From be5e3922fac7e83fd6a07751e12ccfcf8cb645e1 Mon Sep 17 00:00:00 2001 From: willjnz Date: Mon, 10 Aug 2026 12:13:52 +1000 Subject: [PATCH 1/2] Migrate to uv from poetry --- .vscode/settings.json | 5 +- Dockerfile | 22 +- README.md | 59 +- ldn/training_data.py | 2 +- ldn/utils.py | 13 + notebooks/Compare_LULC_per_class.ipynb | 9 +- notebooks/Test_LoadOne.ipynb | 2 +- notebooks/src/Compare_LULC_func.py | 12 - poetry.lock | 6574 ------------------------ pyproject.toml | 131 +- uv.lock | 3389 ++++++++++++ visualisation/Dockerfile | 17 +- visualisation/deploy.sh | 2 +- 13 files changed, 3533 insertions(+), 6704 deletions(-) delete mode 100644 poetry.lock create mode 100644 uv.lock diff --git a/.vscode/settings.json b/.vscode/settings.json index 8b15ca9a..5a570ec6 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -4,7 +4,6 @@ ], "python.testing.unittestEnabled": false, "python.testing.pytestEnabled": true, - "python-envs.defaultEnvManager": "ms-python.python:poetry", - "python-envs.defaultPackageManager": "ms-python.python:poetry", - "python-envs.pythonProjects": [] + "python-envs.defaultEnvManager": "ms-python.python:venv", + "python-envs.defaultPackageManager": "ms-python.python:pip" } diff --git a/Dockerfile b/Dockerfile index d2a81c44..f019260e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,35 +1,37 @@ -FROM ghcr.io/osgeo/gdal:ubuntu-small-3.12.3 +FROM ghcr.io/osgeo/gdal:ubuntu-small-3.13.1 RUN apt-get update && apt-get install -y \ python3-pip \ python3-venv \ git \ curl \ + build-essential \ + pkg-config \ && apt-get clean \ && rm -rf /var/lib/{apt,dpkg,cache,log} - # Install Rust via rustup (needed to build datacube-compute) ENV CARGO_HOME="/usr/local/cargo" RUSTUP_HOME="/usr/local/rustup" ENV PATH="$CARGO_HOME/bin:$PATH" RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable --profile minimal -RUN pip install --break-system-packages poetry +# Install uv +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /usr/local/bin/ +ENV UV_PROJECT_ENVIRONMENT=/code/.venv \ + UV_LINK_MODE=copy WORKDIR /code -COPY pyproject.toml poetry.lock ./ +COPY pyproject.toml uv.lock ./ # Install dependencies first to leverage Docker caching. -# Keep layer separate from installing the package itself to avoid re-building dependencies when our code changes. -# Make venv in-project (in container's working directory). -RUN poetry config virtualenvs.in-project true && \ - poetry install --no-root +# --no-dev keeps the "dev" group (matplotlib, pytest, etc.) out of the image. +RUN uv sync --frozen --no-install-project --no-dev # Rust is no longer needed after dependencies are built RUN rustup self uninstall -y && rm -rf /usr/local/cargo /usr/local/rustup COPY . . -# Install the package itself. Keep separate from dependencies to avoid re-building dependencies when our code changes. -RUN poetry install --only-root +# Install the package itself. +RUN uv sync --frozen --no-dev ENV PATH="/code/.venv/bin:$PATH" diff --git a/README.md b/README.md index df8c2396..0e767135 100644 --- a/README.md +++ b/README.md @@ -21,39 +21,36 @@ rustup-init export PATH="$HOME/.cargo/bin:$PATH" ``` +3. Install uv if you don't have it already: ```bash -poetry lock --no-update -poetry export -f requirements.txt --output requirements.txt --with dev --with visualisation --without-hashes -uv pip install -r requirements.txt -uv run ldn --help + brew install uv ``` - -3. Install Poetry if you don't have it already: +or ```bash - pip install poetry + curl -LsSf https://astral.sh/uv/install.sh | sh ``` -4. Create and activate a Poetry virtual environment pointing at Homebrew's Python 3.12 and install dependencies: -This installs main group. Deps like `cogeo-mosaic` and `boto3` are in both main and visualisation group. +4. Sync dependencies. uv will create a `.venv` automatically using the Python version pinned by `requires-python` in `pyproject.toml` (installing it if needed). + +This installs the main dependency group plus the `dev` group (synced by default). Deps like `cogeo-mosaic` and `boto3` are in both the main group and the `visualisation` group. ```bash - poetry env use $(brew --prefix python@3.12)/bin/python3.12 - poetry install + uv sync ``` - For development dependencies: + For main dependencies only (no dev tools): ```bash - poetry install --with dev + uv sync --no-dev ``` - For visualisation dependencies: + For visualisation dependencies only (no project, no dev group): ```bash - poetry install --no-root --only visualisation + uv sync --only-group visualisation ``` 5. Run the CLI tool: ```bash - poetry run ldn --help - poetry run make {command from Makefile} + uv run ldn --help + uv run make {command from Makefile} ``` ## AWS @@ -66,15 +63,17 @@ Docs on AWS SSO here: https://github.com/digitalearthpacific/internal-documentat ### To add a dependency -Run: `poetry add --dev pytest` +Run: `uv add --group dev pytest` Others: -poetry add "dep-tools@git+https://github.com/digitalearthpacific/dep-tools.git" -poetry add "datacube-compute@git+https://github.com/auspatious/datacube-compute.git" +```bash +uv add "dep-tools @ git+https://github.com/digitalearthpacific/dep-tools.git" +uv add "datacube-compute @ git+https://github.com/auspatious/datacube-compute.git" +``` ### To run tests -Simply run: `poetry run pytest` or for a specific file: `poetry run pytest ldn/tests/test_mosaic.py` +Simply run: `uv run pytest` or for a specific file: `uv run pytest ldn/tests/test_mosaic.py` ### Pre-commit hooks @@ -84,18 +83,18 @@ Formats Python, YAML, and JSON. To use pre-commit to automatically run ruff, and other checks on each commit, make sure the development dependencies are installed and then run: ```bash -poetry run pre-commit install +uv run pre-commit install ``` -Note that you will need to run `poetry run pre-commit run --all-files` if any of the hooks in `.pre-commit-config.yaml` change. +Note that you will need to run `uv run pre-commit run --all-files` if any of the hooks in `.pre-commit-config.yaml` change. ## Running Commands You can run these: -- `poetry run ldn --help` -- `poetry run ldn version` -- `poetry run ldn grid list-countries` or `make grid-list-countries` +- `uv run ldn --help` +- `uv run ldn version` +- `uv run ldn grid list-countries` or `make grid-list-countries` Future commands could look like: - Get a class: `ldn grid ` e.g. forest or grassland @@ -140,16 +139,16 @@ A tile server for viewing GeoMedian/GeoMAD and predicted LULC mosaics, built wit ### Run locally ```bash -poetry install --with visualisation -poetry run uvicorn visualisation.app:app --host 0.0.0.0 --port 8081 --reload +uv sync --group visualisation +uv run uvicorn visualisation.app:app --host 0.0.0.0 --port 8081 --reload ``` ### Deploy From the project root: ```bash -poetry install --with visualisation # Needed for ldn make-mosaics command. -poetry run bash visualisation/deploy.sh +uv sync --group visualisation # Needed for ldn make-mosaics command. +uv run bash visualisation/deploy.sh ``` This will: diff --git a/ldn/training_data.py b/ldn/training_data.py index 0667ed70..23b14735 100644 --- a/ldn/training_data.py +++ b/ldn/training_data.py @@ -57,8 +57,8 @@ is_bucket_source_coop, owner_for_region, parse_tile_id, + standardise_class, ) -from notebooks.src.Compare_LULC_func import standardise_class logger = logging.getLogger(__name__) diff --git a/ldn/utils.py b/ldn/utils.py index dcfda6fd..d4b7b464 100644 --- a/ldn/utils.py +++ b/ldn/utils.py @@ -4,9 +4,11 @@ from typing import Literal from dep_tools.grids import COUNTRIES_AND_CODES as DEP_COUNTRIES_AND_CODES +from numpy import nan from pystac import ItemCollection from rustac import read_sync from rustac import store as rustac_store +from xarray import full_like from ldn.aws import aws_session, get_credential_provider @@ -337,3 +339,14 @@ def build_prefix( if is_bucket_source_coop(bucket): prefix = f"{source_coop_prefix(dataset)}/{prefix}" return prefix + + +# project the current land cover classes to UNCCD, based on the given mapping directory +def standardise_class(DataArray, mapping): + # Create a copy to preserve original metadata + remapped = full_like(DataArray, fill_value=nan) + + for original, new in mapping.items(): + remapped = remapped.where(DataArray != original, new) + + return remapped diff --git a/notebooks/Compare_LULC_per_class.ipynb b/notebooks/Compare_LULC_per_class.ipynb index e039e10f..9b0702a4 100644 --- a/notebooks/Compare_LULC_per_class.ipynb +++ b/notebooks/Compare_LULC_per_class.ipynb @@ -24,7 +24,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "b749fc44", "metadata": {}, "outputs": [], @@ -49,9 +49,10 @@ " heterogeneity_func,\n", " load_sankey_params,\n", " standard_legend,\n", - " standardise_class,\n", ")\n", - "from src.spatial import get_country_boundary, list_countries" + "from src.spatial import get_country_boundary, list_countries\n", + "\n", + "from ldn.utils import standardise_class" ] }, { @@ -2673,7 +2674,7 @@ ], "metadata": { "kernelspec": { - "display_name": "ldn-TK5rT0MB-py3.12", + "display_name": "ldn (3.12.12)", "language": "python", "name": "python3" }, diff --git a/notebooks/Test_LoadOne.ipynb b/notebooks/Test_LoadOne.ipynb index cb454d7e..f1743ba2 100644 --- a/notebooks/Test_LoadOne.ipynb +++ b/notebooks/Test_LoadOne.ipynb @@ -792,7 +792,7 @@ ], "metadata": { "kernelspec": { - "display_name": "ldn-TK5rT0MB-py3.12", + "display_name": "ldn (3.12.12)", "language": "python", "name": "python3" }, diff --git a/notebooks/src/Compare_LULC_func.py b/notebooks/src/Compare_LULC_func.py index e68e71d5..a524e94f 100644 --- a/notebooks/src/Compare_LULC_func.py +++ b/notebooks/src/Compare_LULC_func.py @@ -1,6 +1,5 @@ # package for comparing LULC products import numpy as np -import xarray as xr from matplotlib.colors import BoundaryNorm, ListedColormap from ldn.typology import classes_flipped as standard_legend @@ -33,17 +32,6 @@ def get_standard_norm(): return BoundaryNorm(ids + [max(ids) + 1], len(ids)) -# project the current land cover classes to UNCCD, based on the given mapping directory -def standardise_class(DataArray, mapping): - 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WORKDIR /var/task -COPY pyproject.toml poetry.lock ./ -RUN poetry config virtualenvs.in-project true && \ - poetry install --no-root --only visualisation -RUN .venv/bin/pip install awslambdaric +COPY pyproject.toml uv.lock ./ +# --only-group excludes the project itself AND default groups (dev), +# giving you just the visualisation group — same as the old +# `poetry install --no-root --only visualisation`. +RUN uv sync --frozen --only-group visualisation -# Copy app.py and static folder. COPY visualisation/app.py ./ COPY visualisation/static/ ./static/ diff --git a/visualisation/deploy.sh b/visualisation/deploy.sh index 32511d38..b2ba9b04 100644 --- a/visualisation/deploy.sh +++ b/visualisation/deploy.sh @@ -28,7 +28,7 @@ terraform -chdir=visualisation/infra apply \ FUNCTION_NAME=$(terraform -chdir=visualisation/infra output -raw function_name) echo "==> Function name: ${FUNCTION_NAME}" -poetry check --lock || { echo "poetry.lock is out of date. Run 'poetry lock' first."; exit 1; } +uv lock --check || { echo "uv.lock is out of date. Run 'uv lock' first."; exit 1; } echo "==> Copying SIDS tiles GeoJSON..." # Copy and minify GeoJSON. From 82da6b3cb5542a5e9982fca9fdeba506ce9edacc Mon Sep 17 00:00:00 2001 From: willjnz Date: Mon, 10 Aug 2026 13:14:44 +1000 Subject: [PATCH 2/2] Test in gh action --- .../workflows/ldn-lint-build-test-push.yml | 32 +++++++++++++----- Dockerfile | 33 +++++++------------ visualisation/Dockerfile | 3 +- 3 files changed, 36 insertions(+), 32 deletions(-) diff --git a/.github/workflows/ldn-lint-build-test-push.yml b/.github/workflows/ldn-lint-build-test-push.yml index 00583378..4e5930db 100644 --- a/.github/workflows/ldn-lint-build-test-push.yml +++ b/.github/workflows/ldn-lint-build-test-push.yml @@ -23,7 +23,7 @@ on: # Limit what triggers the workflow to prevent unnecessary runs on unrelated changes. - "ldn/**" - "pyproject.toml" - - "poetry.lock" + - "uv.lock" - "Dockerfile" - ".github/workflows/ldn-lint-build-test-push.yml" push: @@ -33,7 +33,7 @@ on: # Limit what triggers the workflow to prevent unnecessary runs on unrelated changes. - "ldn/**" - "pyproject.toml" - - "poetry.lock" + - "uv.lock" - "Dockerfile" - ".github/workflows/ldn-lint-build-test-push.yml" release: @@ -56,7 +56,7 @@ jobs: with: src: "ldn" - build-and-test: + build-test-push: runs-on: ubuntu-latest needs: [lint] permissions: @@ -84,30 +84,44 @@ jobs: git fetch --all --tags echo "VERSION=$(git describe --tags --always)" >> $GITHUB_OUTPUT - - name: Build image + - name: Build test image uses: docker/build-push-action@f9f3042f7e2789586610d6e8b85c8f03e5195baf # v7.2.0 with: context: . + target: test load: true tags: ldn-lulc:test cache-from: type=gha cache-to: type=gha,mode=max - name: Run tests - run: docker run --rm ldn-lulc:test pytest ldn/tests/ -v + run: docker run --rm ldn-lulc:test + + - name: Build production image + uses: docker/build-push-action@f9f3042f7e2789586610d6e8b85c8f03e5195baf # v7.2.0 + with: + context: . + target: final + load: true + tags: ldn-lulc:latest + cache-from: type=gha + cache-to: type=gha,mode=max + + - name: Smoketest production image + run: docker run --rm ldn-lulc:latest ldn --help - name: Tag and push if: github.ref == 'refs/heads/main' run: | - docker tag ldn-lulc:test ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.get_version.outputs.VERSION }} - docker tag ldn-lulc:test ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest + docker tag ldn-lulc:latest ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.get_version.outputs.VERSION }} + docker tag ldn-lulc:latest ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest docker push ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.get_version.outputs.VERSION }} docker push ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest - name: Tag and push release if: github.event_name == 'release' run: | - docker tag ldn-lulc:test ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.event.release.tag_name }} - docker tag ldn-lulc:test ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest + docker tag ldn-lulc:latest ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.event.release.tag_name }} + docker tag ldn-lulc:latest ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest docker push ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.event.release.tag_name }} docker push ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest diff --git a/Dockerfile b/Dockerfile index f019260e..49b7fde8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,39 +1,30 @@ -FROM ghcr.io/osgeo/gdal:ubuntu-small-3.13.1 +FROM ghcr.io/osgeo/gdal:ubuntu-small-3.13.1 AS base RUN apt-get update && apt-get install -y \ - python3-pip \ - python3-venv \ - git \ - curl \ - build-essential \ - pkg-config \ - && apt-get clean \ - && rm -rf /var/lib/{apt,dpkg,cache,log} -# Install Rust via rustup (needed to build datacube-compute) + python3-pip python3-venv git curl build-essential pkg-config \ + && apt-get clean && rm -rf /var/lib/{apt,dpkg,cache,log} + ENV CARGO_HOME="/usr/local/cargo" RUSTUP_HOME="/usr/local/rustup" ENV PATH="$CARGO_HOME/bin:$PATH" RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --default-toolchain stable --profile minimal -# Install uv COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /usr/local/bin/ -ENV UV_PROJECT_ENVIRONMENT=/code/.venv \ - UV_LINK_MODE=copy - +ENV UV_PROJECT_ENVIRONMENT=/code/.venv UV_LINK_MODE=copy WORKDIR /code COPY pyproject.toml uv.lock ./ -# Install dependencies first to leverage Docker caching. -# --no-dev keeps the "dev" group (matplotlib, pytest, etc.) out of the image. RUN uv sync --frozen --no-install-project --no-dev - -# Rust is no longer needed after dependencies are built RUN rustup self uninstall -y && rm -rf /usr/local/cargo /usr/local/rustup COPY . . -# Install the package itself. RUN uv sync --frozen --no-dev - ENV PATH="/code/.venv/bin:$PATH" -# Smoketest +# ---- test stage: adds dev deps on top of the production layer ---- +FROM base AS test +RUN uv sync --frozen --group dev +CMD ["uv", "run", "pytest", "ldn/tests/", "-v"] + +# ---- final stage = base, i.e. production image with no dev deps ---- +FROM base AS final RUN ldn --help diff --git a/visualisation/Dockerfile b/visualisation/Dockerfile index 944f803a..ef758ec6 100644 --- a/visualisation/Dockerfile +++ b/visualisation/Dockerfile @@ -15,8 +15,7 @@ WORKDIR /var/task COPY pyproject.toml uv.lock ./ # --only-group excludes the project itself AND default groups (dev), -# giving you just the visualisation group — same as the old -# `poetry install --no-root --only visualisation`. +# giving you just the visualisation group RUN uv sync --frozen --only-group visualisation COPY visualisation/app.py ./