[MNT] Add uv for dependency management

.github/dependabot.yml

@@ -63,7 +63,8 @@ updates:
   # See https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/configuring-dependabot-security-updates#overriding-the-default-behavior-with-a-configuration-file
   # Note: this configuration only has an effect in repositories that have
   # a requirements.txt file / use python / pip.
-  - package-ecosystem: "pip"
+  # Temporary uv override
+  - package-ecosystem: "uv"
     directory: "/"
     schedule:
       interval: "weekly"

.github/workflows/test.yaml

@@ -16,20 +16,19 @@ jobs:
 
     - uses: actions/checkout@v6
 
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v6
+    - name: Set up Python 3.10 with uv
+      uses: astral-sh/setup-uv@v7
       with:
         python-version: "3.10"
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        uv sync --group dev
 
     - name: Test with pytest
       run: |
-        coverage run -m pytest
-        coverage lcov -o ./coverage/lcov.info
+        uv run coverage run -m pytest
+        uv run coverage lcov -o ./coverage/lcov.info
 
     - name: Upload results to Codecov
       uses: codecov/codecov-action@v5

.pre-commit-config.yaml

@@ -6,9 +6,6 @@ repos:
     rev: 26.3.0
     hooks:
       - id: black
-        args:
-          - --line-length=79
-          - --safe
 
   - repo: https://github.com/PyCQA/flake8
     rev: 7.3.0
@@ -29,7 +26,6 @@ repos:
     rev: 8.0.1
     hooks:
       - id: isort
-        args: ["--profile", "black", "--filter-files"]
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.2

Dockerfile

@@ -1,8 +1,18 @@
+# We are using a two-stage build here because we use uv for dependency management
+# But decide to keep it out of the production image.
+# The Pre-build stage generates a pip compatible lockfile and then installs with pip
+FROM ghcr.io/astral-sh/uv:latest AS prebuild
+
+WORKDIR /build
+
+COPY pyproject.toml uv.lock ./
+RUN uv export --frozen --no-dev --no-hashes -o requirements.txt
+
+# Build stage
 FROM python:3.10
 
 WORKDIR /usr/src/
-
-COPY ./requirements.txt /usr/src/app/requirements.txt
+COPY --from=prebuild /build/requirements.txt /usr/src/requirements.txt
 
 RUN pip install --no-cache-dir --upgrade -r /usr/src/app/requirements.txt
 

README.md

@@ -61,3 +61,28 @@ docker run -d -v ${PWD}/local_nb_nodes.json:/usr/src/local_nb_nodes.json:ro \
     --name=federation -p 8080:8000 neurobagel/federation_api
 ```
 NOTE: You can replace the port number `8080` for the `-p` flag with any port on the host you wish to use for the API.
+
+### 3. Create a local development environment
+
+We [use `uv`](https://docs.astral.sh/uv/getting-started/installation/)
+for our local dev environment.
+
+Once installed, just run
+
+```bash
+uv sync --group dev
+```
+
+to set up things in editable mode.
+
+And then launch the API with 
+
+```bash
+uv run uvicorn app.main:app
+```
+
+Also don't forget to set up precommit with
+
+```bash
+uv run pre-commit install
+```

pyproject.toml

@@ -0,0 +1,64 @@
+[build-system]
+requires = ["hatch-vcs", "hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "federation-api"
+description = "Neurobagel federation API for aggregating queries across multiple Neurobagel nodes."
+readme = "README.md"
+license = { file = "LICENSE" }
+authors = [{ name = "Neurobagel Developers" }]
+maintainers = [
+  { name = "Alyssa Dai", email = "alyssa.dai@mcgill.ca" },
+  { name = "Arman Jahanpour", email = "arman.jahanpour@mcgill.ca" },
+  { name = "Sebastian Urchs", email = "sebastian.urchs@mcgill.ca" }
+]
+dynamic = ["version"]
+requires-python = ">=3.10,<3.14"
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering",
+  "License :: OSI Approved :: MIT License",
+  "Framework :: FastAPI",
+  "Framework :: Pydantic :: 2",
+  "Typing :: Typed",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13"
+]
+
+dependencies = [
+    "fastapi[standard]",
+    "pydantic>=2.10,<3",
+    "PyJWT",
+    "typing-extensions",
+	"jsonschema",
+    "orjson"
+]
+
+[dependency-groups]
+dev = [
+	"coverage",
+	"pytest",
+	"pytest-asyncio",
+	"pre-commit"
+]
+
+[tool.hatch.version]
+source = "vcs"  # use git tags to automatically determine the project version using hatch-vcs
+
+[tool.hatch.build.hooks.vcs]
+version-file = "app/_version.py"  # useful for accessing dynamically calculated version inside the app (e.g., to support a --version option)
+
+[tool.hatch.version.raw-options]
+local_scheme = "no-local-version"  # do not append local version info to the version string to avoid PyPI upload errors
+
+[tool.black]
+line-length = 79
+
+[tool.isort]
+profile = "black"
+filter_files = true
+line_length = 79