Update install to rely on mamba / conda envs only (#214)

* Update to rely on mamba / conda envs only * Update install instructions * Extend CI to cover all platforms and multiple python versions * Remove `:` from filenames to fix Windows error
arup-group · Jan 8, 2024 · a7e484f · a7e484f
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diff --git a/.github/workflows/build_pipeline.yml b/.github/workflows/build_pipeline.yml
diff --git a/.github/workflows/commit-ci.yml b/.github/workflows/commit-ci.yml
@@ -0,0 +1,32 @@
+name: Minimal CI
+
+on:
+  push:
+    branches:
+      - "**"
+    paths-ignore:
+      - README.md
+      - CHANGELOG.md
+      - LICENSE
+      - CONTRIBUTING.md
+      - docs/**
+      - mkdocs.yml
+
+jobs:
+  test:
+    uses: arup-group/actions-city-modelling-lab/.github/workflows/python-install-lint-test.yml@main
+    with:
+      os: ubuntu-latest
+      py3version: "11"
+      notebook_kernel: genet
+      lint: false
+      additional_mamba_args: coin-or-cbc
+
+  aws-upload:
+    needs: test
+    if: needs.test.result == 'success'
+    uses: arup-group/actions-city-modelling-lab/.github/workflows/aws-upload.yml@main
+    secrets:
+      AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+      AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      AWS_S3_CODE_BUCKET: ${{ secrets.AWS_S3_CODE_BUCKET }}
diff --git a/.github/workflows/daily-scheduled-ci.yml b/.github/workflows/daily-scheduled-ci.yml
@@ -1,69 +1,36 @@
-name: Daily GeNet CI Build
+name: Daily CI
 
 on:
   schedule:
-    - cron: '37 14 * * 1-5'
+    - cron: '37 14 * * 1-5'  # checks on the 37th minute of the 14th hour every weekday
 
 jobs:
-  build:
+  get-date:
     runs-on: ubuntu-latest
-
     steps:
-    - name: Checkout
-      uses: actions/checkout@v3
-
-    - uses: actions/setup-python@v1
-      with:
-        python-version: 3.11
-
-    - uses: actions/cache@v1
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-
-    - name: Install dependencies
-      run: |
-        export ACCEPT_EULA=Y
-        sudo apt-get update
-        python -m pip install --upgrade pip
-        sudo apt-get install -y python3-pip libgdal-dev locales
-        sudo apt-get install -y libspatialindex-dev
-        sudo apt-get install -y coinor-cbc
-        export CPLUS_INCLUDE_PATH=/usr/include/gdal
-        export C_INCLUDE_PATH=/usr/include/gdal
-        sudo apt-get install ca-certificates
-        export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
-        pip install GDAL==3.4.1
-        pip install -e '.[dev]'
-
-    - name: Install jupyter kernel
-      run: python -m ipykernel install --user --name genet
-
-    - name: Run tests
-      run: pytest
-
-    - name: Send build success notification
-      if: success()
-      uses: rtCamp/[email protected]
-      env:
-        SLACK_MESSAGE: ${{ github.repository }} Daily scheduled CI Build ${{ github.run_number }} has succeeded
-        SLACK_TITLE: Daily Scheduled CI Build Success
-        SLACK_CHANNEL: city-modelling-feeds
-        SLACK_USERNAME: GitHub Build Bot
-        SLACK_ICON: https://slack-files2.s3-us-west-2.amazonaws.com/avatars/2017-12-19/288981919427_f45f04edd92902a96859_512.png
-        SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
-
-    - name: Send build failure notification
-      if: failure()
-      uses: rtCamp/[email protected]
-      env:
-        SLACK_COLOR: '#FF0000'
-        SLACK_LINK_NAMES: true
-        SLACK_MESSAGE: '<!here> ${{ github.repository }} Daily scheduled CI Build ${{ github.run_number }} has failed'
-        SLACK_TITLE: Daily Scheduled CI Build Failure!
-        SLACK_CHANNEL: city-modelling-feeds
-        SLACK_USERNAME: GitHub Build Bot
-        SLACK_ICON: https://slack-files2.s3-us-west-2.amazonaws.com/avatars/2017-12-19/288981919427_f45f04edd92902a96859_512.png
-        SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
+      - name: Add date to github output env
+        run: echo "DATE=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+
+  test:
+    needs: get-date
+    uses: arup-group/actions-city-modelling-lab/.github/workflows/python-install-lint-test.yml@main
+    with:
+      os: ubuntu-latest
+      py3version: "11"
+      notebook_kernel: genet
+      pytest_args: '--no-cov'  # ignore coverage
+      cache_mamba_env: false
+      lint: false
+      mamba_env_name: daily-ci
+      additional_mamba_args: coin-or-cbc
+
+  slack-notify-ci:
+    needs: test
+    if: always()
+    uses: arup-group/actions-city-modelling-lab/.github/workflows/slack-notify.yml@main
+    secrets:
+      SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}
+    with:
+      result: needs.test.result
+      channel: genet-feed
+      message: Daily CI action
diff --git a/.github/workflows/pr-ci.yml b/.github/workflows/pr-ci.yml
@@ -0,0 +1,48 @@
+name: Pull Request CI
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - README.md
+      - CHANGELOG.md
+      - LICENSE
+      - CONTRIBUTING.md
+      - docs/**
+      - mkdocs.yml
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        os: [windows-latest, ubuntu-latest, macos-latest]
+        py3version: ["9", "11"]
+        include:
+          - os: windows-latest
+            add_args: ""
+          - os: ubuntu-latest
+            add_args: coin-or-cbc
+          - os: macos-latest
+            add_args: coin-or-cbc
+      fail-fast: false
+    uses: arup-group/actions-city-modelling-lab/.github/workflows/python-install-lint-test.yml@main
+    with:
+      os: ${{ matrix.os }}
+      py3version: ${{ matrix.py3version }}
+      notebook_kernel: genet
+      lint: false
+      pytest_args: '--no-cov'  # ignore coverage
+      upload_to_codecov: false
+      additional_mamba_args: ${{ matrix.add_args }}
+
+  test-coverage:
+    uses: arup-group/actions-city-modelling-lab/.github/workflows/python-install-lint-test.yml@main
+    with:
+      os: ubuntu-latest
+      py3version: "11"
+      notebook_kernel: genet
+      lint: false
+      pytest_args: 'tests/'  # ignore example notebooks
+      upload_to_codecov: true
+      additional_mamba_args: coin-or-cbc
diff --git a/Dockerfile b/Dockerfile
@@ -1,13 +1,11 @@
-FROM python:3.11.4-bullseye
+FROM mambaorg/micromamba:1.5.3-bullseye-slim
 
-RUN apt-get update && \
-apt-get upgrade -y && \
-apt-get -y install gcc git libgdal-dev libgeos-dev libspatialindex-dev curl coinor-cbc cmake &&  \
-rm -rf /var/lib/apt/lists/*
+COPY --chown=$MAMBA_USER:$MAMBA_USER . ./src
 
-RUN python -m pip install --no-cache-dir --compile --upgrade pip
+RUN micromamba install -y -n base -c conda-forge -c city-modelling-lab python=3.11 "proj>=9.3" pip coin-or-cbc --file src/requirements/base.txt && \
+    micromamba clean --all --yes
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
-COPY . ./src
-
-RUN pip3 install --no-cache-dir --compile -e ./src && pip cache purge
+RUN pip install --no-deps ./src
 
+ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]