Update dependencies (#50)

spawnia · web-flow · commit 104e8d3161ae · 2025-03-05T10:29:00.000+01:00
diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml
@@ -21,7 +21,7 @@ jobs:
           extensions: mbstring
           php-version: 8.3
 
-      - run: composer install --no-interaction --no-progress --no-suggest
+      - uses: ramsey/composer-install@v3
 
       - run: composer normalize
 
@@ -43,7 +43,7 @@ jobs:
           extensions: mbstring
           php-version: 8.3
 
-      - run: composer install --no-interaction --no-progress --no-suggest
+      - uses: ramsey/composer-install@v3
 
       - run: vendor/bin/php-cs-fixer fix --using-cache=no
 
diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml
@@ -24,21 +24,37 @@ jobs:
   static-code-analysis:
     runs-on: ubuntu-latest
 
+    strategy:
+      fail-fast: false
+      matrix:
+        php-version:
+          # Not including 7.4, as PHPStan is hard to get working there
+          - "8.0"
+          - "8.1"
+          - "8.2"
+          - "8.3"
+          - "8.4"
+        dependencies:
+          - lowest
+          - highest
+
     steps:
       - uses: actions/checkout@v4
 
       - uses: shivammathur/setup-php@v2
         with:
           coverage: none
           extensions: mbstring
-          php-version: 8.3
+          php-version: "${{ matrix.php-version }}"
 
-      - run: composer install --no-interaction --no-progress --no-suggest
+      - uses: ramsey/composer-install@v3
+        with:
+          dependency-versions: "${{ matrix.dependencies }}"
 
-      - run: vendor/bin/phpstan analyse
+      - run: vendor/bin/phpstan analyse --configuration=phpstan.neon
 
   tests:
-    name: "Tests - PHP ${{ matrix.php-version }}, Illuminate ${{ matrix.illuminate }}, ${{ matrix.dependencies }}"
+    name: "Tests - PHP ${{ matrix.php-version }}, ${{ matrix.dependencies }}"
 
     runs-on: ubuntu-latest
 
@@ -51,27 +67,10 @@ jobs:
           - "8.1"
           - "8.2"
           - "8.3"
+          - "8.4"
         dependencies:
           - lowest
           - highest
-        illuminate:
-          - ^8.73
-          - ^9
-          - ^10
-          - ^11
-        exclude:
-          - php-version: "7.4"
-            illuminate: ^9
-          - php-version: "7.4"
-            illuminate: ^10
-          - php-version: "7.4"
-            illuminate: ^11
-          - php-version: "8.0"
-            illuminate: ^10
-          - php-version: "8.0"
-            illuminate: ^11
-          - php-version: "8.1"
-            illuminate: ^11
 
     steps:
       - uses: actions/checkout@v4
@@ -83,15 +82,11 @@ jobs:
           php-version: "${{ matrix.php-version }}"
 
       - if: "! startsWith(matrix.php-version, 8)"
-        run: composer remove --dev --no-update mll-lab/graphql-php-scalars
-
-      - run: composer require "illuminate/support:${{ matrix.illuminate }}" --no-interaction --no-update
+        run: composer remove --dev --no-update rector/rector mll-lab/graphql-php-scalars
 
-      - if: matrix.dependencies == 'lowest'
-        run: composer update --prefer-lowest --no-interaction --no-progress --no-suggest
-
-      - if: matrix.dependencies == 'highest'
-        run: composer update --no-interaction --no-progress --no-suggest
+      - uses: ramsey/composer-install@v3
+        with:
+          dependency-versions: "${{ matrix.dependencies }}"
 
       - run: vendor/bin/phpunit
 
@@ -107,7 +102,7 @@ jobs:
           extensions: mbstring
           php-version: 8.3
 
-      - run: composer install --no-interaction --no-progress --no-suggest
+      - uses: ramsey/composer-install@v3
 
       - run: vendor/bin/phpunit --coverage-clover=.build/logs/clover.xml
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,18 @@ See [GitHub releases](https://github.com/mll-lab/php-utils/releases).
 
 ## Unreleased
 
+## v5.13.0
+
+### Added
+
+- Support `illuminate/support` version 12
+- Support `thecodingmachine/safe` version 3
+- Add error identifiers to custom PHPStan rules
+
+### Changed
+
+- Refine PHPDoc types
+
 ## v5.12.1
 
 ### Fixed
diff --git a/composer.json b/composer.json
@@ -17,27 +17,27 @@
   "require": {
     "php": "^7.4 || ^8",
     "ext-calendar": "*",
-    "illuminate/support": "^8.73 || ^9 || ^10 || ^11",
+    "illuminate/support": "^8.73 || ^9 || ^10 || ^11 || ^12",
     "mll-lab/str_putcsv": "^1",
     "nesbot/carbon": "^2.62.1 || ^3",
     "ramsey/uuid": "^3 || ^4",
-    "thecodingmachine/safe": "^1 || ^2"
+    "thecodingmachine/safe": "^1 || ^2 || ^3"
   },
   "require-dev": {
-    "ergebnis/composer-normalize": "^2",
-    "jangregor/phpstan-prophecy": "^1",
-    "larastan/larastan": "^1 || ^2",
-    "mll-lab/graphql-php-scalars": "^6.3",
-    "mll-lab/php-cs-fixer-config": "^5",
-    "orchestra/testbench": "^6 || ^7 || ^8 || ^9",
+    "ergebnis/composer-normalize": "^2.45",
+    "jangregor/phpstan-prophecy": "^1.0.2 || ^2.1.1",
+    "larastan/larastan": "^1.0.4 || ^2.9.14 || ^3.1",
+    "mll-lab/graphql-php-scalars": "^6.4",
+    "mll-lab/php-cs-fixer-config": "^5.10",
+    "orchestra/testbench": "^6.47.1 || ^7.52 || ^8.33 || ^9.11 || ^10",
     "phpstan/extension-installer": "^1",
-    "phpstan/phpstan": "^1",
-    "phpstan/phpstan-deprecation-rules": "^1",
-    "phpstan/phpstan-phpunit": "^1",
-    "phpstan/phpstan-strict-rules": "^1",
-    "phpunit/phpunit": "^9 || ^10 || ^11",
-    "rector/rector": "^1",
-    "thecodingmachine/phpstan-safe-rule": "^1.2"
+    "phpstan/phpstan": "^1.8.11 || ^2.1.6",
+    "phpstan/phpstan-deprecation-rules": "^1 || ^2.0.1",
+    "phpstan/phpstan-phpunit": "^1 || ^2.0.4",
+    "phpstan/phpstan-strict-rules": "^1 || ^2.0.3",
+    "phpunit/phpunit": "^9.6.22 || ^10.5.45 || ^11.5.10 || ^12.0.5",
+    "rector/rector": "^1.2.10 || ^2.0.9",
+    "thecodingmachine/phpstan-safe-rule": "^1.2.0"
   },
   "suggest": {
     "mll-lab/graphql-php-scalars": "To use the provided scalar types for GraphQL servers, requires version ^6.3"
diff --git a/phpstan.neon b/phpstan.neon
@@ -7,8 +7,13 @@ parameters:
   - tests
   tmpDir: .build/phpstan
   # Install https://plugins.jetbrains.com/plugin/7677-awesome-console to make those links clickable
+  # TODO restore when we can require a newer PHPStan version
   editorUrl: '%%relFile%%:%%line%%'
   editorUrlTitle: '%%relFile%%:%%line%%'
+  # As long as we support multiple PHP versions, there will be some dead spots
+  reportUnmatchedIgnoredErrors: false
   ignoreErrors:
   # This is a library, so it should be extendable
   - '#Unsafe usage of new static.*#'
+  # Not in older PHPUnit versions
+  - '#Attribute class PHPUnit\\Framework\\Attributes\\DataProvider does not exist\.#'
diff --git a/rector.php b/rector.php
@@ -1,9 +1,6 @@
 <?php declare(strict_types=1);
 
-use Rector\CodeQuality\Rector\Concat\JoinStringConcatRector;
 use Rector\Config\RectorConfig;
-use Rector\PHPUnit\CodeQuality\Rector\Class_\PreferPHPUnitSelfCallRector;
-use Rector\PHPUnit\CodeQuality\Rector\Class_\PreferPHPUnitThisCallRector;
 use Rector\PHPUnit\Set\PHPUnitSetList;
 use Rector\Set\ValueObject\SetList;
 
@@ -23,12 +20,15 @@
         PHPUnitSetList::PHPUNIT_CODE_QUALITY,
     ])
     ->withPhpSets()
-    ->withRules([PreferPHPUnitSelfCallRector::class])
+    ->withRules([
+        Rector\PHPUnit\CodeQuality\Rector\Class_\PreferPHPUnitSelfCallRector::class,
+    ])
     ->withSkip([
-        PreferPHPUnitThisCallRector::class, // breaks tests
-        JoinStringConcatRector::class => [
+        Rector\PHPUnit\CodeQuality\Rector\Class_\PreferPHPUnitThisCallRector::class, // breaks tests
+        Rector\CodeQuality\Rector\Concat\JoinStringConcatRector::class => [
             __DIR__ . '/tests/CSVArrayTest.php', // keep `\r\n` for readability
         ],
+        Rector\PHPUnit\CodeQuality\Rector\MethodCall\AssertCountWithZeroToAssertEmptyRector::class, // sloppy
     ])
     ->withPaths([__DIR__ . '/src', __DIR__ . '/tests'])
     ->withBootstrapFiles([
diff --git a/src/DnaSequence.php b/src/DnaSequence.php
@@ -16,7 +16,10 @@ public function __construct(string $sequence)
 
     public function reverse(): string
     {
-        return implode(array_reverse(mb_str_split($this->sequence)));
+        $parts = mb_str_split($this->sequence); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)
+        $reversedParts = array_reverse($parts);
+
+        return implode($reversedParts);
     }
 
     public function complement(): string
diff --git a/src/FluidXPlate/FluidXPlate.php b/src/FluidXPlate/FluidXPlate.php
@@ -24,7 +24,7 @@ public function __construct(string $rackID)
             throw new InvalidRackIDException($rackID);
         }
         $this->rackID = $rackID;
-        $this->microplate = new Microplate(self::coordinateSystem());
+        $this->microplate = new Microplate(self::coordinateSystem()); // @phpstan-ignore assign.propertyType (generic not inferred)
     }
 
     public static function coordinateSystem(): CoordinateSystem12x8
diff --git a/src/IlluminaSampleSheet/V1/DataSection.php b/src/IlluminaSampleSheet/V1/DataSection.php
@@ -37,11 +37,10 @@ public function convertSectionToString(): string
     {
         $this->validate();
 
-        if ($this->rows->isEmpty()) {
+        $firstRow = $this->rows->first();
+        if ($firstRow === null) {
             throw new IlluminaSampleSheetException('Data section must contain at least one row.');
         }
-        /** @var Row $firstRow */
-        $firstRow = $this->rows->first();
 
         $rowsData = $this->rows
             ->map(fn (Row $row): string => $row->toString())
diff --git a/src/IlluminaSampleSheet/V2/BclConvert/BclSample.php b/src/IlluminaSampleSheet/V2/BclConvert/BclSample.php
@@ -40,7 +40,7 @@ public function __construct(
     /** @return array<int|string> */
     public function toArray(): array
     {
-        return array_filter([
+        return array_filter([ // @phpstan-ignore arrayFilter.strict (we want truthy comparison)
             $this->lane,
             $this->sample_ID,
             $this->index,
diff --git a/src/IlluminaSampleSheet/V2/BclConvert/OverrideCycles.php b/src/IlluminaSampleSheet/V2/BclConvert/OverrideCycles.php
@@ -31,12 +31,14 @@ public function toString(): string
         $dataSection = $this->dataSection;
         $dataSection->assertNotEmpty();
 
-        return implode(';', array_filter([
+        $filledParts = array_filter([ // @phpstan-ignore arrayFilter.strict (we want truthy comparison)
             $this->read1->toString($dataSection->maxRead1Cycles(), null),
             $this->index1->toString($dataSection->maxIndex1Cycles(), null),
             $this->index2(),
             $this->read2(),
-        ]));
+        ]);
+
+        return implode(';', $filledParts);
     }
 
     public function makeOverrideCycle(string $cycleString): OverrideCycle
diff --git a/src/Microplate/AbstractMicroplate.php b/src/Microplate/AbstractMicroplate.php
@@ -118,6 +118,7 @@ public function toWellWithCoordinateMapper(): callable
     /** @return callable(TWell $content, string $coordinatesString): WellWithCoordinates<TWell, TCoordinateSystem> */
     public function toWellWithCoordinatesMapper(): callable
     {
+        // @phpstan-ignore return.type (generic not inferred)
         return fn ($content, string $coordinatesString): WellWithCoordinates => new WellWithCoordinates(
             $content,
             Coordinates::fromString($coordinatesString, $this->coordinateSystem)
@@ -137,6 +138,16 @@ public function isConsecutive(FlowDirection $flowDirection): bool
                 fn ($content, string $coordinatesString): int => Coordinates::fromString($coordinatesString, $this->coordinateSystem)->position($flowDirection)
             );
 
-        return ($positions->max() - $positions->min() + 1) === $positions->count();
+        if ($positions->isEmpty()) {
+            return false;
+        }
+
+        $max = $positions->max();
+        assert(is_int($max));
+
+        $min = $positions->min();
+        assert(is_int($min));
+
+        return ($max - $min + 1) === $positions->count();
     }
 }
diff --git a/src/Microplate/CoordinateSystem.php b/src/Microplate/CoordinateSystem.php
@@ -41,7 +41,9 @@ public function padColumn(int $column): string
 
     public function rowForRowFlowPosition(int $position): string
     {
-        return $this->rows()[floor(($position - 1) / $this->columnsCount())];
+        $index = (int) floor(($position - 1) / $this->columnsCount());
+
+        return $this->rows()[$index];
     }
 
     public function rowForColumnFlowPosition(int $position): string
@@ -56,7 +58,9 @@ public function columnForRowFlowPosition(int $position): int
 
     public function columnForColumnFlowPosition(int $position): int
     {
-        return $this->columns()[floor(($position - 1) / $this->rowsCount())];
+        $index = (int) floor(($position - 1) / $this->rowsCount());
+
+        return $this->columns()[$index];
     }
 
     public function positionsCount(): int
diff --git a/src/Microplate/Coordinates.php b/src/Microplate/Coordinates.php
@@ -87,6 +87,7 @@ public static function fromString(string $coordinatesString, CoordinateSystem $c
             $coordinateSystemClass = \get_class($coordinateSystem);
             throw new \InvalidArgumentException("Expected coordinates between {$firstValidExample} and {$lastValidExample} for {$coordinateSystemClass}, got: {$coordinatesString}.");
         }
+        /** @var array{1: string, 2: string} $matches */
 
         return new static($matches[1], (int) $matches[2], $coordinateSystem);
     }
@@ -136,10 +137,10 @@ public function toPaddedString(): string
 
     public function position(FlowDirection $direction): int
     {
-        /** @var int $rowIndex Must be found, since __construct enforces $this->row is valid */
+        /** @var int<0, max> $rowIndex Must be found, since __construct enforces $this->row is valid */
         $rowIndex = array_search($this->row, $this->coordinateSystem->rows(), true);
 
-        /** @var int $columnIndex Must be found, since __construct enforces $this->column is valid */
+        /** @var int<0, max> $columnIndex Must be found, since __construct enforces $this->column is valid */
         $columnIndex = array_search($this->column, $this->coordinateSystem->columns(), true);
 
         switch ($direction->value) {
diff --git a/src/PHPStan/Rules/NoAssignmentInIfRule.php b/src/PHPStan/Rules/NoAssignmentInIfRule.php
@@ -8,6 +8,7 @@
 use PhpParser\NodeFinder;
 use PHPStan\Analyser\Scope;
 use PHPStan\Rules\Rule;
+use PHPStan\Rules\RuleErrorBuilder;
 
 /**
  * Inspired by https://github.com/odan/phpstan-rules/blob/388db4cdf7c99e2978f20b1ed8801d748984812a/src/Rules/AssignmentInConditionRule.php.
@@ -35,6 +36,10 @@ public function processNode(Node $node, Scope $scope): array
             return [];
         }
 
-        return ['Assignment in conditional expression is not allowed.'];
+        return [
+            RuleErrorBuilder::message('Assignment in conditional expression is not allowed.')
+                ->identifier('mll.noAssignmentInIf')
+                ->build(),
+        ];
     }
 }
diff --git a/src/PHPStan/Rules/ThrowableClassNameRule.php b/src/PHPStan/Rules/ThrowableClassNameRule.php
diff --git a/src/PHPStan/Rules/VariableNameIdToIDRule.php b/src/PHPStan/Rules/VariableNameIdToIDRule.php
diff --git a/src/StringUtil.php b/src/StringUtil.php
diff --git a/src/Tecan/CustomCommands/DispenseParameters.php b/src/Tecan/CustomCommands/DispenseParameters.php
diff --git a/tests/Microplate/MicroplateTest.php b/tests/Microplate/MicroplateTest.php
diff --git a/tests/SpecificationTest.php b/tests/SpecificationTest.php

Original file line number	Diff line number	Diff line change
`@@ -16,7 +16,10 @@ public function __construct(string $sequence)`
`16`	`16`
`17`	`17`	`public function reverse(): string`
`18`	`18`	`{`
`19`		`- return implode(array_reverse(mb_str_split($this->sequence)));`
	`19`	`+ $parts = mb_str_split($this->sequence); // @phpstan-ignore-line theCodingMachineSafe.function (safe from PHP 8.0)`
	`20`	`+ $reversedParts = array_reverse($parts);`
	`21`	`+`
	`22`	`+ return implode($reversedParts);`
`20`	`23`	`}`
`21`	`24`
`22`	`25`	`public function complement(): string`
Original file line number	Diff line number	Diff line change
`@@ -24,7 +24,7 @@ public function __construct(string $rackID)`
`24`	`24`	`throw new InvalidRackIDException($rackID);`
`25`	`25`	`}`
`26`	`26`	`$this->rackID = $rackID;`
`27`		`- $this->microplate = new Microplate(self::coordinateSystem());`
	`27`	`+ $this->microplate = new Microplate(self::coordinateSystem()); // @phpstan-ignore assign.propertyType (generic not inferred)`
`28`	`28`	`}`
`29`	`29`
`30`	`30`	`public static function coordinateSystem(): CoordinateSystem12x8`
Original file line number	Diff line number	Diff line change
`@@ -37,11 +37,10 @@ public function convertSectionToString(): string`
`37`	`37`	`{`
`38`	`38`	`$this->validate();`
`39`	`39`
`40`		`- if ($this->rows->isEmpty()) {`
	`40`	`+ $firstRow = $this->rows->first();`
	`41`	`+ if ($firstRow === null) {`
`41`	`42`	`throw new IlluminaSampleSheetException('Data section must contain at least one row.');`
`42`	`43`	`}`
`43`		`- /** @var Row $firstRow */`
`44`		`- $firstRow = $this->rows->first();`
`45`	`44`
`46`	`45`	`$rowsData = $this->rows`
`47`	`46`	`->map(fn (Row $row): string => $row->toString())`
Original file line number	Diff line number	Diff line change
`@@ -40,7 +40,7 @@ public function __construct(`
`40`	`40`	`/** @return array<int\|string> */`
`41`	`41`	`public function toArray(): array`
`42`	`42`	`{`
`43`		`- return array_filter([`
	`43`	`+ return array_filter([ // @phpstan-ignore arrayFilter.strict (we want truthy comparison)`
`44`	`44`	`$this->lane,`
`45`	`45`	`$this->sample_ID,`
`46`	`46`	`$this->index,`