Fix creation of api index

Author: lauraporta

derotation/analysis/full_derotation_pipeline.py

@@ -1133,9 +1133,7 @@ def derotate_frames_line_by_line(self) -> np.ndarray:
     def find_image_offset(img):
         """Find the "F0", also called "image offset" for a given image.
 
-        Explanations
-        ------------
-        What is the image offset?
+        Explanations: What is the image offset?
         The PMT (photo-multiplier tube) adds an arbitrary offset to the
         image that corresponds to 0 photons received. We can use a Gaussian
         Mixture Model to find this offset by assuming that it will be the

docs/make_api_index.py

@@ -1,42 +1,65 @@
-"""
-Generate the API index page for all modules.
-Inspired by `movement` package.
-"""
-
 import os
 from pathlib import Path
 
 # Modules to exclude from the API index
-exclude_modules = [
-    "cli_entrypoint",
-    "loader_widgets",
-    "meta_widget",
-]
+EXCLUDE_MODULES = {"cli_entrypoint", "loader_widgets", "meta_widget"}
 
 # Set the current working directory to the directory of this script
-script_dir = Path(__file__).resolve().parent
-os.chdir(script_dir)
+SCRIPT_DIR = Path(__file__).resolve().parent
+os.chdir(SCRIPT_DIR)
 
 
 def make_api_index():
-    """Create a doctree of all ``movement`` modules."""
-    doctree = "\n"
+    """Generate a properly formatted `api_index.rst` file for Sphinx documentation."""
+
     api_path = Path("../derotation")
+    module_entries = []
+
     for path in sorted(api_path.rglob("*.py")):
         # Convert file path to module name
         rel_path = path.relative_to(api_path.parent)
         module_name = str(rel_path.with_suffix("")).replace(os.sep, ".")
-        if rel_path.stem not in exclude_modules:
-            doctree += f"    {module_name}\n"
-    # # Get the header
-    api_head_path = Path("source") / "_templates" / "api_index_head.rst"
-    api_head = api_head_path.read_text()
-    # Write api_index.rst with header + doctree
+
+        if rel_path.stem not in EXCLUDE_MODULES:
+            module_entries.append(module_name)
+
+    # Construct the API index content
+    api_index_content = """\
+.. _target-api:
+
+API Reference
+=============
+
+This section contains automatically generated documentation for the `derotation` package.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API Documentation
+
+"""
+
+    # Add module entries for the toctree
+    api_index_content += "\n".join(f"   {module}" for module in module_entries) + "\n\n"
+
+    # Add the autosummary directive
+    api_index_content += """\
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree: api
+   :nosignatures:
+
+"""
+
+    # Add module entries for autosummary
+    api_index_content += "\n".join(f"   {module}" for module in module_entries) + "\n"
+
+    # Write the generated content to `api_index.rst`
     output_path = Path("source") / "api_index.rst"
-    with output_path.open("w") as f:
-        f.write(api_head)
-        f.write(doctree)
+    output_path.write_text(api_index_content, encoding="utf-8")
+
+    print(f"Generated {output_path}")
 
 
 if __name__ == "__main__":
-    make_api_index()
+    make_api_index()

docs/source/api/derotation.__init__.rst

@@ -0,0 +1,6 @@
+derotation.\_\_init\_\_
+=======================
+
+.. currentmodule:: derotation
+
+.. autofunction:: __init__

docs/source/api/derotation.analysis.bayesian_optimization.rst

@@ -0,0 +1,12 @@
+derotation.analysis.bayesian\_optimization
+==========================================
+
+.. automodule:: derotation.analysis.bayesian_optimization
+
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      BO_for_derotation
+   

docs/source/api/derotation.analysis.full_derotation_pipeline.rst

@@ -0,0 +1,12 @@
+derotation.analysis.full\_derotation\_pipeline
+==============================================
+
+.. automodule:: derotation.analysis.full_derotation_pipeline
+
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      FullPipeline
+   

docs/source/api/derotation.analysis.incremental_derotation_pipeline.rst

@@ -0,0 +1,12 @@
+derotation.analysis.incremental\_derotation\_pipeline
+=====================================================
+
+.. automodule:: derotation.analysis.incremental_derotation_pipeline
+
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      IncrementalPipeline
+   

docs/source/api/derotation.analysis.mean_images.rst

@@ -0,0 +1,12 @@
+derotation.analysis.mean\_images
+================================
+
+.. automodule:: derotation.analysis.mean_images
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      calculate_mean_images
+   

docs/source/api/derotation.analysis.metrics.rst

@@ -0,0 +1,12 @@
+derotation.analysis.metrics
+===========================
+
+.. automodule:: derotation.analysis.metrics
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      ptd_of_most_detected_blob
+   

docs/source/api/derotation.derotate_batch.rst

@@ -0,0 +1,13 @@
+derotation.derotate\_batch
+==========================
+
+.. automodule:: derotation.derotate_batch
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      derotate
+      update_config_paths
+   

docs/source/api/derotation.simulate.synthetic_data.rst

@@ -0,0 +1,12 @@
+derotation.simulate.synthetic\_data
+===================================
+
+.. automodule:: derotation.simulate.synthetic_data
+
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      SyntheticData
+