Standardize .yml and .yaml Extensions for Consistency (#488)

* Changed .yml to .yaml files

* Reverted changes in the main directories of the cellfinder repository

* Fixed the dependency errors in the Code

* Fixed the train_yml issue

* Modified train_yml to train_yaml in the train.py file on both lines 10 and 29

* Modified train_yml to train_yaml in the train.py file on both lines 10 and 29

---------

Co-authored-by: nischitkumar <[email protected]>

Author: nischitkumar

cellfinder/core/classify/classify.py

@@ -11,7 +11,7 @@
 from cellfinder.core import logger, types
 from cellfinder.core.classify.cube_generator import CubeGeneratorFromFile
 from cellfinder.core.classify.tools import get_model
-from cellfinder.core.train.train_yml import depth_type, models
+from cellfinder.core.train.train_yaml import depth_type, models
 
 
 def main(

cellfinder/core/main.py

@@ -6,7 +6,7 @@
 
 from cellfinder.core import logger
 from cellfinder.core.download.download import model_type
-from cellfinder.core.train.train_yml import depth_type
+from cellfinder.core.train.train_yaml import depth_type
 
 
 def main(

cellfinder/core/train/train_yml.py cellfinder/core/train/train_yaml.py

@@ -406,7 +406,7 @@ def save_training_data(
             self.update_status_label("Ready")
 
     def __prep_directories_for_save(self):
-        self.yaml_filename = self.output_directory / "training.yml"
+        self.yaml_filename = self.output_directory / "training.yaml"
         self.cell_cube_dir = self.output_directory / "cells"
         self.no_cell_cube_dir = self.output_directory / "non_cells"
 

cellfinder/napari/curation.py

@@ -7,7 +7,7 @@
 from napari.utils.notifications import show_info
 from qtpy.QtWidgets import QScrollArea
 
-from cellfinder.core.train.train_yml import run as train_yml
+from cellfinder.core.train.train_yaml import run as train_yaml
 from cellfinder.napari.utils import cellfinder_header, html_label_widget
 
 from .train_containers import (
@@ -26,7 +26,7 @@ def run_training(
     misc_training_inputs: MiscTrainingInputs,
 ):
     print("Running training")
-    train_yml(
+    train_yaml(
         **training_data_inputs.as_core_arguments(),
         **optional_network_inputs.as_core_arguments(),
         **optional_training_inputs.as_core_arguments(),

cellfinder/napari/train/train.py

@@ -5,7 +5,7 @@
 from magicgui.types import FileDialogMode
 
 from cellfinder.core.download.download import model_filenames
-from cellfinder.core.train.train_yml import models
+from cellfinder.core.train.train_yaml import models
 from cellfinder.napari.input_container import InputContainer
 from cellfinder.napari.utils import html_label_widget
 
@@ -31,7 +31,7 @@ def widget_representation(cls) -> dict:
                 "yaml_files",
                 custom_label="YAML files",
                 mode=FileDialogMode.EXISTING_FILES,
-                filter="*.yml",
+                filter="*.yaml",
             ),
             output_directory=cls._custom_widget(
                 "output_directory", mode=FileDialogMode.EXISTING_DIRECTORY

cellfinder/napari/train/train_containers.py

@@ -66,7 +66,7 @@ napari = [
 
 [project.scripts]
 cellfinder_download = "cellfinder.core.download.cli:main"
-cellfinder_train = "cellfinder.core.train.train_yml:cli"
+cellfinder_train = "cellfinder.core.train.train_yaml:cli"
 cellfinder = "cellfinder.cli_migration_warning:cli_catch"
 
 [project.urls]

pyproject.toml

@@ -3,14 +3,14 @@
 
 import pytest
 
-from cellfinder.core.train.train_yml import cli as train_run
+from cellfinder.core.train.train_yaml import cli as train_run
 
 data_dir = os.path.join(
     os.getcwd(), "tests", "data", "integration", "training"
 )
 cell_cubes = os.path.join(data_dir, "cells")
 non_cell_cubes = os.path.join(data_dir, "non_cells")
-training_yml_file = os.path.join(data_dir, "training.yml")
+training_yaml_file = os.path.join(data_dir, "training.yaml")
 
 
 EPOCHS = "2"
@@ -26,7 +26,7 @@ def test_train(tmpdir):
     train_args = [
         "cellfinder_train",
         "-y",
-        training_yml_file,
+        training_yaml_file,
         "-o",
         tmpdir,
         "--epochs",

tests/core/test_integration/test_train.py

@@ -85,7 +85,7 @@ def test_cell_marking(curation_widget, tmp_path):
     widget.output_directory = tmp_path
     widget.save_training_data(prompt_for_directory=False, block=True)
 
-    assert (tmp_path / "training.yml").exists()
+    assert (tmp_path / "training.yaml").exists()
     # Check that two .tif files are saved for both cells and non_cells
     assert len(list((tmp_path / "non_cells").glob("*.tif"))) == 2
     assert len(list((tmp_path / "cells").glob("*.tif"))) == 2

tests/data/integration/training/training.yml tests/data/integration/training/training.yaml

@@ -2,7 +2,7 @@
 
 import pytest
 
-from cellfinder.core.train.train_yml import run
+from cellfinder.core.train.train_yaml import run
 from cellfinder.napari.train.train_containers import (
     MiscTrainingInputs,
     OptionalNetworkInputs,

tests/napari/test_curation.py

@@ -30,7 +30,7 @@ def test_reset_to_defaults(get_training_widget):
     Checks widgets of a few different types are reset as expected.
     """
     # change a few widgets to non-default values
-    get_training_widget.yaml_files.value = ["file_1.yml", "file_2.yml"]
+    get_training_widget.yaml_files.value = ["file_1.yaml", "file_2.yaml"]
     get_training_widget.continue_training.value = True
     get_training_widget.epochs.value = 50
     get_training_widget.test_fraction.value = 0.20
@@ -65,11 +65,11 @@ def test_run_with_virtual_yaml_files(get_training_widget):
     Checks that training is run with expected set of parameters.
     """
     with patch("cellfinder.napari.train.train.run_training") as run_training:
-        # make default input valid - need yml files (they don't technically
+        # make default input valid - need yaml files (they don't technically
         # have to exist)
         virtual_yaml_files = (
-            Path.home() / "file_1.yml",
-            Path.home() / "file_2.yml",
+            Path.home() / "file_1.yaml",
+            Path.home() / "file_2.yaml",
         )
         get_training_widget.yaml_files.value = virtual_yaml_files
         get_training_widget.call_button.clicked()