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Important

These docs (including this README.md) are a work-in-progress. If you run into any obstacles developing these docs, or if there is any obfuscated, inaccurate, or missing content, please raise awareness by submitting an issue. Thanks!

Onix1 Bonsai Docs

Documentation for the Onix1 Bonsai package.

These docs are built using docfx.

Initialize the local Onix1 Bonsai Repository for Building Locally

These actions only need to be performed once when setting up the repo locally.

Download and install dotnet if it is not installed already.

Download and install git if it is not installed already.

Note

The docfx program provides very little feedback about its state on the command line. It often appears to hang because it does not output any status information. Usually, the command will eventually return.

  1. Clone the documentation repository:

    git clone https://github.com/open-ephys/onix1-bonsai-docs
cd onix1-bonsai-docs

  2. Pull in the latest files from the submodules according to the commit that the submodules point to:

    git submodule update --recursive --init

    In particular, the source code is available in this repo as a submodule. This will update the source code to the latest commit on main.

  3. Configure the docfx version and restore docfx companion tools such as DocLinkChecker.

    dotnet tool restore --configfile ./.bonsai/NuGet.config

  4. To make the docfx command available after restoring the config file from the previous step, run:

    dotnet tool restore

  5. Set up a local Bonsai environment for automatically exporting SVGs, run:

    ./.bonsai/Setup.cmd

Build Documentation Locally

To build the docs and serve locally, run in PowerShell:

./build.ps1 --serve

If SVGs are already exported and do not need to be updated, they don't need to be re-exported. In that case, to build the docs and serve locally more quickly, run:

dotnet docfx --serve

Update Submodules

It is best practice to develop docs with the submodule directories containing the latest commits in their respective main branches (unless you are intentionally testing local changes to or another branch of the source code, for example). To update all submodules, run:

git submodule update --recursive --remote

Before Pushing

The following three commands are run remotely by remote GitHub Actions serve upon pushing to a branch. The branch will not be able to merge to main unless all three commands complete successfully without any errors. Confirm that they can complete successfully without errors locally before committing and pushing. Otherwise, the branch becomes cluttered with potentially several attempts to pass the link-check process. Run:

.\build.ps1 --logLevel Suggestion --warningsAsErrors
dotnet DocLinkChecker -v -f .github/workflows/DocLinkChecker.config

If the above command fails because "you must install or update .NET", follow the URL from the failed command's output or this one to download and install .NET runtime 6. Dotnet supports simultaneous installation of several .NET runtime versions, and version 6 is required to run the DocLinkChecker.

The above set of commands can also be run using the docfx-utils.ps1 Powershell script. Specifically, run ./docfx-utils.ps1 -d in the repo's root directory to run DocLinkChecker, and run ./docfx-utils.ps1 -b to build the site.

To run the next command, install Lychee by following these instructions. If you are use Windows and download a Lychee executable, amend the below command according to the location and version of your Lychee executable, and run it.

<lychee/installation/directory>/lychee-v<x.xx.x>-windows-x86_64.exe --verbose --no-progress --base _site --exclude ^https://github\.com.*merge.* --exclude ^https://github\.com.*apiSpec.* '_site/**/*.html'

If you use a different operating systems and a different methods of installation, the above command might require additional amendments.

The above command can also be run using the docfx-utils.ps1 Powershell script. Specifically, run ./docfx-utils.ps1 -l <path/to/lychee.exe> in the repo's root directory.

All three link-checking commands can be run with the following command: ./docfx-utils.ps1 -a in the repo's root directory. This command additionally cleans remaining artifacts from past builds before performing all the link-checking commands. This is the most robust and expedient way to confirm that the repo will pass the link checks when pushed.

docfx-utils.ps1

This is summary of docfx-utils.ps1 list members. They are described above, but they are also described below for ease-of-finding:

  • docfx-utils.ps1 -c cleans cached files/removes artifacts from previous builds.
  • docfx-utils.ps1 -b exports SVGs and builds the docs.
  • docfx-utils.ps1 -d check the markdown files for broken references using DocLinkChecker.
  • docfx-utils.ps1 -l <path/to/lychee.exe> checks for broken/missing links and references using lychee.
  • docfx-utils.ps1 -a <path/to/lychee.exe> performs all of the above steps.

docfx-utils.ps1 -l and docfx-utils.ps1 -a will not run without a path to a lychee executable.

Note

The docfx-utils.ps1 script (.ps1 PowerShell scripts in general) must be run in PowerShell.

These commands do not serve the docs. Serve them by running dotnet docfx serve _site. Note that this will not work if the documentation website has not been previously built. If the SVGs have been created, but the _site folder is empty and the only option that needs to be run is building the documentation pages, run dotnet docfx --serve to build the pages and automatically serve them.

dotnet docfx

Running dotnet docfx runs both the dotnet docfx metadata command and the dotnet docfx build command in that order. Unless specified otherwise, dotnet docfx uses the docfx.json as its config file.

metadata

The metadata command generates a .yml files containing metadata from the source code. These files contain information about class members, class inheritance, enum fields, etc. and <xml> comments from the source code. The input files for the metadata command are specified in metadata.src of the docfx.json file, and the output directory of the metadata command is specified in metadata.dest of the docfx.json file.

build

The build command generates raw and view data models for each .yml file generated by the metadata command and uses those raw and view data models to populate a template with data.

The build process involves multiple steps:

  1. Generates a raw data model from each .yml file.
  2. Uses template to generate view data model from the raw data model. To see the raw model, refer to the relevant command in the Troubleshooting section of this readme.
  3. Uses template to populate pages with data from the view data model. To see the view models, refer to the relevant command in the Troubleshooting section of this readme.

The user can hook into and modify the build process at each of these steps by editing the template.

All of the files involved in defining the template are specified in the build.template of the docfx.json file. The order in which the templates are defined matters. If the templates contain files with conflicting names, the template specified later overrides the template specified earlier with its conflicting file(s). This is helpful because it enables building custom templates on top of other templates. To see the docfx default and modern templates, refer to the relevant command in the Troubleshooting section of this README.md.

The input files for the build command are specified in build.content of the docfx.json file, and the output directory of the build command is specified in build.output of the docfx.json file.

Docfx Template System

The docfx template system comprises of two primary components: the .js preprocessor files and the .tmpl renderer files. The preprocessor files are used to transform the raw data model into a view data model. The renderer files are templates that use data from the view data model to populate pages.

Preprocessor

There are two functions that are called during the preprocessor step. They are getOptions() and transform(). They are called for every .yml file generated by the metadata command. getOptions() provides the user with the opportunity to modify the raw data model. transform() provides the user with the opportunity to modify the view data model.

When getOptions() is called for a given .yml file, setting the isShared flag as true incorporates the raw data model for every other .yml file into the raw data model of the .yml file whose isShared flag as true. This provides access to other classes', enums', namespaces', etc. metadata when transform() is called. This flag greatly expands the possibilities so it's worth explicitly mentioning. Setting the isShared flag as true would correspond with hooking into step 1 of the build process.

The transform() function transforms the raw data model to the view data model. Through this transformation process, the user can add logic to the template and process the source code's metadata. The default transform() function can be overwritten by writing your own transform() function in <xyz>.overwrite.js or can be extended by writing your own preTransform and postTransform in the <xyz>.extension.js file. Extending or overwriting the transform() function would correspond with hooking into step 2 of the build process.

Renderer

The renderer step utilizes mustache syntax to create a template which is populated with data from the view model data. Writing custom .tmpl files would correspond with hooking into step 3 of the build process.

Troubleshooting

The template in this repo builds upon the default and modern templates built into docfx. It might be helpful to reference those templates. To view them, run:

dotnet docfx template export default modern

It might be helpful to view the intermediate data models involved in the build process. To view those models, build, and serve the docs locally, run:

dotnet docfx --exportRawModel --rawModelOutputFolder _raw --exportViewModel --viewModelOutputFolder _view --serve

Strip the --serve option and append --dryRun option if you want to export the models without completing the build process and serving.

If local html pages don't appear to be updating, hard refresh website pages in browser. Ctrl+Shift+R and Ctrl+F5 are common hotkeys for hard refreshes.

If there are discrepancies between local and remote builds:

  • Confirm local and remote docfx versions are consistent. This inconsistency can occur when, for example, running docfx instead of dotnet docfx or running dotnet tool restore --configfile <configfile> on another config file other than the one in this repo.
  • Clear any locally cached files that aren't available remotely. Such files exist in the api directory (though care to not delete the .gitignore in that directory), the _site directory, and the workflows directory. Run ./docfx-utils.ps1 -c to clean artifacts from previous builds.

Docs Maintainability

Creating Edited Screenshots

There are webpages with edited screenshots of Bonsai. The source material (.xcf GIMP files) belongs in the img-src directory for ease of maintenance. The headers below describe how you can quickly create a new screenshot.

To take the screenshot (in Windows), use the Windows+Shift+S hotkey, select the Window option, and select the window you would like to screenshot. The preference is to take a screenshot against a grey background (e.g. create a (R: 127, G: 127, B: 127) background in GIMP) because some of the background makes it into the screenshot.

Bonsai Package Manager Screenshot Edits

The layer group consisting of the highlight layer and 1,2,3,4 layers of the screenshots in the bonsai-install*.xcf or bonsai-update*.xcf files can be copy and pasted on top of other screenshots. This enables an expedited editing process for creating new edited screenshots. When creating the screenshot, do not change the size of the package manager after opening it.