refactor: broaden container settings args

Snakefile

@@ -25,7 +25,7 @@ algorithm_params = _config.config.algorithm_params
 algorithm_directed = _config.config.algorithm_directed
 pca_params = _config.config.pca_params
 hac_params = _config.config.hac_params
-FRAMEWORK = _config.config.container_settings.framework
+container_settings = _config.config.container_settings
 include_aggregate_algo_eval = _config.config.analysis_include_evaluation_aggregate_algo
 
 # Return the dataset or gold_standard dictionary from the config file given the label
@@ -281,7 +281,7 @@ rule reconstruct:
         # Remove the default placeholder parameter added for algorithms that have no parameters
         if 'spras_placeholder' in params:
             params.pop('spras_placeholder')
-        params['container_framework'] = FRAMEWORK
+        params['container_settings'] = container_settings
         runner.run(wildcards.algorithm, params)
 
 # Original pathway reconstruction output to universal output
@@ -313,7 +313,7 @@ rule viz_cytoscape:
     output: 
         session = SEP.join([out_dir, '{dataset}-cytoscape.cys'])
     run:
-        cytoscape.run_cytoscape(input.pathways, output.session, FRAMEWORK)
+        cytoscape.run_cytoscape(input.pathways, output.session, container_settings)
 
 
 # Write a single summary table for all pathways for each dataset

config/config.yaml

@@ -28,17 +28,17 @@ containers:
     # For example, "reedcompbio" if the image is available as docker.io/reedcompbio/allpairs
     owner: reedcompbio
 
-# Enabling profiling adds a file called 'usage-profile.tsv' to the output directory of each algorithm.
-# The contents of this file describe the CPU utilization and peak memory consumption of the algorithm
-# as seen by its runtime container.
-# NOTE: Profiling is currently supported only when the container framework is set to apptainer/singularity
-#       and when the host system supports the 'cgroup' filesystem.
-#       When profiling via HTCondor, this assumes the current process is already in a two-level nested cgroup
-#       (introduced in HTCondor 24.8.0). To specify a minimum HTCondor version, use the following `requirements`
-#       expression:
-#
-#       requirements = versionGE(split(Target.CondorVersion)[1], "24.8.0") && (isenforcingdiskusage =!= true)
-enable_profiling: false
+  # Enabling profiling adds a file called 'usage-profile.tsv' to the output directory of each algorithm.
+  # The contents of this file describe the CPU utilization and peak memory consumption of the algorithm
+  # as seen by its runtime container.
+  # NOTE: Profiling is currently supported only when the container framework is set to apptainer/singularity
+  #       and when the host system supports the 'cgroup' filesystem.
+  #       When profiling via HTCondor, this assumes the current process is already in a two-level nested cgroup
+  #       (introduced in HTCondor 24.8.0). To specify a minimum HTCondor version, use the following `requirements`
+  #       expression:
+  #
+  #       requirements = versionGE(split(Target.CondorVersion)[1], "24.8.0") && (isenforcingdiskusage =!= true)
+  enable_profiling: false
 
 # This list of algorithms should be generated by a script which checks the filesystem for installs.
 # It shouldn't be changed by mere mortals. (alternatively, we could add a path to executable for each algorithm

spras/allpairs.py

@@ -1,6 +1,7 @@
 import warnings
 from pathlib import Path
 
+from spras.config.container_schema import ProcessedContainerSettings
 from spras.containers import prepare_volume, run_container_and_log
 from spras.dataset import Dataset
 from spras.interactome import (
@@ -69,14 +70,15 @@ def generate_inputs(data: Dataset, filename_map):
                                       header=["#Interactor1", "Interactor2", "Weight"])
 
     @staticmethod
-    def run(nodetypes=None, network=None, directed_flag=None, output_file=None, container_framework="docker"):
+    def run(nodetypes=None, network=None, directed_flag=None, output_file=None, container_settings=None):
         """
         Run All Pairs Shortest Paths with Docker
         @param nodetypes: input node types with sources and targets (required)
         @param network: input network file (required)
-        @param container_framework: choose the container runtime framework, currently supports "docker" or "singularity" (optional)
+        @param container_settings: configure the container runtime
         @param output_file: path to the output pathway file (required)
         """
+        if not container_settings: container_settings = ProcessedContainerSettings()
         if not nodetypes or not network or not output_file or not directed_flag:
             raise ValueError('Required All Pairs Shortest Paths arguments are missing')
 
@@ -85,16 +87,16 @@ def run(nodetypes=None, network=None, directed_flag=None, output_file=None, cont
         # Each volume is a tuple (src, dest)
         volumes = list()
 
-        bind_path, node_file = prepare_volume(nodetypes, work_dir)
+        bind_path, node_file = prepare_volume(nodetypes, work_dir, container_settings)
         volumes.append(bind_path)
 
-        bind_path, network_file = prepare_volume(network, work_dir)
+        bind_path, network_file = prepare_volume(network, work_dir, container_settings)
         volumes.append(bind_path)
 
         # Create the parent directories for the output file if needed
         out_dir = Path(output_file).parent
         out_dir.mkdir(parents=True, exist_ok=True)
-        bind_path, mapped_out_file = prepare_volume(output_file, work_dir)
+        bind_path, mapped_out_file = prepare_volume(output_file, work_dir, container_settings)
         volumes.append(bind_path)
 
         command = ['python',
@@ -108,12 +110,12 @@ def run(nodetypes=None, network=None, directed_flag=None, output_file=None, cont
         container_suffix = "allpairs:v4"
         run_container_and_log(
             'All Pairs Shortest Paths',
-            container_framework,
             container_suffix,
             command,
             volumes,
             work_dir,
-            out_dir)
+            out_dir,
+            container_settings)
 
     @staticmethod
     def parse_output(raw_pathway_file, standardized_pathway_file, params):

spras/analysis/cytoscape.py

@@ -2,16 +2,18 @@
 from shutil import rmtree
 from typing import List, Union
 
+from spras.config.container_schema import ProcessedContainerSettings
 from spras.containers import prepare_volume, run_container_and_log
 
 
-def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, container_framework="docker") -> None:
+def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, container_settings=None) -> None:
     """
     Create a Cytoscape session file with visualizations of each of the provided pathways
     @param pathways: a list of pathways to visualize
     @param output_file: the output Cytoscape session file
-    @param container_framework: choose the container runtime framework, currently supports "docker" or "singularity" (optional)
+    @param container_settings: configure the container runtime
     """
+    if not container_settings: container_settings = ProcessedContainerSettings()
     work_dir = '/spras'
 
     # To work with Singularity, /spras must be mapped to a writeable location because that directory is fixed as
@@ -33,25 +35,28 @@ def run_cytoscape(pathways: List[Union[str, PurePath]], output_file: str, contai
     volumes.append((cytoscape_output_dir, PurePath(work_dir, 'CytoscapeConfiguration')))
 
     # Map the output file
-    bind_path, mapped_output = prepare_volume(output_file, work_dir)
+    bind_path, mapped_output = prepare_volume(output_file, work_dir, container_settings)
     volumes.append(bind_path)
 
     # Create the initial Python command to run inside the container
     command = ['python', '/py4cytoscape/cytoscape_util.py', '--output', mapped_output]
 
     # Map the pathway filenames and add them to the Python command
     for pathway in pathways:
-        bind_path, mapped_pathway = prepare_volume(pathway, work_dir)
+        bind_path, mapped_pathway = prepare_volume(pathway, work_dir, container_settings)
         volumes.append(bind_path)
         # Provided the mapped pathway file path and the original file path as the label Cytoscape
         command.extend(['--pathway', f'{mapped_pathway}|{pathway}'])
 
     container_suffix = "py4cytoscape:v3"
     run_container_and_log('Cytoscape',
-                         container_framework,
                          container_suffix,
                          command,
                          volumes,
                          work_dir,
+                         # TODO: doesn't work on Singularity
+                         # (https://github.com/Reed-CompBio/spras/pull/390/files#r2485100875)
+                         None,
+                         container_settings,
                          env)
     rmtree(cytoscape_output_dir)

spras/btb.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+from spras.config.container_schema import ProcessedContainerSettings
 from spras.containers import prepare_volume, run_container_and_log
 from spras.interactome import (
     convert_undirected_to_directed,
@@ -68,15 +69,16 @@ def generate_inputs(data, filename_map):
 
     # Skips parameter validation step
     @staticmethod
-    def run(sources=None, targets=None, edges=None, output_file=None, container_framework="docker"):
+    def run(sources=None, targets=None, edges=None, output_file=None, container_settings=None):
         """
         Run BTB with Docker
         @param sources:  input source file (required)
         @param targets:  input target file (required)
         @param edges:    input edge file (required)
         @param output_file: path to the output pathway file (required)
-        @param container_framework: choose the container runtime framework, currently supports "docker" or "singularity" (optional)
+        @param container_settings: configure the container runtime
         """
+        if not container_settings: container_settings = ProcessedContainerSettings()
 
         # Tests for pytest (docker container also runs this)
         # Testing out here avoids the trouble that container errors provide
@@ -105,19 +107,19 @@ def run(sources=None, targets=None, edges=None, output_file=None, container_fram
         # Each volume is a tuple (src, dest)
         volumes = list()
 
-        bind_path, source_file = prepare_volume(sources, work_dir)
+        bind_path, source_file = prepare_volume(sources, work_dir, container_settings)
         volumes.append(bind_path)
 
-        bind_path, target_file = prepare_volume(targets, work_dir)
+        bind_path, target_file = prepare_volume(targets, work_dir, container_settings)
         volumes.append(bind_path)
 
-        bind_path, edges_file = prepare_volume(edges, work_dir)
+        bind_path, edges_file = prepare_volume(edges, work_dir, container_settings)
         volumes.append(bind_path)
 
         # Use its --output argument to set the output file prefix to specify an absolute path and prefix
         out_dir = Path(output_file).parent
         out_dir.mkdir(parents=True, exist_ok=True)
-        bind_path, mapped_out_dir = prepare_volume(str(out_dir), work_dir)
+        bind_path, mapped_out_dir = prepare_volume(str(out_dir), work_dir, container_settings)
         volumes.append(bind_path)
         mapped_out_prefix = mapped_out_dir + '/raw-pathway.txt'  # Use posix path inside the container
 
@@ -133,14 +135,13 @@ def run(sources=None, targets=None, edges=None, output_file=None, container_fram
                    mapped_out_prefix]
 
         container_suffix = "bowtiebuilder:v2"
-        run_container_and_log(
-            'BowTieBuilder',
-            container_framework,
-            container_suffix,
-            command,
-            volumes,
-            work_dir,
-            out_dir)
+        run_container_and_log('BowTieBuilder',
+                              container_suffix,
+                              command,
+                              volumes,
+                              work_dir,
+                              out_dir,
+                              container_settings)
         # Output is already written to raw-pathway.txt file
 
 

spras/config/config.py

@@ -66,8 +66,6 @@ def __init__(self, raw_config: dict[str, Any]):
 
         # Directory used for storing output
         self.out_dir = parsed_raw_config.reconstruction_settings.locations.reconstruction_dir
-        # A Boolean indicating whether to enable container runtime profiling (apptainer/singularity only)
-        self.enable_profiling = False
         # A dictionary to store configured datasets against which SPRAS will be run
         self.datasets = None
         # A dictionary to store configured gold standard data against output of SPRAS runs
@@ -292,9 +290,8 @@ def process_config(self, raw_config: RawConfig):
         # Set up a few top-level config variables
         self.out_dir = raw_config.reconstruction_settings.locations.reconstruction_dir
 
-        if raw_config.enable_profiling and raw_config.containers.framework not in ["singularity", "apptainer"]:
+        if raw_config.containers.enable_profiling and raw_config.containers.framework not in ["singularity", "apptainer"]:
             warnings.warn("enable_profiling is set to true, but the container framework is not singularity/apptainer. This setting will have no effect.", stacklevel=2)
-        self.enable_profiling = raw_config.enable_profiling
 
         self.process_datasets(raw_config)
         self.process_algorithms(raw_config)

spras/config/container_schema.py

@@ -33,15 +33,18 @@ class ContainerRegistry(BaseModel):
 class ContainerSettings(BaseModel):
     framework: ContainerFramework = ContainerFramework.docker
     unpack_singularity: bool = False
+    enable_profiling: bool = False
+    "A Boolean indicating whether to enable container runtime profiling (apptainer/singularity only)"
     registry: ContainerRegistry
 
-    model_config = ConfigDict(extra='forbid')
+    model_config = ConfigDict(extra='forbid', use_attribute_docstrings=True)
 
 @dataclass
 class ProcessedContainerSettings:
     framework: ContainerFramework = ContainerFramework.docker
     unpack_singularity: bool = False
     prefix: str = DEFAULT_CONTAINER_PREFIX
+    enable_profiling: bool = False
     hash_length: int = 7
     """
     The hash length for container-specific usage. This does not appear in

spras/config/schema.py

@@ -139,7 +139,6 @@ class ReconstructionSettings(BaseModel):
 
 class RawConfig(BaseModel):
     containers: ContainerSettings
-    enable_profiling: bool = False
 
     hash_length: int = DEFAULT_HASH_LENGTH
     "The length of the hash used to identify a parameter combination"