Replace GTFS operations with DuckDB and fix station sequence bugs

[yu-ta-sato]

Description

This PR refactors GTFS transportation graph processing in transportation.py, by replacing pandas operations with duckdb.

It also fixed an issue of not handling station sequences as integers due to the alphabetical order of strings (e.g., "1", "10", "11", ... , "2", "3" -> 1, 2, ... 9, 10).

Other changes:

• Allow directed graph as nx.DiGraph() if directed=True.
• Use frequencies.txt for calculating the frequencies if given and use_frequencies=True.

This is a major change where load_gtfs produces duckdb.DuckDBPyConnection instead of a dictionary of Pandas Dataframe, as well as the inputs for travel_summary_graph and get_od_pair.

Related Issues

NA

Checklist

• I have read the Contributing Guide.
• I have updated the documentation, if necessary.
• I have added tests to cover my changes.
• All new and existing tests passed.
• Pre-commit checks passed locally.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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