cellfinder 1.1.1__tar.gz → 1.1.2__tar.gz

{cellfinder-1.1.1 → cellfinder-1.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.1.1
+Version: 1.1.2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -22,8 +22,8 @@ Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: brainglobe-utils
-Requires-Dist: brainglobe-napari-io
+Requires-Dist: brainglobe-utils>=0.4.2
+Requires-Dist: brainglobe-napari-io>=0.3.4
 Requires-Dist: dask[array]
 Requires-Dist: fancylog>=0.0.7
 Requires-Dist: natsort

{cellfinder-1.1.1 → cellfinder-1.1.2}/cellfinder/core/download/cli.py

@@ -3,7 +3,7 @@ from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
 from pathlib import Path
 
 from cellfinder.core.download import models
-from cellfinder.core.download.download import amend_cfg
+from cellfinder.core.download.download import amend_user_configuration
 
 home = Path.home()
 DEFAULT_DOWNLOAD_DIRECTORY = home / ".cellfinder"
@@ -65,7 +65,7 @@ def main():
         model_path = models.main(args.model, args.install_path)
 
     if not args.no_amend_config:
-        amend_cfg(new_model_path=model_path)
+        amend_user_configuration(new_model_path=model_path)
 
 
 if __name__ == "__main__":

{cellfinder-1.1.1 → cellfinder-1.1.2}/cellfinder/core/download/download.py

@@ -7,8 +7,8 @@ from brainglobe_utils.general.config import get_config_obj
 from brainglobe_utils.general.system import disk_free_gb
 
 from cellfinder.core.tools.source_files import (
-    source_config_cellfinder,
-    source_custom_config_cellfinder,
+    default_configuration_path,
+    user_specific_configuration_path,
 )
 
 
@@ -75,16 +75,45 @@ def download(
         os.remove(download_path)
 
 
-def amend_cfg(new_model_path=None):
-    print("Ensuring custom config file is correct")
-
-    original_config = source_config_cellfinder()
-    new_config = source_custom_config_cellfinder()
-    if new_model_path is not None:
-        write_model_to_cfg(new_model_path, original_config, new_config)
+def amend_user_configuration(new_model_path=None) -> None:
+    """
+    Amends the user configuration to contain the configuration
+    in new_model_path, if specified.
 
+    Parameters
+    ----------
+    new_model_path : str, optional
+        The path to the new model configuration.
+    """
+    print("(Over-)writing custom user configuration")
 
-def write_model_to_cfg(new_model_path, orig_config, custom_config):
+    original_config = default_configuration_path()
+    new_config = user_specific_configuration_path()
+    if new_model_path is not None:
+        write_model_to_config(new_model_path, original_config, new_config)
+
+
+def write_model_to_config(new_model_path, orig_config, custom_config):
+    """
+    Update the model path in the custom configuration file, by
+    reading the lines in the original configuration file, replacing
+    the line starting with "model_path =" and writing these
+    lines to the custom file.
+
+    Parameters
+    ----------
+    new_model_path : str
+        The new path to the model.
+    orig_config : str
+        The path to the original configuration file.
+    custom_config : str
+        The path to the custom configuration file to be created.
+
+    Returns
+    -------
+    None
+
+    """
     config_obj = get_config_obj(orig_config)
     model_conf = config_obj["model"]
     orig_path = model_conf["model_path"]

{cellfinder-1.1.1 → cellfinder-1.1.2}/cellfinder/core/tools/prep.py

@@ -14,8 +14,8 @@ from brainglobe_utils.general.system import get_num_processes
 import cellfinder.core.tools.tf as tf_tools
 from cellfinder.core import logger
 from cellfinder.core.download import models as model_download
-from cellfinder.core.download.download import amend_cfg
-from cellfinder.core.tools.source_files import source_custom_config_cellfinder
+from cellfinder.core.download.download import amend_user_configuration
+from cellfinder.core.tools.source_files import user_specific_configuration_path
 
 home = Path.home()
 DEFAULT_INSTALL_PATH = home / ".cellfinder"
@@ -49,18 +49,18 @@ def prep_models(
     if model_weights_path is None:
         logger.debug("No model supplied, so using the default")
 
-        config_file = source_custom_config_cellfinder()
+        config_file = user_specific_configuration_path()
 
         if not Path(config_file).exists():
             logger.debug("Custom config does not exist, downloading models")
             model_path = model_download.main(model_name, install_path)
-            amend_cfg(new_model_path=model_path)
+            amend_user_configuration(new_model_path=model_path)
 
         model_weights = get_model_weights(config_file)
         if not model_weights.exists():
             logger.debug("Model weights do not exist, downloading")
             model_path = model_download.main(model_name, install_path)
-            amend_cfg(new_model_path=model_path)
+            amend_user_configuration(new_model_path=model_path)
             model_weights = get_model_weights(config_file)
     else:
         model_weights = Path(model_weights_path)

cellfinder-1.1.2/cellfinder/core/tools/source_files.py

@@ -0,0 +1,27 @@
+from pathlib import Path
+
+
+def default_configuration_path():
+    """
+    Returns the default configuration path for cellfinder.
+
+    Returns:
+        Path: The default configuration path.
+    """
+    return Path(__file__).parent.parent / "config" / "cellfinder.conf"
+
+
+def user_specific_configuration_path():
+    """
+    Returns the path to the user-specific configuration file for cellfinder.
+
+    This function returns the path to the user-specific configuration file
+    for cellfinder. The user-specific configuration file is located in the
+    user's home directory under the ".cellfinder" folder and is named
+    "cellfinder.conf.custom".
+
+    Returns:
+        Path: The path to the custom configuration file.
+
+    """
+    return Path.home() / ".cellfinder" / "cellfinder.conf.custom"

{cellfinder-1.1.1 → cellfinder-1.1.2}/cellfinder.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cellfinder
-Version: 1.1.1
+Version: 1.1.2
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -22,8 +22,8 @@ Classifier: Topic :: Scientific/Engineering :: Image Recognition
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: brainglobe-utils
-Requires-Dist: brainglobe-napari-io
+Requires-Dist: brainglobe-utils>=0.4.2
+Requires-Dist: brainglobe-napari-io>=0.3.4
 Requires-Dist: dask[array]
 Requires-Dist: fancylog>=0.0.7
 Requires-Dist: natsort

{cellfinder-1.1.1 → cellfinder-1.1.2}/cellfinder.egg-info/requires.txt

@@ -1,5 +1,5 @@
-brainglobe-utils
-brainglobe-napari-io
+brainglobe-utils>=0.4.2
+brainglobe-napari-io>=0.3.4
 dask[array]
 fancylog>=0.0.7
 natsort

{cellfinder-1.1.1 → cellfinder-1.1.2}/pyproject.toml

@@ -20,8 +20,8 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "brainglobe-utils",
-    "brainglobe-napari-io",
+    "brainglobe-utils>=0.4.2",
+    "brainglobe-napari-io>=0.3.4",
     "dask[array]",
     "fancylog>=0.0.7",
     "natsort",

cellfinder-1.1.1/cellfinder/core/tools/source_files.py

@@ -1,9 +0,0 @@
-from pathlib import Path
-
-
-def source_config_cellfinder():
-    return Path(__file__).parent.parent / "config" / "cellfinder.conf"
-
-
-def source_custom_config_cellfinder():
-    return Path(__file__).parent.parent / "config" / "cellfinder.conf.custom"