Cdlib

**Emperor of the Galaxy** is the perfect codename for (a release of) a community detection library.


> Many millennia prior to the events of the series (_The Hitchhiker's Guide to the Galaxy_), the final Emperor of the [Galactic Empire](https://en.wikipedia.org/w/index.php?title=Galactic_Empire_(Hitchhiker%27s_Guide_to_the_Galaxy)&action=edit&redlink=1) (in the Hitchhiker's universe) was placed into a stasis field during his dying moments: thus leaving the Empire with a technically ruling, but actually near-dead Emperor, with all his heirs long since dead. And so today, an Imperial President, elected by the Galactic Assembly, has all the trappings of power, without actually wielding any. This was the office held by [Yooden Vranx](https://en.wikipedia.org/wiki/Yooden_Vranx) and [Zaphod Beeblebrox](https://en.wikipedia.org/wiki/Zaphod_Beeblebrox).

**Emperor of the Galaxy** comes with several new features and bugfixes, in particular:

- A completely reorganized readthedocs documentation;
- Support for [Dynamic Community Events](https://cdlib.readthedocs.io/en/latest/reference/events.html) detection, analysis, validation and I/O;
- Novel measures for clustering comparisons (leveraging [clusim](https://github.com/Hoosier-Clusters/clusim/tree/master) as optional dependency)
- Novel CD algorithms;
- Novel and updated viz (community-graph and community events);

What's Changed
* 📝 Fix description of the cut ratio formula [ci skip] by EdGeber in https://github.com/GiulioRossetti/cdlib/pull/224
* Updating vizualisation of communities by amineitji in https://github.com/GiulioRossetti/cdlib/pull/234
* pass partition as 2nd input parameter to the Louvain by Praveer1981 in https://github.com/GiulioRossetti/cdlib/pull/232
* New function - viz.plot_network_highlighted_clusters (collaborating with Remy Cazabet at UCBL) by amineitji in https://github.com/GiulioRossetti/cdlib/pull/235
* Clustering comparison by GiulioRossetti in https://github.com/GiulioRossetti/cdlib/pull/237
* Community events by GiulioRossetti in https://github.com/GiulioRossetti/cdlib/pull/238

New Contributors
* EdGeber made their first contribution in https://github.com/GiulioRossetti/cdlib/pull/224
* amineitji made their first contribution in https://github.com/GiulioRossetti/cdlib/pull/234
* Praveer1981 made their first contribution in https://github.com/GiulioRossetti/cdlib/pull/232

**Full Changelog**: https://github.com/GiulioRossetti/cdlib/compare/v0.3.0...v0.4.0

Deep Thought is the perfect codename for (a release of) a community detection library.

> [she] is a computer that was created by a pan-dimensional, hyper-intelligent species of beings (whose three-dimensional protrusions into our universe are ordinary white mice) to come up with the [Answer to The Ultimate Question of Life, the Universe, and Everything](https://en.wikipedia.org/wiki/Answer_to_The_Ultimate_Question_of_Life,_the_Universe,_and_Everything). Deep Thought is the size of a small city.
>
>When, after seven and a half million years of calculation, the answer finally turns out to be [42](https://en.wikipedia.org/wiki/42_(number)#The_Hitchhiker's_Guide_to_the_Galaxy), Deep Thought admonishes Loonquawl and Phouchg (the receivers of the Ultimate Answer) that:
> **"[she] checked it very thoroughly, and that quite definitely is the answer. I think the problem, to be quite honest with you is that you've never actually known what the question was."**
>
> Douglas Adams - Hitchhiker's Guide to the Galaxy

Deep Thought captures the main aspects of Community Detection:
- Algorithms might take a long time to compute;
- Practitioners search for insights when they decide to apply CD to their data;
- Being the problem ill-posed the answer an algorithm provides makes sense only if the research question, the data, and the assumptions are well-stated and understood from the very beginning.


What's Changed
This version reduces the number of available algorithms to simplify the dependency chain and installation process.

Dependencies upgraded (major breaking changes)
- networkx >= 3.0

Dependencies removed:
- karateclub (hopefully, it will be reintroduced in a later release)

Dependencies made optional:
- pyclustering
- leidenalg
- pycombo
- networkit
- infomap

New CD algorithms:
- Bayan (depends on bayanpy - optional dependency)

Additional notes:
- PiPy installation now has four modalities: vanilla; [C] that includes packages depending on C code (safe for *nix OS); [pypi] that provides for all those pypi dependencies that are not satisfiable on conda; [all] that includes all (pip installable - except for graph-tool) dependencies.
- `graph-tool` support is maintained, but its dependency is not explicitly introduced (neither in pypi nor in the conda distributions). Its installation has to be fulfilled separately from `cdlib`.
- `bayanpy` depends on [Gouroby](https://www.gurobi.com/) solver that needs to be installed separately.
- if the `infomap` package is not installed, `cdlib` will fall back on the `python-igraph` implementation of such an algorithm.


**Full Changelog**: https://github.com/GiulioRossetti/cdlib/compare/v0.2.6...v0.3.0

:new: CDlib light version (python only dependencies)

:arrow_up: python-infomap 1.7.1 support