Skip to content

Commit

Permalink
Initial commit
Browse files Browse the repository at this point in the history
  • Loading branch information
wdduncan authored Dec 19, 2022
0 parents commit 15e096f
Show file tree
Hide file tree
Showing 56 changed files with 256 additions and 0 deletions.
32 changes: 32 additions & 0 deletions .github/workflows/build-deploy-documentation.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@
name: Build and Deploy Static Mkdocs Documentation

# Controls when the action will run. Triggers the workflow on push
on:
push:
branches:
- main
paths:
- 'mkdocs.yml'
- 'docs/*'
- 'docs/images/*'
- 'docs/papers/*'
- 'docs/slides/*'
- 'docs/flash-talks/*'
workflow_dispatch:

# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
github-pages:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
with:
python-version: 3.x

# install dependencies
- run: pip install --upgrade pip
- run: pip install mkdocs

# deploy documentation (note: requires documentation is in docs dir)
- run: mkdocs gh-deploy --remote-branch gh-pages --force --theme readthedocs
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
.DS_Store
21 changes: 21 additions & 0 deletions LICENSE
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
MIT License

Copyright (c) 2022 International Conference on Biomedical Ontologies (ICBO)

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
127 changes: 127 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,127 @@
# ICBO Template
This repository is a template for creating ICBO conference repositories. Instructions for using this template to create a specific ICBO conference repository is included below. For more speci instructions, see the [GitHub instructions](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template) for how to create a repository from a template.

Once your repository has been created, you are free to configure your ICBO repisitory as you desire. Any suggestions or contributions on how to make the instructions for (this) the template repository are welcome.

## Using the template

To create your repository, start by clicking the **Use this template** button:

![use-this-template-button](readme-images/github-use-template-button.png)

Next, fill in the name of your repository:

![use-template-repo-name](readme-images/github-use-template-repo-name.png)

Be sure to mark your repository as **Public** and **Include all branches**:

![use-template-config.](readme-images/github-use-template-config.png)

This will deploy the website on the `gh-pages` branch of your repository. If for some reason the deployment branch is not in your repository, you can add it by going into the repository settings:

![repo-settings](readme-images/github-repo-settings.png)

selecting the **pages** content:

![setting-pages](readme-images/github-setting-pages.png)

and choosing/adding the branch on which to deploy the website:

![pages-setting-gh-pages-branch](readme-images/github-pages-setting-gh-pages-branch.png)


## Add github.io website
To make website available, you have to associate the repository with a `github.io` website (e.g., [https://icbo-conference.github.io/icbo2022](https://icbo-conference.github.io/icbo2022)). The is done be clicking on the settings icon next to **About**:
![about-setting-icon](readme-images/github-repo-about-setting.png)

and then setting the necessary information for **Webpage**:

![about-setting-icon](readme-images/github-repo-webpage-setting.png)

## Github mkdocs actions configuration

The template is set up to use [mkdocs](https://www.mkdocs.org/) to configure a `github.io` website. The deployment of the website is controlled using the GitHub action `.github/workflows/build-deploy-documentation.yaml`. The GitHub action has been configured to run if any changes are made to mkdocs.yaml, files in the `docs/`, `docs/images/`, `docs/papers/`, `docs/slides/`, or `docs/flash-talks/` directories, or after a pull request is merged. Using pull requests allows you to closely track changes made to the repository (if desired). The [icbo2022 conference repository](https://github.com/ICBO-conference/icbo2022) is an example of how a repository can be configured using [mkdocs](https://www.mkdocs.org/).

## Default content

The template provides a set of default webpages in the `docs/` folder. These include:
```
call-for-submissions.md
co-organizers.md
contact-information.md
icbo-hotels.md
icbo-registration.md
icbo-schedule.md
icbo-travel.md
keynote-speakers.md
papers-and-poster-abstracts.md
proceeding-publication-requirements.md
program-committee.md
submit-jbms-icbo.md (optional)
workshops-and-tutorials.md
```
The content for the landing page is in the `index.md` file. You can add or remove content as needed (see below).

The website navigation menu is controlled by associating menu labels with markdown files in `mkdocs.yml` file.

## Editing website content

The website content is contained in the `docs/`, `docs/images/`, `docs/papers/`, `docs/slides/`, and `docs/flash-talks/` directories. Editing any of the `*.md` files or adding/changing an image **should** fire off an action to build and deploy the website. This GitHub action can be checked by navigating to the `Actions` page:

![github-actions-link](readme-images/github-actions-link.png)

and verifying that the changes fired off an action. For example, here is an action that started as a result of an update the to the `call-for-submissions.md`:

![github-actions-call-for-submissions-example](readme-images/github-actions-call-for-submissions-example.png)

After the action has finished running (it will have green check), verify that the edits are displayed on the website.

## Adding new webpages

Adding new webpage takes two steps:

1. Create the new `md` file in the `docs/` directory.
2. Edit the `nav` section of `mkdocs.yml` to reference the new document and its title.

## Adding new images

A new image is added to the website is done by simply saving a the image to the `docs/images/` directory. However, referencing the image from the `md` file is a bit nuanced.

If you reference the image using markdown syntax, you include the `images` directory in the path to the images. For example, in the `docs/call-for-submissions.md` document, the reference to a image is done like so:
```
![submission type](images/test-image.png)
```

However, if you are customizing the image with an HTML `<img>` tag, you use the `../images` directory in the path to the image. For example, `src='../images/test-image.png'` is the path needed when setting the margins of an image like this:
```
<img src='../images/test-image.png' align='left' style='margin:10px 20px 0px 0px' />
```
The reason for this has to do with how `read the docs` processes images, but I don't know the details of why.

## Manually deploying the website

If (for some reason) the GitHub action does not fire, you can manually run it. First, on the `Actions` page, select the `Build and Deploy Static Mkdocs Documentation` workflow.


![github-actions-select-workflow](readme-images/github-actions-select-workflow.png)


Next, click on the `Run workflow` button.


![github-actions-run-build-workflow](readme-images/github-actions-run-build-workflow.png)


Once the workflow starts running, you will see yellow dot beside the workflow name.

![github-actions-build-running](readme-images/github-actions-build-running.png)


After the workflow, completes you will see a green check beside the workflow name.


![github-actions-build-complete](readme-images/github-actions-build-complete.png)


Verify that the edits are displayed on the website.

2 changes: 2 additions & 0 deletions docs/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# docs
Place documents for ICBO website here.
3 changes: 3 additions & 0 deletions docs/call-for-submissions.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
# ICBO Call For Submissions

Fill in details.
Binary file added docs/ceur-author-agreement-ccby-ntp-for-ICBO.pdf
Binary file not shown.
2 changes: 2 additions & 0 deletions docs/co-organizers.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Co-chairs
Fill in information about co-chairs/organizers.
2 changes: 2 additions & 0 deletions docs/contact-information.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Contact Information
Fill in contact information.
2 changes: 2 additions & 0 deletions docs/flash-talks/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# flash-talks
Place slides/posters used for flash-talks here.
Binary file added docs/github-actions-build-complete.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-actions-build-running.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-actions-link.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-actions-run-build-workflow.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-actions-select-workflow.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-pages-setting-gh-pages-branch.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-repo-about-setting.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-repo-settings.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-repo-webpage-setting.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-setting-pages.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-use-template-button.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-use-template-config.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/github-use-template-repo-name.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 2 additions & 0 deletions docs/icbo-hotels.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# ICBO Hotel Options
Fill in information about hotels for participants.
2 changes: 2 additions & 0 deletions docs/icbo-registration.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# ICBO Registration
Fill in registration details.
2 changes: 2 additions & 0 deletions docs/icbo-schedule.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# ICBO Schedule
Fill in schedule details.
2 changes: 2 additions & 0 deletions docs/icbo-travel.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Travel to ICBO
Fill in details about how to best travel to ICBO (e.g., local airports).
Binary file added docs/images/ICBO_Author_Footnote.jpg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 2 additions & 0 deletions docs/images/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# images
Place images used for the ICBO website here.
Binary file added docs/images/test-image.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 2 additions & 0 deletions docs/index.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# ICBO: International Conference on Biomedical Ontology
This is main webpage that is the root of the website. Fill in details about the website, and links to other pages.
2 changes: 2 additions & 0 deletions docs/keynote-speakers.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Keynote Speakers
Fill in information about keynote speakers.
2 changes: 2 additions & 0 deletions docs/papers-and-poster-abstracts.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Papers and Poster Abstracts
Fill in information about papers and poster abstracts.
2 changes: 2 additions & 0 deletions docs/papers/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# papers
Place papers and/or abstracts presented at ICBO here.
17 changes: 17 additions & 0 deletions docs/proceeding-publication-requirements.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
# ICBO Conference Proceeding Publication Requirements

**ICBO conference proceedings are often published in CEUR. Below, we have included language for the requirements to do this. Edit the content indicated by '-> <-' to suite your specific conference.**

**An example from a past conference can be seen [here](https://icbo-conference.github.io/icbo2022/workshop-publication-requirements/)**


Conference submissions will be published in the [CEUR Workshop Proceedings](http://ceur-ws.org/). In order for this to happen, the following requirements must be satisfied.

1. Ensure that the conference name, date, and place, and email addresses and ORCIDs of all authors are added to the footnote on the lower left of the first page. An example of how this should look can be found [here](images/ICBO_Author_Footnote.jpg). The copyright should read **-> INSERT YEAR <-** as well.



2. All papers for ICBO need an accompanying signed **Author Agreement to Publish a Contribution as Open-Access on CEUR-WS.org** prepared by the corresponding author. Please download the ICBO customized form [here](ceur-author-agreement-ccby-ntp-for-ICBO.pdf) **-> CHANGE FORM FOR SPECIFIC CONFERENCE <-**.
Fill in the fields on the form, print it out, sign it in ink, then scan or photograph the form and send it to **-> INSERT EMAIL ADDRESS <-** with a subject heading that reads "Author Agreement for submission [*PAPER-ID*]". Do NOT digitally sign the pdf, as CEUR-WS.org will not accept it. CEUR-WS.org allows an alternative method to provide a signature if you are unable to print the form, as shown here: [http://ceur-ws.org/agreement-paper1.jpg](http://ceur-ws.org/agreement-paper1.jpg)

Please contact us if you have questions.
2 changes: 2 additions & 0 deletions docs/program-committee.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Program Committee
Fill in information about the program committee.
2 changes: 2 additions & 0 deletions docs/slides/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# slides
Place slide decks used for presentations here.
4 changes: 4 additions & 0 deletions docs/submit-jbms-icbo.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Journal of Biomedical Semantics ICBO Thematic Series
If your conference has reached a publication agreement with the Journal of Biomedical Semantics, fill in the details here and add a reference to page in [mkdocs.yml](../mkdocs.yml).

An example of the details can be seen on [ICBO 2022 website](https://icbo-conference.github.io/icbo2022/submit-jbms-icbo/).
2 changes: 2 additions & 0 deletions docs/workshops-and-tutorials.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
# Workshops & Tutorials
Fill in information about workshops and tutorials.
19 changes: 19 additions & 0 deletions mkdocs.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
site_name: "ICBO: International Conference on Biomedical Ontology"
# repo_url: add info to link to your github repository
theme:
name: readthedocs
nav:
- Home: index.md
- Call for Submissions: call-for-submissions.md
- Keynote Speakers: keynote-speakers.md
# - Journal of Biomedical Semantics ICBO Thematic Series: submit-jbms-icbo.md # uncomment to see page on website
- Workshops & Tutorials: workshops-and-tutorials.md
- Conference Proceeding Publication Requirements: proceeding-publication-requirements.md
- Registration: icbo-registration.md
- ICBO Hotel Options: icbo-hotels.md
- Travel to ICBO: icbo-travel.md
- Schedule: icbo-schedule.md
- Papers and Poster Abstracts: papers-and-poster-abstracts.md
- Contact Information: contact-information.md
- Co-organizers: co-organizers.md
- Program Committee: program-committee.md
Binary file added readme-images/.DS_Store
Binary file not shown.
Binary file added readme-images/github-actions-build-complete.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added readme-images/github-actions-build-running.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added readme-images/github-actions-link.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added readme-images/github-actions-select-workflow.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added readme-images/github-repo-about-setting.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added readme-images/github-repo-settings.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added readme-images/github-repo-webpage-setting.png
Binary file added readme-images/github-setting-pages.png
Binary file added readme-images/github-use-template-button.png
Binary file added readme-images/github-use-template-config.png
Binary file added readme-images/github-use-template-repo-name.png

0 comments on commit 15e096f

Please sign in to comment.