Bring in BART Transit Fixes/Improvements

[yueshuaing]

TODO:
get model mechanically running with MTC version tm2py + BART version network

• uncongested transit assignment went through
• add extra parameters to configs
• prepare transit network, add necessary attributes

Fare system:

• update zone-to-zone fare calculation
• update fare system grouping method
• add fare_2015_to_2000_deflator

Skimming:

• multiply skim by 100 (except for XBOATIME and BOARD), https://github.com/BayAreaMetro/modeling-website/wiki/TransitSkims
• Fix OMX (double to float)
• add "DDIST","DTIME","WACC","WEGR","WAUX","CROWD","XBOATIME","DTOLL" skims to _skim_properties, update current skim names
• add "DDIST","DTIME","WACC","WEGR","WAUX","CROWD","XBOATIME","DTOLL" skim calculation
• divide drive time skims by drive perception factors
• walk time skims are calculated by using walk distance/walk_speed (because of we have two walk perception factors)
• matrix calculation didn't work (Error: Current environment is inadequate to perform a parallel matrix calculation) solved: install numexpr 2.7.3
• test mask_above_max_transfers and mask_if_not_required_modes

Test congested transit assignment:

• add congested transit assignment method
• update assignment specifications
• add customized segment congestion function
• update demand tables (three sets --> five classes)
• mixed-mode journey level files
• add trim demand option and trim demand report
• remove "prepare_network_transit" from global iteration
• check the zero_matrix method. The zero demand initialization doesn't work, but won't affect the assignment test

Warmstart:

• add warmstart feature (transit only)
• add warmstart feature (other components)

Other features:

• peaking factors
• PNR parking penalties
• update bus time calculation
• add summaries (segment level report, bart-to-bart transfer, boardings at rail stations by access mode, transfer at stops)
• had some issues with the current summary report (output_stop_usage, export_boardings_by_line)

temp fix:

• comment out highway part in create_tod_scenarios.py (line268-line283, line49, line393), need to uncomment when bring in highway changes

Validate assignment results:

• compare to survey data
• compare to BART results

code review:

• everything is addressed correctly
• cosmetic changes

[DavidOry]

Closes #125

[DavidOry]

Replaced by #127