Merge branch 'bart_transit_improvements' into acceptance-criteria-int…

…egration

.github/ISSUE_TEMPLATE/bug_report.md

@@ -22,13 +22,16 @@ Progress:
 - [ ] Test passes
 
 ## To Reproduce
+
 Steps to reproduce the behavior:
+
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
 4. See error
 
 ### Failing tests
+
 - [ ] No applicable test failed, need to create.
 - [ ] other...specify
 

.github/ISSUE_TEMPLATE/feature_request.md

@@ -6,6 +6,7 @@ labels: enhancement
 assignees: ''
 ---
 ### User Story
+
 *As a ...insert type of user... I'd like to ...insert desired feature or behavior...*
 
 Progress:

.github/pull_request_template.md

@@ -1,27 +1,23 @@
 ## What existing problem does the pull request solve and why should we include it?
 
-
 ## What is the testing plan?
 
 *Demonstrate the code is solid by discussing how results are verified and covered by tests*
 
- - [ ] Code for this PR is covered in tests 
- - [ ] Code passes all existing tests
+- [ ] Code for this PR is covered in tests
+- [ ] Code passes all existing tests
 
 ## Code formatting
+
 *Code should be PEP8 compliant before merging by running a package like [`black`](https://pypi.org/project/black/)*
 
- - [ ] Code linted
+- [ ] Code linted
 
 ## Applicable Issues
+
 *Please do not create a Pull Request without creating an issue first.*
 
 *Put `closes #XXXX` in your comment to auto-close the issue that your PR fixes.*
 
-
-#### Issues List
-
- -  closes...
- -  closes...
-
-
+- closes...
+- closes...

.github/workflows/clean.yml

@@ -0,0 +1,30 @@
+name: Clean Docs for Deleted References
+on:
+  delete:
+
+env:
+  PYTHON_VERSION: 3.8
+
+jobs:
+  clean:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Set up Python $PYTHON_VERSION
+      uses: actions/setup-python@v2
+      with:
+        python-version: $PYTHON_VERSION
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install mike
+    - name: Configure Git user
+      run: |
+        git config --local user.email "github-actions[bot]@users.noreply.github.com"
+        git config --local user.name "github-actions[bot]"
+    - name: Delete defunct docs versions
+      run: |
+        echo "Deleting ${{ github.event.ref_name }} version from docs"
+        mike delete --rebase --push ${{ github.event.ref_name }}

.github/workflows/flake.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main, develop]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+    - uses: pre-commit/[email protected]

.github/workflows/test.yml → .github/workflows/push.yml

@@ -1,4 +1,4 @@
-name: Python package
+name: Push Workflow
 
 on: [push]
 
@@ -9,20 +9,28 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'skip ci')"
     strategy:
       matrix:
-        python-version: [3.7, 3.8]
+        python-version: [3.8]
 
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Document branch
+      run: echo ${{ github.ref_name }}
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
+        sudo apt-get update
+        sudo apt-get install gdal-bin libgdal-dev
+        pip install GDAL==3.2.3
         pip install -r requirements.txt
         pip install -r dev-requirements.txt
-    - name: Lint with flake8
+    - name: Lint
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

.github/workflows/release.yml

@@ -0,0 +1,69 @@
+name: Release Workflow
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-test-deploy:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8]
+    env:
+      DEPLOY_TARGET: ${{ matrix.python-version == '3.8' }}
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Document python/os version
+      run: |
+        echo "Python V ${{ matrix.python-version }}"
+        echo "Targeted Deployment Combo? $DEPLOY_TARGET"
+    - name: Document branch
+      run: echo ${{ github.ref_name }}
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r dev-requirements.txt
+    - name: Lint
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install package
+      run: |
+        pip install -e .
+    - name: Test with pytest
+      run: |
+        pytest -s -m "not skipci"
+    - name: Configure Git user
+      if: ${{DEPLOY_TARGET}}
+      run: |
+        git config --local user.email "github-actions[bot]@users.noreply.github.com"
+        git config --local user.name "github-actions[bot]"
+    - name: Build docs
+      if: ${{DEPLOY_TARGET}}
+      run: |
+        mike deploy --push --rebase --update-aliases ${{ github.ref_name }} latest
+    - name: Install deployment dependencies
+      if: ${{DEPLOY_TARGET}}
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Publish to PyPI
+      if: ${{DEPLOY_TARGET}}
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

.gitignore

@@ -18,7 +18,7 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
+#lib/
 lib64/
 parts/
 sdist/
@@ -41,9 +41,19 @@ MANIFEST
 pip-log.txt
 pip-delete-this-directory.txt
 *.log
+
 # except logs in the example
 !examples/**/*.log
 
+# dowloaded example files
+examples/example_union_test_highway.zip
+examples/UnionCity/demand_matrices/
+examples/UnionCity/emme_project/
+examples/UnionCity/inputs/
+examples/UnionCity/ref_skim_matrices/
+examples/UnionCity/skim_matrices
+examples/UnionCity/
+
 #temp files
 tests/scratch/*
 !tests/scratch/readme.md

.markdownlint.yaml

@@ -5,5 +5,17 @@ default: true
 MD007:
   indent: 4
 
-# Remove line length limit 
-MD013: false
+# Remove line length limit
+MD013: false
+
+# Allow us to skip levels of headings
+MD001: false
+
+# Allow us to use emphasis on whole lines.
+MD036: false
+
+# Allow us to use lower-level headings to start files
+MD041: false
+
+# Fenced code blocks in tabbed views will flag
+MD046: false

.pre-commit-config.yaml

@@ -0,0 +1,47 @@
+default_stages: [commit]
+repos:
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
+    hooks:
+      - id: black
+        language_version: python3
+      - id: black-jupyter
+  - repo: https://github.com/PyCQA/pydocstyle
+    rev: 6.1.1
+    hooks:
+      - id: pydocstyle
+        stages: [manual]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.4.0
+    hooks:
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: check-added-large-files
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+        args: [--unsafe]
+      - id: requirements-txt-fixer
+      - id: check-executables-have-shebangs
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.27.1
+    hooks:
+      - id: markdownlint
+        stages: [manual]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+    - id: isort
+      args: ["--profile", "black"]
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.14.3
+    hooks:
+    - id: check-github-workflows
+    - id: check-github-actions
+  - repo: http://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+    - id: flake8
+      stages: [manual]

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Changelog
 
 ## Version (date)
+
 - a list
 - of things
-- that have changed
+- that have changed

CODEOWNERS

@@ -0,0 +1,36 @@
+# Helps auto-assign code reviews for pull requests
+# The last match will 'win'
+
+# Global owners
+*                               @lmz    @FlaviaTsang
+
+# DevOps / Quality Assurance
+/.github/                       @e-lo    @lmz
+setup.config                    @e-lo    @lmz
+pre-commit-config.yaml          @e-lo    @lmz
+.markdownlint.yaml              @e-lo    @lmz
+
+# Documentation Setup
+/docs/                         @e-lo    @lmz
+mkdocs.yml                     @e-lo    @lmz
+
+# Documentation Content
+*.md                            @lmz     @FlaviaTsang
+
+# Tests should be reviewed by dev team
+pytest.ini                      @e-lo   @inrokevin  @lmz
+/tests/                         @e-lo   @inrokevin  @lmz
+
+# EMME related things should be reviewed by INRO
+/tm2py/emme/                    @inrokevin
+
+# Packaging
+setup.py                         @e-lo          @lmz
+*requirements*.txt               @inrokevin     @lmz
+manifest.in                      @e-lo          @lmz
+environment.yml                  @inrokevin     @lmz
+Dockerfile                       @inrokevin     @lmz
+/bin/                            @inrokevin     @lmz         @e-lo
+
+# Examples
+/examples/                       @FlaviaTsang   @i-am-sijia

CONTRIBUTING.md

@@ -1,2 +1,3 @@
 # Contribution Guide
 
+Please refer to contribution documentation website: [](https://bayareametro.github.io/tm2py/contributing)

Dockerfile

@@ -1,5 +1,5 @@
 # docker build -t mypackage .
-# docker run --rm -v "$PWD":/home/jovyan/work mypackage /bin/bash 
+# docker run --rm -v "$PWD":/home/jovyan/work mypackage /bin/bash
 FROM jupyter/minimal-notebook
 
 COPY ../requirements.txt /tmp/requirements.txt
@@ -28,4 +28,4 @@ RUN conda clean --all --yes && \
 WORKDIR /home/jovyan/work
 
 # set default command to launch when container is run
-CMD ["jupyter", "lab", "--ip='0.0.0.0'", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.password=''"]
+CMD ["jupyter", "lab", "--ip='0.0.0.0'", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.password=''"]