Merge pull request #304 from NCEAS/feature-303-dockerfile-refactor

Feature-303: Dockerfile `venv`

Author: doulikecookiedough

.github/workflows/python-app.yaml

@@ -0,0 +1,31 @@
+name: Python CI with uv and pytest
+
+on:
+  push:
+    branches: [ "main", "develop" ]
+  pull_request:
+    branches: [ "main", "develop" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:  
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.13", "3.14" ]
+    steps:
+    - uses: actions/checkout@v5
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        version: '0.9.15'
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install the project
+      run: uv sync --all-extras --dev
+
+    - name: Run tests with pytest
+      run: uv run pytest tests

.github/workflows/uv-package-test.yml

@@ -151,6 +151,9 @@ ENV/
 env.bak/
 venv.bak/
 
+# uv package manager
+bin/
+
 # Spyder project settings
 .spyderproject
 .spyproject

.gitignore

@@ -77,6 +77,64 @@ commits can be run, for example, for the mac with:
 
 - `act --container-architecture linux/amd64`
 
+### Installing `vegbank` using the `uv` package manager
+
+We are using `uv` as our python environment and dependency manager. To get started locally, follow these instructions below:
+
+```sh
+# Step 1: Set your `VIRTUAL_ENV` path (if not already set)
+$ export VIRTUAL_ENV=/data/venv
+
+# Step 2: Install `uv` (if not already installed)
+$ python -m pip install uv --root-user-action ignore
+
+# Step 3: Navigate to your project root
+$ cd /path/to/vegbank2
+
+# Step 4: Create/reuse the venv and activate it
+$ uv venv --allow-existing ${VIRTUAL_ENV}
+$ source ${VIRTUAL_ENV}/bin/activate
+
+# Step 5: Install all dependencies into the venv
+$ uv sync --active
+
+```
+
+### Adding project dependencies
+
+To add a dependency to this project, you will need to update `pyproject.toml` with the library that you are trying to add, as well as the minimum version required.
+- Note: An easy way to add dependencies to pyproject.toml is to add them with `uv` or other package management tools using a command like `uv add some_package`.
+
+- If the library is required at runtime, add it under `dependencies`
+- If the library is used only for development or testing, add it under `dependency-groups.dev`
+
+```py
+# pyproject.toml
+
+...
+
+dependencies = [
+    "psycopg>=3.3.2",
+    "flask>=3.1.2",
+    "pandas>=3.0.0",
+    "pyarrow>=23.0.0",
+    "numpy>=2.4.2",
+    "DEPENDENCYNAME>=#.#.#", # Add runtime dependencies here
+]
+
+[dependency-groups]
+dev = [
+    # Add development dependencies here
+    "pytest>=8.3.3",
+    "pylint>=3.2.7",
+    "black>=24.8.0",
+]
+
+```
+
+Lastly, build and deploy your Docker image. If you are unsure of how to, please follow the `README.md` under `/docker`.
+
+
 ## Current Contributors
 
 - Matthew B. Jones (jones@nceas.ucsb.edu): [ORCID: 0000-0003-0077-4738](https://orcid.org/0000-0003-0077-4738)

README.md

@@ -2,17 +2,32 @@ FROM python:3.13
 
 LABEL org.opencontainers.image.title="vegbank2 Flask API"
 LABEL org.opencontainers.image.source="http://github.com/nceas/vegbank2"
-LABEL org.opencontainers.image.version="0.0.3-289-importbugs"
+LABEL org.opencontainers.image.version="0.0.3-303-docker-venv"
+
+# Add Docker VENV path
+ENV VIRTUAL_ENV=/data/venv
+# Do not create __pycache__/ directories
+ENV PYTHONDONTWRITEBYTECODE=1
+# Ensure logs behave correctly by flushing out stdout/stderr immediately
+ENV PYTHONUNBUFFERED=1
 
 WORKDIR /app
 
+COPY pyproject.toml uv.lock* /app/
+
+# Install uv
+RUN python -m pip install uv --root-user-action ignore
+
+# Create (or reuse) the venv at $VIRTUAL_ENV
+RUN uv venv --allow-existing "${VIRTUAL_ENV}"
+
+# Activate uv venv
+RUN . "${VIRTUAL_ENV}/bin/activate" && uv sync --active
+
+# TODO: We should be able to simply copy the application code instead of two directories
+# Ex. COPY . /app
 COPY vegbank /app/vegbank
 COPY queries /app/queries
 
-RUN pip install flask
-RUN pip install psycopg
-RUN pip install pandas
-RUN pip install pyarrow
-
 ENV PYTHONPATH=/app
-CMD [ "flask", "--app",  "vegbank.vegbankapi:app", "run", "--host=0.0.0.0", "--port=80"]
+CMD ["/data/venv/bin/python", "-m", "flask", "--app", "vegbank.vegbankapi:app", "run", "--host=0.0.0.0", "--port=80"]

docker/Dockerfile

@@ -1,33 +1,37 @@
-[tool.poetry]
+[project]
 name = "vegbank"
 version = "2.0.0-alpha1"
 description = "VegBank database and data access service"
 authors = [
-    "Robert Shelton <shelton@nceas.ucsb.edu>",
-    "Dou Mok <mok@nceas.ucsb.edu>",
-    "Jim Regetz <regetz@nceas.ucsb.edu>",
-    "Matthew B. Jones <jones@nceas.ucsb.edu>"
-    ]
-license = "Apache2"
-readme = "README.md"
+    { name = "Robert Shelton", email = "shelton@nceas.ucsb.edu" },
+    { name = "Dou Mok", email = "douming.mok@gmail.com" },
+    { name = "Jim Regetz", email = "regetz@nceas.ucsb.edu" },
+    { name = "Matthew B. Jones", email = "jones@nceas.ucsb.edu" },
+]
+license = { text = "Apache-2.0" }
+requires-python = ">=3.13"
+
+dependencies = [
+    "psycopg>=3.3.2",
+    "flask>=3.1.2",
+    "pandas>=3.0.0",
+    "pyarrow>=23.0.0",
+    "numpy>=2.4.2",
+]
 
-[tool.poetry.dependencies]
-python = "^3.12"
+[dependency-groups]
+dev = [
+    "pytest>=8.3.3",
+    "pylint>=3.2.7",
+    "black>=24.8.0",
+]
 
-[tool.poetry.group.dev.dependencies]
-poetry = ">=1.8.3"
-pytest = ">=8.3.3"
-pylint = ">=3.2.7"
-black = ">=24.8.0"
-psycopg = ">=3.3.2"
-flask = ">=3.1.2"
-pandas = ">=3.0.0"
-pyarrow = ">=23.0.0"
-numpy = ">=2.4.2"
+[tool.hatch.build.targets.wheel]
+packages = ["vegbank"]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [tool.pytest.ini_options]
 addopts = [