Update config variable names

I updated `registry` to `container_registry` in anticipation of a future where we
support different data registries as well, per @agitter's suggestion. I also changed
the `config.framework` variable to `config.container_framework` to be more clear
what this variable is supposed to contain.

Snakefile

@@ -24,7 +24,7 @@ algorithm_directed = _config.config.algorithm_directed
 pca_params = _config.config.pca_params
 hac_params = _config.config.hac_params
 
-FRAMEWORK = _config.config.framework
+FRAMEWORK = _config.config.container_framework
 print(f"Running {FRAMEWORK} containers")
 
 # Return the dataset dictionary from the config file given the label

config/config.yaml

@@ -9,7 +9,7 @@ singularity: false
 # Allow the user to configure which container registry containers should be pulled from
 # Note that this assumes container names are consistent across registries, and that the
 # registry being passed doesn't require authentication for pull actions
-registry:
+container_registry:
    base_url: docker.io
    # The owner or project of the registry
    # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs

src/allpairs.py

@@ -85,7 +85,7 @@ def run(nodetypes=None, network=None, output_file=None):
 
         print('Running All Pairs Shortest Paths with arguments: {}'.format(' '.join(command)), flush=True)
 
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "allpairs"
 
         out = run_container(

src/config.py

@@ -6,7 +6,7 @@
 # value. For example
 #
 # import spras.config as config
-# container_framework = config.config.framework
+# container_framework = config.config.container_framework
 #
 # will grab the top level registry configuration option as it appears in the config file
 
@@ -65,13 +65,13 @@ def process_config(self, raw_config):
         self.out_dir = raw_config["reconstruction_settings"]["locations"]["reconstruction_dir"]
 
         if "singularity" in raw_config and raw_config["singularity"]:
-            self.framework = "singularity"
+            self.container_framework = "singularity"
         else:
-            self.framework = "docker"
+            self.container_framework = "docker"
 
         # Grab registry from the config, and if none is provided default to docker
-        if "registry" in raw_config and raw_config["registry"]["base_url"] != "" and raw_config["registry"]["owner"] != "":
-            self.container_prefix = raw_config["registry"]["base_url"] + "/" + raw_config["registry"]["owner"]
+        if "container_registry" in raw_config and raw_config["container_registry"]["base_url"] != "" and raw_config["container_registry"]["owner"] != "":
+            self.container_prefix = raw_config["container_registry"]["base_url"] + "/" + raw_config["container_registry"]["owner"]
         else:
             self.container_prefix = DEFAULT_CONTAINER_PREFIX
 

src/containers.py

@@ -63,7 +63,7 @@ def run_container(framework: str, container_suffix: str, command: List[str], vol
     elif normalized_framework == 'singularity':
         return run_container_singularity(container, command, volumes, working_dir, environment)
     else:
-        raise ValueError(f'{config.config.framework} is not a recognized container framework. Choose "docker" or "singularity".')
+        raise ValueError(f'{config.config.container_framework} is not a recognized container framework. Choose "docker" or "singularity".')
 
 
 # TODO any issue with creating a new client each time inside this function?

src/domino.py

@@ -98,7 +98,7 @@ def run(network=None, active_genes=None, output_file=None, slice_threshold=None,
 
         print('Running slicer with arguments: {}'.format(' '.join(slicer_command)), flush=True)
 
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "domino"
         slicer_out = run_container(container_framework,
                                    container_suffix,

src/meo.py

@@ -140,7 +140,7 @@ def run(edges=None, sources=None, targets=None, output_file=None, max_path_lengt
         print('Running Maximum Edge Orientation with arguments: {}'.format(' '.join(command)), flush=True)
 
         # TODO consider making this a string in the config file instead of a Boolean
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "meo"
         out = run_container(container_framework,
                             container_suffix,

src/mincostflow.py

@@ -96,7 +96,7 @@ def run(sources=None, targets=None, edges=None, output_file=None, flow=None, cap
             command.extend(['--capacity', str(capacity)])
 
         # choosing to run in docker or singularity container
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "mincostflow"
 
         # constructs a docker run call

src/omicsintegrator1.py

@@ -146,7 +146,7 @@ def run(edges=None, prizes=None, dummy_mode=None, mu_squared=None, exclude_terms
         print('Running Omics Integrator 1 with arguments: {}'.format(' '.join(command)), flush=True)
 
         # TODO consider making this a string in the config file instead of a Boolean
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "omics-integrator-1:no-conda" # no-conda version is the default
 
         out = run_container(container_framework,

src/omicsintegrator2.py

@@ -103,7 +103,7 @@ def run(edges=None, prizes=None, output_file=None, w=None, b=None, g=None, noise
 
         print('Running Omics Integrator 2 with arguments: {}'.format(' '.join(command)), flush=True)
 
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "omics-integrator-2:v2"
         out = run_container(container_framework,
                             container_suffix,

src/pathlinker.py

@@ -97,7 +97,7 @@ def run(nodetypes=None, network=None, output_file=None, k=None):
 
         print('Running PathLinker with arguments: {}'.format(' '.join(command)), flush=True)
 
-        container_framework = config.config.framework
+        container_framework = config.config.container_framework
         container_suffix = "pathlinker"
         out = run_container(container_framework,
                             container_suffix,

test/AllPairs/test_ap.py

@@ -44,13 +44,13 @@ def test_allpairs_singularity(self):
         out_path = Path(OUT_DIR+'sample-out.txt')
         out_path.unlink(missing_ok=True)
         # Only include required arguments and run with Singularity
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         AllPairs.run(
             nodetypes=TEST_DIR+'input/sample-in-nodetypes.txt',
             network=TEST_DIR+'input/sample-in-net.txt',
             output_file=str(out_path)
         )
-        config.config.framework = "docker"
+        config.config.container_framework = "docker"
         assert out_path.exists()
 
     def test_allpairs_correctness(self):

test/DOMINO/test_domino.py

@@ -85,13 +85,13 @@ def test_domino_singularity(self):
         out_path = Path(OUT_FILE_DEFAULT)
         out_path.unlink(missing_ok=True)
         # Only include required arguments and run with Singularity
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         DOMINO.run(
             network=TEST_DIR+'input/domino-network.txt',
             active_genes=TEST_DIR+'input/domino-active-genes.txt',
             output_file=OUT_FILE_DEFAULT)
         assert out_path.exists()
-    config.config.framework = "docker"
+    config.config.container_framework = "docker"
     def test_pre_id_transform(self):
         """
         Test the node ID transformation run before DOMINO executes

test/MEO/test_meo.py

@@ -62,10 +62,10 @@ def test_meo_singularity(self):
         out_path = Path(OUT_FILE)
         out_path.unlink(missing_ok=True)
         # Only include required arguments and run with Singularity
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         MEO.run(edges=TEST_DIR + 'input/meo-edges.txt',
                 sources=TEST_DIR + 'input/meo-sources.txt',
                 targets=TEST_DIR + 'input/meo-targets.txt',
                 output_file=OUT_FILE)
-        config.config.framework = "docker"
+        config.config.container_framework = "docker"
         assert out_path.exists()

test/MinCostFlow/test_mcf.py

@@ -106,13 +106,13 @@ def test_mincostflow_singularity(self, graph):
         out_path = Path(OUT_FILE)
         out_path.unlink(missing_ok=True)
         # Include all optional arguments
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         MinCostFlow.run(sources=TEST_DIR + 'input/' + graph + '/sources.txt',
                         targets=TEST_DIR + 'input/' + graph + '/targets.txt',
                         edges=TEST_DIR + 'input/' + graph + '/edges.txt',
                         output_file=OUT_FILE,
                         flow=1,
                         capacity=1)
-        config.config.framework = "docker"
+        config.config.container_framework = "docker"
         assert out_path.exists()
 

test/OmicsIntegrator1/test_oi1.py

@@ -88,12 +88,12 @@ def test_oi1_singularity(self):
         out_path = Path(OUT_FILE)
         out_path.unlink(missing_ok=True)
         # Only include required arguments and run with Singularity
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         OmicsIntegrator1.run(edges=TEST_DIR + 'input/oi1-edges.txt',
                              prizes=TEST_DIR + 'input/oi1-prizes.txt',
                              output_file=OUT_FILE,
                              w=5,
                              b=1,
                              d=10)
-        config.config.framework = "docker"
+        config.config.container_framework = "docker"
         assert out_path.exists()

test/OmicsIntegrator2/test_oi2.py

@@ -64,9 +64,9 @@ def test_oi2_missing(self):
     def test_oi2_singularity(self):
         # Only include required arguments
         OUT_FILE.unlink(missing_ok=True)
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         OmicsIntegrator2.run(edges=EDGE_FILE,
                              prizes=PRIZE_FILE,
                              output_file=OUT_FILE)
-        config.config.framework = "docker"
+        config.config.container_framework = "docker"
         assert OUT_FILE.exists()

test/PathLinker/test_pathlinker.py

@@ -56,11 +56,11 @@ def test_pathlinker_singularity(self):
         out_path = Path(OUT_FILE_DEFAULT)
         out_path.unlink(missing_ok=True)
         # Only include required arguments and run with Singularity
-        config.config.framework = "singularity"
+        config.config.container_framework = "singularity"
         PathLinker.run(
             nodetypes=TEST_DIR+'input/sample-in-nodetypes.txt',
             network=TEST_DIR+'input/sample-in-net.txt',
             output_file=OUT_FILE_DEFAULT,
         )
-        config.config.framework = "docker"
+        config.config.container_framework = "docker"
         assert out_path.exists()