Changelogs

0.1.11

Background stuff:

• Added testing section for unit tests (simple assert statements inside the notebooks)

Bioinfo cli:

• Added numpy/torch checks to dereference

• Renamed sample to peek

• Added infiniteFrom, joinStreamsRandom, batched, collate, splitList

• Added infiniteF

• Added toTensor

• Replaced infinite in favor of repeat

• Updated all cli tools to use super().__init__()

• Added _ctx module, with Promise, enum, identity classes, and getC(), setC() methods

DL:

• Added k1lib.data.CyclicRandomSampler and k1lib.data.DatasetWithSampler

• Added highlight feature in callbacks.Callbacks.checkpointGraph()

• Added k1lib.viz.Carousel.pop(), k1lib.viz.Carousel.__getitem__()

• Added k1lib.Learner.sample()

• Disallow k1lib.executeNb() to execute lines that starts with “!”, also removed parameter catchErrors, as it’s quite useless

• Added k1lib.Object()

0.1.10

Background stuff:

• Added notebook regression tests

• Added tutorials automated building tool

• Added k1lib.ignoreWarnings

• Tutorials part moved to official docs (rather than .md files on github)

• Added covid tutorial

Bioinfo cli:

• Reintroduced permute, as rows is inadequate

• Added lengths, applySingle

• Exposed serial, oneToMany, manyToMany, and manyToManySpecific

DL:

• Added confusionMatrix.ConfusionMatrix and k1lib.viz.confusionMatrix()

• Added callbacks.Callbacks.checkpointGraph()

• Added torch.nn.modules.Module.paramsContext()

• Modified k1lib.Object to allow setting getdoc field

• Added k1lib.viz.Carousel.saveBytes(), k1lib.viz.Carousel.saveFile(), k1lib.viz.Carousel.saveGraphviz(), and handle different image formats much better now

0.1.9

Bioinfo cli:

• Added k1lib.Domain class

• Added __invert__ option for rows and columns by incorporating k1lib.Domain

• Sped up rows significantly

• Removed cli tool every as rows is good enough

• Added __invert__ option for head. As a result, removed nhead

• Added till() mechanism to grep cli tool

• Added gb cli module to deal with genbank file format

• Added tableFromList() as alias of listToTable()

• Renamed avg to toAvg

• Added toSum

DL:

• Added Callbacks tab completion to k1lib.Learner and Callbacks

• Refactored lossLandscape.LossLandscape to landscape.Landscape that can be used by any other callbacks, right now it’s Loss and Accuracy

• Added callbacks.Callback.pause() to help with Accuracy’s Landscape

0.1.8

• Fixed installation bug where readme.md would be absent, and setup.py won’t work at all.

Bioinfo cli:

• Huge revamp of how tables are treated. Before, row elements are in a single string, separated by a delimiter. Now each row is a full fledged list

• Added grepToTable, joinList, contains, table, stitch, listToTable, insertColumn cli tools

• Removed joinRows but still keep joinStreams as “joinRows” is not really obvious

• Removed permute as columns is pretty much identical

• Renamed inside to inSet

• Cut out nested functionality from grep to grepToTable

0.1.7

Interface with external modules:

• Swapped out register_backward_hook with register_full_backward_hook() in HookModule callback

• Added torch.nn.Module.preserveDevice() context manager

Callbacks:

• Changed Callbacks.suspend() to take in names only

• Added Callbacks.suspendClasses() to take in classes

• Changed Callbacks.suspendEvaluation() to Callbacks.suspendEval(), also added functionality for white and black lists

• Ripped out complex Callback.__getattr__() mechanism (that automatically searches the parent learner for missing attributes) to improve speed

• Added k1lib.callbacks.core callbacks CoreNormal and CoreRNN

• Added more plot decorators for MemoryProfiler, including backward-forward separator with their text

• Changed LossLandscape callback so that it follows the common flow structure. Before, it implements a whole new cbs(...) schema that essentially duplicated the loop inside of k1lib.Learner

Learner:

• Implemented grace stop handling for Learner. Before, if someone throws CancelRunException while executing a batch, then it will immediately jump to the end of the run. Changed it so that it will be caught in the batch loop, execute checkpoints cancelBatch and endBatch and rethrow it. Same thing with CancelEpochException

• Moved loss function from being a core functionality inside Learner to an external callback, so that adapting multiple loss functions are possible

• Added Learner.__call__()

Bioinfo cli:

• Added isValue, intersection, AA_, infinite, dereference cli tools

• Modified cat to be able to take in file name by pipe

• Added new joining operator “+” between init.BaseCli

Style changes:

• Changed Callbacks.learner to Callbacks.l

• Changed Callback.learner to Callbacks.l

• Removed k1lib.eqn from k1lib.imports’s namespace

0.1.6

I don’t really keep track of things 0.1.6 and before, so nothing here really.