Merge branch 'refs/heads/master' into tecan-mix-command

CHANGELOG.md

@@ -9,6 +9,24 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v5.5.1
+
+### Fixed
+
+- Fix generic inference for `MLL\Utils\Microplate\Coordinates::fromPosition()`
+
+## v5.5.0
+
+### Added
+
+- Add scalar `Column6`
+
+## v5.4.0
+
+### Added
+
+- Add command `SetDiTiType` to tecan worklist
+
 ## v5.3.0
 
 ### Added

src/Microplate/Coordinates.php

@@ -92,9 +92,11 @@ public static function fromString(string $coordinatesString, CoordinateSystem $c
     }
 
     /**
-     * @param TCoordinateSystem $coordinateSystem
+     * @template TCoord of CoordinateSystem
+     *
+     * @param TCoord $coordinateSystem
      *
-     * @return static<TCoordinateSystem>
+     * @return static<TCoord>
      */
     public static function fromPosition(int $position, FlowDirection $direction, CoordinateSystem $coordinateSystem): self
     {

src/Microplate/MicroplateSet/MicroplateSet.php

@@ -42,7 +42,6 @@ public function locationFromPosition(int $setPosition, FlowDirection $direction)
         $plateIndex = (int) floor(($setPosition - 1) / $this->coordinateSystem->positionsCount());
         $positionOnSinglePlate = $setPosition - ($plateIndex * $this->coordinateSystem->positionsCount());
 
-        /** @phpstan-ignore-next-line Generic inference is too weak to recognize this code is correct */
         return new Location(
             Coordinates::fromPosition($positionOnSinglePlate, $direction, $this->coordinateSystem),
             $this->plateIDs()[$plateIndex]

src/Microplate/Scalars/Column6.php

@@ -0,0 +1,20 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Microplate\Scalars;
+
+use MLL\GraphQLScalars\IntRange;
+
+class Column6 extends IntRange
+{
+    public ?string $description = 'Represents a column in a coordinate system with 6 columns. Allowed values range from 1-6.';
+
+    protected static function min(): int
+    {
+        return 1;
+    }
+
+    protected static function max(): int
+    {
+        return 6;
+    }
+}

src/Tecan/BasicCommands/SetDiTiType.php

@@ -0,0 +1,23 @@
+<?php declare(strict_types=1);
+
+namespace MLL\Utils\Tecan\BasicCommands;
+
+/**
+ * Can only be used at the very beginning of the worklist or directly after a Break command.
+ *
+ * @see BreakCommand
+ */
+class SetDiTiType extends Command
+{
+    private int $indexOfDiTi;
+
+    public function __construct(int $indexOfDiTi)
+    {
+        $this->indexOfDiTi = $indexOfDiTi;
+    }
+
+    public function toString(): string
+    {
+        return "S;{$this->indexOfDiTi}";
+    }
+}

src/Tecan/TecanProtocol.php

@@ -10,6 +10,7 @@
 use MLL\Utils\Tecan\BasicCommands\BreakCommand;
 use MLL\Utils\Tecan\BasicCommands\Command;
 use MLL\Utils\Tecan\BasicCommands\Comment;
+use MLL\Utils\Tecan\BasicCommands\SetDiTiType;
 use MLL\Utils\Tecan\BasicCommands\UsesTipMask;
 use MLL\Utils\Tecan\TipMask\TipMask;
 
@@ -20,19 +21,28 @@ class TecanProtocol
 
     public const GEMINI_WORKLIST_FILENAME_SUFFIX = '.gwl';
 
+    private TipMask $tipMask;
+
+    private string $protocolName;
+
     /** @var Collection<int, Command> */
     private Collection $commands;
 
-    private TipMask $tipMask;
+    public ?int $defaultDiTiTypeIndex;
 
-    private string $protocolName;
+    public ?int $currentDiTiTypeIndex;
 
-    public function __construct(TipMask $tipMask, ?string $protocolName = null, ?string $userName = null)
-    {
-        $this->protocolName = $protocolName ?? Str::uuid()->toString();
+    public function __construct(
+        TipMask $tipMask,
+        ?string $protocolName = null,
+        ?string $userName = null,
+        ?int $defaultDiTiTypeIndex = null
+    ) {
         $this->tipMask = $tipMask;
-
-        $this->commands = $this->initHeader($userName, $protocolName);
+        $this->protocolName = $protocolName ?? Str::uuid()->toString();
+        $this->commands = $this->buildHeader($userName, $protocolName);
+        $this->defaultDiTiTypeIndex = $defaultDiTiTypeIndex;
+        $this->currentDiTiTypeIndex = $defaultDiTiTypeIndex;
     }
 
     public function addCommand(Command $command): void
@@ -43,7 +53,8 @@ public function addCommand(Command $command): void
     /** @param Command&UsesTipMask $command */
     public function addCommandCurrentTip(Command $command): void
     {
-        $command->setTipMask($this->tipMask->currentTip ?? TipMask::firstTip());
+        $tip = $this->tipMask->currentTip ?? TipMask::firstTip();
+        $this->setTipMask($command, $tip);
 
         $this->commands->add($command);
     }
@@ -55,11 +66,37 @@ public function addCommandForNextTip(Command $command): void
             $this->commands->add(new BreakCommand());
         }
 
-        $command->setTipMask($this->tipMask->nextTip());
+        $this->setTipMask($command, $this->tipMask->nextTip());
 
         $this->commands->add($command);
     }
 
+    private function shouldUseDifferentTipTypeIndex(): bool
+    {
+        return $this->defaultDiTiTypeIndex !== null
+            && $this->defaultDiTiTypeIndex !== $this->currentDiTiTypeIndex;
+    }
+
+    private function setTipMask(UsesTipMask $command, int $tip): void
+    {
+        $command->setTipMask($tip);
+
+        if (! $this->shouldUseDifferentTipTypeIndex()) {
+            return;
+        }
+
+        if ($this->currentDiTiTypeIndex === null) {
+            return;
+        }
+
+        if ($this->commands->isEmpty()
+            || $this->commandsAreOnlyComments()
+            || $this->commands->last() instanceof BreakCommand
+        ) {
+            $this->commands->add(new SetDiTiType($this->currentDiTiTypeIndex));
+        }
+    }
+
     public function buildProtocol(): string
     {
         return $this->commands
@@ -73,8 +110,24 @@ public function fileName(): string
         return $this->protocolName . self::GEMINI_WORKLIST_FILENAME_SUFFIX;
     }
 
+    public function setCurrentDiTiTypeIndex(int $currentDiTiTypeIndex): void
+    {
+        if (! $this->commandsAreOnlyComments()
+            && ! $this->commands->last() instanceof BreakCommand
+        ) {
+            throw new TecanException('Cannot change the DiTi type index if the last command is not a break command.');
+        }
+
+        $this->currentDiTiTypeIndex = $currentDiTiTypeIndex;
+    }
+
+    private function commandsAreOnlyComments(): bool
+    {
+        return $this->commands->every(fn (Command $command): bool => $command instanceof Comment);
+    }
+
     /** @return Collection<int, Command> */
-    private function initHeader(?string $userName, ?string $protocolName): Collection
+    private function buildHeader(?string $userName, ?string $protocolName): Collection
     {
         $package = Meta::PACKAGE_NAME;
         $version = InstalledVersions::getPrettyVersion($package);
@@ -90,6 +143,7 @@ private function initHeader(?string $userName, ?string $protocolName): Collectio
         if ($userName !== null) {
             $commentCommands->add(new Comment("User: {$userName}"));
         }
+
         if ($protocolName !== null) {
             $commentCommands->add(new Comment("Protocol name: {$protocolName}"));
         }