Merge pull request #211 from geo-engine/ge_test

test geo engine against actual instance in unit tests
geo-engine · Jan 13, 2025 · 2848c68 · 2848c68
2 parents ef00121 + 2ff8af1
commit 2848c68
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diff --git a/.github/.backend_git_ref b/.github/.backend_git_ref
@@ -0,0 +1 @@
+main
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -10,18 +10,63 @@ jobs:
   check:
     runs-on: ubuntu-22.04
 
+    services:
+      postgres:
+        image: postgis/postgis
+        env:
+          POSTGRES_USER: geoengine
+          POSTGRES_PASSWORD: geoengine
+          POSTGRES_DB: geoengine
+        ports:
+          - 5432:5432
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
     strategy:
       fail-fast: false
       matrix:
         # use all supported versions from https://devguide.python.org/versions/
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
+    defaults:
+      run:
+        working-directory: library
+
     steps:
-      - uses: actions/checkout@v3
-      - name: APT update
-        run: sudo apt-get update
-      - name: Install system dependencies
-        run: sudo apt-get install libgeos-dev libproj-dev
+      - name: Checkout library code
+        uses: actions/checkout@v4
+        with:
+          path: library
+      - name: Read backend version
+        id: read-backend-version
+        run: echo "GEOENGINE_VERSION=$(cat .github/.backend_git_ref)" >> $GITHUB_OUTPUT
+      - name: Checkout Geo Engine code
+        uses: actions/checkout@v4
+        with:
+          repository: geo-engine/geoengine
+          ref: ${{ steps.read-backend-version.outputs.GEOENGINE_VERSION }}
+          path: backend
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          tool-cache: true
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
+      - name: Install lld & GDAL & Protobuf
+        run: |
+          sudo apt-get update
+          sudo apt-get install lld libgdal-dev gdal-bin build-essential clang curl protobuf-compiler libgeos-dev libproj-dev
+          sudo apt-get clean
+          export C_INCLUDE_PATH=/usr/include/gdal:$C_INCLUDE_PATH
+          export CPLUS_INCLUDE_PATH=/usr/include/gdal:$CPLUS_INCLUDE_PATH
+          sudo ldconfig
+      - name: Install Rustup
+        run: |
+          curl --proto '=https' --tlsv1.2 --retry 10 --retry-connrefused -fsSL "https://sh.rustup.rs" | sh -s -- --profile minimal --default-toolchain none -y
+          echo "${CARGO_HOME:-$HOME/.cargo}/bin" >> $GITHUB_PATH
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -53,12 +98,37 @@ jobs:
           python -m mypy tests
       - name: Test
         run: pytest
+        env:
+          GEOENGINE_TEST_CODE_PATH: ${{ github.workspace }}/backend
+          GEOENGINE_TEST_BUILD_TYPE: "release"
+      - name: Examples
+        run: |
+          python -m pip install -e .[examples]
+          python test_all_notebooks.py
+        env:
+          GEOENGINE_TEST_CODE_PATH: ${{ github.workspace }}/backend
+          GEOENGINE_TEST_BUILD_TYPE: "release"
 
   # Checks the library using minimum version resolution
   # `uv` has this feature built-in, c.f. https://github.com/astral-sh/uv
   check-min-version:
     runs-on: ubuntu-22.04
 
+    services:
+      postgres:
+        image: postgis/postgis
+        env:
+          POSTGRES_USER: geoengine
+          POSTGRES_PASSWORD: geoengine
+          POSTGRES_DB: geoengine
+        ports:
+          - 5432:5432
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    defaults:
+      run:
+        working-directory: library
+
     env:
       # use minimum supported versions from https://devguide.python.org/versions/
       python-version: "3.9"
@@ -67,11 +137,41 @@ jobs:
       resolution: "lowest-direct"
 
     steps:
-      - uses: actions/checkout@v3
-      - name: APT update
-        run: sudo apt-get update
-      - name: Install system dependencies
-        run: sudo apt-get install libgeos-dev libproj-dev
+      - name: Checkout library code
+        uses: actions/checkout@v4
+        with:
+          path: library
+      - name: Read backend version
+        id: read-backend-version
+        run: echo "GEOENGINE_VERSION=$(cat .github/.backend_git_ref)" >> $GITHUB_OUTPUT
+      - name: Checkout Geo Engine code
+        uses: actions/checkout@v4
+        with:
+          repository: geo-engine/geoengine
+          ref: ${{ steps.read-backend-version.outputs.GEOENGINE_VERSION }}
+          path: backend
+      - name: Free Disk Space (Ubuntu)
+        uses: jlumbroso/free-disk-space@main
+        with:
+          tool-cache: true
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
+      - name: Install lld & GDAL & Protobuf
+        run: |
+          sudo apt-get update
+          sudo apt-get install lld libgdal-dev gdal-bin build-essential clang curl protobuf-compiler libgeos-dev libproj-dev
+          sudo apt-get clean
+          export C_INCLUDE_PATH=/usr/include/gdal:$C_INCLUDE_PATH
+          export CPLUS_INCLUDE_PATH=/usr/include/gdal:$CPLUS_INCLUDE_PATH
+          sudo ldconfig
+      - name: Install Rustup
+        run: |
+          curl --proto '=https' --tlsv1.2 --retry 10 --retry-connrefused -fsSL "https://sh.rustup.rs" | sh -s -- --profile minimal --default-toolchain none -y
+          echo "${CARGO_HOME:-$HOME/.cargo}/bin" >> $GITHUB_PATH
       - name: Set up Python ${{ env.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -84,17 +184,32 @@ jobs:
           uv venv
           source .venv/bin/activate
 
-          uv pip install --resolution=${{ env.resolution}} -e .
-          uv pip install --resolution=${{ env.resolution}} -e .[dev]
+          uv pip install --resolution=${{ env.resolution }} -e .
+          uv pip install --resolution=${{ env.resolution }} -e .[dev]
       - name: Build
         run: |
           source .venv/bin/activate
           python -m build .
       - name: Install test dependencies
         run: |
           source .venv/bin/activate
-          uv pip install --resolution=${{ env.resolution}} -e .[test]
+          uv pip install --resolution=${{ env.resolution }} -e .[test]
       - name: Test
         run: |
           source .venv/bin/activate
-          pytest
+          pytest --cov=geoengine --cov-report=lcov
+        env:
+          GEOENGINE_TEST_CODE_PATH: ${{ github.workspace }}/backend
+          GEOENGINE_TEST_BUILD_TYPE: "release"
+      - name: Upload coverage to Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          base-path: library
+      - name: Examples
+        run: |
+          source .venv/bin/activate
+          uv pip install --resolution=${{ env.resolution }} -e .[examples]
+          python test_all_notebooks.py
+        env:
+          GEOENGINE_TEST_CODE_PATH: ${{ github.workspace }}/backend
+          GEOENGINE_TEST_BUILD_TYPE: "release"
diff --git a/README.md b/README.md
@@ -47,6 +47,34 @@ Run tests with:
 pytest
 ```
 
+#### Test instance
+
+You have to set the environment variable `GEOENGINE_TEST_CODE_PATH` to the code folder of the Geo Engine instance you want to test against.
+Dotenv is supported, so you can create a `.env` file in the root of the project.
+
+#### Coverage
+
+You can check the coverage with:
+
+```bash
+pytest --cov=geoengine
+```
+
+### Test examples
+
+You can test the examples with:
+
+```bash
+python3 -m pip install -e .[examples]
+./test_all_notebooks.py
+```
+
+Or you can test a single example with:
+
+```bash
+./test_notebook.py examples/ndvi_ports.ipynb
+```
+
 ## Dependencies
 
 Since we use `cartopy`, you need to have the following system dependencies installed.

diff --git a/check.sh b/check.sh
@@ -11,10 +11,6 @@ function echoerr() {
     echo "$@" 1>&2;
 }
 
-echoerr "Running tests"
-
-pytest
-
 echoerr "Check code style"
 
 python3 -m pycodestyle
@@ -28,3 +24,11 @@ echoerr "Check code with type checker"
 
 python3 -m mypy geoengine
 python3 -m mypy tests
+
+echoerr "Running tests"
+
+pytest
+
+echoerr "Running examples"
+
+python3 test_all_notebooks.py
diff --git a/examples/interactive_ml/app/Dockerfile b/examples/interactive_ml/app/Dockerfile
@@ -0,0 +1,37 @@
+# Setup a Debian 12 based image with a Python virtualenv
+FROM debian:12-slim AS build
+RUN apt-get update && \
+    apt-get install --no-install-suggests --no-install-recommends --yes python3-venv gcc libpython3-dev && \
+    python3 -m venv /venv && \
+    /venv/bin/pip install --upgrade pip setuptools wheel
+
+# Install Geo Engine library and its dependencies
+FROM build AS build-venv
+COPY pyproject.toml setup.cfg setup.py /library/
+COPY geoengine /library/geoengine
+WORKDIR /library
+RUN /venv/bin/pip install --disable-pip-version-check .[dev,test,examples]
+
+# Copy the virtualenv into a distroless image
+# Hint: Use the `:debug` tag to get a shell in the image
+FROM gcr.io/distroless/python3-debian12
+COPY --from=build-venv /venv /venv
+
+# Copy the example notebook to run
+COPY examples/interactive_ml /app
+
+WORKDIR /app
+
+ENV GEOENGINE_INSTANCE_URL=https://zentrale.app.geoengine.io/api
+ENV GEOENGINE_SESSION_TOKEN=<SESSION_TOKEN>
+
+EXPOSE 8866
+
+ENTRYPOINT [ \
+    "/venv/bin/python3", \
+    "-m", \
+    "voila", \
+    "--no-browser", \
+    "--Voila.ip='0.0.0.0'", \
+    "app/Simple Random Forest Two-Class Classifier on Sentinel-2 Images.ipynb" \
+    ]
diff --git a/examples/interactive_ml/app/README.md b/examples/interactive_ml/app/README.md
@@ -0,0 +1,42 @@
+# Interactive ML App
+
+This app demonstrates a complete workflow for binary classification using Sentinel-2 satellite imagery and a Random Forest classifier. The workflow includes data acquisition, preprocessing, model training, and result visualization. Initially, the environment is set up and necessary libraries are imported. The spatial and temporal bounds for the data query are then defined through a query rectangle. A workflow is created to fetch and preprocess Sentinel-2 data, which is followed by the use of a labeling tool to create training data for water and non-water classes.
+
+## Local setup
+
+To run the app locally, you need to install the dependencies and start the app. You can install the dependencies with:
+
+```bash
+pip install --disable-pip-version-check -e .[dev,test,examples]
+
+GEOENGINE_INSTANCE_URL=https://zentrale.app.geoengine.io/api \
+GEOENGINE_SESSION_TOKEN=<SESSION_TOKEN> \
+./examples/interactive_ml/app/app.sh
+```
+
+The app will be available at [http://localhost:8866](http://localhost:8866).
+
+## Container setup
+
+To run the app in a container, you need to build the container image and start the container.
+You can build the container image with:
+
+```bash
+./examples/interactive_ml/app/build.sh
+
+podman run --rm \
+    -p 8866:8866 \
+    -e GEOENGINE_INSTANCE_URL=https://zentrale.app.geoengine.io/api \
+    -e GEOENGINE_SESSION_TOKEN=<SESSION_TOKEN> \
+    geoengine-interactive-ml:latest
+```
+
+### Upload to quay.io
+
+To upload the container image to quay.io, you need to log in and push the image.
+You can do this with:
+
+```bash
+podman login quay.io
+podman push geoengine-interactive-ml:latest quay.io/geoengine/geoengine-interactive-ml:latest
+```
diff --git a/...s/interactive_ml/app/Simple Random Forest Two-Class Classifier on Sentinel-2 Images.ipynb b/...s/interactive_ml/app/Simple Random Forest Two-Class Classifier on Sentinel-2 Images.ipynb
@@ -18,6 +18,8 @@
    "outputs": [],
    "source": [
     "import ipyvuetify as vue\n",
+    "import IPython.display\n",
+    "import base64\n",
     "from dataclasses import dataclass\n",
     "from collections.abc import Callable, Coroutine\n",
     "from enum import Enum\n",
@@ -341,6 +343,22 @@
     "\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(\"assets/favicon.ico\", \"rb\") as image_file:\n",
+    "    favicon = base64.b64encode(image_file.read()).decode()\n",
+    "\n",
+    "favicon_changer = IPython.display.Javascript(f'''\n",
+    "    document.querySelector(\"link[rel='icon']\").href = \"data:image/x-icon;base64,{favicon}\";\n",
+    "''')\n",
+    "\n",
+    "IPython.display.display(favicon_changer)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -399,7 +417,7 @@
     "    padding: 0 !important;\n",
     "    margin: 0 !important;\n",
     "  }\n",
-    "</style>\n"
+    "</style>"
    ]
   },
   {
@@ -489,7 +507,7 @@
     "                self.error_bar,\n",
     "                vue.Html(tag='br'),\n",
     "            ]),\n",
-    "            vue.Footer(children=[vue.Col(children=['2024 – Geo Engine GmbH'], class_='text-center')], app=True),\n",
+    "            vue.Footer(children=[vue.Col(children=['2025 – Geo Engine GmbH'], class_='text-center')], app=True),\n",
     "        ]\n",
     "\n",
     "    def register_location_button(self, callback: Callable[[Location, str, str], None]) -> None:\n",
@@ -742,7 +760,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.3"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

diff --git a/examples/interactive_ml/app/assets/favicon.ico b/examples/interactive_ml/app/assets/favicon.ico
diff --git a/examples/interactive_ml/app/build.sh b/examples/interactive_ml/app/build.sh
@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
+
+podman build -f $SCRIPT_DIR/Dockerfile --tag geoengine-interactive-ml:latest .