Merge pull request #22 from DerThorsten/master

Dependencies using  kipoi-conda and kipoi-utils

Author: DerThorsten

.circleci/config.yml

@@ -16,12 +16,17 @@ variables:
       name: Update pytorch
       command: |
         conda install --yes pytorch-cpu -c pytorch
-  install_pip_deps: &install_pip_deps
+  icondaall_pip_deps: &install_pip_deps
     run:
       name: Install pip dependencies
       command: |
         pip install genomelake --no-deps
         pip install pyfaidx
+  install_conda_deps: &install_conda_deps
+    run:
+      name: Install conda dependencies
+      command: |
+        conda install genomelake pyfaidx -c bioconda
   install_kipoi: &install_kipoi
     run:
       name: Install Kipoi
@@ -72,7 +77,7 @@ jobs:
       - *update_conda
       - *install_git_lfs
       - *update_pytorch
-      - *install_pip_deps
+      - *install_conda_deps
       - *install_kipoi
       - *install_kipoiseq
       - *kipoi_ls
@@ -90,7 +95,7 @@ jobs:
       - *update_conda
       - *install_git_lfs
       - *update_pytorch
-      - *install_pip_deps
+      - *install_conda_deps
       - *install_kipoi
       - *install_kipoiseq
       - *kipoi_ls

kipoiseq/dataloaders/sequence.py

@@ -7,8 +7,9 @@
 from kipoi.specs import DataLoaderArgument, ArraySpecialType
 from kipoi.plugin import is_installed
 from kipoi.data import Dataset, kipoi_dataloader
-from kipoi.specs import Author, Dependencies
-from kipoi.utils import default_kwargs
+from kipoi_conda.dependencies import Dependencies
+from kipoi.specs import Author
+from kipoi_utils.utils import default_kwargs
 
 from kipoiseq.extractors import FastaStringExtractor
 from kipoiseq.transforms import SwapAxes, DummyAxis, Compose, OneHot, ReorderedOneHot

setup.py

@@ -15,7 +15,9 @@
     # "related>=0.6.0",
     # sometimes required
     # "h5py",
-    "gffutils"
+    "gffutils",
+    "kipoi-utils>=0.1.1",
+    "kipoi-conda>=0.1.0"
 ]
 
 test_requirements = [