WIP api index

Author: lauraporta

docs/make_api_index.py

@@ -0,0 +1,42 @@
+"""
+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",
+]
+
+# Set the current working directory to the directory of this script
+script_dir = Path(__file__).resolve().parent
+os.chdir(script_dir)
+
+
+def make_api_index():
+    """Create a doctree of all ``movement`` modules."""
+    doctree = "\n"
+    api_path = Path("../derotation")
+    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
+    output_path = Path("source") / "api_index.rst"
+    with output_path.open("w") as f:
+        f.write(api_head)
+        f.write(doctree)
+
+
+if __name__ == "__main__":
+    make_api_index()

docs/requirements.txt

@@ -8,3 +8,4 @@ sphinx
 sphinx-argparse
 sphinx-autodoc-typehints
 sphinx_design
+-e .

docs/source/_templates/api_index_head.rst

@@ -0,0 +1,16 @@
+..
+    This file is auto-generated.
+
+.. _target-api:
+
+API reference
+=============
+
+Information on specific functions, classes, and methods.
+
+.. rubric:: Modules
+
+.. autosummary::
+    :toctree: api
+    :recursive:
+    :nosignatures:

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

@@ -0,0 +1,12 @@
+derotation.analysis.blob\_detection
+===================================
+
+.. automodule:: derotation.analysis.blob_detection
+
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      BlobDetection
+   

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

@@ -0,0 +1,14 @@
+derotation.analysis.fit\_ellipse
+================================
+
+.. automodule:: derotation.analysis.fit_ellipse
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      derive_angles_from_ellipse_fits
+      fit_ellipse_to_points
+      plot_ellipse_fit_and_centers
+   

docs/source/api/derotation.derotate_by_line.rst

@@ -0,0 +1,13 @@
+derotation.derotate\_by\_line
+=============================
+
+.. automodule:: derotation.derotate_by_line
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      apply_homography
+      derotate_an_image_array_line_by_line
+   

docs/source/api/derotation.load_data.custom_data_loaders.rst

@@ -0,0 +1,14 @@
+derotation.load\_data.custom\_data\_loaders
+===========================================
+
+.. automodule:: derotation.load_data.custom_data_loaders
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      convert_to_volts
+      get_analog_signals
+      read_randomized_stim_table
+   

docs/source/api/derotation.plotting_hooks.for_derotation.rst

@@ -0,0 +1,13 @@
+derotation.plotting\_hooks.for\_derotation
+==========================================
+
+.. automodule:: derotation.plotting_hooks.for_derotation
+
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      image_completed
+      line_addition
+   

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

@@ -0,0 +1,12 @@
+derotation.simulate.line\_scanning\_microscope
+==============================================
+
+.. automodule:: derotation.simulate.line_scanning_microscope
+
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      Rotator
+   

docs/source/api_index.rst

@@ -1,16 +1,25 @@
-API
-====
+..
+    This file is auto-generated.
 
-Full derotation
----------------
+.. _target-api:
 
-.. currentmodule:: derotation.analysis.full_rotation_pipeline
+API reference
+=============
 
-.. autoclass:: FullPipeline
+Information on specific functions, classes, and methods.
 
-Incremental derotation
-----------------------
+.. rubric:: Modules
 
-.. currentmodule:: derotation.analysis.incremental_rotation_pipeline
-
-.. autoclass:: IncrementalPipeline
+.. autosummary::
+    :toctree: api
+    :recursive:
+    :nosignatures:
+    derotation.analysis.blob_detection
+    derotation.analysis.fit_ellipse
+    derotation.analysis.full_derotation_pipeline
+    derotation.analysis.incremental_derotation_pipeline
+    derotation.derotate_by_line
+    derotation.load_data.custom_data_loaders
+    derotation.plotting_hooks.for_derotation
+    derotation.simulate.line_scanning_microscope
+    derotation.simulate.synthetic_data