Jover Lee

**Current Behavior** Within [annotate_metadata_with_index](https://github.com/nextstrain/ncov/blob/08cd17c2521001e370bfaaed24620ebda0411356/scripts/annotate_metadata_with_index.py#L18), the index TSV is read without explicitly set dtypes. This can lead to numerical id strain values to be interpreted as numbers, leading to a `ValueError`...

### Context Strings need to be normalized for predictable string comparisons, especially in cases where strings contain diacritics (see https://unicode.org/faq/normalization.html). In a chain of `augur curate` commands, we would want...

augur curate apply-geolocation-rules

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### Context We have a great list of [manually curated geolocation rules in ncov-ingest](https://github.com/nextstrain/ncov-ingest/blob/d5703c4af88f5d1532f9065422e1764ee7d47875/source-data/gisaid_geoLocationRules.tsv) that would be helpful to be used as standard geolocation rules that can be applied to...

### Context Augur commands expect dates to be in ISO 8601 format so we should provide a robust way for users to convert any date format to ISO 8601. We've...

### Context It is common to want to titlecase strings in metadata such a location names. However, the default [Python `str.title()` method ](https://docs.python.org/3/library/stdtypes.html#str.title)groups words as consecutive letters, so letters following...

### Context In internal discussions on how to implement #860 and through my prototype in [monkeypox/ingest](https://github.com/nextstrain/monkeypox/blob/78d5b0e65f80c1817e6175f77c4154d9972e57f9/ingest/workflow/snakemake_rules/transform.smk#L36-L93), it seems like we've agreed to use the NDJSON format for streaming records between...

io.read_metadata does not always set index dtype as expected

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### Current Behavior We try to explicitly set the dtype for the index column within `io.read_metadata`: https://github.com/nextstrain/augur/blob/139ba041a54f0c6aec5bba34df78030c1a8d6ff5/augur/io.py#L116-L121 However, this does not work as expected because of a [bug in pandas](https://github.com/pandas-dev/pandas/issues/9435)...

tree: Unable to use IQ-TREE `-g` option if strain name contains certain characters

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### Current Behavior Within `augur tree` we replace certain characters in strain names with random strings before passing the renamed FASTA to IQ-TREE. https://github.com/nextstrain/augur/blob/945b49af50cc72c4343673491531ae630db40040/augur/tree.py#L214-L219 This results in IQ-TREE being unable...

augur measurements proposal

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## Context A new measurements panel has been [added to Auspice](https://github.com/nextstrain/auspice/pull/1452) which displays data from a measurements sidecar JSON file. A [previous PR](https://github.com/nextstrain/augur/pull/859) added the measurements JSON schema and a...

Create docs version of auspice config schema

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Create docs version of the [auspice config schema](https://github.com/nextstrain/augur/blob/master/augur/data/schema-auspice-config-v2.json) so that users can easily find all available configuration options for auspice. We would want to auto-generate this from the schema so...