basic fix avoiding writing to package files

cellfinder/core/download/cli.py

@@ -3,7 +3,7 @@
 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/core/download/download.py

@@ -7,8 +7,8 @@
 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/core/tools/prep.py

@@ -14,8 +14,8 @@
 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/core/tools/source_files.py

@@ -1,9 +1,27 @@
 from pathlib import Path
 
 
-def source_config_cellfinder():
+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 source_custom_config_cellfinder():
-    return Path(__file__).parent.parent / "config" / "cellfinder.conf.custom"
+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"