Metalation Calculator

This calculator is based on Nature Communications 12 1195- (2021) and is supported by grant BB/V006002/1 from the Biotechnology and Biological Sciences Research Council.

A single rendered calculator is available at https://durhamarc.github.io/metalation-calculator/, and a set of calculators for E. coli is available on the MiB Elements of Bioremediation, Biomanufacturing and Bioenergy site.

If you spot any problems with the calculator, please log an issue to help us improve it.

Notes on security can be found in security.md.

Wordpress Plugin

The calculator can be installed as a Wordpress block plugin, allowing admin users can add a calculator to any page. The plugin can be installed by downloading the metalation-calculator-wp.zip file from the latest release, and uploading the file to the plugins section of the Wordpress admin interface.

Note that in order to update the plugin via the 'Upload' feature, the filename needs to be kept as metalation-calculator-wp.zip, otherwise it will be treated as a new plugin but will conflict with the existing one. (If this happens, it can be fixed by deactivating and deleting the old plugin.)

Development

The code for the calculator is in two parts:

• The typescript directory contains code for a static web app. It uses TypeScript with gulp to generate the static website. GitHub Actions builds the main branch from the typescript directory and pushes the compiled site to GitHub Pages (on the gh-pages branch).
• The metalation-calculator-wp directory contains a Wordpress block plugin, which

TypeScript Calculator

Ensure you have Node.js v16 and npm installed.

Run:

sudo npm install -g gulp-cli

Enter your password to install gulp globally as admin. See Gulp for further information.

To work within the typescript directory and install the necessary packages, run:

bash cd typescript npm install

All necessary packages should now be installed.

Commands below should also be run from the typescript directory.

To compile the website with gulp, run:

bash gulp

To compile on-the-fly, run:

bash gulp watch

Open dist/index.html (from the typescript directory) to view the calculator.

After making changes to the calculator, ensure you run gulp wp to update the files in the Wordpress plugin and commit the modified files in metalation-calculator-wp/include.

Wordpress Plugin

The Wordpress Plugin allows Wordpress authors to add a calculator as a new block in a Wordpress page, allowing Wordpress authors to customise the default values for availability.

To work on/test the plugin, follow the development instructions at https://developer.wordpress.org/block-editor/getting-started/devenv/ to set up a Wordpress development environment.

Then do:

bash cd metalation-calculator-wp npm run build wp-env start

You should then be able to access your local Wordpress instance at http://localhost:8888, and to log in at http://localhost:8888/wp-admin.

Enable the Metalation Calculator plugin, then add a 'metalation calculator' block to a post or page to test it out.

Releases

To create a new release:

1. Update the version number in the following files in metalation-calculator-wp, e.g. if the previous version was 1.0.2 then use 1.0.3.
   • block.json
   • metalation-calculator-wp.php
   • package.json
   • readme.txt: as well as updating the 'stable tag' at the top, add a new section to the Changelog with the new version number and notes on what has changed.

Run npm install to update version number in package-lock.json. Commit and push the changes to the main branch on GitHub.

1. Create a new (lightweight) git tag from main to match the new version number, following the vX.Y.Z formatting (e.g. v1.0.3): bash git tag v1.0.3

2. Push the tag to GitHub: bash git push origin v1.0.3 You can check the tag has been created from the tags page of the repository.

3. GitHub Actions should run on the tag push, including the jobs to release the Wordpress plugin.

4. Go to the releases page and check that the release, including a file metalation-calculator-wp.zip, has been created.

To publish the updated plugin to https://mib-nibb.webspace.durham.ac.uk, contact the web team at Durham University CIS and give them the details of the new release.