Move PyChaste website

[kwabenantim]

Description Move the PyChaste website to the Chaste organisation under chaste.github.io

Related PRs

• https://github.com/Chaste/Chaste.github.io/pull/17

To Do

• [x] Add PyChaste markdown pages to site (https://github.com/Chaste/Chaste.github.io/pull/17)
• [x] Automatically generate tutorial markdown (https://github.com/Chaste/PyChaste/pull/50)
• [x] Add landing page for PyChaste (https://github.com/Chaste/Chaste.github.io/issues/22)
• [x] Fix tutorial syntax highlighting (https://github.com/Chaste/Chaste.github.io/issues/22)
• [ ] Move PyChaste Python API docs (https://github.com/Chaste/Chaste.github.io/issues/22)
• [ ] Update PyChaste pages for trunk merge: https://github.com/Chaste/Chaste.github.io/pull/101

[kwabenantim]

Previous deployment failed, possibly due to permissions issues.

[kwabenantim]

The old Jekyll site is now deployed to https://chaste.github.io/PyChaste. It probably needs redoing to match the modern Hugo theme on https://chaste.github.io.

[kwabenantim]

It probably needs redoing to match the modern Hugo theme on https://chaste.github.io.

As part of #46, content from the PyChaste website will be moved into chaste.github.io

[kwabenantim]

The PyChaste website is being re-created in markdown directly under chaste.github.io (see PR https://github.com/Chaste/Chaste.github.io/pull/17).

Things to consider for python notebook tutorials:

• Generate markdown from ipynb automatically to keep them in sync.
• Create cron job to periodically check current ipynb against markdown and update markdown manually.

[kwabenantim]

nbconvert can help with the automatic conversion of Jupyter notebooks to markdown.

[kwabenantim]

Generating markdown for the website is fixed in this PR: https://github.com/Chaste/PyChaste/pull/50

[kwabenantim]

Python is not specified in the code blocks for some of the generated tutorial markdown, which affects syntax highlighting on the website.

Bad Example

import os
def main:
    print("Code block without 'python'")

https://chaste.github.io/pychaste/tutorials/pottsbasedcellsimulations/

Good Example

import os
def main:
    print("Code block with 'python'")

https://chaste.github.io/pychaste/tutorials/cellsorting/

Resolution The bad examples are duplicate tutorials that were not overwritten with autogenerated ones. They will be removed.

[kwabenantim]

As part of #46, PyChaste API generation will be moved to Chaste infra.