Dadb bump and uv shift

.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:

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
 

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"]):

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",
+    "marshmallow-sqlalchemy",
+    "requests",
+    "cachetools",
+]
+
+[dependency-groups]
+dev = [
+    "pytest>=3.0.5",
+    "pytest-cov>=2.2.1",
+    "pytest-postgresql",
+    "pytest-env",
+    "pytest-mock",
+    "requests-mock",
+    "docker",
+    "coverage",
+]
+
+[tool.hatch.version]
+path = "annotationengine/__init__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["annotationengine"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/annotationengine",
+    "/test",
+    "/README.md",
+    "/LICENSE",
+    "/requirements.txt",
+    "/requirements.in",
+    "/test_requirements.txt",
+]

requirements.in

@@ -1,6 +1,6 @@
 Flask<2.0
 emannotationschemas>=5.26.3
-dynamicannotationdb>=5.5.1
+dynamicannotationdb>=5.15.0
 caveclient>=4.20.2
 multiwrapper
 jsonschema<4.0

test/conftest.py

@@ -10,6 +10,7 @@
 import psycopg2
 import pytest
 from annotationengine import create_app, db
+from annotationengine.anno_database import clear_db_cache
 from flask import appcontext_pushed, g, current_app
 
 logging.basicConfig(level=logging.DEBUG)
@@ -67,6 +68,8 @@ def client():
         with flask_app.app_context():
             db.create_all()
             yield testing_client
+            clear_db_cache()
+            db.session.remove()
             db.drop_all()