If you are new to GitHub or would prefer to work in your browser, please follow the directions in this section.
Have you ever frantically edited a paper, then realized you liked your original version better? Git is a tool that allows you to track all the changes made to a document over time. Have you ever been writing something as a team and found that someone was editing an old version of the document? Git tracks different people's contributions and manages how they get merged together to avoid the headache of figuring out what changed when.
We are managing this project through GitHub with the goal of a) allowing for the manuscript to evolve rapidly as new information comes out, and b) give everyone credit for their contributions. While we believe this is a great tool, we know it can sometimes be intimidating to get started. We don't want the medium to turn anyone away from contributing, so please let us know if you're having problems.
GitHub is an online platform that visualizes changes made with git (think of a really elegant "Track Changes"). You can make an account here. As long as you do this first step of making a GitHub account, you will always be able to open an issue to ask us for help!
- Repository: The set of files, issue tracker issues, etc. related to this manuscript.
- Issue: The ticketing system for GitHub. A ticket can be a question, concern, problem, bug, or anything else you want to bring to the attention of the people working on a repository. Here, we will use tickets not only for problems or questions, but also to gather papers and preprints that come out about diagnostics and therapeutics related to COVID-19.
- Issue Template: A way of pre-specifying what an "issue" should look like to be useful. There might be a template that fits your needs (e.g., New Paper, or asking for help with GitHub). If not, just try to explain why you're opening the issue (e.g., "I was doing X and ran into problem Y", or "I saw the paper linked here and thought it might be interesting for X reason").
- Manuscript Source: The files that comprise the manuscript. These are located in the "content" folder that you see. These are written in a language called "markdown" which is essentially plain text (thankfully!) We have separate a file for each section of the manuscript (Introduction, Pathogenesis, Diagnostics, and Therapeutics right now).
- Pull Request or PR: A request to change the content of the repository in some way. Here, this will usually mean you are adding or editing text.
- Look in the Manuscript Source for the file you want to edit (for example, the Abstract).
- Click the "Edit" button, which looks like a pencil in the upper right corner.
- Make any desired changes.
- Scroll down to the bottom; there you will see a section that says "Commit changes" Give your submission a title in the top box and briefly summarize your changes in the bottom box.
- Click the box that says "Create a new branch for this commit and start a pull request" This will submit a request to add your changes to the underlying document and will notify us to integrate your text into the document!
- Don't forget to add your information to the author list. If you don't have an ORCID, you can make one here.
If you've made a pull request, congratulations! This is a huge step in getting your contributions into the review. It's possible to see what the document will look like with your changes incorporated. The first thing that Manubot does is rebuild the document with your changes included. You'll know this is completed when you can scroll down to the bottom of your pull request and see "All checks have passed." At this point, you can click "Show all checks".
Next, you'll see the various checks that have completed. There might be a few of these, and the one you want will be the one from Manubot. Click the details link to the right of Manubot.
This will take you to a screen describing what was run. You should see a dropdown titled "Artifacts" Clicking on that dropdown should reveal something that says "manuscript-..."
Clicking on the manuscript link will download a zip file to your computer containing the manuscript. You should be able to open the PDF in your favorite PDF reader.
If you are new to GitHub and struggling to follow these directions, we want to know how to help you and how to improve them. If you find something confusing, please open an issue and tell us what you're trying to do, what's going on wrong, or where you're stuck. We want this review to be a collaborative effort that brings scientists of all skillsets together -- not just people who already know how to use tools like GitHub. Opening an issue means your question will be available for others to learn from in the future! It will also us help continually update this document to provide the information people really need as they start contributing.
Thanks to GitHub, you won't be able to change anything we can't change back-- so you can't really make a mistake!
If you're already someone who uses Git, you can instead:
- Fork the repository greenelab/covid19-review
- Push your modifications. If writing full paragraphs, please put one sentence per line.
- Submit a pull request to add your changes to greenelab/covid19-review
- Submit a second pull request to add your information to the bottom of the metadata file using the format outlined here
The easiest way to run Manubot is to use continuous integration to rebuild the manuscript when the content changes.
If you want to build a Manubot manuscript locally, install the conda environment as described in build.
Then, you can build the manuscript on POSIX systems by running the following commands from this root directory.
# 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.serverSometimes 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:
bash build/autobuild.shWhenever 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 master branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the gh-pages and output branches.
The gh-pages branch uses GitHub Pages to host the following URLs:
- HTML manuscript at https://greenelab.github.io/covid19-review/
- PDF manuscript at https://greenelab.github.io/covid19-review/manuscript.pdf
For continuous integration configuration details, see .github/workflows/manubot.yaml if using GitHub Actions or .travis.yml if using Travis CI.
See the .github/workflows/update-external-resources.yaml for more information about the scheduled workflow that updates the contents of the external-resources branch.
Only maintainers need to update Appendix 1, which contains reviews from https://github.com/ismms-himc/covid-19_sinai_reviews, referred to below as the "upstream" repository.
(Maintainers have been explicitly invited to take on this role.
Very few contributors are acting as maintainers.)
The appendix content content/95-ismms-himc-appendix.md is automatically generated from the upstream repository.
Therefore, it should not to be manually edited.
Any errors in the appendix are corrected by submitting a pull request in the upstream repository.
To manually edit a review, fork the repository at https://github.com/ismms-himc/covid-19_sinai_reviews.
Files in the ISMMS markdown_files directory are labeled by DOI, with the / character replaced by a -.
Create a PR to request changes to these files.
Edits made in these files will propagate to the appendix once you follow the directions below.
When the upstream repository is updated, a maintainer can run the following commands from the base directory of this repository:
# checkout a new branch, named using the current date, e.g. ismms-2020-04-09
git checkout -b ismms-$(date '+%Y-%m-%d')
# download the latest reviews from the upstream repository and re-write content/95-ismms-himc-appendix.md
bash build/mssm-jc.shThen, they can proceed to add and commit content/95-ismms-himc-appendix.md in the new branch and make a pull request.
The script build/mssm-jc.sh will add a comment to the top of the appendix that contains the SHA-1 hash of the upstream repository.
For example,
<!-- Appendix source: https://github.com/ismms-himc/covid-19_sinai_reviews/tree/b8d8df55b4f2416da4ca3b7c765c8fff48acf5e3 -->
This can be used to track which version of the reviews appear in this manuscript.