-
Notifications
You must be signed in to change notification settings - Fork 81
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
69 changed files
with
16,110 additions
and
1,494 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -3,6 +3,8 @@ on: | |
| schedule: | ||
| # Run every day at 00:00 | ||
| - cron: '0 0 * * *' | ||
| # Enable manually updating the external resources | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| update_external_resources: | ||
|
|
@@ -21,6 +23,9 @@ jobs: | |
| environment-file: environment.yml | ||
| auto-activate-base: false | ||
| miniconda-version: 'latest' | ||
| - name: List packages in conda environment | ||
| shell: bash --login {0} | ||
| run: conda list | ||
| - name: Update JHU CSSE data | ||
| shell: bash --login {0} | ||
| run: bash csse/generate-csse-stats.sh | ||
|
|
@@ -30,26 +35,32 @@ jobs: | |
| - name: Update OWID data | ||
| shell: bash --login {0} | ||
| run: bash owiddata/generate-owiddata-stats.sh | ||
| - name: Commit JHU CSSE and EBM Data Lab figures | ||
| - name: Update CORD-19 data | ||
| shell: bash --login {0} | ||
| run: bash CORD-19/generate-cord19-stats.sh | ||
| # - name: Update manuscript statistics data | ||
| # shell: bash --login {0} | ||
| # run: bash analyze-ms-stats/calc-manuscript-stats.sh | ||
| - name: Commit JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth figures | ||
| uses: EndBug/add-and-commit@v4 | ||
| with: | ||
| add: '*/*.png */*.svg' | ||
| add: '*/*.png */*.svg */*/*.png */*/*.svg' | ||
| author_name: GitHub Actions | ||
| author_email: [email protected] | ||
| message: 'Update JHU CSSE and EBM Data Lab figures' | ||
| message: 'Update JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth figures' | ||
| ref: external-resources | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
| - name: Update figure versions | ||
| shell: bash --login {0} | ||
| run: bash version-figures.sh | ||
| - name: Commit JHU CSSE, EBM Data Lab, and OWID statistics | ||
| - name: Commit JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth statistics | ||
| uses: EndBug/add-and-commit@v4 | ||
| with: | ||
| add: '*/*.json' | ||
| author_name: GitHub Actions | ||
| author_email: [email protected] | ||
| message: 'Update JHU CSSE, EBM Data Lab, and OWID statistics' | ||
| message: 'Update JHU CSSE, EBM Data Lab, OWID, CORD-19, and manuscript growth statistics' | ||
| ref: external-resources | ||
| env: | ||
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -41,6 +41,7 @@ Thumbs.db | |
|
|
||
| ## Text Editors | ||
| .vscode | ||
| .idea | ||
|
|
||
| ## Spellcheck script | ||
| spellcheck.lua | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,8 @@ | ||
| # Table of contents | ||
|
|
||
| - [Creating a new manuscript](#creating-a-new-manuscript) | ||
| * [Configuration](#configuration) | ||
| * [Using setup script](#using-setup-script) | ||
| * [Manual configuration](#manual-configuration) | ||
| * [Create repository](#create-repository) | ||
| * [Continuous integration](#continuous-integration) | ||
| + [GitHub Actions](#github-actions) | ||
|
|
@@ -27,8 +28,33 @@ These steps should be performed in a command-line shell (terminal), starting in | |
| Setup is supported on Linux, macOS, and Windows. | ||
| Windows setup requires [Git Bash](https://gitforwindows.org/) or [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/faq). | ||
|
|
||
| ## Configuration | ||
| ## Using setup script | ||
| Creating a new manuscript using GitHub actions, the recommended default CI service (see below), can be achieved easily using the [setup script](https://github.com/manubot/rootstock/blob/main/setup.bash). | ||
| This simply runs the steps detailed below in the manual configuration. | ||
|
|
||
| Use the command below to copy `setup.bash` and run it. | ||
| You can check the code that will be executed [here](https://github.com/manubot/rootstock/blob/main/setup.bash). | ||
|
|
||
| ````sh | ||
| bash <( curl --location https://github.com/manubot/rootstock/raw/main/setup.bash ) | ||
| ```` | ||
| The script will then take you through the process of cloning the rootstock repo, make the changes required to use GitHub actions, edit the README to point to your repo and commit the changes. | ||
| Your new manuscript repo is then ready for you to start adding your own content. | ||
|
|
||
| This script does not not create the remote repo for you, so you will be prompted to manually create an empty GitHub repository at <https://github.com/new>. | ||
| Do not initialize the repository, other than optionally adding a description. | ||
|
|
||
| ### CLI | ||
| There is also a command line interface for users who want to create manuscripts at scale and in an automated way. | ||
| See the help for details. | ||
|
|
||
| ````sh | ||
| bash setup.bash --help | ||
| ```` | ||
|
|
||
| ## Manual configuration | ||
|
|
||
| If you do not wish to use the above setup script to configure your new manuscript repository, you can instead execute the steps manually. | ||
| First, you must configure two environment variables (`OWNER` and `REPO`). | ||
| These variables specify the GitHub repository for the manuscript (i.e. `https://github.com/OWNER/REPO`). | ||
| Make sure that the case of `OWNER` matches how your username is displayed on GitHub. | ||
|
|
@@ -63,7 +89,8 @@ git remote set-url origin https://github.com/$OWNER/$REPO.git | |
| git remote set-url origin [email protected]:$OWNER/$REPO.git | ||
| ``` | ||
|
|
||
| Next, you must manually create an empty GitHub repository at <https://github.com/new>. | ||
| Then create an empty repository on GitHub. | ||
| You can do this at <https://github.com/new> or via the [GitHub command line interface](https://github.com/cli/cli) (if installed) with `gh repo create`. | ||
| Make sure to use the same "Owner" and "Repository name" specified above. | ||
| Do not initialize the repository, other than optionally adding a Description. | ||
| Next, push your cloned manuscript: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| % Adaptation of the template by Wouter Groeneveld | ||
| % https://brainbaking.com/post/2021/02/writing-academic-papers-in-markdown/ | ||
|
|
||
| \documentclass[sigconf]{acmart} | ||
|
|
||
| \usepackage{balance} % balancing bibstyles as per request in accepted submission | ||
|
|
||
|
|
||
| %% These commands are for a PROCEEDINGS abstract or paper. | ||
| $for(acm)$ | ||
| \copyrightyear{$acm.copyrightyear$} | ||
| \acmYear{$acm.copyrightyear$} | ||
| \setcopyright{$acm.copyright$} | ||
| \acmConference[$acm.conference$]{$acm.conferencetitle$}{$acm.date$}{$acm.location$} | ||
| \acmBooktitle{$acm.booktitle$} | ||
| \acmPrice{$acm.price$} | ||
| \acmISBN{$acm.bookisbn$} | ||
| \acmDOI{$acm.doi$} | ||
| $endfor$ | ||
|
|
||
| $for(header-includes)$ | ||
| $header-includes$ | ||
| $endfor$ | ||
|
|
||
|
|
||
| $for(author)$ | ||
| \author{$author.name$} | ||
| $if(author.orcid)$ | ||
| \orcid{$author.orcid$} | ||
| $endif$ | ||
| $for(author.affiliations)$ | ||
| \affiliation{ | ||
| $if(author.affiliations.institution)$ | ||
| \institution{$author.affiliations.institution$} | ||
| $endif$ | ||
| $if(author.affiliations.department)$ | ||
| \department{$author.affiliations.department$} | ||
| $endif$ | ||
| $if(author.affiliations.city)$ | ||
| \city{$author.affiliations.city$} | ||
| $endif$ | ||
| $if(author.affiliations.state)$ | ||
| \state{$author.affiliations.state$} | ||
| $endif$ | ||
| $if(author.affiliations.country)$ | ||
| \country{$author.affiliations.country$} | ||
| $endif$ | ||
| } | ||
| $endfor$ | ||
| $for(author.additionalaffiliations)$ | ||
| \additionalaffiliation{ | ||
| $if(author.additionalaffiliations.institution)$ | ||
| \institution{$author.additionalaffiliations.institution$} | ||
| $endif$ | ||
| $if(author.additionalaffiliations.department)$ | ||
| \department{$author.additionalaffiliations.department$} | ||
| $endif$ | ||
| $if(author.additionalaffiliations.city)$ | ||
| \city{$author.additionalaffiliations.city$} | ||
| $endif$ | ||
| $if(author.additionalaffiliations.state)$ | ||
| \state{$author.additionalaffiliations.state$} | ||
| $endif$ | ||
| $if(author.additionalaffiliations.country)$ | ||
| \country{$author.additionalaffiliations.country$} | ||
| $endif$ | ||
| } | ||
| $endfor$ | ||
| $if(author.email)$ | ||
| \email{$author.email$} | ||
| $endif$ | ||
| $endfor$ | ||
|
|
||
| $if(final)$ | ||
| $if(poster)$ | ||
| \settopmatter{printacmref=false, printfolios=false} | ||
| $else$ | ||
| \settopmatter{printacmref=true} | ||
| $endif$ | ||
| $endif$ | ||
|
|
||
| \begin{document} | ||
|
|
||
| $if(final)$ | ||
| \fancyhead{} | ||
| $endif$ | ||
|
|
||
| $if(title)$ | ||
| \title{$title$} | ||
| $endif$ | ||
| $if(subtitle)$ | ||
| \subtitle{$subtitle$} | ||
| $endif$ | ||
|
|
||
|
|
||
| $if(abstract)$ | ||
| \begin{abstract} | ||
| $abstract$ | ||
| \end{abstract} | ||
| $endif$ | ||
|
|
||
|
|
||
| \renewcommand{\shortauthors}{$shortauthors$} | ||
|
|
||
|
|
||
| \maketitle | ||
| \bibliographystyle{ACM-Reference-Format} | ||
|
|
||
| $if(conflicts)$ | ||
| {\let\thefootnote\relax\footnote{$conflicts$}} | ||
| $endif$ | ||
|
|
||
| $body$ | ||
|
|
||
| % Add funding statement as a comment so it can be manually reviewed and condensed | ||
| $if(funding)$ | ||
| %{$funding$} | ||
| $endif$ | ||
|
|
||
| $if(bibfile)$ | ||
| \balance | ||
| \bibliography{$bibfile$} | ||
| $endif$ | ||
|
|
||
| \end{document} | ||
| \endinput |
Oops, something went wrong.