Kipoi

Bugfix

- `test-source` command encoding

Features

- added `--interpret` to `kipoi env` commands to install `kipoi_interpret` packages

Bugfixes

- `--singularity` now uses `source activate $(kipoi env get <model>) && kipoi predict ...` instead of `kipoi env get_cli`. This is required since `pybedtools` uses other binary executables (e.g. `sortBed`) which have to present in the environment, hence `source activate` needs to be explicitly ran.

Features

- https://github.com/kipoi/kipoi/pull/383 - added `kipoi.writers.ParquetBatchWriter`
- https://github.com/kipoi/kipoi/pull/388 - enabled installing all (common) environments for a model source with `kipoi env create all --source=kipoi`
- https://github.com/kipoi/kipoi/pull/394 added `--singularity` to `kipoi predict`. This allows the user to run model prediction in the singularity container without having to worry about conda environments. Make sure you have `singularity` installed and that you can successfully run it (try `singularity shell shub://GodloveD/lolcow`).
Kipoi example:

bash
Download the example files
kipoi get-example MMSplice/deltaLogitPSI -o example

run kipoi predict for MMSplice
kipoi predict MMSplice/deltaLogitPSI --dataloader_args='{"gtf_file":
"example/gtf_file", "fasta_file": "example/fasta_file", "vcf_file":
"example/vcf_file"}' -o '/tmp/MMSplice|deltaLogitPSI.example_pred.tsv'
--singularity

check the results
head '/tmp/MMSplice|deltaLogitPSI.example_pred.tsv'


Bugfix
- https://github.com/kipoi/kipoi/pull/396 `kipoi get-example` now doesn't download the model files and doesn't require the framework (say pytorch) to be installed.
- https://github.com/kipoi/kipoi/pull/392 - required for `--singularity`
- https://github.com/kipoi/kipoi/pull/393 Explicitly use utf-8 encoding and don't rely on user's environment variables for it
- https://github.com/kipoi/kipoi/pull/391 `KerasModel.input_grad` support for keras2.2

Major features update from 0.4 explained here: https://medium.com/zigaavsec/kipoi-0-6-release-notes-854a45bd6fdc

- Implemented `kipoi get-example` and added `download_example` method to the dataloader
- added `dependencies` to model source' `config.yaml` file
- display a warning if the dependency is not satisfied
- merged `GitLFSSource` and `GitSource` into `GitSource` with `use_lfs` flag
- addd `auto_update` flag to model source

Bugfix

- fix kipoi test (355)
- allow to use urls with tensorflow models (353)
- Fix model.schema.target.column_names loading (357)

Features
- Nicer `kipoi ls` (358)