Migrate dependency management from Poetry to uv

.github/workflows/ci.yml

@@ -0,0 +1,71 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  # Lint only the files changed in the PR rather than the whole tree: the repo
+  # predates this CI and still carries flake8 debt in older modules, so
+  # `--all-files` would fail on unrelated code. This runs on pull requests only,
+  # where the diff against the base branch is well defined. pre-commit runs each
+  # hook in its own isolated env, so this does not install the heavy project
+  # dependencies (torch, etc.).
+  lint:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request'
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        python-version: "3.12"
+        enable-cache: true
+
+    - name: Cache pre-commit hooks
+      uses: actions/cache@v4
+      with:
+        path: ~/.cache/pre-commit
+        key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }}
+
+    - name: Run pre-commit on changed files
+      run: |
+        git fetch --no-tags origin "$GITHUB_BASE_REF"
+        uvx pre-commit run \
+          --from-ref "origin/$GITHUB_BASE_REF" --to-ref HEAD \
+          --show-diff-on-failure
+
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        python-version: "3.12"
+        enable-cache: true
+
+    - name: Install dependencies
+      run: uv sync --frozen --extra dev --extra research
+
+    - name: Test CLI commands
+      run: |
+        uv run ami-dataset --help
+        uv run ami-classification --help
+
+    - name: Run test suite
+      run: uv run pytest tests/ -v
+
+    - name: Verify imports
+      run: |
+        uv run python -c "import torch; import numpy; import pandas; print('Core dependencies imported successfully')"
+
+    - name: Verify optional dependencies (research)
+      run: |
+        uv run python -c "import awscli; import absl; print('Research dependencies imported successfully')"

.python-version

@@ -0,0 +1 @@
+3.12

README.md

@@ -21,30 +21,46 @@ Software, algorithms and research related to the Automated Monitoring of Insects
 
 ## Setup
 
-Poetry is used to manage the dependencies common to all scripts and sub-projects. Some sub-projects may manage their own dependencies if necessary.
+[uv](https://github.com/astral-sh/uv) is used to manage the dependencies common to all scripts and sub-projects. uv is a fast, modern Python package manager.
 
-1. Install [Poetry](https://python-poetry.org/docs/#installation)
+1. Install [uv](https://docs.astral.sh/uv/getting-started/installation/)
+   ```bash
+   # On macOS and Linux
+   curl -LsSf https://astral.sh/uv/install.sh | sh
+
+   # On Windows
+   powershell -c "irm https://astral.sh/uv/install.ps1 | iex"
+   ```
 2. Clone this repository
-2. Create a `.env` or copy `.env.example` and update the values
-3. Run `poetry install` in the root of the repository
-4. Install pre-commit hooks `poetry run pre-commit install`
+3. Create a `.env` or copy `.env.example` and update the values
+4. Install dependencies in the root of the repository (`--extra dev` adds the development tools, including pre-commit):
+   ```bash
+   uv sync --extra dev
+   ```
+5. Install pre-commit hooks:
+   ```bash
+   uv run pre-commit install
+   ```
+
+### [Optional] Conda + uv
+An optional way to setup the environment is to use [Conda](https://conda.io/projects/conda/en/latest/index.html) for creating and managing the Python environment, while using [uv](https://docs.astral.sh/uv/) for managing the packages and dependencies.
 
-### [Optional] Conda + Poetry
-An optional way to setup the environment is to use [Conda](https://conda.io/projects/conda/en/latest/index.html) for creating and managing the environment, while using [Poetry](https://python-poetry.org/) for managing the packages and dependencies. Run the following steps to setup:
 1. [Install Conda](https://docs.anaconda.com/free/miniconda/)
 2. Create conda environment using the `environment.yml`: `conda env create -f environment.yml`
 3. Activate the conda environment: `conda activate ami-ml`
-4. Install packages in the root of the repository using Poetry: `poetry install`
+4. Install packages in the root of the repository using uv: `uv sync`
 
 ## Usage
 
 Activate the virtual environment before running scripts
 
 ```bash
-poetry shell
+source .venv/bin/activate     # On Linux/macOS
+# or, on Windows PowerShell
+.\.venv\Scripts\Activate.ps1
 ```
 
-Example for running a script (in the poetry shell):
+Example for running a script (in the activated environment):
 
 ```bash
 python src/localization/inference_localization.py \
@@ -53,8 +69,10 @@ python src/localization/inference_localization.py \
   --model_type fasterrcnn_mobilenet_v3_large_fpn
 ```
 
-Alternatively, one can run the scripts without activating poetry's shell:
+Alternatively, one can run scripts without activating the environment:
 
 ```bash
- poetry run python <script>
+uv run python <script>
 ```
+
+`uv run` automatically uses the project's virtual environment, so there is no need to activate it first.

environment.yml

@@ -3,5 +3,5 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.11
-  - poetry
+  - python=3.12
+  - uv