Migrate from Poetry to uv, bump deps for H100/Python 3.12

.github/workflows/test-ml.yml

@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
-
 name: Test ML pipeline
 
 on:
@@ -17,16 +14,23 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
       - name: Set up Python 3.10
-        uses: actions/setup-python@main # Need latest version to use pyproject.toml instead of requirements.txt
-        with:
-          python-version: "3.10"
-          cache: "pip"
+        run: uv python install 3.10
+
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .
+        run: uv sync --no-default-groups
+
+      - name: Cache ML models
+        uses: actions/cache@v4
+        with:
+          path: ~/.config/AMI/models
+          key: ml-models-v1
+
       - name: Run ML tests
         run: |
-          ami test pipeline
+          uv run ami test pipeline

.github/workflows/test.yml

@@ -13,40 +13,25 @@ jobs:
   test:
     name: Run Python Tests
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-          cache: "pip"
-          cache-dependency-path: |
-            poetry.lock
-            pyproject.toml
-
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: latest
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-
-      - name: Load cached Poetry virtualenv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v3
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
 
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction
+        run: uv sync
 
       - name: Run tests
         run: |
-          # Clean any cached Python files before running tests
           find . -type d -name "__pycache__" -exec rm -r {} +
           find . -type f -name "*.pyc" -delete
-          poetry run pytest --import-mode=importlib
+          uv run pytest --import-mode=importlib

README.md

@@ -18,7 +18,7 @@ Desktop app for analyzing images from autonomous insect monitoring stations usin
 
 ## Dependencies
 
-- Requires Python 3.10. Use [Anaconda](https://www.anaconda.com/) (or [miniconda](https://docs.conda.io/en/latest/miniconda.html)) if you need to maintain multiple versions of Python or are unfamiliar with using Python and scientific packages, it is especially helpful on Windows. [PyEnv](https://github.com/pyenv/pyenv) is also a popular tool for managing multiple versions of python if you are familiar with the command line.
+- Requires Python >=3.10, <3.13 (tested on 3.10 and 3.12). Use [uv](https://docs.astral.sh/uv/) (recommended), [Anaconda](https://www.anaconda.com/), or [PyEnv](https://github.com/pyenv/pyenv) to manage Python versions.
 
 ## Installation (for non-developers)
 
@@ -36,37 +36,30 @@ ami test pipeline
 
 ## Installation (for developers)
 
-Create an environment just for AMI and the data companion using conda (or virtualenv)
-
-```sh
-conda create -n ami python=3.10 anaconda
-```
-
-Clone the repository using the command line or the GitHub desktop app.
+Install [uv](https://docs.astral.sh/uv/getting-started/installation/) then clone and sync:
 
 ```sh
 git clone git@github.com:RolnickLab/ami-data-companion.git
+cd ami-data-companion
+uv sync
 ```
 
-Install as an editable package. This will install the dependencies and install the `trapdata` console command
+To include the desktop GUI dependencies:
 
 ```sh
-cd ami-data-companion
-pip install -e .
+uv sync --extra gui
 ```
 
 Test the whole backend pipeline without the GUI using this command
 
 ```sh
-python trapdata/tests/test_pipeline.py
-# or
-ami test pipeline
+uv run ami test pipeline
 ```
 
 Run all other tests with:
 
 ```sh
-ami test all
+uv run ami test all
 ```
 
 ## GUI Usage