dates: Consolidate date parsing logic

[victorlin]

Context

Date parsing across Augur has come about in the form of convergent evolution, with separate functions trying to do roughly the same thing. A summary:

• numeric_date()
  • is used by --min-date/--max-date options to augur filter and augur frequencies (via numeric_date_type())
  • is used by some example snippets in docstrings
• get_numerical_date_from_value()
  • is used to parse the metadata date column in augur filter, augur frequencies, augur refine (via get_numerical_dates())
  • is used to parse the metadata date column in augur parse
• is_date_ambiguous()
  • is used by augur filter --exclude-ambiguous-dates-by
  • can only handle <year>-<month>-<day>, <year>-<month>, or <year> dates
• get_iso_year_week()
  • is used by augur filter when called with --group-by week

Also note there is some date parsing that currently lives outside of augur.dates:

• augur filter when called with --group-by <year|month|week> parses dates in the form of <year>-<month>-<day>, <year>-<month>, or <year> (src)

Potential solutions

• Merge numeric_date() and get_numerical_date_from_value() since these are serving similar purposes.
• Leave is_date_ambiguous() as-is since it serves its purpose and is not duplicated. No point in trying to use numeric_date() internally since ambiguous dates must be in ISO format.
• Leave get_iso_year_week() as-is since it serves its purpose and is not duplicated. No point in trying to use numeric_date() internally since this is only used by augur filter --group-by which requires ISO format.
• For augur filter --group-by <year|month|week>, first run the date string through numeric_date() then convert to ISO date which can be split into year/month/date parts. If the conversion is not possible (i.e. negative date), just drop the sequence.
• Explicitly drop support for numeric dates in most part of the code? This may be more for Add documentation page on supported date formats #882

Progress

• dates.py created: 2b9ba06
• dates: Move date logic from utils to dates #923
• dates: Rewrite using regular expressions #928
• dates: Use same date parsing functions for both CLI arguments and metadata #938
• dates: Consolidate date logic #1144
• incorporate parse.fix_dates()
• frequency_estimators.py: incorporate float_to_datestring(), timestamp_to_float()

Issues that should be fixed as a result of this work

• Incomplete dates are not interpreted as ambiguous by augur filter #747
• Augur filter does not support the integer.float input date format for --min/max-date filtering #748
• filter: --max-date with year only is not inclusive #893