Migrate dependency management from Poetry to uv

.github/workflows/ci.yml

@@ -0,0 +1,50 @@
+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+        echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+    - name: Verify uv installation
+      run: uv --version
+
+    - name: Install dependencies
+      run: |
+        uv sync --extra dev --extra research
+
+    - name: Test CLI commands
+      run: |
+        uv run ami-dataset --help
+        uv run ami-classification --help
+
+    - name: Run test suite
+      run: |
+        # Placeholder for running the full test suite
+        # TODO: Add proper test command once test infrastructure is ready
+        uv run pytest tests/ -v || echo "Tests not yet configured"
+
+    - 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')"

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:
+   ```bash
+   uv sync
+   ```
+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
+.venv\Scripts\activate     # On Windows
 ```
 
-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 +69,8 @@ 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>
 ```

pyproject.toml

@@ -1,67 +1,68 @@
-[tool.poetry]
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
 name = "ami-ml"
 version = "0.1.0"
 description = "Software & research related to the automated monitoring of insects"
+readme = "README.md"
+license = {text = "MIT"}
+requires-python = ">=3.10"
 authors = [
-    "Aditya Jain <aditya.jain@mila.quebec>",
-    "Michael Bunsen <michael.bunsen@mila.quebec>",
-    "Fagner Cunha <fagner.cunha@icomp.ufam.edu.br>",
-    "Léonard Pasi <leonardpasi@gmail.com>",
+    {name = "Aditya Jain", email = "aditya.jain@mila.quebec"},
+    {name = "Michael Bunsen", email = "michael.bunsen@mila.quebec"},
+    {name = "Fagner Cunha", email = "fagner.cunha@icomp.ufam.edu.br"},
+    {name = "Léonard Pasi", email = "leonardpasi@gmail.com"},
 ]
-license = "MIT"
-readme = "README.md"
-packages = [{ include = "src" }]
-
-[tool.poetry.dependencies]
-python = "^3.9"
-click = "^8.1.6"
-numpy = "^1.25.1"
-torch = "^2.0,!=2.0.1"
-tqdm = "^4.65.0"
-segment-anything = "^1.0"
-torchvision = "^0.15.1,!=0.15.2"
-torchmetrics = "^0.11.4"
-pillow = "^10.0.0"
-matplotlib = "^3.7.2"
-python-dwca-reader = "^0.15.1"
-pandas = "^2.1.0"
-scikit-learn = "^1.3.0"
-webdataset = "^0.2.48"
-timm = "^0.9.8"
-typer = "^0.12.3"
-python-dotenv = "^1.0.1"
-wandb = "^0.17.5"
-pygbif = "^0.6.5"
-opencv-python = "^4.11.0.86"
-
-[tool.poetry.group.research]
-optional = true
 
-[tool.poetry.group.research.dependencies]
-awscli = "^1.33.44"
-awscli-plugin-endpoint = "^0.4"
-absl-py = "^2.1.0"
+dependencies = [
+    "click>=8.1.6",
+    "numpy>=1.25.1",
+    "torch>=2.0,!=2.0.1",
+    "tqdm>=4.65.0",
+    "segment-anything>=1.0",
+    "torchvision>=0.15.1,!=0.15.2",
+    "torchmetrics>=0.11.4",
+    "pillow>=10.0.0",
+    "matplotlib>=3.7.2",
+    "python-dwca-reader>=0.15.1",
+    "pandas>=2.1.0",
+    "scikit-learn>=1.3.0",
+    "webdataset>=0.2.48",
+    "timm>=0.9.8",
+    "typer>=0.12.3",
+    "python-dotenv>=1.0.1",
+    "wandb>=0.17.5",
+    "pygbif>=0.6.5",
+    "opencv-python>=4.11.0.86",
+]
 
-[tool.poetry.group.dev.dependencies]
-pre-commit = "^3.3.3"
-black = "^23.7.0"
-flake8 = "^6.0.0"
-Flake8-pyproject = "^1.2.3"
-isort = "^5.12.0"
-mypy = "^1.4.1"
-ipdb = "^0.13.13"
-python-devtools = "^2"
-ipykernel = "^6.29.4"
-pytest = "^8.1.1"
+[project.optional-dependencies]
+research = [
+    "awscli>=1.33.44",
+    "awscli-plugin-endpoint>=0.4",
+    "absl-py>=2.1.0",
+]
+dev = [
+    "pre-commit>=3.3.3",
+    "black>=23.7.0",
+    "flake8>=6.0.0",
+    "Flake8-pyproject>=1.2.3",
+    "isort>=5.12.0",
+    "mypy>=1.4.1",
+    "ipdb>=0.13.13",
+    "python-devtools>=2",
+    "ipykernel>=6.29.4",
+    "pytest>=8.1.1",
+]
 
-[tool.poetry.scripts]
+[project.scripts]
 ami-dataset = "src.dataset_tools.cli:cli"
 ami-classification = "src.classification.cli:cli"
 
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[tool.hatch.build.targets.wheel]
+packages = ["src"]
 
 [tool.flake8]
 max-line-length = 88