Add combine archive #18
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Windows doing its best to be the biggest headache at cross-platform development again ☕️
Enhanced the Wrapper struct to support custom deserialization logic that iterates through all child elements in an annotation and attempts to deserialize each into the target type, using the first successful match. Added a new test to verify complex annotation deserialization and updated documentation for clarity.
This reverts commit c51482e.
Updated the quick-xml dependency from 0.37.2 to 0.38.0 in Cargo.toml to keep dependencies up to date and benefit from the latest fixes and features.
Replaces instances of format!(...) and println!(...) with inline string interpolation (e.g., println!("{var}")). This modernizes the codebase for improved readability and consistency, without changing functionality.
Introduces methods to retrieve, add, and remove XML namespaces in SBMLDocument, enabling better handling of SBML package extension namespaces. Includes corresponding unit tests for these new methods.
Added #[allow(clippy::mut_from_ref)] to the base() method in the SBase trait to suppress Clippy lint warning. This is necessary due to the method's signature returning a mutable reference from an immutable one, which is required for interoperability with C++ code.
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This pull request introduces multiple changes across the codebase, focusing on dependency updates, improved formatting, new functionality for handling COMBINE archives, and expanded test coverage. Key updates include the addition of test modules for annotations, the introduction of a
CombineArchiveErrorenum for better error handling, and the inclusion of new dependencies for enhanced functionality.Dependency Updates:
quick-xmlto version0.38.0and addedzipversion4.0.0as a new dependency inCargo.toml. Addedtempfileversion3.20.0todev-dependencies. [1] [2]Formatting Improvements:
format!calls with inline formatting syntax (e.g.,format!("{metadata}")) inbuild.rsand various test files to improve code readability. [1] [2] [3] [4] [5] [6] [7] [8] [9]New Features:
examples/create.rs.CombineArchiveErrorenum for detailed error handling when working with COMBINE archives.Test Coverage:
compartments.rs,parameters.rs,reactions.rs,rules.rs,species.rs,unitdefs.rs) to validate serialization and deserialization of annotations. [1] [2] [3] [4] [5] [6]Codebase Organization:
combinemodule insrc/lib.rsto centralize COMBINE-related functionality.get_unit_definition!macro inlocalparameter.rsto retrieve unit definitions for local parameters.