genome-entropy 0.1.1__tar.gz → 0.1.2__tar.gz

{genome_entropy-0.1.1/src/genome_entropy.egg-info → genome_entropy-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genome_entropy
-Version: 0.1.1
+Version: 0.1.2
 Summary: Quantify information content across multiple biological representations derived from genomic sequences
 Author-email: Rob Edwards <raedwards@gmail.com>
 License: MIT
@@ -43,9 +43,10 @@ Dynamic: license-file
 # genome_entropy
 
 [![Edwards Lab](https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4)](https://edwards.flinders.edu.au/)
-
+[![DOI](https://zenodo.org/badge/1132511885.svg)](https://doi.org/10.5281/zenodo.18312206)
 [![Python CI](https://github.com/linsalrob/genome_entropy/workflows/Python%20CI/badge.svg)](https://github.com/linsalrob/genome_entropy/actions)
-[![Documentation](https://github.com/linsalrob/genome_entropy/workflows/Documentation/badge.svg)](https://linsalrob.github.io/genome_entropy/)
+[![GH Pages Docs](https://github.com/linsalrob/genome_entropy/workflows/Documentation/badge.svg)](https://linsalrob.github.io/genome_entropy/)
+[![Read The Docs](https://readthedocs.org/projects/orf-entropy/badge/?version=latest)](https://orf-entropy.readthedocs.io/en/latest/?badge=latest)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/README.md

@@ -1,9 +1,10 @@
 # genome_entropy
 
 [![Edwards Lab](https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4)](https://edwards.flinders.edu.au/)
-
+[![DOI](https://zenodo.org/badge/1132511885.svg)](https://doi.org/10.5281/zenodo.18312206)
 [![Python CI](https://github.com/linsalrob/genome_entropy/workflows/Python%20CI/badge.svg)](https://github.com/linsalrob/genome_entropy/actions)
-[![Documentation](https://github.com/linsalrob/genome_entropy/workflows/Documentation/badge.svg)](https://linsalrob.github.io/genome_entropy/)
+[![GH Pages Docs](https://github.com/linsalrob/genome_entropy/workflows/Documentation/badge.svg)](https://linsalrob.github.io/genome_entropy/)
+[![Read The Docs](https://readthedocs.org/projects/orf-entropy/badge/?version=latest)](https://orf-entropy.readthedocs.io/en/latest/?badge=latest)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "genome_entropy"
-version = "0.1.1"
+version = "0.1.2"
 description = "Quantify information content across multiple biological representations derived from genomic sequences"
 readme = "README.md"
 requires-python = ">=3.10"

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/src/genome_entropy/cli/commands/estimate_tokens.py

@@ -1,5 +1,6 @@
 """Token size estimation command."""
 
+from pathlib import Path
 from typing import Optional
 import traceback
 
@@ -51,6 +52,17 @@ def estimate_token_size_command(
         "-b",
         help="Approximate length of individual proteins (amino acids)",
     ),
+    log_level: str = typer.Option(
+        "INFO",
+        "--log-level",
+        "-l",
+        help="Logging level (DEBUG, INFO, WARNING, ERROR, CRITICAL)",
+    ),
+    log_file: Optional[Path] = typer.Option(
+        None,
+        "--log-file",
+        help="Path to log file (default: log to STDOUT)",
+    ),
 ) -> None:
     """Estimate optimal token size for GPU encoding.
 
@@ -61,8 +73,20 @@ def estimate_token_size_command(
     The recommended token size is returned as 90% of the maximum for safety.
     """
     try:
+        from ...config import VALID_LOG_LEVELS
+        from ...logging_config import configure_logging
         from ...encode3di import ProstT5ThreeDiEncoder, estimate_token_size
 
+        # Validate and configure logging
+        if log_level.upper() not in VALID_LOG_LEVELS:
+            typer.echo(
+                f"Error: Invalid log level '{log_level}'. Must be one of: {', '.join(VALID_LOG_LEVELS)}",
+                err=True,
+            )
+            raise typer.Exit(2)
+
+        configure_logging(level=log_level.upper(), log_file=log_file)
+
         typer.echo("=" * 60)
         typer.echo("Token Size Estimation")
         typer.echo("=" * 60)

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/src/genome_entropy/encode3di/encoder.py

@@ -117,7 +117,7 @@ class ProstT5ThreeDiEncoder:
 
         # only GPUs support half-precision currently; if you want to run on
         # CPU use full-precision (not recommended, much slower)
-        _ = self.model.full() if self.device == "cpu" else self.model.half()
+        _ = self.model.float() if self.device == "cpu" else self.model.half()
 
     def token_budget_batches(
         self,

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/src/genome_entropy/logging_config.py

@@ -48,12 +48,14 @@ def configure_logging(
     global _configured, _log_file, _log_level
 
     # Convert string level to int if needed
+    ori_level = level
     if isinstance(level, str):
         level = getattr(logging, level.upper(), logging.INFO)
 
-    # Skip if already configured (unless force=True)
-    if _configured and not force:
-        return
+    # We always reconfigure, whether or not we are forced to.
+    # this is now here to prevent an error :)
+    if force:
+        logging.info("force is deprecated in logging - we always switch levels")
 
     # Clear any existing handlers
     root_logger = logging.getLogger()

{genome_entropy-0.1.1 → genome_entropy-0.1.2/src/genome_entropy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: genome_entropy
-Version: 0.1.1
+Version: 0.1.2
 Summary: Quantify information content across multiple biological representations derived from genomic sequences
 Author-email: Rob Edwards <raedwards@gmail.com>
 License: MIT
@@ -43,9 +43,10 @@ Dynamic: license-file
 # genome_entropy
 
 [![Edwards Lab](https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4)](https://edwards.flinders.edu.au/)
-
+[![DOI](https://zenodo.org/badge/1132511885.svg)](https://doi.org/10.5281/zenodo.18312206)
 [![Python CI](https://github.com/linsalrob/genome_entropy/workflows/Python%20CI/badge.svg)](https://github.com/linsalrob/genome_entropy/actions)
-[![Documentation](https://github.com/linsalrob/genome_entropy/workflows/Documentation/badge.svg)](https://linsalrob.github.io/genome_entropy/)
+[![GH Pages Docs](https://github.com/linsalrob/genome_entropy/workflows/Documentation/badge.svg)](https://linsalrob.github.io/genome_entropy/)
+[![Read The Docs](https://readthedocs.org/projects/orf-entropy/badge/?version=latest)](https://orf-entropy.readthedocs.io/en/latest/?badge=latest)
 [![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/tests/test_cli_smoke.py

@@ -93,3 +93,25 @@ def test_estimate_tokens_command_help() -> None:
     assert "token size" in result.stdout.lower()
     assert "model" in result.stdout.lower()
     assert "device" in result.stdout.lower()
+    # Remove ANSI codes to check for options
+    import re
+
+    clean_output = re.sub(r"\x1b\[[0-9;]*m", "", result.stdout)
+    assert "--log-level" in clean_output
+    assert "--log-file" in clean_output
+
+
+def test_estimate_tokens_log_level_option() -> None:
+    """Test that estimate-tokens accepts --log-level option."""
+    # Just checking help to ensure the option is recognized
+    result = runner.invoke(app, ["estimate-tokens", "--help"])
+    assert result.exit_code == 0
+    # Remove ANSI codes and check
+    import re
+
+    clean_output = re.sub(r"\x1b\[[0-9;]*m", "", result.stdout)
+    assert "--log-level" in clean_output
+    # Make sure it describes logging level
+    assert (
+        "logging level" in result.stdout.lower() or "log level" in result.stdout.lower()
+    )

{genome_entropy-0.1.1 → genome_entropy-0.1.2}/tests/test_logging_config.py

@@ -134,20 +134,6 @@ def test_configure_logging_creates_parent_dirs():
         assert log_file.parent.exists()
 
 
-def test_configure_logging_no_reconfigure_without_force():
-    """Test that logging is not reconfigured without force=True."""
-    configure_logging(level="INFO", force=True)
-    initial_level = get_log_level()
-
-    # Try to reconfigure without force (should not change)
-    configure_logging(level="DEBUG", force=False)
-    assert get_log_level() == initial_level
-
-    # Reconfigure with force (should change)
-    configure_logging(level="DEBUG", force=True)
-    assert get_log_level() == logging.DEBUG
-
-
 def test_logging_format():
     """Test that logging format includes expected components."""
     with tempfile.TemporaryDirectory() as tmpdir: