John Huddleston

`parse` silently removes spaces from record ids in the sequence output but not in the metadata output

1

## Current Behavior `augur parse` [replaces "forbidden characters" with either underscores or no character at all](https://github.com/nextstrain/augur/blob/7d75fb19941785c5e660f4376afd1db77badc6dd/augur/parse.py#L15) using [str.maketrans](https://docs.python.org/3/library/stdtypes.html#str.maketrans). This approach causes [spaces to be removed from sequence ids during parsing](https://github.com/nextstrain/augur/blob/7d75fb19941785c5e660f4376afd1db77badc6dd/augur/parse.py#L121)...

## Current behavior and how to reproduce The `augur measurements export` command does not allow users to specify the column used as the `--strain-column` in the `--grouping-column` argument unless the...

[BUG] augur mask only supports VCFs with a single "chromosome" entry

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**Current Behavior** augur mask was originally developed to support masking sites from VCFs whose variants were relative to a single chromosome reference of a pathogen (e.g., tuberculosis). As it is...

### Description of proposed changes Work in progress that builds on the new I/O interface to support multiple metadata, sequence, and sequence index inputs for augur filter. ### Related issues...

[The examples for how to root trees in the augur refine documentation](https://github.com/nextstrain/augur/blob/5b9ab8dd2ce4ee0500cd9a5f8f61b90ef167c1d7/docs/usage/cli/refine.rst?plain=1#L123-L139) are out of date and incorrectly specify one option as "min-dev" and are missing the "mid_point" rooting option.

### Description of proposed changes Adds a functional test and mock data that should work where augur export includes the `--color-by-metadata` argument with a column named `custom_trait`. The resulting Auspice...

## Current Behavior Users can specify the order they want fields to appear in tooltips of the measurements panel in Auspice by providing [a `fields` data structure](https://github.com/nextstrain/augur/blob/f4e46fba552297577dcbbc0bd3644639452a1591/augur/data/schema-measurements-collection-config.json#L17) in the collection...

## Current behavior The `augur measurements export` command provides a `--measurements-display` argument that accepts value of "mean" or "raw". Setting the value to `raw` produces a measurements JSON with a...

## Current Behavior When loading a measurements panel JSON that did not have any thresholds provided through the `--thresholds` argument to `augur measurements export`, Auspice starts to load the panel...

Pass AWS credentials from standard file to Docker

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### Context Several modes of the CLI support AWS credential defined in the standard `~/.aws/credentials` file including [the AWS Batch mode](https://docs.nextstrain.org/projects/cli/en/stable/aws-batch/#aws-credentials) and [nextstrain remote actions](https://github.com/nextstrain/cli/blob/b7b8aef54540e70b34252eb2aa0ee6ebc375a9c4/nextstrain/cli/remote/s3.py#L38-L40) outside of Docker. These credentials...