Cleanup after intense rebase

Snakefile

@@ -3,7 +3,6 @@ from spras import runner
 import shutil
 import yaml
 from spras.dataset import Dataset
-from spras.util import process_config
 from spras.analysis import ml, summary, graphspace, cytoscape
 from spras.dataset import Dataset
 from spras.analysis import ml, summary, graphspace, cytoscape

spras/allpairs.py

@@ -3,10 +3,9 @@
 
 import pandas as pd
 
-from spras.prm import PRM
-from spras.util import prepare_volume
-from spras.containers import run_container
 import spras.config as config
+from spras.containers import prepare_volume, run_container
+from spras.prm import PRM
 
 __all__ = ['AllPairs']
 

spras/analysis/cytoscape.py

@@ -2,14 +2,8 @@
 from shutil import rmtree
 from typing import List, Union
 
-<<<<<<< HEAD:spras/analysis/cytoscape.py
 import spras.config as config
-from spras.containers import run_container
-from spras.util import prepare_volume
-=======
-import src.config as config
-from src.containers import prepare_volume, run_container
->>>>>>> 75b746c (Move container framework to algorith run call and fix hash lengths):src/analysis/cytoscape.py
+from spras.containers import prepare_volume, run_container
 
 
 def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, container_framework="docker") -> None:
@@ -55,7 +49,6 @@ def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, contai
 
     print('Running Cytoscape with arguments: {}'.format(' '.join(command)), flush=True)
 
-    # TODO consider making this a string in the config file instead of a Boolean
     container_prefix = "py4cytoscape:v1"
     out = run_container(container_framework,
                         container_prefix,

spras/containers.py

@@ -7,6 +7,7 @@
 import docker
 
 import spras.config as config
+from spras.util import hash_filename
 
 
 def prepare_path_docker(orig_path: PurePath) -> str:

spras/domino.py

@@ -3,10 +3,9 @@
 
 import pandas as pd
 
-from spras.prm import PRM
-from spras.util import prepare_volume
-from spras.containers import run_container
 import spras.config as config
+from spras.containers import prepare_volume, run_container
+from spras.prm import PRM
 
 __all__ = ['DOMINO', 'pre_domino_id_transform', 'post_domino_id_transform']
 

spras/meo.py

@@ -2,10 +2,9 @@
 
 import pandas as pd
 
-from spras.prm import PRM
-from spras.util import prepare_volume
-from spras.containers import run_container
 import spras.config as config
+from spras.containers import prepare_volume, run_container
+from spras.prm import PRM
 
 __all__ = ['MEO', 'write_properties']
 

spras/mincostflow.py

@@ -2,10 +2,9 @@
 
 import pandas as pd
 
-from spras.prm import PRM
-from spras.util import prepare_volume
-from spras.containers import run_container
 import spras.config as config
+from spras.containers import prepare_volume, run_container
+from spras.prm import PRM
 
 __all__ = ['MinCostFlow']
 

spras/omicsintegrator1.py

@@ -2,10 +2,9 @@
 
 import pandas as pd
 
-from spras.prm import PRM
-from spras.util import prepare_volume
-from spras.containers import run_container
 import spras.config as config
+from spras.containers import prepare_volume, run_container
+from spras.prm import PRM
 
 __all__ = ['OmicsIntegrator1', 'write_conf']
 

spras/omicsintegrator2.py

@@ -2,11 +2,11 @@
 
 import pandas as pd
 
+import spras.config as config
+from spras.containers import prepare_volume, run_container
 from spras.dataset import Dataset
 from spras.prm import PRM
-from spras.util import add_rank_column, prepare_volume
-from spras.containers import run_container
-import spras.config as config
+from spras.util import add_rank_column
 
 __all__ = ['OmicsIntegrator2']
 

spras/pathlinker.py

@@ -3,10 +3,9 @@
 
 import pandas as pd
 
-from spras.prm import PRM
-from spras.util import prepare_volume
-from spras.containers import run_container
 import spras.config as config
+from spras.containers import prepare_volume, run_container
+from spras.prm import PRM
 
 __all__ = ['PathLinker']
 

test/test_config.py

@@ -1,6 +1,6 @@
 import pytest
 
-import src.config as config
+import spras.config as config
 
 
 # Set up a dummy config for testing. For now, only include things that MUST exist in the dict

test/test_util.py

@@ -2,20 +2,9 @@
 
 import pytest
 
-
-from spras.util import (
-    hash_params_sha1_base32,
-    prepare_volume,
-)
-
-from spras.containers import (
-    convert_docker_path,
-    prepare_path_docker,
-)
-from src.util import (
-    hash_params_sha1_base32,
-    prepare_volume,
-)
+import spras.config as config
+from spras.containers import convert_docker_path, prepare_path_docker, prepare_volume
+from spras.util import hash_params_sha1_base32
 
 config.init_from_file("config/config.yaml")