diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..a636362 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,15 @@ +# Ignore any local virtual environments +.venv +venv +.cache + +# Ignore the generated runs +data +outputs +intermediates +inputs + + +# Byte-compiled / optimized / DLL files +**/__pycache__/ +**/*.py[cod] \ No newline at end of file diff --git a/.github/workflows/build_docker.yaml b/.github/workflows/build_docker.yaml new file mode 100644 index 0000000..16f87ea --- /dev/null +++ b/.github/workflows/build_docker.yaml @@ -0,0 +1,184 @@ +name: build_docker + +on: + workflow_dispatch: + push: + branches: + - 'main' + tags: + - 'v*' + pull_request: + +env: + REGISTRY: ghcr.io + IMAGE: ghcr.io/openmethane/openmethane-prior + +jobs: + build: + runs-on: ubuntu-latest + + strategy: + matrix: + platform: + # - linux/arm64 + - linux/amd64 + + permissions: + contents: read + packages: write + + outputs: + digest: ${{ steps.build.outputs.digest }} + + # Builds and pushes the image + # Tags the image with the PR that it is linked to + steps: + - name: Checkout code + uses: actions/checkout@v4 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Login to Container registry + uses: docker/login-action@v3 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@v5 + with: + images: "${{ env.IMAGE }}" + tags: | + type=schedule + type=ref,event=branch + type=ref,event=pr + - name: Build and push image + uses: docker/build-push-action@v5 + id: build + with: + platforms: ${{ matrix.platform }} + labels: ${{ steps.meta.outputs.labels }} + tags: ${{ steps.meta.outputs.tags }} + push: true + pull: false + cache-from: type=gha + cache-to: type=gha,mode=max + + test-unit: + # Simple test suite to verify that the docker container works as expected + timeout-minutes: 10 + runs-on: ubuntu-latest + needs: build + permissions: + contents: read + packages: read + container: + image: ghcr.io/openmethane/openmethane-prior@${{ needs.build.outputs.digest }} + credentials: + username: ${{ github.actor }} + password: ${{ secrets.github_token }} + steps: + - name: Run a quick test suite + run: | + cd /opt/project + cp .env.example .env + python -m pytest -r a -v tests/test_domain_json.py + env: + CDSAPI_KEY: ${{ secrets.CDSAPI_ADS_KEY }} + CDSAPI_URL: https://ads.atmosphere.copernicus.eu/api/v2 + - name: Upload artifacts + if: ${{ always() }} + uses: actions/upload-artifact@v4 + with: + name: docker-artifacts + path: /opt/project/data + + # Tag the latest image if running on the main branch + # TODO: Handle tagged builds + tag-latest-image: + runs-on: ubuntu-latest + needs: [ test-unit ] + if: github.ref == 'refs/heads/main' + permissions: + contents: read + packages: write + steps: + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Checkout code + uses: actions/checkout@v4 + - name: Login to Container registry + uses: docker/login-action@v3 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@v5 + with: + images: "${{ env.IMAGE }}" + tags: | + type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main'}} + - name: Push latest image + uses: docker/build-push-action@v5 + id: build + with: + labels: ${{ steps.meta.outputs.labels }} + tags: ${{ steps.meta.outputs.tags }} + cache-from: type=gha + cache-to: type=gha,mode=max + push: true + load: true + + # Push the image to ECR as well + push-ecr: + runs-on: ubuntu-latest + needs: [test-unit, build ] + permissions: + contents: read + packages: read + env: + GHCR_IMAGE_ID: ghcr.io/openmethane/openmethane-prior@${{ needs.build.outputs.digest }} + ECR_IMAGE: 654654509571.dkr.ecr.ap-southeast-2.amazonaws.com/github/openmethane/openmethane-prior + steps: + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Checkout code + uses: actions/checkout@v4 + - name: Login to Container registry + uses: docker/login-action@v3 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + - name: Configure AWS credentials + uses: aws-actions/configure-aws-credentials@v4 + # TODO: Use the OIDC token instead of the access key + with: + aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} + aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + aws-region: ap-southeast-2 + - name: Login to Amazon ECR + uses: aws-actions/amazon-ecr-login@v2 + - name: Pull built docker image + run: | + docker pull ${{ env.GHCR_IMAGE_ID }} + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@v5 + with: + images: "${{ env.ECR_IMAGE }}" + tags: | + type=schedule + type=ref,event=branch + type=ref,event=pr + type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main'}} + - name: Tag and push docker image to Amazon ECR + run: | + echo "${{ steps.meta.outputs.tags }}" + + for tag in "${{ steps.meta.outputs.tags }}"; do + docker tag "${{ env.GHCR_IMAGE_ID }}" "$tag" + docker push "$tag" + done \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..c0030c0 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,57 @@ +# Secret management +FROM segment/chamber:2 AS chamber + +# Build the reqired dependecies +FROM python:3.11 AS builder + +# Creates a standalone environment in /opt/venv +RUN pip install poetry==1.8.2 + +WORKDIR /opt/venv + +COPY pyproject.toml poetry.lock ./ +RUN touch README.md + +# This installs the python dependencies into /opt/venv +RUN python -m venv /opt/venv && \ + poetry export --with dev,tests -f requirements.txt --output requirements.txt && \ + /opt/venv/bin/pip install -r requirements.txt + +# Container for running the project +# This isn't a hyper optimised container but it's a good starting point +FROM python:3.11 + +LABEL org.opencontainers.image.authors="jared.lewis@climate-resource.com" + +# Configure Python +ENV PYTHONFAULTHANDLER=1 \ + PYTHONUNBUFFERED=1 \ + PYTHONHASHSEED=random + +# This is deliberately outside of the work directory +# so that the local directory can be mounted as a volume of testing +ENV VIRTUAL_ENV=/opt/venv \ + PATH="/opt/venv/bin:$PATH" \ + LD_LIBRARY_PATH="/opt/venv/lib:$LD_LIBRARY_PATH" + +WORKDIR /opt/project + +# Install additional apt dependencies +#RUN apt-get update && \ +# apt-get install -y csh bc file make wget && \ +# rm -rf /var/lib/apt/lists/* + +# Secret management +COPY --from=chamber /chamber /bin/chamber + +# Copy across the virtual environment +COPY --from=builder /opt/venv /opt/venv + +# Copy in the rest of the project +# For testing it might be easier to mount $(PWD):/opt/project so that local changes are reflected in the container +COPY . /opt/project + +# Install the local package in editable mode +RUN pip install -e . + +CMD ["/bin/bash"] \ No newline at end of file diff --git a/Makefile b/Makefile index 4ee1e2c..9eecfd9 100644 --- a/Makefile +++ b/Makefile @@ -2,6 +2,10 @@ update-licenseheaders: ## add or update license headers in all python files licenseheaders -y 2023 --owner "The Superpower Institute Ltd" --projname "OpenMethane" --tmpl .copyright.tmpl --ext .py -x "venv/*" +.PHONY: build +build: ## Build the docker container locally + docker build --platform=linux/amd64 -t openmethane-prior . + .PHONY: virtual-environment virtual-environment: ## update virtual environment, create a new one if it doesn't already exist poetry lock --no-update diff --git a/poetry.lock b/poetry.lock index 5d86db0..a86287f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -15,69 +15,6 @@ files = [ dev = ["coveralls", "flake8", "pydocstyle"] test = ["pytest (>=4.6)", "pytest-cov"] -[[package]] -name = "aniso8601" -version = "9.0.1" -description = "A library for parsing ISO 8601 strings." -optional = false -python-versions = "*" -files = [ - 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from openmethane_prior.config import PriorConfig @@ -67,18 +65,3 @@ def check_input_files(config: PriorConfig): ) print("\n".join(errors)) sys.exit(1) - - -def reproject_raster_inputs(config: PriorConfig): - """Re-project raster files to match domain""" - print("### Re-projecting raster inputs...") - sam.reproject( - str(config.as_input_file(config.layer_inputs.land_use_path)), - str(config.as_intermediate_file(config.layer_inputs.land_use_path)), - config.crs, - ) - sam.reproject( - str(config.as_input_file(config.layer_inputs.ntl_path)), - str(config.as_intermediate_file(config.layer_inputs.ntl_path)), - config.crs, - ) diff --git a/src/openmethane_prior/raster.py b/src/openmethane_prior/raster.py new file mode 100644 index 0000000..8c13cda --- /dev/null +++ b/src/openmethane_prior/raster.py @@ -0,0 +1,70 @@ +import os + +import rasterio as rio +from openmethane_prior.config import PriorConfig +from rasterio.warp import Resampling, calculate_default_transform, reproject + + +def reproject_tiff(image, output, dst_crs="EPSG:4326", resampling="nearest", **kwargs): + """Reprojects an image. + + Based on samgeo.common.reproject + + Args: + image (str): The input image filepath. + output (str): The output image filepath. + dst_crs (str, optional): The destination CRS. Defaults to "EPSG:4326". + resampling (Resampling, optional): The resampling method. Defaults to "nearest". + **kwargs: Additional keyword arguments to pass to rasterio.open. + + """ + if isinstance(resampling, str): + resampling = getattr(Resampling, resampling) + + image = os.path.abspath(image) + output = os.path.abspath(output) + + if not os.path.exists(os.path.dirname(output)): + os.makedirs(os.path.dirname(output)) + + with rio.open(image, **kwargs) as src: + transform, width, height = calculate_default_transform( + src.crs, dst_crs, src.width, src.height, *src.bounds + ) + kwargs = src.meta.copy() + kwargs.update( + { + "crs": dst_crs, + "transform": transform, + "width": width, + "height": height, + } + ) + + with rio.open(output, "w", **kwargs) as dst: + for i in range(1, src.count + 1): + reproject( + source=rio.band(src, i), + destination=rio.band(dst, i), + src_transform=src.transform, + src_crs=src.crs, + dst_transform=transform, + dst_crs=dst_crs, + resampling=resampling, + **kwargs, + ) + + +def reproject_raster_inputs(config: PriorConfig): + """Re-project raster files to match domain""" + print("### Re-projecting raster inputs...") + reproject_tiff( + str(config.as_input_file(config.layer_inputs.land_use_path)), + str(config.as_intermediate_file(config.layer_inputs.land_use_path)), + config.crs, + ) + reproject_tiff( + str(config.as_input_file(config.layer_inputs.ntl_path)), + str(config.as_intermediate_file(config.layer_inputs.ntl_path)), + config.crs, + )