Change all master elements in Github URLs to - [nextstrain/docs.n…

…extstrain.org#14]

Feels like a good time to get all these cleaned up…

README.md

@@ -32,7 +32,7 @@ Try out an analysis of real virus data by [completing the Zika tutorial](https:/
 * [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html)
 * [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html)
 * [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html)
-* [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md)
+* [Contributor guide](https://github.com/nextstrain/.github/blob/-/CONTRIBUTING.md)
 * [Developer docs for Augur](./docs/contribute/DEV_DOCS.md)
 * [Changelog](./CHANGES.md)
 

docs/contribute/DEV_DOCS.md

@@ -5,13 +5,13 @@ Thank you for helping us to improve Augur! Use the GitHub markdown preview sideb
 ## Getting started
 
 To be an effective, productive contributor, please start by reading the
-[**Nextstrain contributing guide**](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md)
+[**Nextstrain contributing guide**](https://github.com/nextstrain/.github/blob/-/CONTRIBUTING.md)
 for useful information about how to pick an issue, submit your contributions, and so on.
 
 Please see the "Source" tab in [Augur's installation instructions](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html) for details on how to install Augur for development.
 
 This project strictly adheres to the
-[Contributor Covenant Code of Conduct](https://github.com/nextstrain/.github/blob/master/CODE_OF_CONDUCT.md).
+[Contributor Covenant Code of Conduct](https://github.com/nextstrain/.github/blob/-/CODE_OF_CONDUCT.md).
 
 Please see the [open issues list](https://github.com/nextstrain/augur/issues) for currently available issues.
 
@@ -265,7 +265,7 @@ release, see [this section of the docker-base README](https://github.com/nextstr
 
 ### Maintaining Bioconda package
 
-Bioconda hosts [augur’s conda package](http://bioconda.github.io/recipes/augur/README.html) and defines augur’s dependencies in [a conda recipe YAML file](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/augur/meta.yaml).
+Bioconda hosts [augur’s conda package](http://bioconda.github.io/recipes/augur/README.html) and defines augur’s dependencies in [a conda recipe YAML file](https://github.com/bioconda/bioconda-recipes/blob/-/recipes/augur/meta.yaml).
 New releases on GitHub automatically trigger a new Bioconda release.
 
 To modify augur’s dependencies or other aspects of its conda environment, [follow Bioconda’s contributing guide](https://bioconda.github.io/contributor/index.html).

docs/faq/lat_longs.md

@@ -1,6 +1,6 @@
 # Adding Custom Lat-Long Data
 
-To place sequences on a map, auspice needs to know where the locations you specify are on the globe. These coordinates are provided by augur and augur has preset coordinates for many places. For example, for `region`, `country`, and some `division`s augur already knows many lat-long coordinates (see which ones it already knows by checking the list [here](https://github.com/nextstrain/augur/blob/master/augur/data/lat_longs.tsv)).
+To place sequences on a map, auspice needs to know where the locations you specify are on the globe. These coordinates are provided by augur and augur has preset coordinates for many places. For example, for `region`, `country`, and some `division`s augur already knows many lat-long coordinates (see which ones it already knows by checking the list [here](https://github.com/nextstrain/augur/blob/-/augur/data/lat_longs.tsv)).
 
 Some places, however, are inevitably missing and you need to tell augur the latitudes and longitude of all locations not covered by defaults. The file for latitude and longitude needs to be a tab-delimited table with four columns:
 

docs/faq/metadata.rst

@@ -61,7 +61,7 @@ Geographic locations can be broken down, for example, into ``region``,
 geographic information as you wish. For ``region``, ``country``, and
 some ``division``\ s augur already knows many lat-long coordinates (see
 which ones it already knows by checking the list
-`here <https://github.com/nextstrain/augur/blob/master/augur/data/lat_longs.tsv>`__).
+`here <https://github.com/nextstrain/augur/blob/-/augur/data/lat_longs.tsv>`__).
 
 It is important that these are spelled consistently.
 

docs/releases/migrating-v5-v6.md

@@ -261,7 +261,7 @@ The config file is a JSON file, and as such it's important that everything in yo
 These can be on a separate line at the very top and very bottom of your file.
 Syntax is important - if you are getting errors, ensure all your brackets and quotation marks match up, and that commas separate items in the same pair of brackets.
 
-Export v2 config files are generally very similar to export v1, _but there are a few changes_. They are explained in detail below, or you can see [an example of converting a v1 config to v2](#updating-your-config-file). For more details, see [the complete JSON schema for v2 config files](https://github.com/nextstrain/augur/blob/master/augur/data/schema-auspice-config-v2.json).
+Export v2 config files are generally very similar to export v1, _but there are a few changes_. They are explained in detail below, or you can see [an example of converting a v1 config to v2](#updating-your-config-file). For more details, see [the complete JSON schema for v2 config files](https://github.com/nextstrain/augur/blob/-/augur/data/schema-auspice-config-v2.json).
 
 Here are the top-level keys of the config JSON in plain English:
 

setup.py

@@ -44,7 +44,7 @@
     url = "https://github.com/nextstrain/augur",
     project_urls = {
         "Bug Reports": "https://github.com/nextstrain/augur/issues",
-        "Change Log": "https://github.com/nextstrain/augur/blob/master/CHANGES.md#next",
+        "Change Log": "https://github.com/nextstrain/augur/blob/-/CHANGES.md#next",
         "Source": "https://github.com/nextstrain/augur",
     },
     packages = setuptools.find_packages(),