AGENTS.md

=== .ai/project-context rules ===

Project Context (BIOSPEX)

Data Stores

• Relational DB: MySQL (e.g., Expeditions, Projects).
• NoSQL DB: MongoDB via the mongodb/laravel-mongodb package (e.g., Subject data, Occurrences).

Where to Work

• For web app logic, controllers, services, Eloquent models, etc., look in biospex/app/.

Running Commands

• Run Artisan commands from the biospex/ directory.

=== .ai/workflow rules ===

Workflow (Solo / BIOSPEX)

These rules exist to prevent “wrong place / wrong assumptions” work. They intentionally do not repeat Boost’s generic guidance (tests, Pint, Laravel/Livewire/Pest/Filament rules, etc.). Follow Boost for those.

1) Pick the correct execution surface

• This is a Laravel application repository. Most changes belong in the Laravel app code.
• If the request smells like OCR, SQS, image processing, exports, or “pipeline” work, verify what components/services/jobs are involved before coding, and identify any external dependencies.

2) Prefer existing patterns, but allow small cleanups

• Check sibling files and follow local conventions.
• Reuse existing services/actions/jobs/components when they exist.
• Small refactors are OK when they:
  • reduce duplication,
  • improve naming/clarity,
  • or make testing easier, and they do not change behavior beyond the request.

3) Make cross-system impacts explicit

• If a change affects more than one subsystem (for example: web request → queue job → external service), state that clearly:
  • what changes where,
  • how data/IDs/events move between them,
  • and what to verify at each step.

4) Finish with a tight verification recipe

• Rely on Boost’s existing expectations for formatting/testing/build steps.
• End with 3 bullets: what changed, where, and the fastest way to verify.

=== foundation rules ===

Laravel Boost Guidelines

The Laravel Boost guidelines are specifically curated by Laravel maintainers for this application. These guidelines should be followed closely to ensure the best experience when building Laravel applications.

Foundational Context

This application is a Laravel application and its main Laravel ecosystems package & versions are below. You are an expert with them all. Ensure you abide by these specific packages & versions.

• php - 8.5
• filament/filament (FILAMENT) - v5
• laravel/framework (LARAVEL) - v13
• laravel/prompts (PROMPTS) - v0
• laravel/reverb (REVERB) - v1
• laravel/sanctum (SANCTUM) - v4
• livewire/livewire (LIVEWIRE) - v4
• laravel/boost (BOOST) - v2
• laravel/breeze (BREEZE) - v2
• laravel/mcp (MCP) - v0
• laravel/pail (PAIL) - v1
• laravel/pint (PINT) - v1
• pestphp/pest (PEST) - v4
• phpunit/phpunit (PHPUNIT) - v12
• alpinejs (ALPINEJS) - v3
• laravel-echo (ECHO) - v1
• tailwindcss (TAILWINDCSS) - v3

Skills Activation

This project has domain-specific skills available in **/skills/**. You MUST activate the relevant skill whenever you work in that domain—don't wait until you're stuck.

Conventions

• You must follow all existing code conventions used in this application. When creating or editing a file, check sibling files for the correct structure, approach, and naming.
• Use descriptive names for variables and methods. For example, isRegisteredForDiscounts, not discount().
• Check for existing components to reuse before writing a new one.

Verification Scripts

• Do not create verification scripts or tinker when tests cover that functionality and prove they work. Unit and feature tests are more important.

Application Structure & Architecture

• Stick to existing directory structure; don't create new base folders without approval.
• Do not change the application's dependencies without approval.

Frontend Bundling

• If the user doesn't see a frontend change reflected in the UI, it could mean they need to run yarn run build, yarn run dev, or composer run dev. Ask them.

Documentation Files

• You must only create documentation files if explicitly requested by the user.

Replies

• Be concise in your explanations - focus on what's important rather than explaining obvious details.

=== boost rules ===

Laravel Boost

Tools

• Laravel Boost is an MCP server with tools designed specifically for this application. Prefer Boost tools over manual alternatives like shell commands or file reads.
• Use database-query to run read-only queries against the database instead of writing raw SQL in tinker.
• Use database-schema to inspect table structure before writing migrations or models.
• Use get-absolute-url to resolve the correct scheme, domain, and port for project URLs. Always use this before sharing a URL with the user.

Searching Documentation (IMPORTANT)

• Always use search-docs before making code changes. Do not skip this step. It returns version-specific docs based on installed packages automatically.
• Pass a packages array to scope results when you know which packages are relevant.
• Use multiple broad, topic-based queries: ['rate limiting', 'routing rate limiting', 'routing']. Expect the most relevant results first.
• Do not add package names to queries because package info is already shared. Use test resource table, not filament 4 test resource table.

Search Syntax

1. Use words for auto-stemmed AND logic: rate limit matches both "rate" AND "limit".
2. Use "quoted phrases" for exact position matching: "infinite scroll" requires adjacent words in order.
3. Combine words and phrases for mixed queries: middleware "rate limit".
4. Use multiple queries for OR logic: queries=["authentication", "middleware"].

Artisan

• Run Artisan commands directly via the command line (e.g., php artisan route:list). Use php artisan list to discover available commands and php artisan [command] --help to check parameters.
• Inspect routes with php artisan route:list. Filter with: --method=GET, --name=users, --path=api, --except-vendor, --only-vendor.
• Read configuration values using dot notation: php artisan config:show app.name, php artisan config:show database.default. Or read config files directly from the config/ directory.
• To check environment variables, read the .env file directly.

Tinker

• Execute PHP in app context for debugging and testing code. Do not create models without user approval, prefer tests with factories instead. Prefer existing Artisan commands over custom tinker code.
• Always use single quotes to prevent shell expansion: php artisan tinker --execute 'Your::code();'
  • Double quotes for PHP strings inside: php artisan tinker --execute 'User::where("active", true)->count();'

=== php rules ===

PHP

• Always use curly braces for control structures, even for single-line bodies.
• Use PHP 8 constructor property promotion: public function __construct(public GitHub $github) { }. Do not leave empty zero-parameter __construct() methods unless the constructor is private.
• Use explicit return type declarations and type hints for all method parameters: function isAccessible(User $user, ?string $path = null): bool
• Use TitleCase for Enum keys: FavoritePerson, BestLake, Monthly.
• Prefer PHPDoc blocks over inline comments. Only add inline comments for exceptionally complex logic.
• Use array shape type definitions in PHPDoc blocks.

=== deployments rules ===

Deployment

• Laravel can be deployed using Laravel Cloud, which is the fastest way to deploy and scale production Laravel applications.

=== tests rules ===

Test Enforcement

• Every change must be programmatically tested. Write a new test or update an existing test, then run the affected tests to make sure they pass.
• Run the minimum number of tests needed to ensure code quality and speed. Use php artisan test --compact with a specific filename or filter.

=== laravel/core rules ===

Do Things the Laravel Way

• Use php artisan make: commands to create new files (i.e. migrations, controllers, models, etc.). You can list available Artisan commands using php artisan list and check their parameters with php artisan [command] --help.
• If you're creating a generic PHP class, use php artisan make:class.
• Pass --no-interaction to all Artisan commands to ensure they work without user input. You should also pass the correct --options to ensure correct behavior.

Model Creation

• When creating new models, create useful factories and seeders for them too. Ask the user if they need any other things, using php artisan make:model --help to check the available options.

APIs & Eloquent Resources

• For APIs, default to using Eloquent API Resources and API versioning unless existing API routes do not, then you should follow existing application convention.

URL Generation

• When generating links to other pages, prefer named routes and the route() function.

Testing

• When creating models for tests, use the factories for the models. Check if the factory has custom states that can be used before manually setting up the model.
• Faker: Use methods such as $this->faker->word() or fake()->randomDigit(). Follow existing conventions whether to use $this->faker or fake().
• When creating tests, make use of php artisan make:test [options] {name} to create a feature test, and pass --unit to create a unit test. Most tests should be feature tests.

Vite Error

• If you receive an "Illuminate\Foundation\ViteException: Unable to locate file in Vite manifest" error, you can run yarn run build or ask the user to run yarn run dev or composer run dev.

=== livewire/core rules ===

Livewire

• Livewire allow to build dynamic, reactive interfaces in PHP without writing JavaScript.
• You can use Alpine.js for client-side interactions instead of JavaScript frameworks.
• Keep state server-side so the UI reflects it. Validate and authorize in actions as you would in HTTP requests.

=== pint/core rules ===

Laravel Pint Code Formatter

• If you have modified any PHP files, you must run vendor/bin/pint --dirty --format agent before finalizing changes to ensure your code matches the project's expected style.
• Do not run vendor/bin/pint --test --format agent, simply run vendor/bin/pint --format agent to fix any formatting issues.

=== pest/core rules ===

Pest

• This project uses Pest for testing. Create tests: php artisan make:test --pest {name}.
• The {name} argument should not include the test suite directory. Use php artisan make:test --pest SomeFeatureTest instead of php artisan make:test --pest Feature/SomeFeatureTest.
• Run tests: php artisan test --compact or filter: php artisan test --compact --filter=testName.
• Do NOT delete tests without approval.

=== filament/filament rules ===

Filament

• Filament is a Laravel UI framework built on Livewire, Alpine.js, and Tailwind CSS. UIs are defined in PHP via fluent, chainable components. Follow existing conventions in this app.
• Use the search-docs tool for official documentation on Artisan commands, code examples, testing, relationships, and idiomatic practices. If search-docs is unavailable, refer to https://filamentphp.com/docs.

Artisan

• Always use Filament-specific Artisan commands to create files. Find available commands with the list-artisan-commands tool, or run php artisan --help.
• Inspect required options before running, and always pass --no-interaction.

Patterns

Always use static make() methods to initialize components. Most configuration methods accept a Closure for dynamic values.

Use Get $get to read other form field values for conditional logic:

use Filament\Forms\Components\Select; use Filament\Forms\Components\TextInput; use Filament\Schemas\Components\Utilities\Get;

Select::make('type') ->options(CompanyType::class) ->required() ->live(),

TextInput::make('company_name') ->required() ->visible(fn (Get $get): bool => $get('type') === 'business'),

Use Set $set inside ->afterStateUpdated() on a ->live() field to mutate another field reactively. Prefer ->live(onBlur: true) on text inputs to avoid per-keystroke updates:

use Filament\Schemas\Components\Utilities\Set; use Illuminate\Support\Str;

TextInput::make('title') ->required() ->live(onBlur: true) ->afterStateUpdated(fn (Set $set, ?string $state) => $set( 'slug', Str::slug($state ?? ''), )),

TextInput::make('slug') ->required(),

Compose layout by nesting Section and Grid. Children need explicit ->columnSpan() or ->columnSpanFull():

use Filament\Schemas\Components\Grid; use Filament\Schemas\Components\Section;

Section::make('Details') ->schema([ Grid::make(2)->schema([ TextInput::make('first_name') ->columnSpan(1), TextInput::make('last_name') ->columnSpan(1), TextInput::make('bio') ->columnSpanFull(), ]), ]),

Use Repeater for inline HasMany management. ->relationship() with no args binds to the relationship matching the field name:

use Filament\Forms\Components\Repeater;

Repeater::make('qualifications') ->relationship() ->schema([ TextInput::make('institution') ->required(), TextInput::make('qualification') ->required(), ]) ->columns(2),

Use state() with a Closure to compute derived column values:

use Filament\Tables\Columns\TextColumn;

TextColumn::make('full_name') ->state(fn (User $record): string => "{$record->first_name} {$record->last_name}"),

Use SelectFilter for enum or relationship filters, and Filter with a ->query() closure for custom logic:

use Filament\Tables\Filters\Filter; use Filament\Tables\Filters\SelectFilter; use Illuminate\Database\Eloquent\Builder;

SelectFilter::make('status') ->options(UserStatus::class),

SelectFilter::make('author') ->relationship('author', 'name'),

Filter::make('verified') ->query(fn (Builder $query) => $query->whereNotNull('email_verified_at')),

Actions are buttons that encapsulate optional modal forms and behavior:

use Filament\Actions\Action;

Action::make('updateEmail') ->schema([ TextInput::make('email') ->email() ->required(), ]) ->action(fn (array $data, User $record) => $record->update($data)),

Testing

Testing setup (requires pestphp/pest-plugin-livewire in composer.json):

• Always call $this->actingAs(User::factory()->create()) before testing panel functionality.
• For edit pages, pass ['record' => $user->id], use ->call('save') (not ->call('create')), and do not assert ->assertRedirect() (edit pages do not redirect after save).

use function Pest\Livewire\livewire;

livewire(ListUsers::class) ->assertCanSeeTableRecords($users) ->searchTable($users->first()->name) ->assertCanSeeTableRecords($users->take(1)) ->assertCanNotSeeTableRecords($users->skip(1));

use function Pest\Laravel\assertDatabaseHas;

livewire(CreateUser::class) ->fillForm([ 'name' => 'Test', 'email' => 'test@example.com', ]) ->call('create') ->assertNotified() ->assertHasNoFormErrors() ->assertRedirect();

assertDatabaseHas(User::class, [ 'name' => 'Test', 'email' => 'test@example.com', ]);

livewire(EditUser::class, ['record' => $user->id]) ->fillForm(['name' => 'Updated']) ->call('save') ->assertNotified() ->assertHasNoFormErrors();

assertDatabaseHas(User::class, [ 'id' => $user->id, 'name' => 'Updated', ]);

livewire(CreateUser::class) ->fillForm([ 'name' => null, 'email' => 'invalid-email', ]) ->call('create') ->assertHasFormErrors([ 'name' => 'required', 'email' => 'email', ]) ->assertNotNotified();

Use ->callAction(DeleteAction::class) for page actions, or ->callAction(TestAction::make('name')->table($record)) for table actions:

use Filament\Actions\Testing\TestAction;

livewire(ListUsers::class) ->callAction(TestAction::make('promote')->table($user), [ 'role' => 'admin', ]) ->assertNotified();

Correct Namespaces

• Form fields (TextInput, Select, Repeater, etc.): Filament\Forms\Components\
• Infolist entries (TextEntry, IconEntry, etc.): Filament\Infolists\Components\
• Layout components (Grid, Section, Fieldset, Tabs, Wizard, etc.): Filament\Schemas\Components\
• Schema utilities (Get, Set, etc.): Filament\Schemas\Components\Utilities\
• Table columns (TextColumn, IconColumn, etc.): Filament\Tables\Columns\
• Table filters (SelectFilter, Filter, etc.): Filament\Tables\Filters\
• Actions (DeleteAction, CreateAction, etc.): Filament\Actions\. Never use Filament\Tables\Actions\, Filament\Forms\Actions\, or any other sub-namespace for actions.
• Icons: Filament\Support\Icons\Heroicon enum (e.g., Heroicon::PencilSquare)

Common Mistakes

• Never assume public file visibility. File visibility is private by default. Always use ->visibility('public') when public access is needed.
• Never assume full-width layout. Grid, Section, Fieldset, and Repeater do not span all columns by default.
• Use Select::make('author_id')->relationship('author', 'name') for BelongsTo fields. BelongsToSelect does not exist in v4.
• Repeater uses ->schema(), not ->fields().
• Never add ->dehydrated(false) to fields that need to be saved. It strips the value from form state before ->action() or the save handler runs. Only use it for helper/UI-only fields.
• Use correct property types when overriding Page, Resource, and Widget properties. These properties have union types or changed modifiers that must be preserved:
  • $navigationIcon: protected static string | BackedEnum | null (not ?string)
  • $navigationGroup: protected static string | UnitEnum | null (not ?string)
  • $view: protected string (not protected static string) on Page and Widget classes