Sourcing python-remove-tests-dir-hook
Sourcing python-catch-conflicts-hook.sh
Sourcing python-remove-bin-bytecode-hook.sh
Sourcing pypa-build-hook
Using pypaBuildPhase
Sourcing python-runtime-deps-check-hook
Using pythonRuntimeDepsCheckHook
Sourcing pypa-install-hook
Using pypaInstallPhase
Sourcing python-imports-check-hook.sh
Using pythonImportsCheckPhase
Sourcing python-metadata-check-hook.sh
Using pythonMetadataCheckPhase
Sourcing python-namespaces-hook
Sourcing python-catch-conflicts-hook.sh
Sourcing pytest-check-hook
Using pytestCheckPhase
Using checkPhaseThreadLimitHook
Running phase: unpackPhase
unpacking source archive /nix/store/9mmjdsvm7djnn602nrq97pbfwpl14cg6-source
source root is source
setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/tests/tests_from_genbanks/test_from_genbanks.py"
Running phase: patchPhase
Running phase: updateAutotoolsGnuConfigScriptsPhase
Running phase: configurePhase
no configure script, doing nothing
Running phase: buildPhase
Executing pypaBuildPhase
Creating a wheel...
pypa build flags: --no-isolation --outdir dist/ --wheel
* Getting build dependencies for wheel...
running egg_info
creating dnachisel.egg-info
writing dnachisel.egg-info/PKG-INFO
writing dependency_links to dnachisel.egg-info/dependency_links.txt
writing entry points to dnachisel.egg-info/entry_points.txt
writing requirements to dnachisel.egg-info/requires.txt
writing top-level names to dnachisel.egg-info/top_level.txt
writing manifest file 'dnachisel.egg-info/SOURCES.txt'
reading manifest file 'dnachisel.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'dnachisel.egg-info/SOURCES.txt'
* Building wheel...
running bdist_wheel
running build
running build_py
creating build/lib/dnachisel
copying dnachisel/cli.py -> build/lib/dnachisel
copying dnachisel/Location.py -> build/lib/dnachisel
copying dnachisel/__init__.py -> build/lib/dnachisel
copying dnachisel/version.py -> build/lib/dnachisel
creating build/lib/dnachisel/DnaOptimizationProblem
copying dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py -> build/lib/dnachisel/DnaOptimizationProblem
copying dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py -> build/lib/dnachisel/DnaOptimizationProblem
copying dnachisel/DnaOptimizationProblem/NoSolutionError.py -> build/lib/dnachisel/DnaOptimizationProblem
copying dnachisel/DnaOptimizationProblem/__init__.py -> build/lib/dnachisel/DnaOptimizationProblem
creating build/lib/dnachisel/MutationSpace
copying dnachisel/MutationSpace/MutationChoice.py -> build/lib/dnachisel/MutationSpace
copying dnachisel/MutationSpace/MutationSpace.py -> build/lib/dnachisel/MutationSpace
copying dnachisel/MutationSpace/__init__.py -> build/lib/dnachisel/MutationSpace
creating build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/DnaNotationPattern.py -> build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/EnzymeSitePattern.py -> build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/HomopolymerPattern.py -> build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/MotifPssmPattern.py -> build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/RepeatedKmerPattern.py -> build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/SequencePattern.py -> build/lib/dnachisel/SequencePattern
copying dnachisel/SequencePattern/__init__.py -> build/lib/dnachisel/SequencePattern
creating build/lib/dnachisel/Specification
copying dnachisel/Specification/FeatureRepresentationMixin.py -> build/lib/dnachisel/Specification
copying dnachisel/Specification/Specification.py -> build/lib/dnachisel/Specification
copying dnachisel/Specification/SpecificationSet.py -> build/lib/dnachisel/Specification
copying dnachisel/Specification/__init__.py -> build/lib/dnachisel/Specification
creating build/lib/dnachisel/biotools
copying dnachisel/biotools/blast_sequence.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/bowtie.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/__init__.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/biotables.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/enzymes_operations.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/formatting_operations.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/gc_content.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/genbank_operations.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/indices_operations.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/random_sequences.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/sequences_differences.py -> build/lib/dnachisel/biotools
copying dnachisel/biotools/sequences_operations.py -> build/lib/dnachisel/biotools
creating build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AllowPrimer.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidBlastMatches.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidChanges.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidHairpins.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidHeterodimerization.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidMatches.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidPattern.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/AvoidStopCodons.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/CodonSpecification.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceChanges.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceChoice.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceGCContent.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceMeltingTemperature.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforcePatternOccurence.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceRegionsCompatibility.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceSequence.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceTerminalGCContent.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/EnforceTranslation.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/SequenceLengthBounds.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/TerminalSpecification.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/UniquifyAllKmers.py -> build/lib/dnachisel/builtin_specifications
copying dnachisel/builtin_specifications/__init__.py -> build/lib/dnachisel/builtin_specifications
creating build/lib/dnachisel/reports
copying dnachisel/reports/SpecAnnotationsTranslator.py -> build/lib/dnachisel/reports
copying dnachisel/reports/__init__.py -> build/lib/dnachisel/reports
copying dnachisel/reports/colors_cycle.py -> build/lib/dnachisel/reports
copying dnachisel/reports/optimization_reports.py -> build/lib/dnachisel/reports
copying dnachisel/reports/tools.py -> build/lib/dnachisel/reports
creating build/lib/dnachisel/utils
copying dnachisel/utils/__init__.py -> build/lib/dnachisel/utils
copying dnachisel/utils/utils.py -> build/lib/dnachisel/utils
creating build/lib/dnachisel/DnaOptimizationProblem/mixins
copying dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins
copying dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins
copying dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins
copying dnachisel/DnaOptimizationProblem/mixins/__init__.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins
creating build/lib/dnachisel/Specification/SpecEvaluation
copying dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py -> build/lib/dnachisel/Specification/SpecEvaluation
copying dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py -> build/lib/dnachisel/Specification/SpecEvaluation
copying dnachisel/Specification/SpecEvaluation/SpecEvaluation.py -> build/lib/dnachisel/Specification/SpecEvaluation
copying dnachisel/Specification/SpecEvaluation/SpecEvaluations.py -> build/lib/dnachisel/Specification/SpecEvaluation
copying dnachisel/Specification/SpecEvaluation/__init__.py -> build/lib/dnachisel/Specification/SpecEvaluation
creating build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
copying dnachisel/builtin_specifications/codon_optimization/__init__.py -> build/lib/dnachisel/builtin_specifications/codon_optimization
creating build/lib/dnachisel/reports/constraints_reports
copying dnachisel/reports/constraints_reports/GraphicTranslator.py -> build/lib/dnachisel/reports/constraints_reports
copying dnachisel/reports/constraints_reports/__init__.py -> build/lib/dnachisel/reports/constraints_reports
copying dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py -> build/lib/dnachisel/reports/constraints_reports
copying dnachisel/reports/constraints_reports/constraints_reports.py -> build/lib/dnachisel/reports/constraints_reports
running egg_info
writing dnachisel.egg-info/PKG-INFO
writing dependency_links to dnachisel.egg-info/dependency_links.txt
writing entry points to dnachisel.egg-info/entry_points.txt
writing requirements to dnachisel.egg-info/requires.txt
writing top-level names to dnachisel.egg-info/top_level.txt
reading manifest file 'dnachisel.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file 'dnachisel.egg-info/SOURCES.txt'
creating build/lib/dnachisel/biotools/data
copying dnachisel/biotools/data/README.md -> build/lib/dnachisel/biotools/data
copying dnachisel/biotools/data/complements.csv -> build/lib/dnachisel/biotools/data
copying dnachisel/biotools/data/iupac_notation.csv -> build/lib/dnachisel/biotools/data
copying dnachisel/biotools/data/nucleotide_to_regexpr.csv -> build/lib/dnachisel/biotools/data
creating build/lib/dnachisel/reports/assets
copying dnachisel/reports/assets/logo.png -> build/lib/dnachisel/reports/assets
copying dnachisel/reports/assets/optimization_report.pug -> build/lib/dnachisel/reports/assets
copying dnachisel/reports/assets/style.css -> build/lib/dnachisel/reports/assets
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/dnachisel
copying build/lib/dnachisel/cli.py -> build/bdist.linux-x86_64/wheel/./dnachisel
copying build/lib/dnachisel/Location.py -> build/bdist.linux-x86_64/wheel/./dnachisel
copying build/lib/dnachisel/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel
copying build/lib/dnachisel/version.py -> build/bdist.linux-x86_64/wheel/./dnachisel
creating build/bdist.linux-x86_64/wheel/dnachisel/DnaOptimizationProblem
copying build/lib/dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem
copying build/lib/dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem
copying build/lib/dnachisel/DnaOptimizationProblem/NoSolutionError.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem
copying build/lib/dnachisel/DnaOptimizationProblem/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem
creating build/bdist.linux-x86_64/wheel/dnachisel/DnaOptimizationProblem/mixins
copying build/lib/dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins
copying build/lib/dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins
copying build/lib/dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins
copying build/lib/dnachisel/DnaOptimizationProblem/mixins/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins
creating build/bdist.linux-x86_64/wheel/dnachisel/MutationSpace
copying build/lib/dnachisel/MutationSpace/MutationChoice.py -> build/bdist.linux-x86_64/wheel/./dnachisel/MutationSpace
copying build/lib/dnachisel/MutationSpace/MutationSpace.py -> build/bdist.linux-x86_64/wheel/./dnachisel/MutationSpace
copying build/lib/dnachisel/MutationSpace/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/MutationSpace
creating build/bdist.linux-x86_64/wheel/dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/DnaNotationPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/EnzymeSitePattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/HomopolymerPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/MotifPssmPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/RepeatedKmerPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/SequencePattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
copying build/lib/dnachisel/SequencePattern/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern
creating build/bdist.linux-x86_64/wheel/dnachisel/Specification
copying build/lib/dnachisel/Specification/FeatureRepresentationMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification
copying build/lib/dnachisel/Specification/Specification.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification
copying build/lib/dnachisel/Specification/SpecificationSet.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification
copying build/lib/dnachisel/Specification/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification
creating build/bdist.linux-x86_64/wheel/dnachisel/Specification/SpecEvaluation
copying build/lib/dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation
copying build/lib/dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation
copying build/lib/dnachisel/Specification/SpecEvaluation/SpecEvaluation.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation
copying build/lib/dnachisel/Specification/SpecEvaluation/SpecEvaluations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation
copying build/lib/dnachisel/Specification/SpecEvaluation/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation
creating build/bdist.linux-x86_64/wheel/dnachisel/biotools
copying build/lib/dnachisel/biotools/blast_sequence.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/bowtie.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/biotables.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/enzymes_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/formatting_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/gc_content.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/genbank_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/indices_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/random_sequences.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/sequences_differences.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
copying build/lib/dnachisel/biotools/sequences_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools
creating build/bdist.linux-x86_64/wheel/dnachisel/biotools/data
copying build/lib/dnachisel/biotools/data/README.md -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data
copying build/lib/dnachisel/biotools/data/complements.csv -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data
copying build/lib/dnachisel/biotools/data/iupac_notation.csv -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data
copying build/lib/dnachisel/biotools/data/nucleotide_to_regexpr.csv -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data
creating build/bdist.linux-x86_64/wheel/dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AllowPrimer.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidBlastMatches.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidChanges.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidHairpins.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidHeterodimerization.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidMatches.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/AvoidStopCodons.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/CodonSpecification.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceChanges.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceChoice.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceGCContent.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceMeltingTemperature.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforcePatternOccurence.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceRegionsCompatibility.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceSequence.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceTerminalGCContent.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/EnforceTranslation.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/SequenceLengthBounds.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/TerminalSpecification.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/UniquifyAllKmers.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
copying build/lib/dnachisel/builtin_specifications/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications
creating build/bdist.linux-x86_64/wheel/dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
copying build/lib/dnachisel/builtin_specifications/codon_optimization/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization
creating build/bdist.linux-x86_64/wheel/dnachisel/reports
copying build/lib/dnachisel/reports/SpecAnnotationsTranslator.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports
copying build/lib/dnachisel/reports/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports
copying build/lib/dnachisel/reports/colors_cycle.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports
copying build/lib/dnachisel/reports/optimization_reports.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports
copying build/lib/dnachisel/reports/tools.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports
creating build/bdist.linux-x86_64/wheel/dnachisel/reports/constraints_reports
copying build/lib/dnachisel/reports/constraints_reports/GraphicTranslator.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports
copying build/lib/dnachisel/reports/constraints_reports/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports
copying build/lib/dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports
copying build/lib/dnachisel/reports/constraints_reports/constraints_reports.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports
creating build/bdist.linux-x86_64/wheel/dnachisel/reports/assets
copying build/lib/dnachisel/reports/assets/logo.png -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/assets
copying build/lib/dnachisel/reports/assets/optimization_report.pug -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/assets
copying build/lib/dnachisel/reports/assets/style.css -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/assets
creating build/bdist.linux-x86_64/wheel/dnachisel/utils
copying build/lib/dnachisel/utils/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/utils
copying build/lib/dnachisel/utils/utils.py -> build/bdist.linux-x86_64/wheel/./dnachisel/utils
running install_egg_info
Copying dnachisel.egg-info to build/bdist.linux-x86_64/wheel/./dnachisel-3.2.16-py3.14.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/dnachisel-3.2.16.dist-info/WHEEL
creating '/build/source/dist/.tmp-4txx5rml/dnachisel-3.2.16-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'dnachisel/Location.py'
adding 'dnachisel/__init__.py'
adding 'dnachisel/cli.py'
adding 'dnachisel/version.py'
adding 'dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py'
adding 'dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py'
adding 'dnachisel/DnaOptimizationProblem/NoSolutionError.py'
adding 'dnachisel/DnaOptimizationProblem/__init__.py'
adding 'dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py'
adding 'dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py'
adding 'dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py'
adding 'dnachisel/DnaOptimizationProblem/mixins/__init__.py'
adding 'dnachisel/MutationSpace/MutationChoice.py'
adding 'dnachisel/MutationSpace/MutationSpace.py'
adding 'dnachisel/MutationSpace/__init__.py'
adding 'dnachisel/SequencePattern/DnaNotationPattern.py'
adding 'dnachisel/SequencePattern/EnzymeSitePattern.py'
adding 'dnachisel/SequencePattern/HomopolymerPattern.py'
adding 'dnachisel/SequencePattern/MotifPssmPattern.py'
adding 'dnachisel/SequencePattern/RepeatedKmerPattern.py'
adding 'dnachisel/SequencePattern/SequencePattern.py'
adding 'dnachisel/SequencePattern/__init__.py'
adding 'dnachisel/Specification/FeatureRepresentationMixin.py'
adding 'dnachisel/Specification/Specification.py'
adding 'dnachisel/Specification/SpecificationSet.py'
adding 'dnachisel/Specification/__init__.py'
adding 'dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py'
adding 'dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py'
adding 'dnachisel/Specification/SpecEvaluation/SpecEvaluation.py'
adding 'dnachisel/Specification/SpecEvaluation/SpecEvaluations.py'
adding 'dnachisel/Specification/SpecEvaluation/__init__.py'
adding 'dnachisel/biotools/__init__.py'
adding 'dnachisel/biotools/biotables.py'
adding 'dnachisel/biotools/blast_sequence.py'
adding 'dnachisel/biotools/bowtie.py'
adding 'dnachisel/biotools/enzymes_operations.py'
adding 'dnachisel/biotools/formatting_operations.py'
adding 'dnachisel/biotools/gc_content.py'
adding 'dnachisel/biotools/genbank_operations.py'
adding 'dnachisel/biotools/indices_operations.py'
adding 'dnachisel/biotools/random_sequences.py'
adding 'dnachisel/biotools/sequences_differences.py'
adding 'dnachisel/biotools/sequences_operations.py'
adding 'dnachisel/biotools/data/README.md'
adding 'dnachisel/biotools/data/complements.csv'
adding 'dnachisel/biotools/data/iupac_notation.csv'
adding 'dnachisel/biotools/data/nucleotide_to_regexpr.csv'
adding 'dnachisel/builtin_specifications/AllowPrimer.py'
adding 'dnachisel/builtin_specifications/AvoidBlastMatches.py'
adding 'dnachisel/builtin_specifications/AvoidChanges.py'
adding 'dnachisel/builtin_specifications/AvoidHairpins.py'
adding 'dnachisel/builtin_specifications/AvoidHeterodimerization.py'
adding 'dnachisel/builtin_specifications/AvoidMatches.py'
adding 'dnachisel/builtin_specifications/AvoidPattern.py'
adding 'dnachisel/builtin_specifications/AvoidStopCodons.py'
adding 'dnachisel/builtin_specifications/CodonSpecification.py'
adding 'dnachisel/builtin_specifications/EnforceChanges.py'
adding 'dnachisel/builtin_specifications/EnforceChoice.py'
adding 'dnachisel/builtin_specifications/EnforceGCContent.py'
adding 'dnachisel/builtin_specifications/EnforceMeltingTemperature.py'
adding 'dnachisel/builtin_specifications/EnforcePatternOccurence.py'
adding 'dnachisel/builtin_specifications/EnforceRegionsCompatibility.py'
adding 'dnachisel/builtin_specifications/EnforceSequence.py'
adding 'dnachisel/builtin_specifications/EnforceTerminalGCContent.py'
adding 'dnachisel/builtin_specifications/EnforceTranslation.py'
adding 'dnachisel/builtin_specifications/SequenceLengthBounds.py'
adding 'dnachisel/builtin_specifications/TerminalSpecification.py'
adding 'dnachisel/builtin_specifications/UniquifyAllKmers.py'
adding 'dnachisel/builtin_specifications/__init__.py'
adding 'dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py'
adding 'dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py'
adding 'dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py'
adding 'dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py'
adding 'dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py'
adding 'dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py'
adding 'dnachisel/builtin_specifications/codon_optimization/__init__.py'
adding 'dnachisel/reports/SpecAnnotationsTranslator.py'
adding 'dnachisel/reports/__init__.py'
adding 'dnachisel/reports/colors_cycle.py'
adding 'dnachisel/reports/optimization_reports.py'
adding 'dnachisel/reports/tools.py'
adding 'dnachisel/reports/assets/logo.png'
adding 'dnachisel/reports/assets/optimization_report.pug'
adding 'dnachisel/reports/assets/style.css'
adding 'dnachisel/reports/constraints_reports/GraphicTranslator.py'
adding 'dnachisel/reports/constraints_reports/__init__.py'
adding 'dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py'
adding 'dnachisel/reports/constraints_reports/constraints_reports.py'
adding 'dnachisel/utils/__init__.py'
adding 'dnachisel/utils/utils.py'
adding 'dnachisel-3.2.16.dist-info/licenses/LICENSE'
adding 'dnachisel-3.2.16.dist-info/METADATA'
adding 'dnachisel-3.2.16.dist-info/WHEEL'
adding 'dnachisel-3.2.16.dist-info/entry_points.txt'
adding 'dnachisel-3.2.16.dist-info/top_level.txt'
adding 'dnachisel-3.2.16.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built dnachisel-3.2.16-py3-none-any.whl
Finished creating a wheel...
Finished executing pypaBuildPhase
Running phase: pythonRuntimeDepsCheckHook
Executing pythonRuntimeDepsCheck
Checking runtime dependencies for dnachisel-3.2.16-py3-none-any.whl
Finished executing pythonRuntimeDepsCheck
Running phase: installPhase
Executing pypaInstallPhase
Successfully installed dnachisel-3.2.16-py3-none-any.whl
Finished executing pypaInstallPhase
Running phase: pythonOutputDistPhase
Executing pythonOutputDistPhase
Finished executing pythonOutputDistPhase
Running phase: fixupPhase
shrinking RPATHs of ELF executables and libraries in /nix/store/25zm6m11d1caax11snlgcr577m2w4h0y-python3.14-dnachisel-3.2.16
checking for references to /build/ in /nix/store/25zm6m11d1caax11snlgcr577m2w4h0y-python3.14-dnachisel-3.2.16...
patching script interpreter paths in /nix/store/25zm6m11d1caax11snlgcr577m2w4h0y-python3.14-dnachisel-3.2.16
stripping (with command strip and flags -S -p) in /nix/store/25zm6m11d1caax11snlgcr577m2w4h0y-python3.14-dnachisel-3.2.16/lib /nix/store/25zm6m11d1caax11snlgcr577m2w4h0y-python3.14-dnachisel-3.2.16/bin
shrinking RPATHs of ELF executables and libraries in /nix/store/n9ivapbyxlvi737krh3cf0myy3wdf17y-python3.14-dnachisel-3.2.16-dist
checking for references to /build/ in /nix/store/n9ivapbyxlvi737krh3cf0myy3wdf17y-python3.14-dnachisel-3.2.16-dist...
patching script interpreter paths in /nix/store/n9ivapbyxlvi737krh3cf0myy3wdf17y-python3.14-dnachisel-3.2.16-dist
Rewriting #!/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7/bin/python3.14 to #!/nix/store/d64q19q1xjdwfhqx6czvrjgrhq0n3lcc-python3-3.14.7
wrapping `/nix/store/25zm6m11d1caax11snlgcr577m2w4h0y-python3.14-dnachisel-3.2.16/bin/dnachisel'...
Executing pythonRemoveTestsDir
Finished executing pythonRemoveTestsDir
Running phase: installCheckPhase
setting known thread variables to default: 1
 OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1 BLIS_NUM_THREADS=1 VECLIB_MAXIMUM_THREADS=1 NUMBA_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1
no Makefile or custom installCheckPhase, doing nothing
Running phase: pythonCatchConflictsPhase
Running phase: pythonRemoveBinBytecodePhase
Running phase: pythonImportsCheckPhase
Executing pythonImportsCheckPhase
Check whether the following modules can be imported: dnachisel
mkdir -p failed for path /homeless-shelter/.config/matplotlib: [Errno 13] Permission denied: '/homeless-shelter'
Matplotlib created a temporary cache directory at /build/matplotlib-ep99kx6u because there was an issue with the default path ({configdir}); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Fontconfig error: Cannot load default config file: File not found

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	/var/cache/fontconfig
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Running phase: pythonMetadataCheckPhase
Executing pythonMetadataCheckPhase
Running phase: pytestCheckPhase
Executing pytestCheckPhase
setting known thread variables to default: 1
 OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1 BLIS_NUM_THREADS=1 VECLIB_MAXIMUM_THREADS=1 NUMBA_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1
pytest flags: -m pytest tests -k not\ \(test_avoid_phage_blast_matches\)\ and\ not\ \(test_avoid_matches_with_phage\)
============================= test session starts ==============================
platform linux -- Python 3.14.7, pytest-9.1.1, pluggy-1.6.0
rootdir: /build/source
configfile: pyproject.toml
collected 149 items / 2 deselected / 147 selected                              

tests/builtin_specifications/test_AllowPrimer.py .                       [  0%]
tests/builtin_specifications/test_AvoidBlastMatches.py .                 [  1%]
tests/builtin_specifications/test_AvoidChanges.py .....                  [  4%]
tests/builtin_specifications/test_AvoidHairpins.py ..                    [  6%]
tests/builtin_specifications/test_AvoidMatches.py .                      [  6%]
tests/builtin_specifications/test_AvoidPattern.py .........              [ 12%]
tests/builtin_specifications/test_AvoidRareCodons.py ....                [ 15%]
tests/builtin_specifications/test_AvoidStopCodons.py .                   [ 16%]
tests/builtin_specifications/test_CodonOptimize.py .......               [ 21%]
tests/builtin_specifications/test_EnforceChanges.py ...........          [ 28%]
tests/builtin_specifications/test_EnforceChoice.py .                     [ 29%]
tests/builtin_specifications/test_EnforceGCContent.py ..                 [ 30%]
tests/builtin_specifications/test_EnforceMeltingTemperature.py .         [ 31%]
tests/builtin_specifications/test_EnforcePatternOccurence.py ...         [ 33%]
tests/builtin_specifications/test_EnforceRegionsCompatibility.py .       [ 34%]
tests/builtin_specifications/test_EnforceSequence.py ..                  [ 35%]
tests/builtin_specifications/test_EnforceTerminalGCContent.py .          [ 36%]
tests/builtin_specifications/test_EnforceTranslation.py ......           [ 40%]
tests/builtin_specifications/test_SequenceLengthBounds.py .              [ 40%]
tests/builtin_specifications/test_UniquifyAllKmers.py ......             [ 44%]
tests/test_Location.py .........................................         [ 72%]
tests/test_MutationChoices.py ...                                        [ 74%]
tests/test_NoSolutionError.py ...                                        [ 76%]
tests/test_biotools.py .......                                           [ 81%]
tests/test_circular_sequences.py ..                                      [ 82%]
tests/test_constraints_reports.py .                                      [ 83%]
tests/test_determinism/test_determinism.py ..                            [ 85%]
tests/test_features_annotations.py ...                                   [ 87%]
tests/test_io.py ....                                                    [ 89%]
tests/test_optimization_with_report.py ....                              [ 92%]
tests/test_patterns.py ...                                               [ 94%]
tests/test_scenarios/test_primers_collection.py .                        [ 95%]
tests/test_utils.py .                                                    [ 95%]
tests/tests_from_genbanks/test_from_genbanks.py ......                   [100%]

=============================== warnings summary ===============================
tests/builtin_specifications/test_AllowPrimer.py::test_AllowPrimer
tests/builtin_specifications/test_EnforceMeltingTemperature.py::test_enforce_melting_temperature
tests/tests_from_genbanks/test_from_genbanks.py::test_all_shorthands
  /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/bindings.py:489: UserWarning: Function deprecated please use "calc_tm" instead
    return THERMO_ANALYSIS.calcTm(seq)

tests/builtin_specifications/test_AllowPrimer.py::test_AllowPrimer
tests/test_scenarios/test_primers_collection.py::test_primers_collection_example
  /nix/store/ic3bvg1qr4lvbm0lslgcvr6ni9qf9wbl-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/bindings.py:305: UserWarning: Function deprecated please use "calc_heterodimer" instead
    return THERMO_ANALYSIS.calcHeterodimer(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================ 147 passed, 2 deselected, 5 warnings in 12.72s ================
Finished executing pytestCheckPhase
Running phase: pytestcachePhase
Running phase: pytestRemoveBytecodePhase