Merge branch 'main' into fix-reading-java-array

.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 }}

.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/action-slack-notify@v2.2.0
-      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/action-slack-notify@v2.2.0
-      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

.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

.gitignore

@@ -54,6 +54,7 @@ coverage.xml
 *.cover
 .hypothesis/
 .pytest_cache/
+reports/
 
 # Translations
 *.mo
@@ -122,15 +123,5 @@ dmypy.json
 .pyre/
 .idea
 
-tests/test_outputs/
-test_chunks.csv
-reports/
-mprofile*
-benchmark-outputs/
-working-dir/
-scripts/secrets-mgr-exploration.py
-*.nbconvert.*
-example_data/pt2matsim_network/genet_output/*
-genet_output/*
-example_data/output_*/*
-example_data/api_requests_send.json
+# Project specific
+examples/example_data/outputs

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## [Unreleased]
 
 ### Fixed
+* Fixed problem snapping and routing PT services with stops whose names started with 'x' [#225](https://github.com/arup-group/genet/pull/225)
 * Fixed summary report:
   * Intermodal Access/Egress reporting is more general (not expecting just car and bike mode access to PT) [#204](https://github.com/arup-group/genet/pull/204)
   * Node/Links numbers were reported incorrectly (switched) [#207](https://github.com/arup-group/genet/pull/207)

CONTRIBUTING.md

@@ -65,14 +65,15 @@ automated `PEP8` checks and runs unit tests in a fresh environment, as well as i
 8. Update/add to or generate a new jupyter notebook in `notebooks` directory which takes the user through your new feature or
 change.
    1. Jupyter notebooks are closely linked to the [wiki pages](https://github.com/arup-group/genet/wiki).
-      1. Make sure you follow the naming convention: `number.number. Theme: Catchy Title`
-      2. Make sure you structure the notebook in a way that you would like to see it in a wiki page, with a lot of
+      1. Make sure you follow the naming convention to title your page: `number.number. Theme: Catchy Title`
+      2. Make sure to also name the notebook so that it is machine readable: `number_number_theme_catchy_title.ipynb`
+      3. Make sure you structure the notebook in a way that you would like to see it in a wiki page, with a lot of
       markdown cells containing quality descriptions. Use existing notebook as examples.
    2. After your changes have been merged, you may like to update the wiki pages. To do this in an automated way:
       1. Clone the wiki part of the repo: ```git clone https://github.com/arup-group/genet.wiki.git```
-      2. Run the `notebooks/generate_usage_wiki_from_notebooks.py` script, pointing at the folder containing the
+      2. Run the `examples/generate_usage_wiki_from_notebooks.py` script, pointing at the folder containing the
       notebooks and the wiki repo folder to receive the output.
-   3. You may use example data already in `example_data` directory of this repo, or add more (small amount of) data to
+   3. You may use example data already in `examples/example_data` directory of this repo, or add more (small amount of) data to
    it to show off your new features.
 9. Add section in the `README.md` which shows usage of your new feature. This can be paraphrased from the jupyter
 notebook in point above.

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"]