Merge branch 'develop' of github.com:ECP-CANDLE/Benchmarks into develop

Author: jmohdyusof

Pilot1/Uno/planargs.py

@@ -4,70 +4,82 @@
 
 import argparse
 
-partitioning_strategies = ['windows', 'undefine1', 'undefined2']         # to be completed ?????????????
+partitioning_strategies = [
+    "windows",
+    "undefine1",
+    "undefined2",
+]  # to be completed ?????????????
 
 
 def parse_arguments():
-    parser = argparse.ArgumentParser(
-        description='feature-set partioning'
-    )
+    parser = argparse.ArgumentParser(description="feature-set partioning")
 
-    parser.add_argument('--in_dir',
-                        type=str,
-                        help='Directory containing feature-set list files')
+    parser.add_argument(
+        "--in_dir", type=str, help="Directory containing feature-set list files"
+    )
 
-    parser.add_argument('--out_dir',
-                        default='results',
-                        type=str,
-                        help='Directory to contain generated plan files')
+    parser.add_argument(
+        "--out_dir",
+        default="results",
+        type=str,
+        help="Directory to contain generated plan files",
+    )
 
-    parser.add_argument('--json',
-                        action='store_true',
-                        help='Generate plan in JSON format')
+    parser.add_argument(
+        "--json", action="store_true", help="Generate plan in JSON format"
+    )
 
-    parser.add_argument('--overwrite',
-                        action='store_true',
-                        help='Accept non-empty out_dir, contents overwritten')
+    parser.add_argument(
+        "--overwrite",
+        action="store_true",
+        help="Accept non-empty out_dir, contents overwritten",
+    )
 
-    parser.add_argument('--partition_strategy',
-                        choices=partitioning_strategies,
-                        default=partitioning_strategies[0],
-                        help='Specify a feature-set partitioning strategy')
+    parser.add_argument(
+        "--partition_strategy",
+        choices=partitioning_strategies,
+        default=partitioning_strategies[0],
+        help="Specify a feature-set partitioning strategy",
+    )
 
     # The following fs_* arguments are required, the number of values specified for each
     # must match, and at least two values are required for each
 
-    parser.add_argument('--fs_names',
-                        required=True,
-                        type=str,
-                        nargs='+',
-                        help='Specify a list of (arbitrary) feature-set names')
-
-    parser.add_argument('--fs_paths',
-                        required=True,
-                        type=str,
-                        nargs='+',
-                        help='Specify a list of feature-set file paths')
-
-    parser.add_argument('--fs_parts',
-                        required=True,
-                        type=int,
-                        nargs='+',
-                        help='Specify a list of partition counts')
-
-    parser.add_argument('--verbose',
-                        action='store_true',
-                        help='Verbosity')
-
-    parser.add_argument('--debug',
-                        action='store_true',
-                        help='Data structure dumps, etc')
-
-    parser.add_argument('--test',
-                        action='store_true',
-                        help='Test plan navigation and entry retrieval')
-
-    parser.add_argument('--maxdepth', type=int, default=0)
-    parser.add_argument('--print_tree', action='store_true')
+    parser.add_argument(
+        "--fs_names",
+        required=True,
+        type=str,
+        nargs="+",
+        help="Specify a list of (arbitrary) feature-set names",
+    )
+
+    parser.add_argument(
+        "--fs_paths",
+        required=True,
+        type=str,
+        nargs="+",
+        help="Specify a list of feature-set file paths",
+    )
+
+    parser.add_argument(
+        "--fs_parts",
+        required=True,
+        type=int,
+        nargs="+",
+        help="Specify a list of partition counts",
+    )
+
+    parser.add_argument("--verbose", action="store_true", help="Verbosity")
+
+    parser.add_argument(
+        "--debug", action="store_true", help="Data structure dumps, etc"
+    )
+
+    parser.add_argument(
+        "--test", action="store_true", help="Test plan navigation and entry retrieval"
+    )
+
+    parser.add_argument("--maxdepth", type=int, default=0)
+    parser.add_argument("--print_tree", action="store_true")
     args = parser.parse_args()
     return args

Pilot1/Uno/plangen.py

@@ -4,7 +4,6 @@
 import os
 import sqlite3
 import sys
-import planargs
 from abc import ABC, abstractmethod  # abstract class support
 from collections import OrderedDict, deque, namedtuple
 from datetime import datetime
@@ -13,6 +12,7 @@
 from sqlite3 import Error as db_Error
 
 import numpy as np
+import planargs
 from scipy.special import comb
 
 ISO_TIMESTAMP = "seconds"  # timestamp to ISO string

README.md

@@ -1,5 +1,9 @@
 # Benchmarks
 
+IMPORTANT
+
+The latest version of Benchmarks uses a separate candle_lib package to replace the functionality formerly found in Benchmarks/common. In order to run the Benchmarks, you will first need to download candle_lib from https://github.com/ECP-CANDLE/candle_lib and install it using the instructions found there.
+
 ECP-CANDLE Benchmarks
 
 This repository contains the CANDLE benchmark codes. These codes implement deep learning architectures that are relevant to problems in cancer. These architectures address problems at different biological scales, specifically problems at the molecular, cellular and population scales.