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Nextflow's v2 syntax parser requires ConfigScope implementations to have a no-arg constructor so it can reflectively instantiate them at parse time to discover and validate config options. Without this, the co2footprint scope and its sub-scopes are not registered, causing "Unrecognized config option" warnings for all co2footprint.* settings. This adds no-arg constructors to CO2FootprintConfig and all BaseFileConfig subclasses (TraceFileConfig, SummaryFileConfig, ReportFileConfig, DataFileConfig), following the same pattern used by nf-schema's ValidationConfig. Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> Signed-off-by: Jonathan Manning <[email protected]>
Per Ben's review, only the top-level scope needs @ScopeName, a no-arg constructor, and extension point registration. Nested scopes are discovered via fields on the parent class. - Register CO2FootprintConfig in build.gradle extensionPoints - Remove @ScopeName from nested scope classes (Trace/Summary/Report/DataFileConfig) - Remove no-arg constructors from nested scopes and BaseFileConfig - Remove unnecessary types=[...] from @ConfigOption annotations (kept types=[Number, BigDecimal] on ci since it constructs CiRecord from a number) Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]> Signed-off-by: Jonathan Manning <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
…separation) Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
…c values in report Documentation: Added changed to CHANGELOG.md Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Refactor: Changed default of `emissionMetricsOnly` to `true` Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Test: Adjusted tests and file checks Signed-off-by: Josua Carl <[email protected]>
Refactor: Renamed emission metrics to camel case Test: Adjusted tests to new naming Chore: Intermediate save Signed-off-by: Josua Carl <[email protected]>
Refactor: Renamed emission metrics to camel case Test: Adjusted tests to new naming Signed-off-by: Josua Carl <[email protected]>
Co-authored-by: Nadja Volkmann <[email protected]>
Co-authored-by: Nadja Volkmann <[email protected]>
Fix: Improve report quality for extension / CLI runs
# Conflicts: # src/testResources/cli/data_test.yaml # src/testResources/cli/file_checks.json # src/testResources/cli/report_test.html
Signed-off-by: Josua Carl <[email protected]>
Refactor: Move to provenance file and update related tests
…org/bioschemas.org classes annotations to enabled machine processing Test: Adjusted file checks Signed-off-by: Josua Carl <[email protected]>
Documentation: Included changed into CHANGELOG.md Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
…t plugin version Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
# Conflicts: # CHANGELOG.md # src/testResources/cli/file_checks.json # src/testResources/cli/report_test.html # src/testResources/observer/file_checks.json # src/testResources/report/test_payload.json
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: nadnein <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: nadnein <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: nadnein <[email protected]>
Signed-off-by: nadnein <[email protected]>
Fix: zero division crashes when task realtime is 0
Fix floating point error and refactor Bytes for value types
Signed-off-by: Josua Carl <[email protected]>
Signed-off-by: Josua Carl <[email protected]>
Add --delimiter argument to CLI post-run docs
JosuaCarl
added
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May 4, 2026
Chore: Version 1.3.0 bump
…or-2 Fix/config scope noarg constructor 2
Resolves conflicts in:
- src/main/nextflow/co2footprint/Config/BaseFileConfig.groovy
(drop @ConfigOption imports; the annotations live on each subclass now)
- src/main/nextflow/co2footprint/Logging/CustomCaptureAppender.groovy
(take dev's 26.04.0 LogObserver adaptation)
- src/testResources/{cli,observer,report}/* (take dev's calculator outputs)
- Mark file/enabled/overwrite/maxTasks final on the four nested file scopes and final on name/ending/defaultEnabled in BaseFileConfig (each is assigned exactly once in a constructor body) - Normalise whitespace: drop trailing spaces and double-space after `=` - Add CHANGELOG entry under New > Bug Fixes Signed-off-by: Jonathan Manning <[email protected]>
…tructor Fix: Add no-arg constructors for v2 config parser scope registration
… file name Test: Adapted file tests Documentation: Added changes to CHANGELOG.md Documentation: Moved fix into this release Signed-off-by: Josua Carl <[email protected]>
Fix: CI plot threw error due to changed variable name -> Inserted new…
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Merge
dev->masterfor Release 1.3.0