Next Version (2.1.0 | 2.1.0-rc3) #264
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WalkthroughThe changes update dependency versions and Gradle wrapper, add version property generation tasks, introduce provenance management with versioned metadata tracking, and extend the Changes
Sequence Diagram(s)sequenceDiagram
participant CrateReader
participant RoCrate
participant Crate
CrateReader->>RoCrate: rebuildCrate(...)
RoCrate->>RoCrate: markAsImported()
RoCrate-->>CrateReader: return marked crate
sequenceDiagram
participant CrateWriter
participant ProvenanceManager
participant Crate
CrateWriter->>Crate: validate()
CrateWriter->>ProvenanceManager: addProvenanceInformation(crate)
ProvenanceManager->>Crate: add or update provenance entities and actions
CrateWriter->>CrateWriter: delegate save operation
sequenceDiagram
participant RoCrateBuilder
participant RoCrateMetadataContext
RoCrateBuilder->>RoCrateMetadataContext: checkEntity(entity)
RoCrateMetadataContext-->>RoCrateBuilder: validation result
alt valid
RoCrateBuilder->>RoCrateBuilder: add entity to payload
else invalid
RoCrateBuilder->>User: print error, do not add entity
end
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Pull Request Test Coverage Report for Build #478Details
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Add context prefix support
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Actionable comments posted: 2
🔭 Outside diff range comments (1)
src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java (1)
136-203: 🛠️ Refactor suggestionConsider improving error handling mechanism.
The validation logic is comprehensive and handles prefixes well. However, printing errors to
System.erris not ideal for a library. Consider using a logging framework or collecting errors for the caller to handle.Consider refactoring the error handling:
- System.err.println("type " + s + " is missing from the context!"); + // Consider using SLF4J logger instead + // logger.error("type {} is missing from the context!", s); return false;- System.err.println("attribute name " + s + " is missing from context;"); + // Consider using SLF4J logger instead + // logger.error("attribute name {} is missing from context", s); return false;Alternatively, consider collecting validation errors and returning them to the caller for better error handling flexibility.
🧹 Nitpick comments (1)
src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java (1)
263-271: Consider simplifying the getValueOf implementation.The current implementation uses Optional but then falls back to the same map lookup. Since
contextMapshould contain all entries fromother, this might be redundant.Consider simplifying:
- public String getValueOf(String key) { - return Optional.ofNullable(this.contextMap.get(key)) - .orElseGet(() -> this.other.get(key)); - } + public String getValueOf(String key) { + return this.contextMap.get(key); + }If there's a specific reason for checking both maps, please add a comment explaining the logic.
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📒 Files selected for processing (5)
build.gradle(2 hunks)gradle/wrapper/gradle-wrapper.properties(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java(11 hunks)src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java(5 hunks)
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src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java (2)
src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java (1)
RoCrate(43-531)src/test/java/edu/kit/datamanager/ro_crate/HelpFunctions.java (1)
HelpFunctions(27-178)
🔇 Additional comments (14)
gradle/wrapper/gradle-wrapper.properties (1)
3-3: LGTM!Gradle wrapper patch version update from 8.14 to 8.14.1 is appropriate for bug fixes and improvements.
src/main/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContext.java (7)
15-15: LGTM!The Function import is correctly added to support the new validation logic.
42-43: Excellent documentation improvements!The clarifications about the default context not being automatically included are crucial for API users to understand the behavior of these constructors.
Also applies to: 50-52, 62-63
91-134: Well-implemented context serialization method!The method correctly handles different context structures and provides clear documentation with examples. The conditional logic for single vs. multiple context entries is appropriate for JSON-LD standards.
205-212: LGTM!Good documentation addition for the existing method.
273-295: LGTM!The
getKeys()andgetPairs()methods provide clean, immutable views of the context data with appropriate documentation.
306-312: Verify the impact of URL deletion on context entries.The
deleteUrlFromContextmethod removes the URL but doesn't remove the corresponding entries fromcontextMapthat were added when the URL was processed. This could leave orphaned context entries.Consider whether entries added from the deleted URL should also be removed from the context maps, or document this behavior if it's intentional.
251-261: LGTM!The
addToContextmethod correctly maintains consistency between both internal maps.src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java (1)
385-385: Same validation concern as previous method.Good addition of validation before adding contextual entities. Please refer to the previous comment about verifying the
checkEntityerror handling behavior.src/test/java/edu/kit/datamanager/ro_crate/context/RoCrateMetadataContextTest.java (5)
9-9: LGTM!Import addition is necessary for the new test functionality.
24-24: LGTM!Class rename improves clarity and follows standard test naming conventions.
36-36: LGTM!Resource stream update is necessary after the class rename.
102-103: LGTM!Good catch fixing the typos in the test URLs.
290-305: Excellent test coverage for prefixed type validation.This test comprehensively validates the new prefixed type functionality. It properly tests the integration between
RoCrateandRoCrateMetadataContextwith a realistic scenario using "rdfs:Property".The test structure is good:
- Sets up context with prefix mapping
- Creates entity with prefixed type
- Adds to crate (triggering validation)
- Explicitly validates the entity
Note: The test's behavior depends on how
checkEntityhandles validation failures in theaddDataEntitymethod (see previous comments about error handling).
…g implicitly or explicitly
…nd action handling
…a creation so that checks stay as simple as possible
…ies file in ProvenanceManager
…eval and refactor ProvenanceManager to use it
…anager instance This allows disabling provenance management with null, but also enable to implement derived or completely new implementations.
…ility during read
…pertiesVersionProvider
…bility during crate updates
…-crates-about-the-tool-which-created-it 265 store provenance in crates about the tool which created it
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Actionable comments posted: 4
🧹 Nitpick comments (9)
src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java (4)
11-11: Fix documentation reference.The
{@see JsonUtilFunctions}reference appears to be incorrect. Use{@link JsonUtilFunctions}if the class exists, or remove the reference if it doesn't.- * {@see JsonUtilFunctions}. + * {@link JsonUtilFunctions}.
26-33: Consider using Stream API for consistency.For consistency with the other methods, consider refactoring this method to use Stream API instead of traditional iteration.
public static JsonNode findEntityById(JsonNode graph, String id) { - for (JsonNode entity : graph) { - if (entity.has("@id") && entity.get("@id").asText().equals(id)) { - return entity; - } - } - return null; + return StreamSupport.stream(graph.spliterator(), false) + .filter(entity -> entity.has("@id") && entity.get("@id").asText().equals(id)) + .findFirst() + .orElse(null); }
42-47: Add null safety check.Consider adding a null safety check similar to the
findEntityByIdmethod to ensure robust handling of entities without the@typefield.public static JsonNode findEntityByType(JsonNode graph, String type) { return StreamSupport.stream(graph.spliterator(), false) - .filter(entity -> entity.path("@type").asText().equals(type)) + .filter(entity -> entity.has("@type") && entity.get("@type").asText().equals(type)) .findFirst() .orElse(null); }
56-60: Apply same null safety improvement.Apply the same null safety improvement as suggested for
findEntityByType.public static JsonNode[] findEntitiesByType(JsonNode graph, String type) { return StreamSupport.stream(graph.spliterator(), false) - .filter(entity -> entity.path("@type").asText().equals(type)) + .filter(entity -> entity.has("@type") && entity.get("@type").asText().equals(type)) .toArray(JsonNode[]::new); }src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java (2)
105-112: Extract action types as constants.Consider extracting the action type strings as constants to improve maintainability and reduce the risk of typos.
+ private static final String CREATE_ACTION_TYPE = "CreateAction"; + private static final String UPDATE_ACTION_TYPE = "UpdateAction"; + protected ContextualEntity buildNewActionEntity(boolean isFirstWrite, String libraryId) { return new ContextualEntityBuilder() - .addType(isFirstWrite ? "CreateAction" : "UpdateAction") + .addType(isFirstWrite ? CREATE_ACTION_TYPE : UPDATE_ACTION_TYPE) .addIdProperty("result", "./") .addProperty("startTime", Instant.now().toString()) .addIdProperty("agent", libraryId) .build(); }
114-137: Consider extracting entity properties as constants.The hardcoded metadata properties could be extracted as constants for better maintainability.
+ private static final String RO_CRATE_JAVA_NAME = "ro-crate-java"; + private static final String RO_CRATE_JAVA_URL = "https://github.com/kit-data-manager/ro-crate-java"; + private static final String RO_CRATE_JAVA_LICENSE = "Apache-2.0"; + private static final String RO_CRATE_JAVA_DESCRIPTION = "A Java library for creating and manipulating RO-Crates"; + private static final String SOFTWARE_APPLICATION_TYPE = "SoftwareApplication"; protected ContextualEntity buildRoCrateJavaEntity( Crate crate, String newActionId, String libraryId ) { String version = this.versionProvider.getVersion(); ContextualEntity self = crate.getAllContextualEntities().stream() .filter(contextualEntity -> libraryId.equals(contextualEntity.getId())) .findFirst() .orElseGet(() -> new ContextualEntityBuilder() .setId(libraryId) - .addType("SoftwareApplication") - .addProperty("name", "ro-crate-java") - .addProperty("url", "https://github.com/kit-data-manager/ro-crate-java") + .addType(SOFTWARE_APPLICATION_TYPE) + .addProperty("name", RO_CRATE_JAVA_NAME) + .addProperty("url", RO_CRATE_JAVA_URL) .addProperty("version", version) .addProperty("softwareVersion", version) - .addProperty("license", "Apache-2.0") - .addProperty("description", "A Java library for creating and manipulating RO-Crates") + .addProperty("license", RO_CRATE_JAVA_LICENSE) + .addProperty("description", RO_CRATE_JAVA_DESCRIPTION) .addIdProperty("Action", newActionId) .build() );src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java (3)
240-241: Extract regex pattern as a constant.The semantic versioning regex pattern should be extracted as a class constant for reusability and maintainability.
+ private static final String SEMVER_PATTERN = + "(?i)^\\d+\\.\\d+\\.\\d+(?:-(?:rc\\d+|alpha|beta|snapshot)(?:\\.\\d+)?)?(?:\\+[0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*)?$"; + @Test void should_HaveValidVersionFormat_When_WritingCrate(@TempDir Path tempDir) throws IOException { // ... existing code ... - String semverPattern = "(?i)^\\d+\\.\\d+\\.\\d+(?:-(?:rc\\d+|alpha|beta|snapshot)(?:\\.\\d+)?)?(?:\\+[0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*)?$"; - assertTrue(version.matches(semverPattern), + assertTrue(version.matches(SEMVER_PATTERN),
144-212: Consider breaking down this test method.This test method is quite long and tests multiple aspects. Consider breaking it into smaller, more focused test methods for better maintainability and clarity.
This method could be split into:
should_CreateOneCreateAction_When_WritingCrateFirstTimeshould_CreateUpdateActions_When_WritingCrateMultipleTimesshould_MaintainChronologicalOrder_When_WritingMultipleTimes
233-234: Review necessity of @SuppressWarnings annotation.The
@SuppressWarnings("DataFlowIssue")annotation suggests potential null pointer concerns. Consider adding explicit null checks instead of suppressing warnings.// Version format validation - @SuppressWarnings("DataFlowIssue") - String version = roCrateJavaEntity.get("version").asText(); + JsonNode versionNode = roCrateJavaEntity.get("version"); + assertNotNull(versionNode, "Version property should not be null"); + String version = versionNode.asText();
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CITATION.cff(1 hunks)build.gradle(4 hunks)src/main/java/edu/kit/datamanager/ro_crate/Crate.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java(2 hunks)src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java(6 hunks)src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/util/Graph.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java(1 hunks)src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java(2 hunks)src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/reader/CommonReaderTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/writer/FolderWriterTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManagerTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java(1 hunks)src/test/java/edu/kit/datamanager/ro_crate/writer/ZipStreamWriterTest.java(2 hunks)src/test/java/edu/kit/datamanager/ro_crate/writer/ZipWriterTest.java(1 hunks)
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- src/main/java/edu/kit/datamanager/ro_crate/util/VersionProvider.java
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- src/test/java/edu/kit/datamanager/ro_crate/writer/ZipStreamWriterTest.java
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- build.gradle
- src/main/java/edu/kit/datamanager/ro_crate/RoCrate.java
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🧬 Code Graph Analysis (4)
src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java (1)
src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java (1)
Writers(9-42)
src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java (1)
src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java (1)
Writers(9-42)
src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java (1)
src/main/java/edu/kit/datamanager/ro_crate/special/IdentifierUtils.java (1)
IdentifierUtils(23-158)
src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java (1)
src/main/java/edu/kit/datamanager/ro_crate/writer/Writers.java (1)
Writers(9-42)
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🔇 Additional comments (18)
src/test/java/edu/kit/datamanager/ro_crate/writer/FolderWriterTest.java (1)
19-19: LGTM: Appropriate test isolation by disabling automatic provenance.This change ensures test predictability by explicitly disabling automatic provenance metadata addition during crate writing, which is the correct approach for maintaining test isolation.
src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateWriterSpec12Test.java (1)
33-33: LGTM: Essential for test correctness.This change is crucial for the
writeDoesNotModifyTestsince automatic provenance addition would invalidate the test's premise that writing doesn't modify the original crate. Disabling provenance ensures the test accurately validates the write operation's non-invasive behavior.src/test/java/edu/kit/datamanager/ro_crate/reader/FolderReaderTest.java (1)
24-26: LGTM: Ensures clean test data for reader tests.The addition of
.withAutomaticProvenance(null)maintains test data integrity by preventing automatic metadata addition during the save operation used for test setup, ensuring that reader tests work with clean, predictable data.src/test/java/edu/kit/datamanager/ro_crate/reader/ZipReaderTest.java (1)
17-19: LGTM: Consistent provenance handling across writer types.The addition of
.withAutomaticProvenance(null)maintains consistency with other test files while ensuring that zip-based tests also have predictable behavior without automatic provenance metadata addition.src/main/java/edu/kit/datamanager/ro_crate/reader/CrateReader.java (1)
100-100: LGTM: Correctly marks crates as imported when read from external sources.This change appropriately integrates with the new provenance management system by marking crates as imported upon reading, which enables proper provenance handling downstream.
src/test/java/edu/kit/datamanager/ro_crate/reader/ZipStreamReaderTest.java (1)
36-38: LGTM: Proper test isolation by disabling automatic provenance.Explicitly disabling automatic provenance in tests ensures consistent behavior and prevents automatic metadata generation from interfering with test assertions.
src/test/java/edu/kit/datamanager/ro_crate/reader/CommonReaderTest.java (1)
130-135: LGTM: Maintains test correctness by disabling automatic provenance.Disabling automatic provenance is essential here to ensure fair comparison between raw and imported crates, as automatic metadata addition would introduce differences that would break the test logic.
src/main/java/edu/kit/datamanager/ro_crate/preview/CratePreview.java (1)
43-44: LGTM: Appropriate separation of concerns for provenance handling.The assumption that the caller has already handled provenance is reasonable for preview generation, and the explanatory comment clearly documents this design decision.
src/main/java/edu/kit/datamanager/ro_crate/Crate.java (1)
25-45: LGTM! Well-designed interface additions for crate state tracking.The new methods provide a clean way to distinguish between imported and newly created crates, which is essential for proper provenance handling. The fluent interface pattern and comprehensive Javadoc documentation are excellent.
src/main/java/edu/kit/datamanager/ro_crate/writer/CrateWriter.java (2)
18-18: LGTM! Good initialization of provenance manager.The default initialization provides sensible behavior while allowing customization through the fluent interface.
29-39: Well-designed fluent interface for provenance configuration.The method provides clear control over provenance management with good documentation explaining the null behavior for disabling provenance.
src/main/java/edu/kit/datamanager/ro_crate/entities/AbstractEntity.java (4)
115-126: Useful utility method for extracting ID properties.This method provides a clean way to extract
@idvalues from properties, which is commonly needed when working with RO-Crate entities.
257-257: Minor style improvement removing unnecessary braces.Clean simplification of the lambda expression while maintaining readability.
425-425: Excellent safety improvement using orElse() instead of get().This change prevents potential
NoSuchElementExceptionif the encoding fails and returns an empty Optional. UsingorElse(this.id)maintains the current ID value as a fallback, which is the correct behavior.
370-370: Good Javadoc formatting improvements.The consistent use of
<p>tags improves documentation rendering and readability.Also applies to: 462-462, 522-522
src/test/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManagerTest.java (1)
1-182: Excellent test coverage and structure.This test class demonstrates excellent testing practices:
- Clear test naming with should/when structure
- Comprehensive coverage of provenance scenarios
- Good use of Given/When/Then pattern
- Descriptive assertion messages
- Proper verification of entity relationships and properties
The tests effectively validate the core functionality of the ProvenanceManager class.
src/main/java/edu/kit/datamanager/ro_crate/writer/ProvenanceManager.java (1)
22-38: Well-designed IdPrefix record.The
IdPrefixrecord is a clever design that provides type safety and prevents accidental misuse of partial IDs. ThewithSuffixmethod andtoStringoverride are well-implemented.src/test/java/edu/kit/datamanager/ro_crate/writer/RoCrateMetadataGenerationTest.java (1)
1-406: Excellent comprehensive test coverage.This test class provides outstanding integration test coverage for the metadata generation functionality:
- Thorough validation of provenance entity creation and relationships
- Proper file I/O testing with temporary directories
- Good use of JSON parsing and validation
- Comprehensive edge case coverage
- Excellent debugging support with pretty printing
The tests effectively validate the integration between multiple components of the provenance management system.
src/main/java/edu/kit/datamanager/ro_crate/util/ClasspathPropertiesVersionProvider.java
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…alization for version loading
…nance information
…ION.cff during release process
…an now be called without it
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Actionable comments posted: 1
🧹 Nitpick comments (3)
gradle/updateCff.gradle (3)
40-42: Guard against missing input file.
ReadingcffFile.textwithout verifying existence can fail the build unexpectedly. Add a check to throw a clear error or initialize the file if it’s missing.def cffFile = file('CITATION.cff') + if (!cffFile.exists()) { + throw new GradleException("CITATION.cff not found at ${cffFile.absolutePath}") + } def content = cffFile.text
44-48: Refactor version update logic for clarity.
Instead of separatecontains+replaceAll, leverage a regex match to detect existing entries and minimize duplication.- if (content.contains('version:')) { - content = content.replaceAll(/(?m)^version:\s*.+$/, "version: ${version}") - } else { - content = content + "\nversion: ${version}" - } + def versionPattern = /(?m)^version:\s*.+$/ + if (content =~ versionPattern) { + content = content.replaceAll(versionPattern, "version: ${version}") + } else { + content += "\nversion: ${version}" + }
50-55: Apply the same consolidation todate-released.
DRY up the code by reusing the pattern-based approach for updating or inserting the release date.- if (content.contains('date-released:')) { - content = content.replaceAll(/(?m)^date-released:\s*.+$/, "date-released: ${today}") - } else { - content = content + "\ndate-released: ${today}" - } + def datePattern = /(?m)^date-released:\s*.+$/ + if (content =~ datePattern) { + content = content.replaceAll(datePattern, "date-released: ${today}") + } else { + content += "\ndate-released: ${today}" + }
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🔇 Additional comments (3)
gradle/updateCff.gradle (3)
1-2: No import issues.
TheLocalDateandDateTimeFormatterimports are correct and required.
63-65: Task ordering aligns with release workflow.
UsingmustRunAfter(confirmReleaseVersion)ensuresupdateCffruns at the correct point.
68-70: Dependency integration is correct.
AddingdependsOn('updateCff')tocheckSnapshotDependenciesproperly hooks the task into the release chain.
| tasks.register('updateCff') { | ||
| group = 'release' | ||
| description = 'Updates the version in CITATION.cff file' | ||
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| outputs.file("CITATION.cff") | ||
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🛠️ Refactor suggestion
Declare task inputs for up-to-date checks.
Gradle tasks should declare both inputs and outputs to support incremental builds. Add inputs.file("CITATION.cff") alongside the existing output.
tasks.register('updateCff') {
group = 'release'
description = 'Updates the version in CITATION.cff file'
- outputs.file("CITATION.cff")
+ inputs.file("CITATION.cff")
+ outputs.file("CITATION.cff")
...
}📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| tasks.register('updateCff') { | |
| group = 'release' | |
| description = 'Updates the version in CITATION.cff file' | |
| outputs.file("CITATION.cff") | |
| tasks.register('updateCff') { | |
| group = 'release' | |
| description = 'Updates the version in CITATION.cff file' | |
| inputs.file("CITATION.cff") | |
| outputs.file("CITATION.cff") | |
| ... | |
| } |
🤖 Prompt for AI Agents
In gradle/updateCff.gradle around lines 30 to 35, the 'updateCff' task declares
outputs but lacks declared inputs, which is necessary for Gradle's incremental
build checks. Add an inputs declaration by including inputs.file("CITATION.cff")
within the task configuration to properly specify the input file for up-to-date
checks.
Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Chores