What is next#

Graphs#

  • IDEA: to GFA function

Graph views#

  • IDEA: graphs views

    • See graphtools python package

    • See backup folder

Vertices#

Virtual suppress#

  • IDEA: virtual suppress vertices

Vertex is not suppressed in memory:

  • index will not change

Real suppress#

  • Real suppress vertices

Vertex is suppressed in memory:

  • Vertex index will change

  • Dichotomy on number of removing pull update times \(|E|\)

  • Delete attributes -> \(O(|V|)\) if list

  • DOC: explain complexity, verify with preprint

  • TODO: verify if in code is same as in the preprint

Edges#

Add edges#

  • Add several edges \((u, v)\) same orientations?

    • Then search for e_index method should yield on them

Edge indices#

  • TODO: forward and reverse edge should not have the same index

    • Do it as described in the preprint

Virtual suppress#

  • Virtual suppress edges

Edge is not suppressed in memory:

  • Edge indices will not change

  • DOC: explain complexity

  • TODO: verify if in code is same as in the preprint

Real suppress#

  • IDEA: Real suppress edges

  • Edge is suppressed in memory:

    • Edge indices will change

    • Dichotomy on number of removing pull update times \(|E|\)

    • delete attributes -> \(O(|E|)\) if list

  • XXX: explain complexity, not sure about this result

SplitStrandsEdges#

  • REFACTOR: orientations method (from _vertices attribute before) should be a shared attribute with vertices and edges

  • IDEA: this class is for object representing one connected component, should I verify when delete/add the connectivity? -> fully dynamic connectivity

    • XXX: for now, we can have an attribute to say: certain or not to be in only one cc

Packaging and Gitlab#

CI/CD#

  • TODO: script bump_release.sh (see https://nvie.com/posts/a-successful-git-branching-model/) that modify version in pyptoject.toml

  • TODO: don’t accept push to master if the version in pyproject.toml is the same as previously

    • TODO: scripts release push

  • auto-release gitlab