dates: Rewrite using regular expressions

[victorlin]

Description of proposed changes

This rewrites the date parsing functions currently used by filter and frequencies --min-date/--max-date parameters, and adds support for ambiguous dates (e.g. 2020-XX-XX) and incomplete dates (e.g. 2020-06, 2020). This means --max-date with year only will be inclusive now.

Motivated by work in #854.

Related issue(s)

• Fixes #893
• Related to #662
• Related to #882

Testing

Added doctests and pytests.

TODO

• [ ] squash 7fb35acbdfff4cd8ed121939d375ee11c9460185...468f3b46b3f056670b1e2b1e6c88ee2776b11d2b into fc297541df179491f4d67a39a901d79ca627306a
• [ ] add tests for 7fb35acbdfff4cd8ed121939d375ee11c9460185...468f3b46b3f056670b1e2b1e6c88ee2776b11d2b

[codecov[bot]]

Codecov Report

Base: 63.32% // Head: 59.47% // Decreases project coverage by -3.85% :warning:

Coverage data is based on head (6229db7) compared to base (8b3c33d). Patch coverage: 93.24% of modified lines in pull request are covered.

:exclamation: Current head 6229db7 differs from pull request most recent head 53cb6c1. Consider uploading reports for the commit 53cb6c1 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #928      +/-   ##
==========================================
- Coverage   63.32%   59.47%   -3.86%     
==========================================
  Files          57       50       -7     
  Lines        6628     6314     -314     
  Branches     1632     1599      -33     
==========================================
- Hits         4197     3755     -442     
- Misses       2147     2295     +148     
+ Partials      284      264      -20     

Impacted Files	Coverage Δ
augur/dates.py	89.74% <92.64%> (-3.32%)	:arrow_down:
augur/filter.py	95.78% <100.00%> (+0.04%)	:arrow_up:
augur/frequencies.py	50.84% <100.00%> (-0.82%)	:arrow_down:
augur/io/vcf.py	42.50% <0.00%> (-43.75%)	:arrow_down:
augur/translate.py	38.18% <0.00%> (-36.43%)	:arrow_down:
augur/utils.py	64.28% <0.00%> (-7.33%)	:arrow_down:
augur/traits.py	80.83% <0.00%> (-4.42%)	:arrow_down:
augur/reconstruct_sequences.py	27.58% <0.00%> (-2.42%)	:arrow_down:
augur/lbi.py	21.91% <0.00%> (-2.09%)	:arrow_down:
... and 38 more

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[victorlin]

Converting to draft, at least until #989 is resolved

[tsibley]

Is the plan to eventually replace the remaining treetime-based functions like augur.date.get_numerical_dates() with the new ones introduced here?

[victorlin]

@tsibley yes, that's my plan with #938