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Relocate repository to manubot/rootstock
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Merges manubot/rootstock#180
Closes manubot/rootstock#175
Closes manubot/rootstock#124 (supersedes)

Relocate repository from https://github.com/greenelab/manubot-rootstock
to https://github.com/manubot/rootstock.

Relocate continuous integration from https://travis-ci.org/greenelab/manubot-rootstock
to https://travis-ci.com/manubot/rootstock
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@dhimmel
dhimmel authored Feb 13, 2019
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22 changes: 11 additions & 11 deletions README.md
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<!-- usage note: edit the H1 title above to personalize the manuscript -->

[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://greenelab.github.io/manubot-rootstock/)
[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://greenelab.github.io/manubot-rootstock/manuscript.pdf)
[![Build Status](https://travis-ci.org/greenelab/manubot-rootstock.svg?branch=master)](https://travis-ci.org/greenelab/manubot-rootstock)
[![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://manubot.github.io/rootstock/)
[![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://manubot.github.io/rootstock/manuscript.pdf)
[![Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=master)](https://travis-ci.com/manubot/rootstock)

## Manuscript description

Expand All @@ -19,10 +19,10 @@ Actual manuscript instances will clone this repository (see [`SETUP.md`](SETUP.m

Manubot is a system for writing scholarly manuscripts via GitHub.
Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub.
The [Manubot Rootstock repository](https://git.io/vQSvo) is a general purpose template for creating new Manubot instances, as detailed in [`SETUP.md`](SETUP.md).
The [rootstock repository](https://git.io/fhQH1) is a general purpose template for creating new Manubot instances, as detailed in [`SETUP.md`](SETUP.md).
See [`USAGE.md`](USAGE.md) for documentation how to write a manuscript.

Please open [an issue](https://github.com/greenelab/manubot-rootstock/issues) for questions related to Manubot usage, bug reports, or general inquiries.
Please open [an issue](https://git.io/fhQHM) for questions related to Manubot usage, bug reports, or general inquiries.

### Repository directories & files

Expand Down Expand Up @@ -69,17 +69,17 @@ sh build/autobuild.sh

### Continuous Integration

[![Build Status](https://travis-ci.org/greenelab/manubot-rootstock.svg?branch=master)](https://travis-ci.org/greenelab/manubot-rootstock)
[![Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=master)](https://travis-ci.com/manubot/rootstock)

Whenever a pull request is opened, Travis CI will test whether the changes break the build process to generate a formatted manuscript.
The build process aims to detect common errors, such as invalid citations.
If your pull request build fails, see the Travis CI logs for the cause of failure and revise your pull request accordingly.

When a commit to the `master` branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/greenelab/manubot-rootstock/tree/gh-pages) and [`output`](https://github.com/greenelab/manubot-rootstock/tree/output) branches.
When a commit to the `master` branch occurs (for example, when a pull request is merged), Travis CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/manubot/rootstock/tree/gh-pages) and [`output`](https://github.com/manubot/rootstock/tree/output) branches.
The `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs:

+ **HTML manuscript** at https://greenelab.github.io/manubot-rootstock/
+ **PDF manuscript** at https://greenelab.github.io/manubot-rootstock/manuscript.pdf
+ **HTML manuscript** at https://manubot.github.io/rootstock/
+ **PDF manuscript** at https://manubot.github.io/rootstock/manuscript.pdf

For continuous integration configuration details, see [`.travis.yml`](.travis.yml).

Expand All @@ -94,7 +94,7 @@ We encourage users to openly license their manuscripts, which is the default as
[![License: CC0 1.0](https://img.shields.io/badge/License%20Parts-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/)

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution.
Please attribute by linking to https://github.com/greenelab/manubot-rootstock.
Please attribute by linking to https://github.com/manubot/rootstock.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication ([`LICENSE-CC0.md`](LICENSE-CC0.md)).
All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:
Expand All @@ -118,4 +118,4 @@ Except for the following files with different licenses:

+ `build/assets/anchors.js` which is [released](https://www.bryanbraun.com/anchorjs/) under an [MIT License](https://opensource.org/licenses/MIT)

Please open [an issue](https://github.com/greenelab/manubot-rootstock/issues) for any question related to licensing.
Please open [an issue](https://github.com/manubot/rootstock/issues) for any question related to licensing.
36 changes: 19 additions & 17 deletions SETUP.md
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# Cloning manubot-rootstock to create a new manuscript
# Cloning the manubot/rootstock repository to create a new manuscript

The process to create a new Manubot manuscript is a bit challenging, because it requires a few steps that are difficult to automate.
However, you will only have to perform these steps once for each manuscript.
These steps should be performed in a terminal, starting in the directory where you want the manuscript folder be created.
Setup is supported on Linux and macOS, but [**not on Windows**](https://github.com/greenelab/manubot-rootstock/issues/91).
Setup is supported on Linux and macOS, but [**not on Windows**](https://github.com/manubot/rootstock/issues/91).

## Configuration

Expand All @@ -14,26 +14,26 @@ In general, assume that all commands in this setup are case-sensitive.
**Edit the following commands with your manuscript's information:**

```sh
# GitHub username (change from greenelab)
OWNER=greenelab
# Repository name (change from manubot-rootstock)
REPO=manubot-rootstock
# GitHub username (change from manubot)
OWNER=manubot
# Repository name (change from rootstock)
REPO=rootstock
```

## Create repository

**Execute the remaining commands verbatim.**
They do not need to be edited (if the setup works as intended).

Next you must clone `greenelab/manubot-rootstock` and configure its branches and remotes:
Next you must clone `manubot/rootstock` and configure its branches and remotes:

```sh
# Clone greenelab/manubot-rootstock
git clone https://github.com/greenelab/manubot-rootstock.git $REPO
# Clone manubot/rootstock
git clone https://github.com/manubot/rootstock.git $REPO
cd $REPO

# Configure remotes and branches
git remote add rootstock https://github.com/greenelab/manubot-rootstock.git
git remote add rootstock https://github.com/manubot/rootstock.git
git checkout --orphan gh-pages
git rm -r --force .
git commit --allow-empty \
Expand Down Expand Up @@ -61,7 +61,7 @@ git push --set-upstream origin output

## Continuous integration

Now you must manually enable Travis CI for the new repository at https://travis-ci.org.
Now you must manually enable Travis CI for the new repository at https://travis-ci.com.
Click the `+` sign to "Add New Repository".
If you don't see your repository listed, push the "Sync account" button.
Finally, flick the repository's switch to enable CI.
Expand Down Expand Up @@ -89,10 +89,11 @@ Give the key a descriptive title, such as "Travis CI Manubot".
For the next step, you need the [Travis command line client](https://github.com/travis-ci/travis.rb) installed.
This program is a Ruby gem:
install it with `gem install travis` (not `apt install travis`, which is a different program).
After the install, you will need to provide your credentials to login to travis with `travis login --org`.
After the install, you will need to provide your credentials to login to travis with `travis login`.

```sh
travis encrypt-file \
--com \
--repo=$OWNER/$REPO \
--force \
deploy.key > travis-encrypt-file.log
Expand All @@ -119,6 +120,7 @@ Next, limit [concurrent](https://blog.travis-ci.com/2014-07-18-per-repository-co

```sh
travis settings \
--com \
--repo=$OWNER/$REPO \
maximum_number_of_builds --set 1
```
Expand All @@ -141,8 +143,8 @@ Now update `README.md` files to reference the new repository:

```sh
# Perform substitutions
sed "s/greenelab/$OWNER/g" README.md > tmp && mv -f tmp README.md
sed "s/manubot-rootstock/$REPO/g" README.md > tmp && mv -f tmp README.md
sed "s/manubot\/rootstock/$OWNER\/$REPO/g" README.md > tmp && mv -f tmp README.md
sed "s/manubot\.github\.io\/rootstock/$OWNER\.github\.io\/$REPO/g" README.md > tmp && mv -f tmp README.md

# Remove deletable content file
git rm content/02.delete-me.md
Expand All @@ -168,9 +170,9 @@ git push origin master
You should be good to go now.
A good first step is to modify `content/metadata.yaml` with the relevant information for your manuscript.

# Merging upstream manubot-rootstock changes
# Merging upstream rootstock changes

This section will describe how to incorporate changes to manubot-rootstock that occurred since initializing your manuscript.
This section will describe how to incorporate changes to rootstock that occurred since initializing your manuscript.
You will want to do this if there are new enhancements or bugfixes that you want to incorporate.
This process can be difficult, especially if conflicts have arisen, and is recommended only for advanced git users.

Expand All @@ -182,7 +184,7 @@ First, checkout a new branch to use as the pull request head branch:
git checkout -b rootstock-`date '+%Y-%m-%d'`
```

Second, pull the new commits from manubot-rootstock, but do not automerge:
Second, pull the new commits from rootstock, but do not automerge:

```sh
git pull --no-ff --no-commit rootstock master
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# Manubot usage guidelines

This repository uses [Manubot](https://github.com/greenelab/manubot-rootstock) to automatically produce a manuscript from the source in the [`content`](content) directory.
This repository uses [Manubot](https://manubot.org) to automatically produce a manuscript from the source in the [`content`](content) directory.

## Manubot markdown

Expand Down Expand Up @@ -169,7 +169,7 @@ Note that `affiliations` should be a list to allow for multiple affiliations per

## Manubot feedback

If you experience any issues with the Manubot or would like to contribute to its source code, please visit [`manubot/manubot`](https://github.com/manubot/manubot) or [`greenelab/manubot-rootstock`](https://github.com/greenelab/manubot-rootstock).
If you experience any issues with the Manubot or would like to contribute to its source code, please visit [`manubot/manubot`](https://github.com/manubot/manubot) or [`manubot/rootstock`](https://github.com/manubot/rootstock).

## Examples

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Expand Up @@ -11,7 +11,7 @@ For example, use the command `BUILD_DOCX=true sh build/build.sh`.
To export DOCX for all Travis builds, set a [Travis environment variable](https://docs.travis-ci.com/user/environment-variables/#Defining-Variables-in-Repository-Settings).
Currently, equation numbers via `pandoc-eqnos` are not supported for DOCX output.
There is varying support for embedding images in DOCX output.
Please reference [Pull Request #40](https://github.com/greenelab/manubot-rootstock/pull/40) for possible solutions and continued discussion.
Please reference [Pull Request #40](https://github.com/manubot/rootstock/pull/40) for possible solutions and continued discussion.

## Environment

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Expand Up @@ -5,7 +5,7 @@
<title>Manubot</title>
<id>http://www.zotero.org/styles/manubot</id>
<link href="http://www.zotero.org/styles/manubot" rel="self"/>
<link href="https://github.com/greenelab/manubot-rootstock" rel="documentation"/>
<link href="https://github.com/manubot/rootstock" rel="documentation"/>
<author>
<name>Daniel Himmelstein</name>
<email>[email protected]</email>
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# Continuous integration / analysis directory

[![Build Status](https://travis-ci.org/greenelab/manubot-rootstock.svg?branch=master)](https://travis-ci.org/greenelab/manubot-rootstock)
[![Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=master)](https://travis-ci.com/manubot/rootstock)

This repository uses [continuous analysis](https://doi.org/10.1101/056473 "Reproducible Computational Workflows with Continuous Analysis") to create the manuscript and commit it back to GitHub.
[`deploy.sh`](deploy.sh) runs on successful `master` branch builds that are not pull requests.
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ssh-rsa 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 [email protected]
ssh-rsa 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 [email protected]
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Expand Up @@ -16,8 +16,8 @@ git remote set-url origin [email protected]:$TRAVIS_REPO_SLUG.git

# Decrypt and add SSH key
openssl aes-256-cbc \
-K $encrypted_f2f00aaf6402_key \
-iv $encrypted_f2f00aaf6402_iv \
-K $encrypted_9befd6eddffe_key \
-iv $encrypted_9befd6eddffe_iv \
-in ci/deploy.key.enc \
-out ci/deploy.key -d
eval `ssh-agent -s`
Expand Down Expand Up @@ -49,8 +49,8 @@ This build is based on
https://github.com/$TRAVIS_REPO_SLUG/commit/$TRAVIS_COMMIT.
This commit was created by the following Travis CI build and job:
https://travis-ci.org/$TRAVIS_REPO_SLUG/builds/$TRAVIS_BUILD_ID
https://travis-ci.org/$TRAVIS_REPO_SLUG/jobs/$TRAVIS_JOB_ID
https://travis-ci.com/$TRAVIS_REPO_SLUG/builds/$TRAVIS_BUILD_ID
https://travis-ci.com/$TRAVIS_REPO_SLUG/jobs/$TRAVIS_JOB_ID
[ci skip]
Expand Down

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