BanditPAM v4.0.4

BanditPAM v4.0.4 contains the following changes:

Organization and Functionality:

• Added a new GHA to build the package and run tests on Windows.
• Added a configuration file v2 for our Read the Docs documentation.
• Added a convenience script retrieve_windows_python_files.sh to retrieve clang_rt.asan_dynamic-x86_64.dll automatically for the Windows Python build.

Tests:

• Updated tests/test_smaller.py to use different data types on different platforms when loading data/scrna_reformat.csv.gz to adjust memory usage.

Documentation:

• Updated the Windows installation instructions to use the convenience script retrieve_windows_python_files.sh.

Full Changelog: v4.0.3...v4.0.4

BanditPAM v4.0.3

BanditPAM v4.0.3 contains the following changes:

Organization and Functionality:

• Ensure GHAs don't run on a tag push.
• Automatically upload wheels to TestPyPI on a PR update and PyPI on release in GHAs (fixes #256)
• Add tests/test_initialization to the GHAs that build and test the package.
• Loss issues are resolved in all versions of BanditPAM
• The clustering results are now identical to scikit-learn's implementation. This was achieved by increasing the batch size for accurate estimation of the standard deviation of the arm parameters and by fixing the bug that drops arms whose lower confidence bounds equal the lowest upper confidence bounds (fixes #252).
• Add complexity to scripts/comparison_utils.py, such as printing cache writes.
• Update cache calculations in src/algorithms/kmedoids_algorithm.cpp and add an assertion for better error handling.
• Turn VERSION_INFO into a string in src/python_bindings/kmedoids_pywrapper.cpp.
• Update build_confidence in src/python/kmedoids_pywrapper.cpp to avoid stochasticity issue in tests/test_larger.py.

Tests:

• Update assertion in tests/test_initialization to match with new build_confidence in src/python/kmedoids_pywrapper.cpp.
• Use NumPy and Armadillo seeds for reproducibility.
• Update some tests in tests/test_larger.py to count the proportion of passing cases instead of immediately failing.

Style:

• Ran black, docformatter, flake8, and clang-format.

Documentation:

• Slightly updated the documentation on the CMake build on Windows to clarify how to use retrieve_windows_cmake_files.sh.

Full Changelog: v4.0.2...v4.0.3

BanditPAM v4.0.2

BanditPAM v4.0.2 contains the following changes:

Organization and Functionality:

• We include the files, edits, and instructions to succeed in the CMake and Python builds on Windows, Mac, and Linux.
• Note that carma has now bumped to version v0.6.7.
• Does not require LLVM's clang when running pip install . (Fixes #242)
• Swaps are only performed in banditpam.cpp, banditpam_orig.cpp, fastpam1.cpp, and pam.cpp if k=1 (Fixes #227)
• Uses bool data type when necessary (Fixes #232)
• Implements the buildLoss functionality (Fixes #234)
• Modifies the FastPAM1 implementation such that the runtime is significantly reduced while resulting in the same medoids (Fixes #228)
• Ensures Linux GHA error does not appear anymore (Fixes #250)
• Update GHAs to use python -m pip throughout instead of just pip
• Mac GHAs now run on macos-latest as macos-10.15 is now unsupported.
• Fixes failing GHAs that activated on PR.

Tests:

• Updated incorrect assertion in tests/test_initialization.py

Style:

• Ran black, flake8, a combination of clang-format and cpplint, and our own style definitions over codebase (such as using 2 spaces instead of 4 in C++ code).

Documentation:

• Documented functional CMake and Python builds on Windows.

Full Changelog: v4.0.1...v4.0.2

BanditPAM v4.0.1

BanditPAM v4.0.1 contains a few minor changes:

Organization and Functionality:

• Makes cibuildwheel more verbose
• For CMake builds, checks out the current branch (not main) in GHA
• Changes the CMake build to Release mode to avoid running sanitizers in GHA
• Adds status badges (Fixes #224)
• Fixes the GHA builds by including the proper directory for armadillo (the locally installed version)

Tests:
No changes.

Style:
No changes.

Documentation:

• Updates README.md and other docs

BanditPAM v4.0.0

BanditPAM v4.0.0 contains many big changes:

Organization and Functionality:

• We now rely on C++17 for std::optional
• We implement a new version of BanditPAM that considers only $n$ non-medoids as arms in the SWAP step, each of which has $k$ values. This leads to a significant speedup. The old BanditPAM is still available as BanditPAM_orig
• Update the GHA to use newer machine images and update the dependencies on Ubuntu 22.04
• Split the cmake build into a separate GHA
• Added Python 3.11 to GHA where possible, removed Python 3.6
• Restores the ability to call OpenMP functions omp_get_max_threads and omp_set_num_threads, which should resolve the remaining issues on M1 Macs
• We allow users to pass in a distance matrix (Fixes #164 )
• Now uses buildConfidence and swapConfidence in log (ln) space
• Allows users to retrieve the sample complexities and caching statistics
• Adds scripts/cache_measurements.py, scripts/compare_banditpam_versions.py, scripts/comparison_utils.py, scripts/comparison_with_fasterpam.py, scripts/dist_mat_test.py, scripts/timing_dist_mat.py, scripts/sample_complexity_with_k.py, and scripts/scaling_with_k.py
• Properly builds Mac wheels using Apple Clang and enabling OpenMP. Tested across both Intel and M1 Macs for gcc- and clang- compiled Python.
• Adding parallelize flag that only uses OpenMP parallelization if set to true, i.e., replacing all #pragma omp parallel for with #pragma omp parallel for if (this->parallelize)
• Fixing an issue with the python bindings where variable orderings didn't match so they were getting intialized with each other's values
• Changes max_iter to 100
• Added tests/test_initialization.py, but this is not run by GHA
• Implements caching of distance computations. Also allows for retrieving cache statistics (hits, misses, writes)
• Allows setting cache parameters (useCache, usePerm, etc.) from Python
• Allows setting parallelize from Python

Tests:

• Added tests/test_initialization.py, but this is not run by GHA

Style:

• Ran black over codebase.

Documentation:

• Documented new capabilities.

Full Changelog: v3.0.4...v4.0.0

BanditPAM v3.0.4

BanditPAM v3.0.4 contains a few hotfixes:

Organization and Functionality:

• Fixes the computation of cosine distance (Fixes #182)
• Removes the ability to call OpenMP functions omp_get_max_threads and omp_set_num_threads, which should resolve the remaining issues on M1 Macs (Fixes #167)

Tests:
No changes.

Style:
No changes.

Documentation:
No changes.

Full Changelog: v3.0.3...v3.0.4

BanditPAM v3.0.3

This contains BanditPAM v3.0.3. This update will be largely invisible to users, but allows for building the Linux and Mac (including Apple Silicon/M1) wheels to upload to PyPi.

Organization and Functionality:

• Building wheels automatically for Linux, Intel Mac, and M1 Mac and uploading them to PyPI via Github actions

Tests:

• None, other than verifying the changes in Organization and Functionality work via Github Actions

Style:

• Including newlines between steps of Github Actions

Documentation:

None

Full Changelog: v3.0.2...v3.0.3

BanditPAM v3.0.2

BanditPAM v3.0.2 contains several bugfixes:

Organization and Functionality:

• We now allow the user to set a seed for reproducible results (must be called with banditpam.set_num_threads(1) for deterministic reproducibility) (Fixes #176)
• We have added the KMedoids.average_loss attribute to contain the final average clustering loss after fitting (Fixes #174)
• We throw an std::invalid_argument error properly when specifying an invalid loss function (Fixes #173, Fixes #141)

Tests:

• We now also test PAM in tests/test_smaller.py

Style:

• We change PAM and FastPAM1 to use this->*lossFn instead of KMedoids::cachedLoss to avoid resetting the cache for them; they do not benefit much from a cache anyway
• Nits

Documentation:

• Created documentation for new functions

Full Changelog: v3.0.1...v3.0.2

BanditPAM v3.0.1

BanditPAM v3.0.1 contains a hotfix to ensure it can be installed on Paperspace Gradient and Google Colab.

For Paperspace Gradient:

• allows users to install banditpam==3.0.1 on Paperspace Gradient instances by installing the necessary dependencies and armadillo 10.8 automatically in setup.py
• Builds a recent (>=10.8) armadillo from source

For Google Colab:

• Installs the necessary Ubuntu dependencies
• Fixes a missing space that was conjoining the repo name with the local installation path
• Replaces the MANIFEST.in so the headers are properly included in the source distribution

Full Changelog: v3.0.0...v3.0.1

BanditPAM v3.0.0

BanditPAM v3.0.0 contains several changes:

Organization and Functionality:

• doubles are changed to floats throughout

Tests:

• Python3.10 has been added to the list of python versions to check
• We now verify the package can be built on MacOS
• We separate the different tests into different files

Style:

• We use the appropriate armadillo types throughout for floats

Documentation:

• We have updated the documentation through
• We updated the favicon on readthedocs
• We have updated the installation guides throughout](https://github.com/ThrunGroup/BanditPAM/releases/new)

Full Changelog: v2.0.0...v3.0.0