SBOL Utilities 1.0-alpha17

This release of SBOL Utilities includes the following utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.
• sbol-converter converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats (plus specific converters: sbol2-to-sbol3, sbol3-to-sbol2, sbol-to-genbank, genbank-to-sbol, sbol-to-fasta, and fasta-to-sbol)
• sbol-diff computes and reports the difference between two SBOL3 documents.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

New in this release:

• Experimental python-native converter between GenBank and SBOL3
• Support for Python 3.11
• Utilities with "2" names have been changed to "to" (e.g., "fasta-to-sbol" instead of "fasta2sbol")

Full Changelog: 1.0a16...1.0a17

SBOL Utilities 1.0-alpha16

This release of SBOL Utilities includes the following utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.
• sbol-converter converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats.
• sbol-diff computes and reports the difference between two SBOL3 documents.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

New in this release:

• Fix for local conversion on Windows
• Additional utilities in the component package
• Add with cached_references(doc) form to accelerate lookups

SBOL Utilities 1.0-alpha15

This release of SBOL Utilities includes the following utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.
• sbol-converter converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats.
• sbol-diff computes and reports the difference between two SBOL3 documents.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

New in this release:

• Conversion to/from GenBank without sending materials to online converter service (should be faster, confidental, and able to operate offline)

SBOL Utilities 1.0-alpha14

This release of SBOL Utilities includes the following utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.
• sbol-converter converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats.
• sbol-diff computes and reports the difference between two SBOL3 documents.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

New in this release:

• Addition of high-level functions for building components
• Fixed some SBOL2 <-> SBOL3 conversion bugs
• Improved documentation and error messages

SBOL Utilities 1.0-alpha13

This release of SBOL Utilities includes the following utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.
• sbol-converter converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats.
• sbol-diff computes and reports the difference between two SBOL3 documents.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

This is a patch release fixing a problem in the distribution of 1.0a12 that failed to install some converters when installed via pip

SBOL Utilities 1.0-alpha12

This release of SBOL Utilities includes the following utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.
• sbol-converter converts between any of the SBOL3, SBOL2, GenBank, and FASTA formats.
• sbol-diff computes and reports the difference between two SBOL3 documents.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

New this release:

• sbol-converter and sbol-diff utilities
• Online conversion tools are not used by default: user must explicitly decide to expose information
• Correction of bugs related to whitespace and namespace assignment in excel-to-sbol

SBOL Utilities 1.0-alpha11

Early release of SBOL Utilities with four utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

This is a patch release handling updates in pySBOL3 1.0a8. Specifically:

• Fix breaking changes from pySBOL3 1.0a7 to 1.0a8
• Move id_sort from workarounds to helper_functions
• Deprecate workarounds that are no longer needed

SBOL Utilities 1.0-alpha10

Early release of SBOL Utilities with four utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.

In addition, for python users SBOL Utilities provides sequence and component packages to simplify common tasks with those types of objects.

New this release:

• Compatibility for python 3.7 forward
• New sequence and component packages with higher level functions for working with those types of objects
• Migration of many helper_functions into sequence and workarounds packages not backward compatible
• Fix an excel-to-sbol bug with sequence identities
• Unpin required pySBOL3 version

SBOL Utilities 1.0-alpha9

Early release of SBOL Utilities with four utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.

New this release:

• excel-to-sbol supports sourcing of GenBank and FASTA from arbitrary URLs, trims extensions
• Additional helper functions for file extensions and identity manipulations

SBOL Utilities 1.0-alpha8

Early release of SBOL Utilities with four utilities:

• graph-sbol uses graphviz to render the object tree in an SBOL Document.
• excel-to-sbol extracts SBOL parts and libraries from an Excel file (an SBOL3 version of the SBOL2 Excel-to-SBOL utility)
• sbol-expand-derivations searches through an SBOL file for CombinatorialDerivation objects and expands them to create a library of all of the specific constructs.
• sbol-calculate-sequences attempts to calculate the sequence of any DNA Component that can be fully specified from the sequences of its sub-components.

New this release:

• MIT license
• Version pin on pySBOL3 dependency