0.5.1 model bug fix

senseppi/__init__.py

-__version__ = "0.5.0"
+__version__ = "0.5.1"
 __author__ = "Konstantin Volzhenin"
 
 from . import model, commands, esm2_model, dataset, utils, network_utils

senseppi/commands/predict.py

@@ -68,7 +68,7 @@ def add_args(parser):
     parser._action_groups[0].add_argument("fasta_file", type=pathlib.Path,
                                           help="FASTA file on which to extract the ESM2 representations and then test.",
                                           )
-    predict_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "senseppi.ckpt"),
+    predict_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "default_model", "senseppi.ckpt"),
                                           help="A path to .ckpt file that contains weights to a pretrained model. If "
                                                "None, the senseppi trained version is used.")
     predict_args.add_argument("--pairs_file", type=str, default=None,

senseppi/commands/predict_string.py

@@ -187,7 +187,7 @@ def add_args(parser):
     parser._action_groups[0].add_argument("genes", type=str, nargs="+",
                                           help="Name of gene to fetch from STRING database. Several names can be "
                                                "typed (separated by whitespaces).")
-    string_pred_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "senseppi.ckpt"),
+    string_pred_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "default_model", "senseppi.ckpt"),
                                   help="A path to .ckpt file that contains weights to a pretrained model. If "
                                        "None, the senseppi trained version is used.")
     string_pred_args.add_argument("-s", "--species", type=int, default=9606,

senseppi/commands/test.py

@@ -44,7 +44,7 @@ def add_args(parser):
                                           help="FASTA file on which to extract the ESM2 "
                                                "representations and then evaluate.",
                                           )
-    test_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "senseppi.ckpt"),
+    test_args.add_argument("--model_path", type=str, default=os.path.join(os.path.dirname(__file__), "..", "default_model", "senseppi.ckpt"),
                            help="A path to .ckpt file that contains weights to a pretrained model. If "
                                 "None, the senseppi trained version is used.")
     test_args.add_argument("-o", "--output", type=str, default="test_metrics",

setup.py

@@ -13,7 +13,7 @@ setup(
     url="",
     license="MIT",
     packages=find_packages(),
-
+    package_data={'senseppi': ['default_model/*']},
     long_description=long_description,
     long_description_content_type="text/markdown",
     include_package_data=True,