libbdsg

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When I use python bdsg to deal with a packedgraph, I found a question.

3

 1. I want to use follow_edges to get all the nodes which connect to node2, but i only get node3.(In fact, node3 and node4 are both its' connecting edges)....

pioneer-pi

I wanted `net_handle_t`'s to be used in sets in python so I needed the bindings to include equality and hashing. @adamnovak or maybe @ctcisar, can I do this? It looks...

xchang1

Bumps [certifi](https://github.com/certifi/python-certifi) from 2020.6.20 to 2022.12.7. Commits 9e9e840 2022.12.07 b81bdb2 2022.09.24 939a28f 2022.09.14 aca828a 2022.06.15.2 de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ... b8eb5e9 2022.06.15.1...

dependabot[bot]

Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.25.11 to 1.26.5. Release notes Sourced from urllib3's releases. 1.26.5 :warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap Fixed...

dependabot[bot]

Bumps [babel](https://github.com/python-babel/babel) from 2.8.0 to 2.9.1. Release notes Sourced from babel's releases. Version 2.9.1 Bugfixes The internal locale-data loading functions now validate the name of the locale file to be...

dependabot[bot]

Docs/Python bindings broke because of SnarlDistanceIndex

1

The ReadTheDocs builds have been failing for a while with: ``` ImportError: overloading a method with both static and instance methods is not supported; error while attempting to bind instance...

adamnovak

The libbdsg ReadTheDocs docs, separate from the vg Doxygen docs, have a Doxygen-derived listing of C++ methods for the handle graph API, at https://bdsg.readthedocs.io/en/master/rst/cppapi.html Even in the last successful docs...

adamnovak

Right now, overlays like `PackedPathPositionOverlay` will index all the paths that `for_each_path_handle()` returns. For backward compatibility, I have `for_each_path_handle()` omitting haplotype paths, at least for graphs like GBWTGraph where there...

adamnovak

I added a bunch of path metadata methods in #153 but I never added the stubs to call through to the backing graph in the overlays. So I think right...

adamnovak

Add low level methods for handle graphs

2

I've been using paths quite a lot in bdsg and found that a couple methods would simplify things: ``` pop_path_front/back rename_path ``` Based on the existing methods `prepend_step` and `append_step`,...

rlorigro