<commit_before>## How to run augur:
* see the `README.md` files in the respective pathogen's folder (`flu`, `ebola`, e.t.c.)

## Docs:
* [Fauna](https://github.com/nextstrain/fauna)
* [Prepare](prepare.md)
* [Process](process.md)
* [Format of (auspice) output JSONs](auspice_output.md)

## Tests

Install [pytest](https://docs.pytest.org/en/latest/).

```bash
# Install with pip.
pip install pytest

# Or install with conda.
conda install pytest
```

Checkout augur and temporarily install it as a package.

```bash
git clone --recursive https://github.com/nextstrain/augur
cd augur
pip install -e .
```

Run tests.

```bash
pytest
```

Uninstall the augur package.

```bash
pip uninstall augur
```<commit_msg>Updated testing documents to reflect use of tox.<commit_after>## How to run augur:
* see the `README.md` files in the respective pathogen's folder (`flu`, `ebola`, e.t.c.)

## Docs:
* [Fauna](https://github.com/nextstrain/fauna)
* [Prepare](prepare.md)
* [Process](process.md)
* [Format of (auspice) output JSONs](auspice_output.md)

## Tests

Tests run using [tox](http://tox.readthedocs.io/en/latest/)
and [pytest](https://docs.pytest.org/en/latest/). If you didn't install augur
with the pip `requirements.txt` or with
the
[janus conda environment](https://github.com/nextstrain/janus/#installation),
install them as follows.

```bash
# Install with pip.
pip install pytest tox

# Or install inside a conda environment.
conda install pytest virtualenv
pip install tox
```

Run tests from the augur root directory.

```bash
tox
```

Tox builds an empty virtual environment, installs augur's requirements and a
package of augur built from the local directory, and runs tests with pytest. The
`tox.ini` file defines the test environment and the `pytest.ini` file defines
which tests to run. Tox reuses the virtual environment with subsequent runs. Use
the `-r` flag to force it to rebuild its environment.

```bash
tox -r
```
{'fraction_non_alphanumeric': 0.13126614987080104, 'fraction_numerical': 0.0, 'mean_word_length': 4.515669515669516, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 6, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6108890', 'n_tokens_mistral': 676, 'n_tokens_neox': 635, 'n_words': 225}