From f61093e70e5ec885ca8a1925b5fbbf70b96bb3f3 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 5 Dec 2022 13:46:57 -0800
Subject: [PATCH] Convert installation doc to reST
Commands used:
pandoc -f markdown -t rst --wrap=none docs/introduction/install.md -o docs/introduction/install.rst
rm docs/introduction/install.md
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docs/introduction/install.md | 68 -----------------------------------
docs/introduction/install.rst | 67 ++++++++++++++++++++++++++++++++++
2 files changed, 67 insertions(+), 68 deletions(-)
delete mode 100644 docs/introduction/install.md
create mode 100644 docs/introduction/install.rst
diff --git a/docs/introduction/install.md b/docs/introduction/install.md
deleted file mode 100644
index 87863534b..000000000
--- a/docs/introduction/install.md
+++ /dev/null
@@ -1,68 +0,0 @@
-# Install Auspice
-
-## Prerequisites
-Auspice is a JavaScript program, and requires [Node.js](https://nodejs.org/) to be installed on your system.
-Refer to `engines.node` in [package.json](https://github.com/nextstrain/auspice/blob/-/package.json) for currently supported versions.
-
-We highly recommend using [Conda](https://conda.io/docs/) to manage environments, i.e. use Conda to create an environment with Node.js installed where you can use Auspice.
-It's possible to use other methods, but this documentation presupposes that you have Conda installed.
-
-To run package scripts, the [`bash` shell](https://en.wikipedia.org/wiki/Bash_(Unix_shell)) and the [`env`](https://en.wikipedia.org/wiki/Env) command need to be in your `PATH`.
-You should already have them on Unix-like systems including Linux and macOS.
-If you are working from Windows, you can run the installation under Git Bash, MSYS2, or Cygwin.
-You can also use the Windows Subsystem Linux for a fuller Linux environment.
-
-## Create a Conda Environment
-```bash
-conda create --name auspice nodejs=14
-conda activate auspice
-```
-
-> This parallels [the Nextstrain installation docs](https://nextstrain.org/docs/getting-started/local-installation#install-augur--auspice-with-conda-recommended).
-You're welcome to use those instead!
-
-## Install Auspice from npm
-
-
-```bash
-npm install --global auspice
-```
-Auspice should now be available as a command-line program -- check by running `auspice --help`.
-
-If you look at the [release notes](https://docs.nextstrain.org/projects/auspice/en/stable/releases/changelog.html) you can see the changes that have been made to Auspice (see your version of Auspice via `auspice --version`).
-To upgrade, you can run
-
-```bash
-npm update --global auspice
-```
-
-## Installing from Source
-
-
-This is useful for debugging, modifying the source code, or using an unpublished feature branch.
-We're going to assume that you have used Conda to install Node.js as above.
-
-```bash
-# activate the correct conda enviornment
-conda activate auspice
-
-# grab the GitHub auspice repo
-git clone https://github.com/nextstrain/auspice.git
-cd auspice
-
-# install dependencies and make `auspice` available globally
-npm install --global .
-
-# build auspice (builds the JS client bundle using webpack)
-auspice build
-
-# test it works
-auspice --version
-auspice --help
-
-# Obtain nextstrain.org datasets to view locally (optional)
-npm run get-data
-```
-
-Updating Auspice should only require pulling the new version from GitHub -- it shouldn't require any `npm` commands.
-You will, however, have to re-build Auspice whenever the client-related code has changed, via `auspice build`.
diff --git a/docs/introduction/install.rst b/docs/introduction/install.rst
new file mode 100644
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--- /dev/null
+++ b/docs/introduction/install.rst
@@ -0,0 +1,67 @@
+Install Auspice
+===============
+
+Prerequisites
+-------------
+
+Auspice is a JavaScript program, and requires `Node.js `__ to be installed on your system. Refer to ``engines.node`` in `package.json `__ for currently supported versions.
+
+We highly recommend using `Conda `__ to manage environments, i.e. use Conda to create an environment with Node.js installed where you can use Auspice. It’s possible to use other methods, but this documentation presupposes that you have Conda installed.
+
+To run package scripts, the ```bash`` shell `__ and the ```env`` `__ command need to be in your ``PATH``. You should already have them on Unix-like systems including Linux and macOS. If you are working from Windows, you can run the installation under Git Bash, MSYS2, or Cygwin. You can also use the Windows Subsystem Linux for a fuller Linux environment.
+
+Create a Conda Environment
+--------------------------
+
+.. code:: bash
+
+ conda create --name auspice nodejs=14
+ conda activate auspice
+
+..
+
+ This parallels `the Nextstrain installation docs `__. You’re welcome to use those instead!
+
+Install Auspice from npm
+------------------------
+
+.. code:: bash
+
+ npm install --global auspice
+
+Auspice should now be available as a command-line program – check by running ``auspice --help``.
+
+If you look at the `release notes `__ you can see the changes that have been made to Auspice (see your version of Auspice via ``auspice --version``). To upgrade, you can run
+
+.. code:: bash
+
+ npm update --global auspice
+
+Installing from Source
+----------------------
+
+This is useful for debugging, modifying the source code, or using an unpublished feature branch. We’re going to assume that you have used Conda to install Node.js as above.
+
+.. code:: bash
+
+ # activate the correct conda enviornment
+ conda activate auspice
+
+ # grab the GitHub auspice repo
+ git clone https://github.com/nextstrain/auspice.git
+ cd auspice
+
+ # install dependencies and make `auspice` available globally
+ npm install --global .
+
+ # build auspice (builds the JS client bundle using webpack)
+ auspice build
+
+ # test it works
+ auspice --version
+ auspice --help
+
+ # Obtain nextstrain.org datasets to view locally (optional)
+ npm run get-data
+
+Updating Auspice should only require pulling the new version from GitHub – it shouldn’t require any ``npm`` commands. You will, however, have to re-build Auspice whenever the client-related code has changed, via ``auspice build``.