augur.io.metadata not packaged

[ammaraziz]

Current Behavior

I am trying to import augur.io.metadata to access functions such as read_metadata_with_sequences. However these appear to not be packaged:

from augur.io.metadata import  read_metadata_with_sequences

ImportError: cannot import name 'read_metadata_with_sequences' from 'augur.io.metadata' (~/lib/python3.8/site-packages/augur/io/metadata.py)

This could be intentional but I assume if the files/functions are in the main branch it would be packaged/accessible when installed (but please correct me).

https://github.com/nextstrain/augur/blob/master/augur/io/metadata.py

Your environment: if running Nextstrain locally

• Operating system: Linux Mint 20
• Augur version: 18.1.2 installed via conda

[ammaraziz]

It appears some of the other augur.io files are also not packaged:

• json.py missing
• sequences.py some functions missing

[joverlee521]

Hi @ammaraziz,

These are available on the main branch, but they have not been officially released yet.
You can see a diff of all of the commits that are on the main branch but not in the latest release at 18.1.2...master.

I'm planning on doing a new release this week, so these will be available in the next version of Augur.
However, I do want to warn you that these functions are not officially part of our public Python Development API, so they are potentially subject to breaking changes in the future. (See #1011 for related discussion on our API).

[ammaraziz]

Hi Jover,

That makes a lot of sense. I will treat the augur.io as experimental.

Thanks again,

Ammar