Merge pull request #41 from EOSC-synergy/release/v2.0

Release/v2.0

Author: mariojmdavid

README.md

@@ -43,69 +43,7 @@ Please check our [contribution](CONTRIBUTING.md) guide.
 
 ## Copyright Notice
 
-<<<<<<< HEAD
 Copyright © Members of the EOSC-Synergy collaborations, 2019-2020.
-=======
-### Repository directories & files
-
-The directories are as follows:
-
-+ [`content`](content) contains the manuscript source, which includes markdown files as well as inputs for citations and references.
-  See [`USAGE.md`](USAGE.md) for more information.
-+ [`output`](output) contains the outputs (generated files) from Manubot including the resulting manuscripts.
-  You should not edit these files manually, because they will get overwritten.
-+ [`webpage`](webpage) is a directory meant to be rendered as a static webpage for viewing the HTML manuscript.
-+ [`build`](build) contains commands and tools for building the manuscript.
-+ [`ci`](ci) contains files necessary for deployment via continuous integration.
-
-### Local execution
-
-The easiest way to run Manubot is to use [continuous integration](#continuous-integration) to rebuild the manuscript when the content changes.
-If you want to build a Manubot manuscript locally, install the [conda](https://conda.io) environment as described in [`build`](build).
-Then, you can build the manuscript on POSIX systems by running the following commands from this root directory.
-
-```sh
-# Activate the manubot conda environment (assumes conda version >= 4.4)
-conda activate manubot
-
-# Build the manuscript, saving outputs to the output directory
-bash build/build.sh
-
-# At this point, the HTML & PDF outputs will have been created. The remaining
-# commands are for serving the webpage to view the HTML manuscript locally.
-# This is required to view local images in the HTML output.
-
-# Configure the webpage directory
-manubot webpage
-
-# You can now open the manuscript webpage/index.html in a web browser.
-# Alternatively, open a local webserver at http://localhost:8000/ with the
-# following commands.
-cd webpage
-python -m http.server
-```
-
-Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected.
-The following command, while running, will trigger both the `build.sh` script and `manubot webpage` command upon content changes:
-
-```sh
-bash build/autobuild.sh
-```
-
-### Continuous Integration
-
-Whenever a pull request is opened, CI (continuous integration) 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 CI logs for the cause of failure and revise your pull request accordingly.
-
-When a commit to the `main` branch occurs (for example, when a pull request is merged), 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://manubot.github.io/rootstock/
-+ **PDF manuscript** at https://manubot.github.io/rootstock/manuscript.pdf
-
-For continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml) if using GitHub Actions or [`.travis.yml`](.travis.yml) if using Travis CI.
->>>>>>> 9a448fe6edb477fb98065d5b83d206b1ca489cee
 
 ## License
 
@@ -123,5 +61,4 @@ The EOSC-Synergy project has received funding from the European Union’s Horizo
   <img src="https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcT1WF4g5KH3PnQE_Ve10QFRS-gZ0NpCQ7Qr-_km1RqnOCEF1fQt">
 </p>
 
-
 ###### _Manuscript generated with [Manubot](https://greenelab.github.io/manubot-rootstock/)_

webpage/images

@@ -0,0 +1 @@
+v/latest/images

webpage/index.html

@@ -0,0 +1 @@
+v/latest/index.html

webpage/manuscript.pdf

@@ -0,0 +1 @@
+v/latest/manuscript.pdf