NickleDave/songdkl issues and pull requests

#74 - Use silhouttes scores on clusters

Issue - State: open - Opened by NickleDave over 1 year ago

#73 - Provide prep'd data from Plos Comp Bio dataset

Pull Request - State: closed - Opened by NickleDave almost 2 years ago

#72 - Fix cross validation in numsyls and add parameters/cli args for gaussian mixture

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#71 - Save segmentation as annotation, fix #68

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#70 - ENH: Add GMM init params to cli / numsyls + songdkl.calculate

Issue - State: closed - Opened by NickleDave almost 2 years ago
Labels: enhancement

#69 - BUG: Fix cross-validation in numsyls

Issue - State: closed - Opened by NickleDave almost 2 years ago
Labels: bug

#68 - ENH: Add saving of segmentation

Issue - State: closed - Opened by NickleDave almost 2 years ago
Labels: enhancement

#67 - BUG: Fix how main handles output_dir_path arg

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#66 - Refactor numsyls, add more cli args

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#65 - Add Zenodo DOI + citation.cff

Issue - State: open - Opened by NickleDave almost 2 years ago

#64 - Combine `numsyls` and `em_of_gmm_cluster` function

Issue - State: closed - Opened by NickleDave almost 2 years ago - 1 comment
Labels: enhancement

#63 - ENH: Parallelize data prep with dask, fix #18

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#62 - Decouple data prep from analysis functions, add `prep` command to cli

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#61 - Add script to generate all prep'd data from Dryad dataset + nox session to download from OSF

Issue - State: closed - Opened by NickleDave almost 2 years ago
Labels: enhancement

#60 - Add logging and progress bar

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 2 comments

#59 - Add similarity data from paper

Issue - State: open - Opened by NickleDave almost 2 years ago

#58 - ENH: Use Otsu's method from scikit-image, fix #37

Pull Request - State: closed - Opened by NickleDave almost 2 years ago - 1 comment

#57 - Test what happens to numsyls + songdkl estimates as we increase amount of data

Issue - State: open - Opened by NickleDave almost 2 years ago

#56 - Add more thorough unit tests

Issue - State: open - Opened by NickleDave almost 2 years ago

#55 - Add continuous integration

Pull Request - State: closed - Opened by NickleDave almost 2 years ago

#54 - Switch to pytest and add unit tests

Pull Request - State: closed - Opened by NickleDave almost 2 years ago

#53 - Create and download test data

Pull Request - State: closed - Opened by NickleDave almost 2 years ago

#52 - Create and download test data

Pull Request - State: closed - Opened by NickleDave almost 2 years ago

#51 - Add readme to pyproject.toml

Pull Request - State: closed - Opened by NickleDave almost 2 years ago

#50 - TST: Write script for tests to download/extract test data

Issue - State: closed - Opened by NickleDave about 2 years ago - 1 comment

#49 - DEV: make a conda-forge package

Issue - State: closed - Opened by NickleDave about 2 years ago - 1 comment

#48 - DEV: fix pyproject.toml so README gets put into distribution package

Issue - State: closed - Opened by NickleDave about 2 years ago

#47 - Decouple segment/PSD step and songdkl calculate / numsyls

Issue - State: closed - Opened by NickleDave about 2 years ago - 3 comments
Labels: enhancement

#46 - Understand differences returned by GMM across sklearn versions

Issue - State: open - Opened by NickleDave about 2 years ago - 2 comments

#45 - Refactor code

Pull Request - State: closed - Opened by NickleDave about 2 years ago - 1 comment

#44 - DEV: Add nox conda-install session

Issue - State: open - Opened by NickleDave about 2 years ago

#43 - Add csvs from dataset

Pull Request - State: closed - Opened by NickleDave about 2 years ago

#42 - Estimate syllable number by eye for original dataset

Issue - State: open - Opened by NickleDave about 2 years ago

#41 - Add viz tool for filter?

Issue - State: open - Opened by NickleDave about 2 years ago

#40 - Add syllable number data and relatedness data

Issue - State: closed - Opened by NickleDave about 2 years ago - 2 comments

#39 - Notes to discuss

Issue - State: open - Opened by NickleDave about 2 years ago

#38 - Add scripts from PLOS Comp Bio paper

Pull Request - State: closed - Opened by NickleDave about 2 years ago

#37 - ENH: calculate amplitude threshold w/skimage implementation of Otsu's method

Issue - State: closed - Opened by NickleDave about 2 years ago

#36 - removed the need for mahotas

Pull Request - State: closed - Opened by dgmets about 2 years ago - 1 comment

#35 - ENH: add in the ability to use more than one PSD for the DKL calculations.

Issue - State: open - Opened by NickleDave about 2 years ago

#34 - Fix dev

Pull Request - State: closed - Opened by NickleDave about 2 years ago

#33 - Bump urllib3 from 1.26.2 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#32 - Bump babel from 2.9.0 to 2.9.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#31 - ENH: Add cli flag to apply filter before analysis

Issue - State: open - Opened by NickleDave about 2 years ago

#30 - ENH: add visualization scripts

Issue - State: open - Opened by NickleDave about 2 years ago - 1 comment

#29 - pin scikit-learn version to less than / equal to 0.18.2

Issue - State: closed - Opened by NickleDave over 3 years ago - 11 comments
Labels: bug, High Priority

#28 - add scripts from PCB paper to repo then use to generate "oracle" data for testing

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment
Labels: Build / CI, Testing

#27 - add --n_basis and --random_basis as options / flags for calculate command

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: enhancement

#26 - refactor analysis pipeline so steps are separate functions

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment

#25 - change `calculate` argument commands to be more explicit about what they represent WRT calculate?

Issue - State: closed - Opened by NickleDave almost 4 years ago - 2 comments
Labels: enhancement

#24 - use pathlib for songdkl function

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment
Labels: enhancement

#23 - use pathlib for numsyls function, fix bug with path

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment
Labels: bug, enhancement

#22 - Add logging and progress bar

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: enhancement

#21 - make sure all functions have clear docstrings

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: enhancement, Documentation

#20 - save output of calculate as a file

Issue - State: open - Opened by NickleDave almost 4 years ago
Labels: enhancement

#19 - save PSDs as output files, have `calculate` operate on those output files

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment
Labels: enhancement

#18 - parallelize with Dask

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment
Labels: enhancement

#17 - fix tests, actually use pytests

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: Testing, High Priority

#16 - Fix readme

Pull Request - State: closed - Opened by NickleDave almost 4 years ago

#15 - get rid of `util` sub-package

Issue - State: closed - Opened by NickleDave almost 4 years ago

#14 - remove current test data saved in package

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: Testing

#13 - point to actual test data in README

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: Documentation

#12 - add dev install instructions to README

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: Documentation

#11 - Use poetry for dev

Pull Request - State: closed - Opened by NickleDave almost 4 years ago

#10 - use the actual test data from the paper!!!

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment

#9 - switch to Poetry for dev

Issue - State: closed - Opened by NickleDave almost 4 years ago

#8 - test with MNIST as in paper

Issue - State: open - Opened by NickleDave almost 4 years ago

#7 - put on pypi

Issue - State: closed - Opened by NickleDave almost 4 years ago - 1 comment
Labels: Build / CI

#6 - set up continuous integration

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: Build / CI, High Priority

#5 - fix usage in README

Issue - State: closed - Opened by NickleDave almost 4 years ago
Labels: Documentation

#4 - Add about.py, fix #3

Pull Request - State: closed - Opened by NickleDave almost 4 years ago

#3 - add an about to single-source version, fix description and url

Issue - State: closed - Opened by NickleDave almost 4 years ago

#2 - add mahotas in REQUIRED

Issue - State: closed - Opened by NickleDave almost 6 years ago - 1 comment
Labels: Build / CI

#1 - tensorflow and/or FAISS as a backend?

Issue - State: closed - Opened by NickleDave almost 6 years ago - 1 comment
Labels: enhancement

GitHub / NickleDave/songdkl issues and pull requests