io.read_metadata does not always set index dtype as expected

[joverlee521]

Current Behavior

We try to explicitly set the dtype for the index column within io.read_metadata:

augur/augur/io.py

Lines 116 to 121 in 139ba04

	# If we found a valid column to index the DataFrame, specify that column and
	# also tell pandas that the column should be treated like a string instead
	# of having its type inferred. This latter argument allows users to provide
	# numerical ids that don't get converted to numbers by pandas.
	kwargs["index_col"] = index_col
	kwargs["dtype"] = {index_col: "string"}

However, this does not work as expected because of a bug in pandas where the dtype is ignored for index_col.

Additional context

Found this issue when looking into nextstrain/ncov#948

[victorlin]

Seems like this was fixed in pandas 1.4.0, should we bump minimum requirement in setup.py?

[joverlee521]

Hmm, starting with pandas 1.4.0, they only support Python 3.8 and higher. Maybe we should just work around it to avoid bumping the minimum Python dependency for Augur.

[genehack]

Hmm, starting with pandas 1.4.0, they only support Python 3.8 and higher. Maybe we should just work around it to avoid bumping the minimum Python dependency for Augur.

Augur currently also requires Python 3.8 or higher — could we maybe resolve this old issue by bumping our minimum Pandsas requirement?