0", + "middle-auth-client>=3.11.1", + "flask_sqlalchemy", + "flask_cors", + "flask-marshmallow==0.14.0", + "flask-admin", + "flask-restx", + "flask-accepts", + 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