From c13c73039bf5f16a988698fb68a9f71f13c5f226 Mon Sep 17 00:00:00 2001 From: Michael Bunsen Date: Fri, 20 Feb 2026 23:47:24 -0800 Subject: [PATCH 1/4] feat: migrate from Poetry to uv, bump deps for H100/Python 3.12 Replace Poetry build system with PEP 621 metadata + hatchling, managed by uv. Key dependency bumps: torch>=2.5 (H100 support), pandas>=2.0 and pillow>=10 (Python 3.12 compat). Move GUI deps (kivy, plyer) to optional extras, dev tools to dependency-groups. Update CI to use uv with a Python 3.10/3.12 test matrix. Add example SLURM script for DRAC Alliance HPC clusters. Co-Authored-By: Claude Opus 4.6 --- .github/workflows/test-ml.yml | 22 +- .github/workflows/test.yml | 36 +- MANIFEST.in | 1 - README.md | 23 +- poetry.lock | 3552 --------------------------------- pyproject.toml | 113 +- scripts/job_adc_worker.sh | 53 + uv.lock | 2434 ++++++++++++++++++++++ 8 files changed, 2575 insertions(+), 3659 deletions(-) delete mode 100644 MANIFEST.in delete mode 100644 poetry.lock create mode 100755 scripts/job_adc_worker.sh create mode 100644 uv.lock diff --git a/.github/workflows/test-ml.yml b/.github/workflows/test-ml.yml index 68ca7071..2f9cb4e0 100644 --- a/.github/workflows/test-ml.yml +++ b/.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 +14,17 @@ 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: Run ML tests run: | - ami test pipeline + uv run ami test pipeline diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5b67ecdc..ac90f415 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,40 +13,24 @@ jobs: test: name: Run Python Tests runs-on: ubuntu-latest + strategy: + 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 diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 055d1b4e..00000000 --- a/MANIFEST.in +++ /dev/null @@ -1 +0,0 @@ -include README.rst requirements.txt \ No newline at end of file diff --git a/README.md b/README.md index 778bfaef..d5856158 100644 --- a/README.md +++ b/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 or 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 diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 72cbbd99..00000000 --- a/poetry.lock +++ /dev/null @@ -1,3552 +0,0 @@ -# This file is automatically @generated by Poetry 2.3.1 and should not be changed by hand. - -[[package]] -name = "aiofiles" -version = "23.2.1" -description = "File support for asyncio." -optional = false -python-versions = ">=3.7" -groups = ["main"] -files = [ - {file = "aiofiles-23.2.1-py3-none-any.whl", hash = "sha256:19297512c647d4b27a2cf7c34caa7e405c0d60b5560618a29a9fe027b18b0107"}, - {file = "aiofiles-23.2.1.tar.gz", hash = "sha256:84ec2218d8419404abcb9f0c02df3f34c6e0a68ed41072acfb1cef5cbc29051a"}, -] - -[[package]] -name = "alembic" -version = "1.14.0" -description = "A database migration tool for SQLAlchemy." -optional = false -python-versions = ">=3.8" -groups = ["main"] -files = [ - {file = "alembic-1.14.0-py3-none-any.whl", hash = "sha256:99bd884ca390466db5e27ffccff1d179ec5c05c965cfefc0607e69f9e411cb25"}, - {file = "alembic-1.14.0.tar.gz", hash = "sha256:b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b"}, -] - -[package.dependencies] -Mako = "*" -SQLAlchemy = ">=1.3.0" -typing-extensions = ">=4" - -[package.extras] -tz = ["backports.zoneinfo ; 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insect monitoring stations" -authors = ["Michael Bunsen "] -license = "MIT" +authors = [{ name = "Michael Bunsen", email = "notbot@gmail.com" }] +license = { text = "MIT" } readme = "README.md" -homepage = "https://github.com/RolnickLab/ami-data-manager" -repository = "https://github.com/RolnickLab/ami-data-manager" +requires-python = ">=3.10,<3.13" +urls = { Homepage = "https://github.com/RolnickLab/ami-data-companion", Repository = "https://github.com/RolnickLab/ami-data-companion" } -[build-system] -requires = ["poetry-core>=1.0.0"] -build-backend = "poetry.core.masonry.api" +dependencies = [ + "alembic>=1.10.2", + "boto3>=1.33", + "botocore>=1.33", + "fastapi>=0.100", + "gradio>=4.41", + "imagesize>=1.4.1", + "numpy>=1.26", + "pandas>=2.0", + "pillow>=10.0", + "pydantic>=2.5", + "pydantic-settings>=2.1", + "python-dateutil>=2.8.2", + "python-dotenv>=1.0", + "requests>=2.28", + "rich>=13.3", + "sentry-sdk>=1.18", + "sqlalchemy>=2.0", + "sqlalchemy-utils>=0.40", + "structlog>=22.3", + "timm>=0.6.13", + "torch>=2.5", + "torchvision>=0.20", + "typer>=0.12.3,<1", + "uvicorn>=0.20", +] + +[project.optional-dependencies] +gui = [ + "kivy[base]>=2.3", + "plyer>=2.1", + "pyobjus>=1.2.1; sys_platform == 'darwin'", +] +postgres = [ + "psycopg2-binary>=2.9.5", +] -[tool.poetry.dependencies] -python = "^3.10,<3.12" -pillow = "^9.5.0" -python-dateutil = "^2.8.2" -python-dotenv = "^1.0.0" -pydantic = "^2.5.0" -rich = "^13.3.3" -pandas = "^1.5.3" -sqlalchemy = ">2.0" -sqlalchemy-utils = "^0.40.0" -alembic = "^1.10.2" -psycopg2-binary = { version = "^2.9.5", optional = true } -sentry-sdk = "^1.18.0" -imagesize = "^1.4.1" -torch = "^2.1.0" -torchvision = "^0.16.0" -timm = "^0.6.13" -structlog = "^22.3.0" -kivy = { extras = ["base"], version = "^2.3.0" } -plyer = "^2.1.0" -pyobjus = { version = "^1.2.1", markers = "sys_platform == 'darwin'" } +[dependency-groups] +dev = [ + "black>=23.3", + "flake8>=6.0", + "ipython>=8.11", + "isort>=5.12", + "mypy-boto3-s3>=1.29", + "pytest>=7", + "pytest-asyncio>=0.21", + "pytest-cov>=4.0", +] -# [tool.poetry.group.dev.dependencies] # Can't install these dev deps with pip, so they're in the main deps -black = "^23.3.0" -flake8 = "^6.0.0" -ipython = "^8.11.0" -pytest-cov = "^4.0.0" -pytest-asyncio = "^0.21.0" -pytest = "*" -numpy = "^1.26.2" -pip = "^23.3.1" -pydantic-settings = "^2.1.0" -boto3 = "^1.33.0" -botocore = "^1.33.0" -mypy-boto3-s3 = "^1.29.7" -typer = ">=0.12.3,<1.0.0" -gradio = "^4.41.0" +[project.scripts] +trapdata = "trapdata.ui.main:run" +trapdata-test = "trapdata.tests.test_pipeline:process_deployments" +ami = "trapdata.cli.base:cli" +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" [tool.pytest.ini_options] -asyncio_mode = 'auto' +asyncio_mode = "auto" testpaths = ["trapdata/tests", "trapdata/**/tests"] [tool.isort] profile = "black" - -[tool.poetry.scripts] -trapdata = 'trapdata.ui.main:run' -trapdata-test = 'trapdata.tests.test_pipeline:process_deployments' -ami = 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a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -14,6 +14,7 @@ jobs: name: Run Python Tests runs-on: ubuntu-latest strategy: + fail-fast: false matrix: python-version: ["3.10", "3.12"] diff --git a/README.md b/README.md index d5856158..5cdf3056 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ Desktop app for analyzing images from autonomous insect monitoring stations usin ## Dependencies -- Requires Python 3.10 or 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. +- 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) diff --git a/pyproject.toml b/pyproject.toml index e2c362ed..51bf7fda 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,6 @@ urls = { Homepage = "https://github.com/RolnickLab/ami-data-companion", Reposito dependencies = [ "alembic>=1.10.2", "boto3>=1.33", - "botocore>=1.33", "fastapi>=0.100", "gradio>=4.41", "imagesize>=1.4.1", diff --git a/scripts/job_adc_worker.sh b/scripts/job_adc_worker.sh index 6168bfa1..bce1b182 100755 --- a/scripts/job_adc_worker.sh +++ b/scripts/job_adc_worker.sh @@ -23,6 +23,8 @@ # uv venv ~/venvs/adc --python 3.12 # source ~/venvs/adc/bin/activate # cd ~/projects/ami-data-companion +# # --no-deps: let the lockfile control versions; avoids conflicts with +# # system packages on DRAC nodes. # uv pip install --no-deps -r <(uv export --no-hashes --frozen) # uv pip install --no-deps . # @@ -39,10 +41,20 @@ set -euo pipefail +# Catch unedited placeholder in #SBATCH --account +if [[ "${SLURM_JOB_ACCOUNT:-}" == *YOUR_ACCOUNT* ]]; then + echo "ERROR: Replace --account in this script with your DRAC allocation." >&2 + exit 1 +fi + module load python/3.12 cuda/12.6 source ~/venvs/adc/bin/activate cd ~/projects/ami-data-companion +if [[ ! -f .env ]]; then + echo "ERROR: .env not found in $(pwd). See one-time setup instructions in this script." >&2 + exit 1 +fi set -a; source .env; set +a # Register pipelines on each run (idempotent) diff --git a/trapdata/ml/models/tracking.py b/trapdata/ml/models/tracking.py index 1a2497e4..2549f456 100644 --- a/trapdata/ml/models/tracking.py +++ b/trapdata/ml/models/tracking.py @@ -456,7 +456,7 @@ def post_process_batch(self, output) -> np.ndarray: # output = output.view(-1, output.size(0)).cpu() # output = output.reshape((output.shape[0],)) batch_size = output.shape[0] - num_features = np.product(output.shape[1:]) + num_features = np.prod(output.shape[1:]) output = output.reshape(batch_size, num_features) output = output.cpu().numpy() diff --git a/uv.lock b/uv.lock index e4df3909..aaf96887 100644 --- a/uv.lock +++ b/uv.lock @@ -2240,7 +2240,6 @@ source = { editable = "." } dependencies = [ { name = "alembic" }, { name = "boto3" }, - { name = "botocore" }, { name = "fastapi" }, { name = "gradio" }, { name = "imagesize" }, @@ -2293,7 +2292,6 @@ dev = [ requires-dist = [ { name = "alembic", specifier = ">=1.10.2" }, { name = "boto3", specifier = ">=1.33" }, - { name = "botocore", specifier = ">=1.33" }, { name = "fastapi", specifier = ">=0.100" }, { name = "gradio", specifier = ">=4.41" }, { name = "imagesize", specifier = ">=1.4.1" }, From bf9e4ae7f632355eb77175b505baa89cf06a5051 Mon Sep 17 00:00:00 2001 From: Michael Bunsen Date: Sat, 21 Feb 2026 00:00:21 -0800 Subject: [PATCH 3/4] fix: cache ML model downloads in CI The ML pipeline test downloads ~500MB of model weights on every run. Cache ~/.config/AMI/models between runs with a static key (model URLs are hardcoded in source). Co-Authored-By: Claude Opus 4.6 --- .github/workflows/test-ml.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/test-ml.yml b/.github/workflows/test-ml.yml index 2f9cb4e0..212eebe6 100644 --- a/.github/workflows/test-ml.yml +++ b/.github/workflows/test-ml.yml @@ -25,6 +25,12 @@ jobs: - name: Install dependencies 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: | uv run ami test pipeline From 541374af323664922e043921cc331b8484280e6b Mon Sep 17 00:00:00 2001 From: Michael Bunsen Date: Sat, 21 Feb 2026 00:12:57 -0800 Subject: [PATCH 4/4] fix: SLURM script register args and timeout exit code MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - Remove positional arg from `ami worker register` — service name is read from AMI_ANTENNA_SERVICE_NAME env var, not a CLI argument - Handle timeout exit code 124 as clean exit to avoid SLURM marking the job as FAILED on normal time-limit shutdown - Add AMI_ANTENNA_SERVICE_NAME to .env example in setup comments Co-Authored-By: Claude Opus 4.6 --- scripts/job_adc_worker.sh | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/scripts/job_adc_worker.sh b/scripts/job_adc_worker.sh index bce1b182..0734eff1 100755 --- a/scripts/job_adc_worker.sh +++ b/scripts/job_adc_worker.sh @@ -33,10 +33,12 @@ # AMI_ANTENNA_API_BASE_URL=https://antenna.insectai.org/api/v2 # AMI_ANTENNA_API_AUTH_TOKEN=your_token_here # AMI_ANTENNA_API_BATCH_SIZE=4 +# AMI_ANTENNA_SERVICE_NAME="DRAC Worker" # EOF # -# # Register worker with Antenna (once): -# ami worker register "DRAC Worker" +# # Set service name and register worker with Antenna (once): +# export AMI_ANTENNA_SERVICE_NAME="DRAC Worker" +# ami worker register # ────────────────────────────────────────────────────────────────────── set -euo pipefail @@ -57,9 +59,12 @@ if [[ ! -f .env ]]; then fi set -a; source .env; set +a -# Register pipelines on each run (idempotent) -ami worker register "DRAC Worker - $(hostname)" +# Register pipelines on each run (idempotent). +# Service name is read from AMI_ANTENNA_SERVICE_NAME in .env (hostname appended automatically). +ami worker register # Run with timeout slightly shorter than SLURM --time to allow clean shutdown. # The worker handles SIGTERM gracefully and finishes the current batch. -timeout --signal=SIGTERM 11h55m ami worker +# Exit code 124 from timeout is expected (time limit reached), not an error. +timeout --signal=SIGTERM 11h55m ami worker \ + || { rc=$?; [[ $rc -eq 124 ]] && echo "Worker reached time limit — exiting cleanly." && exit 0; exit $rc; }