John Huddleston

Document case studies to guide interpretation of SARS-CoV-2 evolution based on Nextstrain analyses

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**Context** [Our current ncov tutorial lists an unlinked item for "case studies"](https://github.com/nextstrain/ncov/blob/40ae575/docs/index.md#getting-started-with-visualization--interpretation) and states that these are "coming soon!". These docs were written nearly a year ago and the case...

Report Augur versions on error without `--use-conda`

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## Description of proposed changes If the workflow errors out and the user isn't using the `--use-conda` Snakemake flag, let the user know what Augur version they have installed and...

WIP: Prototype a build showing an overview of all Pangolin lineages

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### Description of proposed changes Adds a Snakemake profile with a single build that subsamples an existing filtered alignment of GISAID data to one sample per Pangolin lineage. The resulting...

Allow users to disable clock filter in augur refine rule

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**Context** In the refine step of the ncov workflow, the `--clock-filter-iqd` argument is hardcoded such that TreeTime will always apply its clock filter to strains that fall beyond the given...

Calling `get_numerical_dates` with a metadata dictionary fails silently

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## Current Behavior The `get_numerical_dates` function in `augur.dates` expects the metadata argument to be a pandas DataFrame. [When the metadata is not a DataFrame, the function returns an empty dictionary](https://github.com/nextstrain/augur/blob/e8392b320123b1422f86a8d61db1711681d9862f/augur/dates.py#L124-L125)....

Remove matplotlib and seaborn dependencies

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## Context Augur supports [a "full" installation](https://github.com/nextstrain/augur/blob/8d69df645b2bfce8778861402ad5cf3a104d8fb3/setup.py#L59-L63) that installs optional dependencies including cvxopt, matplotlib, and seaborn. Although cvxopt is required for titer models to work (arguably a dependency that should...

Report actual missing filename for index paths

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## Description of proposed changes Fixes a confusing error message produced by augur index when the output directory for the sequence index does not exist but the error message says...

Add functional tests for expected behavior of translate command

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## Description of proposed changes Adds functional tests for the expected behavior of the `augur translate` command and then updates related translate logic to make tests pass. The main changes...

## Context Augur's functional tests rely on a lightweight wrapper script around DeepDiff, `scripts/diff_jsons.py`, to support comparisons between JSONs. [Augur's dev requirements specify DeepDiff >=4.3.2](https://github.com/nextstrain/augur/blob/67027a6ae6a7a324c8eb646593cc5c0a89650ccf/setup.py#L72). However, [version 5.2.0 of DeepDiff...

## Current Behavior Nextclade provides gene map GFFs for [its many datasets](https://github.com/nextstrain/nextclade_data/). These gene maps use the `gene_name` qualifier key to define the name of each gene (e.g., [the SARS-CoV-2...