Janggu

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Added various features and bug fixes:

Changes in janggu.data

- Added new dataset wrapper to remove NaNs: NanToNumConverter
- Added new dataset wrappers for data augmentation: RandomOrientation, RandomSignalScale
- Adapted ReduceDim wrapper: added aggregator argument
- plotGenomeTrack added figsize option
- plotGenomeTrack added other plot types, including heatmap and seqplot.
- plotGenomeTrack refactoring of internal code
- Bioseq bugfix: Fixed issue for reverse complementing N's in the sequence.
- GenomicArray: condition, order, resolution are not read from the cache anymore, but from the arguments to avoid inconsistencies
- Normalization of Cover can handle a list of normalizer callables which are applied in turn
- Normaliation and Transformation: Added PercentileTrimming, RegionLengthNormalization, LogTransform
- ZScore and ZScoreLog do not apply RegionLengthNormalization by default anymore.
- janggu.data version-aware caching of datasets included
- Added copy method for janggu datasets.
- split_train_test refactored
- removed obsolete transformations attribute from the datasets
- Adapted the documentation
- Refactoring according to suggestions from isort and pylint

Changes in janggu

- Added input_attribution via integrated gradients for feature importance assignment
- Performance scoring by name for Janggu.evaluate for a number common metrices, including ROC, PRC, correlation, variance explained, etc.
- training.log is stored by default for each model
- Added model_from_json, model_from_yaml wrappers
- inputlayer decorator only instantiates Input layers if inputs == None, which makes the use of inputlayer less restrictive when using nested functions
- Added create_model method to create a keras model directly
- Adapted the documentation
- Refactoring according to suggestions from isort and pylint

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- Bugfix for ROIs that reach beyond the chromosome when loading Bioseq datasets. Now, zero-padding is performed for intervals that stretch over the sequence ends.

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- Updated abstract, added logo
- Utility: janggutrim command line tool for cutting bed file regions to avoid unwanted rounding effects. If rounding issues are detected an error is raised.
- Caching mechanism revisited. Caching of datasets is based on determining the sha256 hash of the dataset. If the data or some parameters change, the files are automatically reloaded. Consequently, the arguments overwrite and datatags become obsolete and have been marked for deprecation.
- Refactored access of GenomicArray
- Added ReduceDim wrapper to convert a 4D Cover object to a 2D table-like object.

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- Updated installation instructions in the readme

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- Fixed issues for loading SparseGenomicArray
- Made GenomicIndexer.filter_by_region aware of flank
- Fixed BedLoader of partially overlapping ROI and bedfiles issue using filter_by_region.
- Adapted classifier, license and keywords in setup.py
- Fixed hyperlinks

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- Bugfix for zero-padding functionality
- Added ndim for keras compatibility