mkdocs-bioinformatic-izsam-theme 1.0.13
MkDocs theme designed for Bioinformatic Unit of the Istituto Zooprofilattico dell' Abruzzo e del Molise G. Caporale
License: MIT
Keywords: MkDocs, Theme, Software documentation

# mkdocs-bioinformatic-izsam-theme

This is an MkDocs theme designed to layout the documentation provided by Bioinformatic Unit of the Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale".

#### Important!

The theme is intended to work with the plugin **mkdocs-izsam-search** [https://pypi.org/project/mkdocs-izsam-search/](https://pypi.org/project/mkdocs-izsam-search/)

```bash
pip install mkdocs-izsam-search
```

## Theme customization

The theme allows you to customize platform title and footer contents by using your mdkdocs configuration file `mkdocs.yml`.

```yaml
extra:
  platform_title: Piattaforma GenPat, Wiki
  language: it
  useful_links:
    link_1:
      label: CRN Sequenze Genomiche
      url: https://www.izs.it/IZS/Eccellenza/Centri_nazionali/CRN_-_Sequenze_Genomiche
    link_2:
      label: IZSAM "G. Caporale"
      url: https://www.izs.it
  support:
    support_1:
      label: bioinformatica@izs.it
      url: mailto:bioinformatica@izs.it
    support_2:
      label: +39 0861 3321
      url: tel:+3908613321
  tools:
    tool_1:
      icon: iconic-print
      label: Versione PDF
      target: _blank
      url: https://genpat.izs.it/genpat_wiki/en/pdf/genpat_platform_wiki.pdf
  copyright: IZSAM "G. Caporale"
```

## Multi language support

The theme supports a localization system written in javascript. At the moment it supports Italian and English but it is possible to add new languages.

### Add a language

1. Create a new language file in `js/i18n` folder by using `en.js` or `it.js` as template and translate values.
2. List it in `js/languages-builder.js`
3. Pack language files in `languages.js` 

#### Pack language files

To pack files we use [**packjs**](https://www.npmjs.com/package/packjs) npm library:

```bash
npm install --save-dev packjs
```

Then from `js` folder:

```bash
  packjs i18n/languages-builder.js languages.js
```

The code will loop through the `wiki.languages` object keys and for each key, it will add an option to the language switcher. By selecting an available language, the code will redirect to the language subfolder.

The theme is designed to handle different builds for each language. Specifically, we will have the documentation in Italian hosted under `https://mywiki.eu/it`, the documentation in English under `https://mywiki.eu/en`, and so on.

> **Please note:** If you have a single language site, just remove the languages you don't need from `js/languages.js`. If you want to modify the behavior of the language switcher, you can override the `js/locales.js` file.

### Language definition

Each build relies on `config.extra.language` parameter to define the wiki language (the default is `en`), on `base.html` we set the html `lang` attribute and a global javascript constant `config_lang` with that value:

```html
<html lang="{{ config.extra.language|default('en') }}">
```

```javascript
const config_lang = "{{ config.extra.language|default('en') }}";
```

The `config.extra.language` variable is used also to set **search functionalities**. There are some limitations on the values it can assume. Allowed languages are: `ar`, `da`, `de`, `du`, `es`, `fi`, `fr`, `hi`, `hu`, `it`, `ja`, `jp`, `nl`, `no`, `pt`, `ro`, `ru`, `sv`, `ta`, `th`, `tr`, `vi`, `zh`. If you want to use a different language, you should not to use **mkdocs-izsam-search** plugin and customize the `base.html` file removing all the code related to it.

```html
{% if config.extra.language and not 'en' in config.extra.language %}
  <script src="{{ 'js/lunr-languages/lunr.stemmer.support.js'|url }}"></script>
  <script src="{{ 'js/lunr-languages/lunr.multi.js'|url }}"></script>
  {% set js_path = 'js/lunr-languages/lunr.' ~ config.extra.language ~ '.js' %}
  <script src="{{ js_path|url }}"></script>
{% endif %}
```

## Theme features

#### Use image caption

If you need to use a caption for images, you can use the markdown image title sintax.

`![](image.png "image title")`

> A function in `theme.js` loops all images and if a title exists will append a `figcaption` tag after the image.

#### Use icons inline

To use icons inline inside the contents, please add the alt attribute `inline-icon`:

```
![inline-icon](icon.png)
```

> Images will have inherent size and displayed inline.

#### Use diagram as images (no plantuml)

To use diagram inside the contents as images, please add the alt attribute `diagram` to avoid box shadow.

```
![diagram](file.png)
```

## Credits

For the icons, we are using the free [Iconic](https://iconic.app/) package, converted to a font with the [IcoMoon app](https://icomoon.io/app/#/select).

# Change log

## [1.0.13] - 2025-11-05

### base.css
- Added specific rules for ordered lists.

## [1.0.12] - 2025-09-29

### wiki.css
- Added `max-height` css rule for inline icons.

## [1.0.11] - 2025-09-08

### search.js
- Added support for the new `meta_text` field introduced by `mkdocs-izsam-search==0.1.9`.
- Implemented a check to display the searched text highlighted with the `<mark>` tag in the summary.

### setup.py
- Fixed a typo in the package name: changed `name='mkdocs-bionformatic-izsam-theme'` to `name='mkdocs-bioinformatic-izsam-theme'`.

## [1.0.10] - 2025-05-28

### 404 page
- Fixed HTML, changed contents and messages, new css rules.

## [1.0.9] - 2025-05-22

### Hyphenation
- Added hyphenation and break-word rules for navigation, toc, contents and titles.

## [1.0.8] - 2025-05-20

### Bug fixes for navigation menu
- Fixed JavaScript DOM selector error.
- Minor changes to submenu icon positions.

## [1.0.7] - 2025-05-20

### Bug fixes and accessibility improvements
- Updated UX/UI for navigation and TOC menu.
- Minor fixes for mobile display.

## [1.0.6] - 2025-03-7

### Bug fixes and improvements 
- Improved handling of `title` and `meta description`, now they take values from the metadata inserted in the markdown of the `docs`.
- Fixed behavior that did not allow independent clicking on the `plus` and `minus` icons in the context menu.
- Added language code to the options of the language switch select box.

## [1.0.5] - 2025-02-25

### Added rules for drawio diagrams
Added css rules to manage images with `class="drawio"`.

## [1.0.4] - 2025-02-04

### Fix for TOC navigation
Fix for TOC navigation expandable functionalities if they contain children.

## [1.0.3] - 2025-01-31

### UX changes and a fix for English UI translation
TOC navigation now has expandable items if they contain children. Scrolling the page will highlight the corresponding TOC item in the context menu. Fixed an incorrect translation for the `search` key in the i18n English object.

## [1.0.2] - 2025-01-31

### Bug fixes
Fix for onload events being called twice for the same element. Fix for TOC navigation theme where the for loop was generating a `ul` tag for each element.

## [1.0.1] - 2025-01-30

### Bug fix and cleaning
Fixed formatting problem with last update date on footer, reoved unused code

## [1.0.0] - 2025-01-28

### Refactoring
Theme code refactoring in order to have greater modularity for overrides, better localization management, and improved flexibility with the use of extra mkdocs configuration variables.

## [0.2.8] - 2024-09-17

### Added css style in order to manage Mermaid diagrams
Added support in general theme css rules for Mermaid diagrams generated by mkdocs-izsam-mermaid-to-images plugin

## [0.2.7] - 2024-09-16

### Added home link for header logo

## [0.2.6] - 2024-09-10

### Fixed style for indented list

## [0.2.5] - 2024-06-17

### Fixed package problem related to build process

## [0.2.4] - 2024-06-17

### New style for table

## [0.2.3] - 2023-12-1

### Added new logo and canged accent color

## [0.2.1] - 2023-08-29

### Small fix related to 0.2 release
- Edited base.html

## [0.2] - 2023-08-29

### Refactoring and bug fix for search
Change in multilingual handling for search in order to resolve issues related to searching for words containing the underscore character (`_`).
- Edited base.html
- Edited js/search.js

## [0.1.9.3] - 2023-05-15

### Ux improvement for main menu in mobile view
- Edited theme.css
- Edited base.html

## [0.1.9.2] - 2023-03-28

### Bug fix for ordered list
- Edited theme.css

## [0.1.9.1] - 2022-12-09

### Ux improvement for main menu in mobile view
- Edited theme.css

## [0.1.9] - 2022-10-24

### Small fix on Ux improvement for main menu in mobile view
- Edited theme.css and base.html

## [0.1.8] - 2022-10-24

### Ux improvement for main menu in mobile view
- Edited theme.css and base.html

## [0.1.7] - 2022-05-12

### Debug and refactoring for theme.js
- Edited theme.js

## [0.1.6] - 2022-05-12

### Fix for image caption function
- Edited theme.css and theme.js

## [0.1.5] - 2022-05-12

### Added support for image caption
- Edited theme.css and theme.js

### Readme improvements
- Edited README.md

## [0.1.4] - 2022-05-2

### CSS: added rule for html video tag
- Edited theme.css

## [0.1.3] - 2022-04-27

### Html base template: changed next and previous buttons in order to integrate parent title
- Edited base.html

## [0.1.2] - 2022-03-18

### Layout improvement.
- Edited theme.css

## [0.1.1] - 2022-01-25

### Layout improvement.
- Edited theme.css

## [0.1.0] - 2022-01-25

### Layout improvement.
- Edited theme.css

## [0.0.9] - 2022-01-25

### Layout changes: form fields and buttons aspect.
- Edited theme.css

## [0.0.8] - 2021-11-24

### Layout improvement.
- Edited theme.css

## [0.0.7] - 2021-11-15

### Project description.
- Edited README.md

## [0.0.6] - 2021-11-15

### Theme localization, integration of a footer.css, ui emprovement.
- Added theme localization for search.html file.
- Added theme localization for 404.html file.
- Added a footer.css file.
- Small changes in the main theme.css style for left menu.

## [0.0.5] - 2021-11-12

### Theme localization
- The theme now support it and en localization and it can be extended with other langauges.

## [0.0.4] - 2021-11-12

### Added support for other languages besides `en` to make theme working with mkdocs-izsam-search plugin
- The theme now support languages present in `js/lunr-languages` and can be defined in `theme.locale` of the `.yml` configuration file. Multilanguage is not supported yet.

## [0.0.2] and [0.0.3] - 2021-11-11

### Debug on setup
- Fixed bugs for the mkdocs entry point in `setup.py` 

## [0.0.1] - 2021-11-11

### First release
- Made stuff necessary to package a theme