19 pkg resources deprecation warning

[r-leyshon]

Description

Following our discussion about upgrading to python 3.11.x with a stripped back requirements.txt today, I went ahead and decided to implement things. A few things to note here:

• A new explicit dependency as suggested by pipdeptools is munkres which seems to be a python internal for resource partition.
• install -e . removed from reqs
• Python needs major minor patch to match in pyproject.toml, environment.yml & installs in CI runners
• Local install (not in editable mode) of transport-performance added to all runners
• This approach would tolerate pkg_resource deprecation warnings
• A deprecation warning originating from kaleido is introduced

Fixes None

Motivation and Context

Reference for deprecation and future warnings associated with upgrading to python 3.11.6

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Housekeeping

How Has This Been Tested?

Test configuration details:

• OS: macos
• Python version: 3.11.6
• Java version: NA
• Python management system: pip

Advice for reviewer

Warnings introduced on pytest are as follows, some of which originate in our source code:

================================================================ warnings summary =================================================================
../../../../opt/anaconda3/envs/transport-performance/lib/python3.11/site-packages/pycountry/__init__.py:10
  /opt/anaconda3/envs/transport-performance/lib/python3.11/site-packages/pycountry/__init__.py:10: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    import pkg_resources

../../../../opt/anaconda3/envs/transport-performance/lib/python3.11/site-packages/pkg_resources/__init__.py:2871
  /opt/anaconda3/envs/transport-performance/lib/python3.11/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

tests/gtfs/test_validation.py::TestGtfsInstance::test__plot_summary_on_pass
  /opt/anaconda3/envs/transport-performance/lib/python3.11/site-packages/kaleido/scopes/base.py:188: DeprecationWarning:
  
  setDaemon() is deprecated, set the daemon attribute instead

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

...

tests/gtfs/test_validation.py::TestGtfsInstance::test__plot_summary_on_pass
  /opt/anaconda3/envs/foobar-tp/lib/python3.11/site-packages/kaleido/scopes/base.py:188: DeprecationWarning:
  
  setDaemon() is deprecated, set the daemon attribute instead

tests/urban_centres/test_urban_centres.py::test_final_output
  /Users/richardleyshon/Documents/transport-network-performance/tests/urban_centres/test_urban_centres.py:554: FutureWarning:
  
  Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`

tests/urban_centres/test_urban_centres.py::test_final_output
  /Users/richardleyshon/Documents/transport-network-performance/tests/urban_centres/test_urban_centres.py:564: FutureWarning:
  
  Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`

Checklist:

• My code follows the intended structure of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings See point above
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

Additional comments

[codecov-commenter]

Codecov Report

All modified lines are covered by tests ✅

Comparison is base (d230227) 96.80% compared to head (b0d6c61) 0.00%.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev    #165       +/-   ##
==========================================
- Coverage   96.80%   0.00%   -96.80%     
==========================================
  Files          11       8        -3     
  Lines        1000     792      -208     
==========================================
- Hits          968       0      -968     
- Misses         32     792      +760     

Flag	Coverage Δ
unittests	0.00% <ø> (-96.80%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
src/transport_performance/gtfs/routes.py	0.00% <ø> (-95.17%)	⬇️

... and 10 files with indirect coverage changes

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