BanditPAM v2.0.0

BanditPAM v2.0.0 PR. Contains many changes:

Organization and Functionality:

• Everything has been migrated to the namespace km for better encapsulation (Fixes #135)
• We now allow for <100 datapoints by setting the batchSize to min(dataset_size, 100) (Fixes #158)
• We now return ints for the medoid indices instead of floats, including a list of a single int if k=1 (Fixes #152)
• We reformatted the functions in each .cpp file to appear in the same order they appear in the corresponding .hpp
• The code has been refactored for better organization
• The code in setup.py is now encapsulated (Fixes #131)
• The check for LLVM clang is now back in setup.py (Fixes #79)
• Attempting to set the build or swap confidences when not using the BanditPAM algorithm results in an error

Tests:

• The code's accuracy is now automatically checked by running test cases via Github actions (Fixes #52)
• An error is now thrown if an empty dataset is passed
• We now use FastPAM1 instead of PAM for the tests, which significantly speeds them up
• We added additional functionality to the tests to error quickly on failures
• The code is now tested on Python3.9 via Github actions (Fixes #46)

Style:

• We have changed variable names to camelCase for C++ variables (Fixes #140)
• The code is now automatically checked for style compliance via Github actions
• The python code now contains typehints
• const qualifiers have been added where possible

Documentation:

• We now publicly host the documentation on ReadTheDocs, via an integration with Sphinx (Fixes #165, Fixes #124)
• We have updated the README with links to the ReadTheDocs and SAIL blog post
• We have deleted duplicate docstrings in the .cpp files, moved all docstrings to the .hpp files, updated the docstrings, and added the necessary @throws and @returns (Fixes #127)

Full Changelog: v1.0.5...v2.0.0

BanditPAM v1.0.5

BanditPAM v1.0.5 Release Notes:

• Removes all logging and the verbosity flag, which were unnecessary
• Enables users to install the package via pip on Google Colab (by using prebuilt armadillo libraries and copying them over to the correct places)
• Bumps the version to v1.0.5
• Cleans up some nits

Implementing tags for release

Creating the first tag, v1.0.2 to keep track of releases.

Tag created by @motiwari .