Merge pull request #7 from DerThorsten/master

Requirements: Using kipoi-utils

.circleci/config.yml

@@ -15,8 +15,14 @@ variables:
     run:
       name: Install pip dependencies
       command: |
-        pip install genomelake --no-deps
-        pip install pyfaidx 'tensorflow>=1.6'
+        pip install 'tensorflow>=1.6'
+
+  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
@@ -43,6 +49,7 @@ variables:
       command: |
         mkdir test-reports
         py.test --cov=kipoi_interpret/ tests/ -n 4 --no-cov-on-fail --junitxml=test-reports/junit.xml
+      no_output_timeout: 20m
   run_coveralls: &run_coveralls
     run:
       name: run coveralls
@@ -66,6 +73,7 @@ jobs:
       - checkout
       - *update_conda
       - *install_git_lfs
+      - *install_conda_deps
       - *install_pip_deps
       - *install_kipoi
       - *install_kipoi_interpret
@@ -83,6 +91,7 @@ jobs:
       - checkout
       - *update_conda
       - *install_git_lfs
+      - *install_conda_deps
       - *install_pip_deps
       - *install_kipoi
       - *install_kipoi_interpret

kipoi_interpret/cli.py

@@ -13,8 +13,8 @@
 import kipoi
 from kipoi.cli.parser_utils import add_model, add_dataloader, file_exists, dir_exists
 from kipoi import writers
-from kipoi.utils import cd
-from kipoi.utils import parse_json_file_str
+from kipoi_utils.utils import cd
+from kipoi_utils.utils import parse_json_file_str
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())

kipoi_interpret/importance_scores/base.py

@@ -1,7 +1,7 @@
 from __future__ import division, absolute_import, print_function
 from tqdm import tqdm
-from kipoi.utils import merge_dicts
-from kipoi.data_utils import numpy_collate_concat
+from kipoi_utils.utils import merge_dicts
+from kipoi_utils.data_utils import numpy_collate_concat
 import abc
 # Abstract declaration of different interpretation APIs, plus any
 # common functionality

kipoi_interpret/importance_scores/cli.py

@@ -14,7 +14,7 @@
 import kipoi
 from kipoi.cli.parser_utils import add_model, add_dataloader, file_exists, dir_exists
 from kipoi import writers
-from kipoi.utils import parse_json_file_str, load_module
+from kipoi_utils.utils import parse_json_file_str, load_module
 import numpy as np
 
 logger = logging.getLogger(__name__)

kipoi_interpret/importance_scores/ism.py

@@ -1,9 +1,9 @@
 from __future__ import division, absolute_import, print_function
 from .base import ImportanceScore
 import numpy as np
-from kipoi.data_utils import numpy_collate_concat, numpy_collate
+from kipoi_utils.data_utils import numpy_collate_concat, numpy_collate
 from kipoi_interpret.utils import get_model_input, set_model_input
-from kipoi.data_utils import get_dataset_item, get_dataset_lens
+from kipoi_utils.data_utils import get_dataset_item, get_dataset_lens
 from kipoi_interpret.utils import apply_within
 from .ism_scores import Score
 import copy

kipoi_interpret/importance_scores/referencebased.py

@@ -2,7 +2,7 @@
 from .base import ImportanceScoreWRef
 from .gradient import Gradient
 from kipoi.model import KerasModel, TensorFlowModel
-from kipoi.data_utils import numpy_collate
+from kipoi_utils.data_utils import numpy_collate
 
 import tempfile
 import numpy as np

setup.py

@@ -5,7 +5,8 @@
 
 
 requirements = [
-    "kipoi",
+    "kipoi>=0.6.7",
+    "kipoi-utils>=0.1.1",
     "tqdm",
     "matplotlib",
     "seaborn",