297 restructure package

.github/workflows/integration-tests.yml

@@ -20,20 +20,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: ["macos-12"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # SHA for v4.1.7
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@9a7ac94420f42ee15fc60ab88d0dca4be1fd5757 # SHA for v5.1.0
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install '.[test]'
     - name: Install java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # SHA for v4.2.1
       with:
         distribution: 'temurin'
         java-version: '11.0.21'
@@ -47,6 +47,9 @@ jobs:
         brew install --build-from-source ./osmosis.rb
         brew info osmosis
       shell: sh
-    - name: Run Integration Tests Only
-      run: |
-        pytest -m runinteg --runinteg --ignore tests/analyse_network --ignore tests/test_analyse_network.py --deselect tests/gtfs/test_gtfs_utils.py::TestBboxFilterGtfs::test_bbox_filter_gtfs_to_date_builds_network
+    - name: Run Integration Tests with retry
+      uses: nick-fields/retry@7152eba30c6575329ac0576536151aca5a72780e # SHA for v3.0.0
+      with:
+        timeout_minutes: 10
+        max_attempts: 3
+        command: pytest -m runinteg --runinteg --ignore tests/analyse_network --ignore tests/test_analyse_network.py

.github/workflows/python-package-linux.yml

@@ -18,21 +18,21 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: ["ubuntu-22.04"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # SHA for v4.1.7
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@9a7ac94420f42ee15fc60ab88d0dca4be1fd5757 # SHA for v5.1.0
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install '.[test]'
     - name: Install java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # SHA for v4.2.1
       with:
         distribution: 'temurin'
         java-version: '11.0.21'
@@ -44,6 +44,9 @@ jobs:
         sudo apt update
         sudo apt install -y libgeos-dev
       shell: sh
-    - name: Test with pytest
-      run: |
-        pytest
+    - name: Test with retry
+      uses: nick-fields/retry@7152eba30c6575329ac0576536151aca5a72780e # SHA for v3.0.0
+      with:
+        timeout_minutes: 10
+        max_attempts: 3
+        command: pytest

.github/workflows/python-package-mac.yml

@@ -19,20 +19,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: ["macos-12"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # SHA for v4.1.7
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@9a7ac94420f42ee15fc60ab88d0dca4be1fd5757 # SHA for v5.1.0
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install '.[dev,test]'
     - name: Install java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # SHA for v4.2.1
       with:
         distribution: 'temurin'
         java-version: '11.0.21'
@@ -48,12 +48,16 @@ jobs:
       run: |
         pre-commit install
         pre-commit run --all-files
-    - name: Run Tests and Generate Coverage Report
-      run: |
-        coverage run -m pytest
-        coverage xml
+    - name: Base tests with retry
+      uses: nick-fields/retry@7152eba30c6575329ac0576536151aca5a72780e # SHA for v3.0.0
+      with:
+        timeout_minutes: 10
+        max_attempts: 3
+        command: |
+          coverage run -m pytest
+          coverage xml
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@ab904c41d6ece82784817410c45d8b8c02684457 # SHA for v3.1.6
       with:
         file: ./coverage.xml
         flags: unittests

.github/workflows/python-package-windows.yml

@@ -1,4 +1,4 @@
-# This workflow will install OS dependencies and run a 'base' set of unit tests with Python 3.9
+# This workflow will install OS dependencies and run a 'base' set of unit tests with Python 3.9, 3.10, 3.11
 # The base set is selected based on dependencies that have previously caused issues on Windows
 # Will look to open up the windows test suite in the future.
 # Fixing OS version to avoid breaking OS changes during development stage.
@@ -20,12 +20,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: ["windows-2022"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # SHA for v4.1.7
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@9a7ac94420f42ee15fc60ab88d0dca4be1fd5757 # SHA for v5.1.0
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -35,8 +35,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install kaleido==0.1.0.post1  # fixing kaleido version within runner, known issue: https://github.com/plotly/Kaleido/issues/134
-    - name: Run 'base' Tests
-      run: |
-          pytest --ignore tests/osm/ --ignore tests/analyse_network --ignore tests/test_analyse_network.py --deselect tests/gtfs/test_gtfs_utils.py::TestBboxFilterGtfs::test_bbox_filter_gtfs_to_date_builds_network
+        pip install '.[test]'
+    - name: Base tests with retry
+      uses: nick-fields/retry@7152eba30c6575329ac0576536151aca5a72780e # SHA for v3.0.0
+      with:
+        timeout_minutes: 10
+        max_attempts: 3
+        command: pytest --ignore tests/osm/ --ignore tests/analyse_network --ignore tests/test_analyse_network.py

.github/workflows/quarto-render.yml

@@ -17,17 +17,17 @@ jobs:
     permissions:
       contents: write
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ env.PYTHON_VERSION }}
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # SHA for v4.1.7
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@9a7ac94420f42ee15fc60ab88d0dca4be1fd5757 # SHA for v5.1.0
       with:
         python-version: ${{ env.PYTHON_VERSION }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install '.[docs]'
     - name: Install java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # SHA for v4.2.1
       with:
         distribution: 'temurin'
         java-version: '11.0.21'
@@ -44,9 +44,9 @@ jobs:
       run: |
         python -m quartodoc build
     - name: Set up Quarto
-      uses: quarto-dev/quarto-actions/setup@v2
+      uses: quarto-dev/quarto-actions/setup@c1b50d36cf3c22b3dc7e530bd1b36634e824e545 # SHA for v2.1.4
     - name: Render and Publish
-      uses: quarto-dev/quarto-actions/publish@v2
+      uses: quarto-dev/quarto-actions/publish@c1b50d36cf3c22b3dc7e530bd1b36634e824e545 # SHA for v2.1.4
       with:
         target: gh-pages
       env:

CONTRIBUTING.md

@@ -30,19 +30,19 @@ Install Dependencies:
 
 Package set-up and installation:
 
-1. Setup a new conda env: `conda create -n r5py python=3.9.13`
+1. Setup a new conda env: `conda create -n r5py python=3.11`
 2. Activate the environment: `conda activate r5py`
 3. Launch terminal and change directory to wherever you keep your GitHub repos: `cd ~/Documents`
 4. Clone this repo, eg with https: `git clone https://github.com/datasciencecampus/transport-network-performance.git`
 5. Change directory to the repo: `cd transport-network-performance`
 6. Install pre-commit hooks: `pre-commit install`
 7. Update pip: `pip install --upgrade pip`
-8. Install r5py & other reqs: `pip install -r requirements.txt`
+8. Install package & dependencies: `pip install -e '.[dev,test,docs]'`
 
 Set-up check:
 
-10. Run set-up pytests: `pytest --runsetup`.
-11. If everything is working as expected, you should see some Java flavoured warnings about `--illegal-access` that you can ignore. But importantly look out for the message: `r5py has created the expected database files.`
+10. Run `pytest --runinteg --runexpensive` to check test suite passes.
+11. If everything is working as expected, you should see some Java flavoured warnings about `--illegal-access` that you can ignore. But importantly look out for any fails or errors in the pytest report.
 12. If you've made it this far, you've earned yourself a coffee.
 
 #### Dependencies

README.md

@@ -34,9 +34,9 @@ We welcome contributions from others. Please check out our
 ## Installation
 *Describe technical set-up. Such as the required dependencies.*
 
-This package is designed to work with python 3.9.13. Full functionality is
-tested on macos only. Other operating systems may be incompatible with
-`transport_performance.osm` specifically.
+This package is designed to work with python 3.9, 3.10 & 3.11. Full
+functionality is tested on macos only. Other operating systems may be
+incompatible with `transport_performance.osm` specifically.
 
 The transport modelling features in `transport_performance.analyse_network`
 depends upon a compatible Java Development Kit (JDK). Please consult the
@@ -63,15 +63,15 @@ or [venv](https://docs.python.org/3/library/venv.html).
 
 With conda:
 ```
-conda create -n transport-performance python=3.9.13 -y
+conda create -n transport-performance python=3.11 -y
 ```
 Once completed, activate the environment:
 ```
 conda activate transport-performance
 ```
-Install the python requirements:
+Install the python package:
 ```
-pip install -r requirements.txt
+pip install .
 ```
 Additional Java dependencies are required for full functionality. See the
 [contributing guidance](./CONTRIBUTING.md) for assistance.

_quarto.yml

@@ -7,7 +7,6 @@ project:
     - "!docs/source/"
     - "!docs/build/"
     - "!*.ipynb"
-    - "!docs/gtfs/*"
   preview:
     port: 1111
     browser: true
@@ -56,14 +55,12 @@ website:
         href: docs/how_to/index.qmd
         contents:
           - "docs/how_to/uc_pop/index.qmd"
-          - "docs/how_to/gtfs/index.qmd"
           - "docs/how_to/osm/index.qmd"
       - section: Tutorials
         href: docs/tutorials/index.qmd
         contents:
           - "docs/tutorials/urban_centre/index.qmd"
           - "docs/tutorials/population/index.qmd"
-          - "docs/tutorials/gtfs/index.qmd"
           - "docs/tutorials/osm/index.qmd"
           - "docs/tutorials/analyse_network/index.qmd"
           - "docs/tutorials/metrics/index.qmd"
@@ -120,18 +117,6 @@ quartodoc:
       package: transport_performance.population.rasterpop
       contents:
         - RasterPop
-    - title: "`gtfs`"
-      desc: >
-        Modules for working with GTFS public transit schedule files.
-      package: transport_performance.gtfs
-      contents:
-        - calendar
-        - cleaners
-        - gtfs_utils
-        - multi_validation
-        - routes
-        - validation
-        - validators
     - title: "`osm`"
       desc: >
         Modules for OpenStreetMap utilities, such are cropping .pbf files to a bounding box.

docs/tutorials/analyse_network/index.qmd

@@ -1,5 +1,5 @@
 ---
-title: "5. Analyse Network"
+title: "4. Analyse Network"
 description: Learn how to use the `transport_performance.analyse_network` module through examples.
 date-modified: 05/17/2024  # must be in MM/DD/YYYY format
 categories: ["Tutorial"]  # see https://diataxis.fr/tutorials-how-to/#tutorials-how-to, delete as appropriate