From 69fb0fd26eec150fc4d8a290d4e59f720b99d7f0 Mon Sep 17 00:00:00 2001 From: Simon Bigelmayr <simon.bigelmayr@mll.com> Date: Mon, 27 Jun 2022 17:14:14 +0200 Subject: [PATCH] feat: Add scan fludix plate with tecan scanner logic --- .github/workflows/autoformat.yml | 26 +- .github/workflows/continuous-integration.yml | 101 +- composer.json | 12 +- composer.lock | 8064 ++++++++++++----- src/FluidXPlate/FluidXPlate.php | 1 + src/FluidXPlate/InvalidRackIdException.php | 2 +- .../InvalidTubeBarcodeException.php | 2 +- src/TecanScanner/NoRackIdException.php | 2 +- src/TecanScanner/TecanScanEmptyException.php | 2 +- src/TecanScanner/TecanScanner.php | 1 - src/TecanScanner/WrongNumberOfWells.php | 2 +- tests/Unit/FluidXPlateTest.php | 8 +- 12 files changed, 6063 insertions(+), 2160 deletions(-) diff --git a/.github/workflows/autoformat.yml b/.github/workflows/autoformat.yml index 3a92603..4763bb0 100644 --- a/.github/workflows/autoformat.yml +++ b/.github/workflows/autoformat.yml @@ -16,7 +16,7 @@ jobs: with: coverage: none extensions: mbstring - php-version: 7.4 + php-version: 8.1 - run: composer install --no-interaction --no-progress --no-suggest @@ -52,7 +52,7 @@ jobs: with: coverage: none extensions: mbstring - php-version: 7.4 + php-version: 8.1 - run: composer install --no-interaction --no-progress --no-suggest @@ -63,3 +63,25 @@ jobs: - uses: stefanzweifel/git-auto-commit-action@v4 with: commit_message: Apply php-cs-fixer changes + + rector: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v2 + with: + ref: ${{ github.head_ref }} + + - uses: shivammathur/setup-php@v2 + with: + coverage: none + extensions: mbstring + php-version: 8.1 + + - run: composer install --no-interaction --no-progress --no-suggest + + - run: vendor/bin/rector process + + - uses: stefanzweifel/git-auto-commit-action@v4 + with: + commit_message: Apply rector changes diff --git a/.github/workflows/continuous-integration.yml b/.github/workflows/continuous-integration.yml index 0e88069..0483ff4 100644 --- a/.github/workflows/continuous-integration.yml +++ b/.github/workflows/continuous-integration.yml @@ -25,98 +25,11 @@ jobs: with: coverage: none extensions: mbstring - php-version: 7.4 + php-version: 8.1 - name: "Validate composer.json and composer.lock" run: composer validate --strict - composer-normalize: - name: "Normalize composer.json" - - runs-on: ubuntu-latest - - steps: - - name: "Checkout" - uses: actions/checkout@v2 - with: - ref: ${{ github.head_ref }} - - - name: "Install PHP with extensions" - uses: shivammathur/setup-php@v2 - with: - coverage: none - extensions: mbstring - php-version: 7.4 - - - name: "Install locked dependencies with composer" - run: composer install --no-interaction --no-progress --no-suggest - - - name: "Run localheinz/composer-normalize" - run: composer normalize - - - name: "Commit fixes" - uses: stefanzweifel/git-auto-commit-action@v4 - with: - commit_message: Normalize composer.json - - php-cs-fixer: - name: "Fix PHP codestyle with php-cs-fixer" - - runs-on: ubuntu-latest - - steps: - - name: "Checkout" - uses: actions/checkout@v2 - with: - ref: ${{ github.head_ref }} - - - name: "Install PHP with extensions" - uses: shivammathur/setup-php@v2 - with: - coverage: none - extensions: mbstring - php-version: 7.4 - - - name: "Install locked dependencies with composer" - run: composer install --no-interaction --no-progress --no-suggest - - - name: "Run php-cs-fixer" - run: vendor/bin/php-cs-fixer fix - - - name: "Commit fixes" - uses: stefanzweifel/git-auto-commit-action@v4 - with: - commit_message: Apply php-cs-fixer changes - - rector: - name: "Apply rector" - - runs-on: ubuntu-latest - - steps: - - name: "Checkout" - uses: actions/checkout@v2 - with: - ref: ${{ github.head_ref }} - - - name: "Install PHP with extensions" - uses: shivammathur/setup-php@v2 - with: - coverage: none - extensions: mbstring - php-version: 7.4 - - - name: "Install locked dependencies with composer" - run: composer install --no-interaction --no-progress --no-suggest - - - name: "Run rector" - run: vendor/bin/rector process - - - name: "Commit fixes" - uses: stefanzweifel/git-auto-commit-action@v4 - with: - commit_message: Apply rector changes - static-code-analysis: name: "Static Code Analysis" @@ -131,7 +44,7 @@ jobs: with: coverage: none extensions: mbstring - php-version: 7.4 + php-version: 8.1 - name: "Install locked dependencies with composer" run: composer install --no-interaction --no-progress --no-suggest @@ -149,14 +62,16 @@ jobs: php-version: - 7.4 - 8.0 - + - 8.1 dependencies: - lowest - highest - illuminate: - ^8 - ^9 + exclude: + - php-version: 7.4 + illuminate: ^9 steps: - name: "Checkout" @@ -201,7 +116,7 @@ jobs: with: coverage: pcov extensions: mbstring - php-version: 7.4 + php-version: 8.1 - name: "Install locked dependencies with composer" run: composer install --no-interaction --no-progress --no-suggest @@ -229,7 +144,7 @@ jobs: with: coverage: pcov extensions: mbstring - php-version: 7.4 + php-version: 8.1 - name: "Install locked dependencies with composer" run: composer install --no-interaction --no-progress --no-suggest diff --git a/composer.json b/composer.json index f86a9f1..5b45e84 100644 --- a/composer.json +++ b/composer.json @@ -17,7 +17,7 @@ "require": { "php": "^7.4 || ^8", "illuminate/support": "^8 || ^9", - "mll-lab/microplate": "^3.5", + "mll-lab/microplate": "^3.6", "mll-lab/php-utils": "^1.2", "rector/rector": "^0.13.6", "thecodingmachine/safe": "^1" @@ -27,13 +27,15 @@ "infection/infection": "~0.25", "jangregor/phpstan-prophecy": "^1", "mll-lab/php-cs-fixer-config": "^4.3", + "nunomaduro/larastan": "^0.7 || ^1", + "orchestra/testbench": "^6 || ^7", "phpstan/extension-installer": "^1", "phpstan/phpstan": "^1", "phpstan/phpstan-deprecation-rules": "^1", "phpstan/phpstan-phpunit": "^1", "phpstan/phpstan-strict-rules": "^1", "phpunit/phpunit": "^9", - "symfony/var-dumper": "^5", + "symfony/var-dumper": "^5 || ^6", "thecodingmachine/phpstan-safe-rule": "^1.1" }, "autoload": { @@ -50,8 +52,10 @@ ] }, "config": { - "platform": { - "php": "7.4.24" + "allow-plugins": { + "infection/extension-installer": true, + "ergebnis/composer-normalize": true, + "phpstan/extension-installer": true }, "preferred-install": "dist", "sort-packages": true diff --git a/composer.lock b/composer.lock index cc89202..b8fd280 100644 --- a/composer.lock +++ b/composer.lock @@ -4,8 +4,143 @@ "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies", "This file is @generated automatically" ], - "content-hash": "8016e819d3ef4d19820d855f07c79305", + "content-hash": "88bdf5b70433baa33d20b4833cdcc327", "packages": [ + { + "name": "brick/math", + "version": "0.9.3", + "source": { + "type": "git", + "url": "https://github.com/brick/math.git", + "reference": "ca57d18f028f84f777b2168cd1911b0dee2343ae" + }, + "dist": { + "type": "zip", + "url": "https://api.github.com/repos/brick/math/zipball/ca57d18f028f84f777b2168cd1911b0dee2343ae", + "reference": "ca57d18f028f84f777b2168cd1911b0dee2343ae", + "shasum": "" + }, + "require": { + "ext-json": "*", + "php": "^7.1 || ^8.0" + }, + "require-dev": { + "php-coveralls/php-coveralls": "^2.2", + "phpunit/phpunit": "^7.5.15 || ^8.5 || ^9.0", + "vimeo/psalm": "4.9.2" + }, + "type": "library", + "autoload": { + "psr-4": { + "Brick\\Math\\": "src/" + } + }, + "notification-url": "https://packagist.org/downloads/", + "license": [ + "MIT" + ], + "description": "Arbitrary-precision arithmetic library", + "keywords": [ + "Arbitrary-precision", + "BigInteger", + "BigRational", + "arithmetic", + "bigdecimal", + "bignum", + "brick", + "math" + ], + "support": { + "issues": "https://github.com/brick/math/issues", + "source": "https://github.com/brick/math/tree/0.9.3" + }, + "funding": [ + { + "url": "https://github.com/BenMorel", + "type": "github" + }, + { + "url": "https://tidelift.com/funding/github/packagist/brick/math", + "type": "tidelift" + } + ], + "time": "2021-08-15T20:50:18+00:00" + }, + { + "name": "dflydev/dot-access-data", + "version": "v3.0.1", + "source": { + "type": "git", + "url": "https://github.com/dflydev/dflydev-dot-access-data.git", + "reference": "0992cc19268b259a39e86f296da5f0677841f42c" + }, + "dist": { + "type": "zip", + "url": "https://api.github.com/repos/dflydev/dflydev-dot-access-data/zipball/0992cc19268b259a39e86f296da5f0677841f42c", + "reference": "0992cc19268b259a39e86f296da5f0677841f42c", + "shasum": "" + }, + "require": { + "php": "^7.1 || ^8.0" + }, + "require-dev": { + "phpstan/phpstan": "^0.12.42", + "phpunit/phpunit": "^7.5 || ^8.5 || ^9.3", + "scrutinizer/ocular": "1.6.0", + "squizlabs/php_codesniffer": "^3.5", + "vimeo/psalm": "^3.14" + }, + "type": "library", + "extra": { + "branch-alias": { + "dev-main": "3.x-dev" + } + }, + "autoload": { + "psr-4": { + "Dflydev\\DotAccessData\\": "src/" + } + }, + "notification-url": "https://packagist.org/downloads/", + "license": [ + "MIT" + ], + "authors": [ + { + "name": "Dragonfly Development Inc.", + "email": "info@dflydev.com", + "homepage": "http://dflydev.com" + }, + { + "name": "Beau Simensen", + "email": "beau@dflydev.com", + "homepage": "http://beausimensen.com" + }, + { + "name": "Carlos Frutos", + "email": "carlos@kiwing.it", + "homepage": "https://github.com/cfrutos" + }, + { + "name": "Colin O'Dell", + "email": "colinodell@gmail.com", + "homepage": "https://www.colinodell.com" + } + ], + "description": "Given a deep data structure, access data by dot notation.", + "homepage": "https://github.com/dflydev/dflydev-dot-access-data", + "keywords": [ + "access", + "data", + "dot", + "notation" + ], + "support": { + "issues": "https://github.com/dflydev/dflydev-dot-access-data/issues", + "source": "https://github.com/dflydev/dflydev-dot-access-data/tree/v3.0.1" + }, + "time": "2021-08-13T13:06:58+00:00" + }, { "name": "doctrine/inflector", "version": "2.0.4", @@ -98,39 +233,32 @@ "time": "2021-10-22T20:16:43+00:00" }, { - 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"https://github.com/webmozart/path-util/tree/2.3.0" + "issues": "https://github.com/zbateson/stream-decorators/issues", + "source": "https://github.com/zbateson/stream-decorators/tree/1.0.6" }, - "abandoned": "symfony/filesystem", - "time": "2015-12-17T08:42:14+00:00" + "funding": [ + { + "url": "https://github.com/zbateson", + "type": "github" + } + ], + "time": "2021-07-08T19:01:59+00:00" } ], "aliases": [], @@ -6791,8 +10754,5 @@ "php": "^7.4 || ^8" }, "platform-dev": [], - "platform-overrides": { - "php": "7.4.24" - }, - "plugin-api-version": "2.0.0" + "plugin-api-version": "2.3.0" } diff --git a/src/FluidXPlate/FluidXPlate.php b/src/FluidXPlate/FluidXPlate.php index 3ea69f4..2f7f801 100644 --- a/src/FluidXPlate/FluidXPlate.php +++ b/src/FluidXPlate/FluidXPlate.php @@ -21,6 +21,7 @@ public function __construct(string $rackId) throw new InvalidRackIdException($rackId); } $this->rackId = $rackId; + parent::__construct(self::coordinateSystem()); } diff --git a/src/FluidXPlate/InvalidRackIdException.php b/src/FluidXPlate/InvalidRackIdException.php index 5b7d25b..0aeaba9 100644 --- a/src/FluidXPlate/InvalidRackIdException.php +++ b/src/FluidXPlate/InvalidRackIdException.php @@ -2,7 +2,7 @@ namespace Mll\LiquidHandlingRobotics\FluidXPlate; -class InvalidRackIdException extends FluidXPlateException +final class InvalidRackIdException extends FluidXPlateException { public function __construct(string $rackId) { diff --git a/src/FluidXPlate/InvalidTubeBarcodeException.php b/src/FluidXPlate/InvalidTubeBarcodeException.php index 3aed4a8..63917fc 100644 --- a/src/FluidXPlate/InvalidTubeBarcodeException.php +++ b/src/FluidXPlate/InvalidTubeBarcodeException.php @@ -2,7 +2,7 @@ namespace Mll\LiquidHandlingRobotics\FluidXPlate; -class InvalidTubeBarcodeException extends FluidXPlateException +final class InvalidTubeBarcodeException extends FluidXPlateException { public function __construct(string $tubeBarcode) { diff --git a/src/TecanScanner/NoRackIdException.php b/src/TecanScanner/NoRackIdException.php index f0e403e..fc41ffc 100644 --- a/src/TecanScanner/NoRackIdException.php +++ b/src/TecanScanner/NoRackIdException.php @@ -2,7 +2,7 @@ namespace Mll\LiquidHandlingRobotics\TecanScanner; -class NoRackIdException extends TecanScanException +final class NoRackIdException extends TecanScanException { public function __construct() { diff --git a/src/TecanScanner/TecanScanEmptyException.php b/src/TecanScanner/TecanScanEmptyException.php index 5ab0cac..e455e44 100644 --- a/src/TecanScanner/TecanScanEmptyException.php +++ b/src/TecanScanner/TecanScanEmptyException.php @@ -2,7 +2,7 @@ namespace Mll\LiquidHandlingRobotics\TecanScanner; -class TecanScanEmptyException extends TecanScanException +final class TecanScanEmptyException extends TecanScanException { public function __construct() { diff --git a/src/TecanScanner/TecanScanner.php b/src/TecanScanner/TecanScanner.php index 1762f39..d9fb600 100644 --- a/src/TecanScanner/TecanScanner.php +++ b/src/TecanScanner/TecanScanner.php @@ -38,7 +38,6 @@ public static function parseRawContent(string $rawContent): FluidXPlate $plate = new FluidXPlate(Str::substr($firstLineWithRackId, 7)); foreach ($lines as $line) { - assert(is_string($line)); $barcode = Str::after($line, ','); if (self::NO_READ !== $barcode) { diff --git a/src/TecanScanner/WrongNumberOfWells.php b/src/TecanScanner/WrongNumberOfWells.php index f14dea8..ca9f637 100644 --- a/src/TecanScanner/WrongNumberOfWells.php +++ b/src/TecanScanner/WrongNumberOfWells.php @@ -2,7 +2,7 @@ namespace Mll\LiquidHandlingRobotics\TecanScanner; -class WrongNumberOfWells extends TecanScanException +final class WrongNumberOfWells extends TecanScanException { public function __construct(int $expectedCount, int $actualCount) { diff --git a/tests/Unit/FluidXPlateTest.php b/tests/Unit/FluidXPlateTest.php index 8ee6962..820ad6b 100644 --- a/tests/Unit/FluidXPlateTest.php +++ b/tests/Unit/FluidXPlateTest.php @@ -41,18 +41,20 @@ public function testCanNotAddInvalidBarcode(): void $barcode = 'testWrongBarcode'; $rackId = 'AB12345678'; $fluidXPlate = new FluidXPlate($rackId); + $coordinate = Coordinate::fromString('A1', new CoordinateSystem96Well()); $this->expectExceptionObject(new InvalidTubeBarcodeException($barcode)); - $fluidXPlate->addWell(Coordinate::fromString('A1', new CoordinateSystem96Well()), $barcode); + $fluidXPlate->addWell($coordinate, $barcode); } public function testCanOnlyAddStringAsBarcode(): void { $rackId = 'AB12345678'; $fluidXPlate = new FluidXPlate($rackId); + $coordinate = Coordinate::fromString('A1', new CoordinateSystem96Well()); $this->expectException(TypeError::class); - // @phpstan-ignore-next-line expecting a type error due to and array as content paramenter - $fluidXPlate->addWell(Coordinate::fromString('A1', new CoordinateSystem96Well()), []); + // @phpstan-ignore-next-line intentionally wrong + $fluidXPlate->addWell($coordinate, []); } }