From 8ec10879d6034bad3218c310d324b4351079f801 Mon Sep 17 00:00:00 2001 From: Benedikt Franke Date: Fri, 16 Jun 2023 14:25:50 +0200 Subject: [PATCH] Require `mll-lab/microplate:^6` --- CHANGELOG.md | 6 + composer.json | 2 +- composer.lock | 231 ++++++++++--------- src/FluidXPlate/FluidXPlate.php | 12 +- src/FluidXPlate/FluidXScanner.php | 10 +- src/TecanScanner/TecanScanner.php | 8 +- tests/Unit/FluidXPlate/FluidXPlateTest.php | 14 +- tests/Unit/TecanScanner/TecanScannerTest.php | 4 +- 8 files changed, 149 insertions(+), 138 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 334242c..658d8a1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Unreleased +## v6.0.0 + +### Changed + +- Require `mll-lab/microplate:^6` + ## v5.3.0 ### Added diff --git a/composer.json b/composer.json index bcdf6a7..312102f 100644 --- a/composer.json +++ b/composer.json @@ -19,7 +19,7 @@ "bensampo/laravel-enum": "^3 || ^4 || ^5 || ^6", "composer/composer": "^2", "illuminate/support": "^8 || ^9 || ^10", - "mll-lab/microplate": "^5", + "mll-lab/microplate": "^6", "mll-lab/php-utils": "^1.2", "thecodingmachine/safe": "^1 || ^2" }, diff --git a/composer.lock b/composer.lock index e01be10..15cbcef 100644 --- a/composer.lock +++ b/composer.lock @@ -4,7 +4,7 @@ "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies", "This file is @generated automatically" ], - "content-hash": "4f076a8ba8dd1a9011707c371ff990d9", + "content-hash": "f17f87b85d668b214d58949c345d9590", "packages": [ { "name": "bensampo/laravel-enum", @@ -147,16 +147,16 @@ }, { "name": "composer/ca-bundle", - "version": "1.3.5", + "version": "1.3.6", "source": { "type": "git", "url": "https://github.com/composer/ca-bundle.git", - "reference": "74780ccf8c19d6acb8d65c5f39cd72110e132bbd" + "reference": "90d087e988ff194065333d16bc5cf649872d9cdb" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/composer/ca-bundle/zipball/74780ccf8c19d6acb8d65c5f39cd72110e132bbd", - "reference": "74780ccf8c19d6acb8d65c5f39cd72110e132bbd", + "url": "https://api.github.com/repos/composer/ca-bundle/zipball/90d087e988ff194065333d16bc5cf649872d9cdb", + "reference": "90d087e988ff194065333d16bc5cf649872d9cdb", "shasum": "" }, "require": { @@ -203,7 +203,7 @@ "support": { "irc": "irc://irc.freenode.org/composer", "issues": "https://github.com/composer/ca-bundle/issues", - 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"reference": "0e5c45c8046298212347a0bfb659126af8e75d2e" + "reference": "2e88e466dd49f20c10a15330b3953d4d49c326e3" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/sanmai/pipeline/zipball/0e5c45c8046298212347a0bfb659126af8e75d2e", - "reference": "0e5c45c8046298212347a0bfb659126af8e75d2e", + "url": "https://api.github.com/repos/sanmai/pipeline/zipball/2e88e466dd49f20c10a15330b3953d4d49c326e3", + "reference": "2e88e466dd49f20c10a15330b3953d4d49c326e3", "shasum": "" }, "require": { @@ -9785,7 +9790,7 @@ }, "require-dev": { "ergebnis/composer-normalize": "^2.8", - "friendsofphp/php-cs-fixer": "^3", + "friendsofphp/php-cs-fixer": "^3.17", "infection/infection": ">=0.10.5", "league/pipeline": "^0.3 || ^1.0", "phan/phan": ">=1.1", @@ -9821,7 +9826,7 @@ "description": "General-purpose collections pipeline", "support": { "issues": "https://github.com/sanmai/pipeline/issues", - "source": "https://github.com/sanmai/pipeline/tree/v6.7" + "source": "https://github.com/sanmai/pipeline/tree/v6.8.1" }, "funding": [ { @@ -9829,7 +9834,7 @@ "type": "github" } ], - "time": "2023-04-29T11:21:51+00:00" + "time": "2023-06-15T09:14:47+00:00" }, { "name": "sebastian/cli-parser", @@ -10797,16 +10802,16 @@ }, { "name": "spatie/backtrace", - "version": "1.4.0", + "version": "1.4.1", "source": { "type": "git", "url": "https://github.com/spatie/backtrace.git", - "reference": "ec4dd16476b802dbdc6b4467f84032837e316b8c" + "reference": "47794d19e3215ace9e005a8f200cd7cc7be52572" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/spatie/backtrace/zipball/ec4dd16476b802dbdc6b4467f84032837e316b8c", - "reference": "ec4dd16476b802dbdc6b4467f84032837e316b8c", + "url": "https://api.github.com/repos/spatie/backtrace/zipball/47794d19e3215ace9e005a8f200cd7cc7be52572", + "reference": "47794d19e3215ace9e005a8f200cd7cc7be52572", "shasum": "" }, "require": { @@ -10843,7 +10848,7 @@ "spatie" ], "support": { - "source": "https://github.com/spatie/backtrace/tree/1.4.0" + "source": "https://github.com/spatie/backtrace/tree/1.4.1" }, "funding": [ { @@ -10855,7 +10860,7 @@ "type": "other" } ], - "time": "2023-03-04T08:57:24+00:00" + "time": "2023-06-13T14:35:04+00:00" }, { "name": "spatie/laravel-ray", @@ -11523,16 +11528,16 @@ }, { "name": "webonyx/graphql-php", - "version": "v15.5.0", + "version": "v15.5.1", "source": { "type": "git", "url": "https://github.com/webonyx/graphql-php.git", - "reference": "0dd4dd8ebe1bc8f3d61b4daedcf66987f39772e7" + "reference": "b305633164a48947e22d53b6b15fcb98613c6592" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/webonyx/graphql-php/zipball/0dd4dd8ebe1bc8f3d61b4daedcf66987f39772e7", - "reference": "0dd4dd8ebe1bc8f3d61b4daedcf66987f39772e7", + "url": "https://api.github.com/repos/webonyx/graphql-php/zipball/b305633164a48947e22d53b6b15fcb98613c6592", + "reference": "b305633164a48947e22d53b6b15fcb98613c6592", "shasum": "" }, "require": { @@ -11543,20 +11548,20 @@ "require-dev": { "amphp/amp": "^2.6", "amphp/http-server": "^2.1", - "dms/phpunit-arraysubset-asserts": "^0.4", + "dms/phpunit-arraysubset-asserts": "dev-master", "ergebnis/composer-normalize": "^2.28", - "mll-lab/php-cs-fixer-config": "^5.0", + "mll-lab/php-cs-fixer-config": "^5", "nyholm/psr7": "^1.5", "phpbench/phpbench": "^1.2", "phpstan/extension-installer": "^1.1", - "phpstan/phpstan": "1.10.15", + "phpstan/phpstan": "1.10.19", "phpstan/phpstan-phpunit": "1.3.13", "phpstan/phpstan-strict-rules": "1.5.1", - "phpunit/phpunit": "^9.5", + "phpunit/phpunit": "^9.5 || ^10", "psr/http-message": "^1 || ^2", "react/http": "^1.6", "react/promise": "^2.9", - "rector/rector": "^0.16.0", + "rector/rector": "^0.17.0", "symfony/polyfill-php81": "^1.23", "symfony/var-exporter": "^5 || ^6", "thecodingmachine/safe": "^1.3 || ^2" @@ -11584,7 +11589,7 @@ ], "support": { "issues": "https://github.com/webonyx/graphql-php/issues", - "source": "https://github.com/webonyx/graphql-php/tree/v15.5.0" + "source": "https://github.com/webonyx/graphql-php/tree/v15.5.1" }, "funding": [ { @@ -11592,7 +11597,7 @@ "type": "open_collective" } ], - "time": "2023-05-30T13:10:49+00:00" + "time": "2023-06-16T12:19:23+00:00" }, { "name": "zbateson/mail-mime-parser", diff --git a/src/FluidXPlate/FluidXPlate.php b/src/FluidXPlate/FluidXPlate.php index 30fa36d..49130a6 100644 --- a/src/FluidXPlate/FluidXPlate.php +++ b/src/FluidXPlate/FluidXPlate.php @@ -3,7 +3,7 @@ namespace Mll\LiquidHandlingRobotics\FluidXPlate; use Illuminate\Support\Collection; -use Mll\Microplate\Coordinate; +use Mll\Microplate\Coordinates; use Mll\Microplate\CoordinateSystem96Well; use Mll\Microplate\Enums\FlowDirection; use Mll\Microplate\Microplate; @@ -35,21 +35,21 @@ public static function coordinateSystem(): CoordinateSystem96Well } /** - * @param Coordinate $coordinate + * @param Coordinates $coordinates */ - public function addWell(Coordinate $coordinate, string $barcode): void + public function addWell(Coordinates $coordinates, string $barcode): void { if (0 === \Safe\preg_match(self::FLUIDX_BARCODE_REGEX, $barcode)) { throw new InvalidTubeBarcodeException($barcode); } - $this->microplate->addWell($coordinate, $barcode); + $this->microplate->addWell($coordinates, $barcode); } /** - * @return Coordinate + * @return Coordinates */ - public function addToNextFreeWell(string $content, FlowDirection $flowDirection): Coordinate + public function addToNextFreeWell(string $content, FlowDirection $flowDirection): Coordinates { return $this->microplate->addToNextFreeWell($content, $flowDirection); } diff --git a/src/FluidXPlate/FluidXScanner.php b/src/FluidXPlate/FluidXScanner.php index 2305c70..0b54b7f 100644 --- a/src/FluidXPlate/FluidXScanner.php +++ b/src/FluidXPlate/FluidXScanner.php @@ -3,7 +3,7 @@ namespace Mll\LiquidHandlingRobotics\FluidXPlate; use Illuminate\Support\Str; -use Mll\Microplate\Coordinate; +use Mll\Microplate\Coordinates; use Mll\Microplate\CoordinateSystem96Well; use MLL\Utils\StringUtil; @@ -72,9 +72,9 @@ public static function parseRawContent(string $rawContent): FluidXPlate } $barcodeScanResult = $content[1]; - $coordinateString = $content[0]; + $coordinatesString = $content[0]; if (self::NO_READ !== $barcodeScanResult && self::NO_TUBE !== $barcodeScanResult) { - $barcodes[$coordinateString] = $barcodeScanResult; + $barcodes[$coordinatesString] = $barcodeScanResult; } } @@ -89,8 +89,8 @@ public static function parseRawContent(string $rawContent): FluidXPlate } $plate = new FluidXPlate($id); - foreach ($barcodes as $coordinate => $barcode) { - $plate->addWell(Coordinate::fromString($coordinate, new CoordinateSystem96Well()), $barcode); + foreach ($barcodes as $coordinates => $barcode) { + $plate->addWell(Coordinates::fromString($coordinates, new CoordinateSystem96Well()), $barcode); } return $plate; diff --git a/src/TecanScanner/TecanScanner.php b/src/TecanScanner/TecanScanner.php index 35c151c..8f0f8e5 100644 --- a/src/TecanScanner/TecanScanner.php +++ b/src/TecanScanner/TecanScanner.php @@ -5,7 +5,7 @@ use Illuminate\Support\Collection; use Illuminate\Support\Str; use Mll\LiquidHandlingRobotics\FluidXPlate\FluidXPlate; -use Mll\Microplate\Coordinate; +use Mll\Microplate\Coordinates; use MLL\Utils\StringUtil; /** @@ -43,11 +43,11 @@ public static function parseRawContent(string $rawContent): FluidXPlate $barcode = Str::after($line, ','); if (self::NO_READ !== $barcode) { - $coordinateString = Str::before($line, ','); + $coordinatesString = Str::before($line, ','); $plate->addWell( - Coordinate::fromString( - $coordinateString, + Coordinates::fromString( + $coordinatesString, $plate::coordinateSystem() ), $barcode diff --git a/tests/Unit/FluidXPlate/FluidXPlateTest.php b/tests/Unit/FluidXPlate/FluidXPlateTest.php index def788d..5a7d179 100644 --- a/tests/Unit/FluidXPlate/FluidXPlateTest.php +++ b/tests/Unit/FluidXPlate/FluidXPlateTest.php @@ -5,7 +5,7 @@ use Mll\LiquidHandlingRobotics\FluidXPlate\FluidXPlate; use Mll\LiquidHandlingRobotics\FluidXPlate\InvalidRackIdException; use Mll\LiquidHandlingRobotics\FluidXPlate\InvalidTubeBarcodeException; -use Mll\Microplate\Coordinate; +use Mll\Microplate\Coordinates; use Mll\Microplate\CoordinateSystem96Well; use Mll\Microplate\Enums\FlowDirection; use PHPUnit\Framework\TestCase; @@ -41,29 +41,29 @@ public function testCanNotAddInvalidBarcode(): void $barcode = 'testWrongBarcode'; $rackId = 'AB12345678'; $fluidXPlate = new FluidXPlate($rackId); - $coordinate = Coordinate::fromString('A1', new CoordinateSystem96Well()); + $coordinates = Coordinates::fromString('A1', new CoordinateSystem96Well()); $this->expectExceptionObject(new InvalidTubeBarcodeException($barcode)); - $fluidXPlate->addWell($coordinate, $barcode); + $fluidXPlate->addWell($coordinates, $barcode); } public function testCanOnlyAddStringAsBarcode(): void { $rackId = 'AB12345678'; $fluidXPlate = new FluidXPlate($rackId); - $coordinate = Coordinate::fromString('A1', new CoordinateSystem96Well()); + $coordinates = Coordinates::fromString('A1', new CoordinateSystem96Well()); $this->expectException(\TypeError::class); // @phpstan-ignore-next-line intentionally wrong - $fluidXPlate->addWell($coordinate, []); + $fluidXPlate->addWell($coordinates, []); } public function testCanAddToNextFreeWell(): void { $rackId = 'AB12345678'; $fluidXPlate = new FluidXPlate($rackId); - $expectedCoordinate = Coordinate::fromString('A1', new CoordinateSystem96Well()); + $expectedCoordinates = Coordinates::fromString('A1', new CoordinateSystem96Well()); $addToNextFreeWell = $fluidXPlate->addToNextFreeWell('test', FlowDirection::COLUMN()); - self::assertEquals($expectedCoordinate, $addToNextFreeWell); + self::assertEquals($expectedCoordinates, $addToNextFreeWell); } } diff --git a/tests/Unit/TecanScanner/TecanScannerTest.php b/tests/Unit/TecanScanner/TecanScannerTest.php index 6725c41..6cf9be8 100644 --- a/tests/Unit/TecanScanner/TecanScannerTest.php +++ b/tests/Unit/TecanScanner/TecanScannerTest.php @@ -29,12 +29,12 @@ public function testCreateFromUnexpectedLineCount(): void TecanScanner::parseRawContent($rawContent); } - public function testMicroplateHandlesDuplicateCoordinate(): void + public function testMicroplateHandlesDuplicateCoordinates(): void { $rawContent = "rackid,SA00411242\nA1,FD13945423\nA1,FD32807353\nC1,NO READ\nD1,NO READ\nE1,NO READ\nF1,NO READ\nG1,NO READ\nH1,NO READ\nA2,NO READ\nB2,NO READ\nC2,NO READ\nD2,NO READ\nE2,NO READ\nF2,NO READ\nG2,NO READ\nH2,NO READ\nA3,NO READ\nB3,NO READ\nC3,NO READ\nD3,NO READ\nE3,NO READ\nF3,NO READ\nG3,NO READ\nH3,NO READ\nA4,NO READ\nB4,NO READ\nC4,NO READ\nD4,NO READ\nE4,NO READ\nF4,NO READ\nG4,NO READ\nH4,NO READ\nA5,NO READ\nB5,NO READ\nC5,NO READ\nD5,NO READ\nE5,NO READ\nF5,NO READ\nG5,NO READ\nH5,NO READ\nA6,NO READ\nB6,NO READ\nC6,NO READ\nD6,NO READ\nE6,NO READ\nF6,NO READ\nG6,NO READ\nH6,NO READ\nA7,NO READ\nB7,NO READ\nC7,NO READ\nD7,NO READ\nE7,NO READ\nF7,NO READ\nG7,NO READ\nH7,NO READ\nA8,NO READ\nB8,NO READ\nC8,NO READ\nD8,NO READ\nE8,NO READ\nF8,NO READ\nG8,NO READ\nH8,NO READ\nA9,NO READ\nB9,NO READ\nC9,NO READ\nD9,NO READ\nE9,NO READ\nF9,NO READ\nG9,NO READ\nH9,NO READ\nA10,NO READ\nB10,NO READ\nC10,NO READ\nD10,NO READ\nE10,NO READ\nF10,NO READ\nG10,NO READ\nH10,NO READ\nA11,NO READ\nB11,NO READ\nC11,NO READ\nD11,NO READ\nE11,NO READ\nF11,NO READ\nG11,NO READ\nH11,NO READ\nA12,NO READ\nB12,NO READ\nC12,NO READ\nD12,NO READ\nE12,NO READ\nF12,NO READ\nG12,NO READ\nH12,NO READ"; self::assertTrue(TecanScanner::isValidRawContent($rawContent)); - $this->expectExceptionObject(new WellNotEmptyException('Well with coordinate "A1" is not empty. Use setWell() to overwrite the coordinate. Well content "s:10:"FD32807353";" was not added.')); + $this->expectExceptionObject(new WellNotEmptyException('Well with coordinates "A1" is not empty. Use setWell() to overwrite the coordinate. Well content "s:10:"FD32807353";" was not added.')); TecanScanner::parseRawContent($rawContent); }