SeqAn3 3.1.0-rc.2
The Modern C++ library for sequence analysis.
Stability and future-proofness

Summary: SeqAn3 adheres to semantic versioning and provides a stable API within one major release (all of seqan-3.*.*) unless otherwise noted. There is no ABI stability.

Many of the rules on this page are derived from the abseil library.

API stability

In general, you can expect all entities within the seqan3 namespace to be usable throughout the entire release cycle of SeqAn3, i.e. if you write an application that includes seqan-3.1.1, you should be able to re-compile it against seqan-3.4.5 without errors.

Exceptions to the previous rule:

  1. Do not depend upon internal details. If something is in a namespace or filename/path that includes the word detail or if it is private to a class type, you are not allowed to depend upon it any way. More generally, if it is not part of the user documentation, it is not part of the API.
  2. Do not depend on entities marked as "experimental" or "NOAPI". Major changes to the library like new modules are often marked as experimental within the first minor release they appear in. This means we do not guarantee stability until the next minor release happens and the experimental flag is removed. Very few entities in namespace seqan3 are permanently marked as "NOAPI" which designates them as subject to unannounced change. This is usually the case for auxiliary data structures that would be part of seqan3::detail were they not needed to generate correct API documentation for entities in seqan3.
  3. Do not depend on the signatures of SeqAn APIs. In particular you may not take the address of APIs in SeqAn and you may not use metaprogramming tricks to depend on those signatures. We reserve the right to:
    • Add new names to namespace seqan3 and any sub-namespaces
    • Add new member functions to types in namespace seqan3
    • Add new overloads to existing functions
    • Add new default arguments to functions and templates
    • Change return-types of functions in compatible ways (void to anything, numeric types in a widening fashion, etc.).
  4. Do not forward declare SeqAn APIs. This is actually a sub-point of the previous one, but can be surprising. Any refactoring that changes template parameters, default parameters, or namespaces will be a breaking change in the face of forward-declarations.
  5. Avoid unnecessary dependency on Argument-Dependent Lookup (ADL) when calling SeqAn APIs. Some APIs are designed to work via ADL (e.g. operator<< for iostreams, unqualified swap in generic code, etc.) For most APIs, however, ADL is not part of the design. Calling functions from namespace seqan3 via ADL, unless that is explicitly intended as part of the design, should be avoided.
  6. Include What You Use. We may make changes to the internal include-graph for SeqAn headers - if you use an API, please include the relevant header file directly.
  7. Do not make unqualified calls in the global namespace. A call like f(a); for a function f in the global namespace can become ambiguous if/when we add seqan3::f (especially if a is a SeqAn type). We generally do not recommend you use the global namespace for anything. If you must, please qualify any call that accepts a type provided by SeqAn.

In the very rare case that we feel a breaking change to the API is unavoidable, we promise to provide the following update path:

  • A new minor version is introduced that supports the new API.
  • The old API is still supported, but might be marked [[deprecated]].
  • We provide very extensive documentation on the change or an automated tool that converts your code from using the old API to using the new API.
  • The next (or another future) minor version removes the old API.
Warning
As a special case of point 2. the entire 3.0.* release is marked as experimental. We will do our best not to break things, but similar to the releases of GCC, you should consider seqan-3.1.0 as the first API-stable release of SeqAn3.

ABI stability

No guarantees of any kind are provided in regard to the in-memory representation of our data structures. We intend for SeqAn to be built from source. The internal layout of our types may change at any point, without notice. In particular, building SeqAn in the presence of different C++ standard library types may change SeqAn types, especially for pre-adopted types in the std module — these will resolve to standard library types as of C++20.

We do promise, however, that SeqAn3 data structures¹ serialised to disk are de-serialisable by later versions of SeqAn3. The reverse is not true, however, and re-serialising a data structure serialised by a previous release might result in a different (updated) on-disk format.

¹ Iff they are API stable.

Platform stability

The main requirement for being able to use SeqAn is a supported compiler and in general all operating systems that provide a supported compiler should be supported. We currently support the following compilers on 64-bit operating systems with little-endian CPU architectures only:

  • GCC7, GCC8, GCC9, GCC10, GCC11

We promise to support all of the above compilers until the last release of SeqAn3, or until all of the following operating systems provide a newer supported compiler:

Operating System Supported Releases¹
RedHat Enterprise Linux the latest release ²
CentOS Linux the latest release ²
SUSE Linux Enterprise Server the latest release
Debian GNU/Linux "stable" and "old-stable"
Ubuntu Linux the two latest LTS releases
macOS the two latest releases
FreeBSD the latest stable release

"Support" in this context does not imply that we package SeqAn for these operating systems (although we do in some cases), it merely states that you should be able to build applications that depend on SeqAn on the given platforms. This implies the availability of a supported compiler in the default package repositories or via easy-to-use third party services.

Note
Only the most recent minor release of a compiler is guaranteed to be supported, e.g. when gcc-10.4 is released, we may drop support for gcc-10.3. Since all platforms with an older version receive minor release updates, this should not be a problem.

More platforms and compilers will be added during the SeqAn3 lifecycle, but some will be marked as experimentally supported which means support may be dropped again later on.

We promise to provide good forward-compatibility with the C++ standard. And we will strive to fix any warnings that are added by newer versions of a supported compiler.

¹ This site provides a good overview of what the current release and its lifecycle is.
² We consider CentOS 7 / RedHat Enterprise Linux (RHEL) 7 as being community-supported. That means issues and patches are welcome, but we do not actively test for those operating systems. See this related issue.

Dependencies

We may add additional dependencies in future minor releases of SeqAn or raise the required versions of current dependencies. However, we promise not to add required dependencies that result in new licensing obligations or link-time dependencies.