augur

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Error when metadata to `get_numerical_dates()` is not a pandas DataFrame

1

### Description of proposed changes See commit messages and #1025. ### Related issue(s) - Fixes #1025 ### Testing - [x] Added 84a4b0397e90c80947a48ab9f1e811382933f323 which fails, then fixed it with the following...

victorlin

chore: use `--cores all` in snakemake CI test, format .sh script

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If testing locally, we have more than 1 core available, so why not make use of it. For CI it shouldn't change anything since the runners only have 1 core.

corneliusroemer

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)....

huddlej

Added installation instructions to developer documentation

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### Description of proposed changes This pull request adds complete installation instructions in the developer documentation (dev docs) and exposes dev docs by adding links in sections related contributing to...

jtboing

DOC/DEV: test `bash tests/builds/runner.sh` not mentioned in dev docs

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There seems to be a test that is only run in CI but missing from the dev documentation. It'd be great if the person who added the line to the...

corneliusroemer

Export fails if node-data contains unhashable items.

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If `node_data` contains data such as lists, validation of the output json in export fails here: https://github.com/nextstrain/augur/blob/cc3b7bdb6faf370c496efc798b10e4a3d014bef4/augur/export_v2.py#L185 While we typically don't have such data, it is a rather difficult to...

rneher

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...

huddlej

filter: re-implement with SQLite and add option to use with `--engine`

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### Description of proposed changes - Rewrite pandas logic with a database approach. - Split logic into smaller files. - [sqlite.py](https://github.com/victorlin/augur/blob/filter/sqlite/augur/filter_support/db/sqlite.py) contains the working class – an implementation of the...

victorlin

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...

huddlej

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...

huddlej