Add H5 GenomicFeatures support for more flexible target datatypes (#200)

* selene changes for methylation model

* remove f1 metric

* bugfix and some temporary profiling

* adjustments to loss breakdown and logging

* adjust return type for get_features_data

* bugfix for get_feature_data

* remove event object init

* initial changes to h5 dataloader

* methylation sampler excl

* add type specification to unpackbits

* change loss

* experimenting w loss

* add pearsonr

* fix metrix nan removal bug

* changes to sampler for positives-only hdf5

* loss weighting

* adjust methylation perf metric output checking

* revert multisampler and add spearmanr to training log

* explicit metric fn checking, refine later

* minor adjustment to dataloader

* non strand specific temp changes

* positives only sampler

* revamp dataloader, seq length flexibility

* attempted a nonstrandspecific utils module, not being used

* evaluation classes

* revert non strand specific module

* trying to figure out unet dataloader changes

* trying to figure out unet dataloader changes - add tgt shift

* remove print debug statements

* addr memory issue in eval

* comment

* troubleshooting dataloader shift

* add strand arg to _retrieve

* shift testing

* adjust casting of targets in dataloader

* minor changes to eval and sampling

* remove unused code in nonstrandspecific module

* remove indicators from dataloader, clean up methylation performance metrics

* remove unused files from version control, adjust multi sampler get dataset batches function

* remove commented out code in shift sections

* remove ind commented out code in multisampler

* add excl chr optional arg

* make adjustments to nonstrandspecific, performancemetrics, for what can be generalized from the methylation specific code

* remove files that we have merged the functionality into existing classes

* clean up indicator code that is no longer used

* integrate changes for methylation prediction in training and metrics

* incorporate changes from previous PR on config yaml and model file saving

* update pytorch version constraint

* variable name fix for copying model file / directory

* remove train methylation model class

* fix bug in random positions sampler with exclude_chrs, overload targets_path in both sampler classes

* remove unused method in genomicfeaturesh5

* adjust strand vs feature (target) column ordering assumptions in tabix-indexed BED file

* adjust descriptions for target classes

* minor adjustments to docstrings

* tuple output handling for non strand specific

* line breaks for formatting in performance metrics file

* adjust CLI config parsing so that a copy of the input config file is made and saved to the output dir

* update versioning

* add new dependency

* adjustment in

* update release notes for 0.6.0

* adjustment for sampling at the end of N_samples

* adjust expected BED file format when strand is included for seqweaver script

* adjust  method in seqweaver script to accept lr input and new config loading function

Adjust lower bound for NumPy/Cython dependency requirements (#199)

* adjust dependencies version requirements

* adjust up pytorch for jenkins

pyx fix for numpy and cython updates (#198)

try adding conda-forge channel to conda install

Merge pull request #144 from kathyxchen/heartenn-updates

Add HeartENN arch to models dir

Merge pull request #142 from kathyxchen/selene-v047

update minor version to 0.4.7 (bugfix)

Merge pull request #140 from kathyxchen/selene-v046

Update selene minor version to 0.4.6

Merge pull request #135 from kathyxchen/pytorch-140-update

Minor changes and updating Selene to be compatible with PyTorch 1.4.0

Merge pull request #127 from kathyxchen/master

Update selene minor version to 0.4.4

Merge pull request #124 from kathyxchen/selene-v043

selene minor release update to 0.4.3