Update docs after refactoring roman_photoz.

docs/conf.py

@@ -7,7 +7,7 @@
 import sys
 
 # Add the project directory to sys.path
-sys.path.insert(0, os.path.abspath('../roman_photoz'))
+sys.path.insert(0, os.path.abspath(".."))
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
@@ -22,6 +22,7 @@
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.napoleon",
+    "sphinxarg.ext",  # For automatic documentation of argparse arguments
 ]
 
 templates_path = ["_templates"]

docs/create_roman_filters.rst

@@ -1,21 +1,21 @@
-====================
+=====================
 Create Roman Filters
-====================
+=====================
 
 This module provides functionality to process Roman Space Telescope filter data, create individual filter files, and generate a configuration file for use with `rail+lephare`.
 
 Module API
 ----------
 
-.. automodule:: create_roman_filters
+.. automodule:: roman_photoz.create_roman_filters
    :members:
    :undoc-members:
    :show-inheritance:
 
-Usage Example
--------------
+Command-line Interface
+----------------------
 
-To use this module, run it as a script with the following command:
+This module can be run as a command-line tool to generate filter definitions:
 
 .. code-block:: bash
 
@@ -25,4 +25,3 @@ To use this module, run it as a script with the following command:
 - `<input_filename>`: The filename containing the monochromatic effective area of each filter per column.
 
 The script will generate individual filter files and a configuration file (`roman_phot.par`) for use with `rail+lephare`.
-

docs/create_simulated_catalog.rst

@@ -7,7 +7,7 @@ This module provides functionality to create a simulated catalog using data from
 Module API
 ----------
 
-.. automodule:: create_simulated_catalog
+.. automodule:: roman_photoz.create_simulated_catalog
    :members:
    :undoc-members:
    :show-inheritance:
@@ -19,26 +19,38 @@ The module can also be executed as a standalone script to create a simulated cat
 
 **Arguments**
 
-- ``--output_path`` (:class:`str`)  
+- ``--output_path`` (:class:`str`)
   Path to save the output catalog (default: ``LEPHAREWORK``).
 
-- ``--output_filename`` (:class:`str`)  
+- ``--output_filename`` (:class:`str`)
   Filename for the output catalog (default: ``roman_simulated_catalog.asdf``).
 
 **Example**
 
 .. code-block:: bash
 
-   python create_simulated_catalog.py --output_path /path/to/output --output_filename my_catalog.asdf
+   python -m roman_photoz.create_simulated_catalog --output_path=/path/to/output/ --output_filename=simulated_catalog.asdf
 
-Dependencies
-------------
+Usage Examples
+--------------
 
-- ``argparse``
-- ``os``
-- ``collections.OrderedDict``
-- ``pathlib.Path``
-- ``lephare``
-- ``numpy``
-- ``rail.core.stage``
-- ``roman_datamodels``
+The following example demonstrates how to programmatically create a simulated catalog:
+
+.. code-block:: python
+
+    from roman_photoz.create_simulated_catalog import CreateSimulatedCatalog
+
+    # Initialize the catalog creator with default parameters
+    creator = CreateSimulatedCatalog()
+
+    # Create a simulated catalog with 100 sources
+    catalog = creator.create_catalog(n_sources=100)
+
+    # Save the catalog to a file
+    creator.save_catalog(
+        catalog,
+        output_path="/path/to/output/",
+        output_filename="simulated_catalog.asdf"
+    )
+
+    print(f"Simulated catalog with {len(catalog)} sources created successfully")

docs/index.rst

@@ -6,6 +6,18 @@ The ``roman_photoz`` package provides tools for processing catalogs
 produced by the Roman Space Telescope Calibration Pipeline (``romancal``)
 to estimate photometric redshift.
 
+Overview
+--------
+
+The Roman Space Telescope will produce large catalogs of astronomical objects.
+This package provides tools for processing these catalogs to estimate photometric
+redshifts. Key features include:
+
+* Processing Roman catalog data in ASDF format
+* Creating filter definitions based on Roman Space Telescope specifications
+* Generating simulated catalogs for development and testing
+* Estimating photometric redshifts using LePhare
+
 .. toctree::
    :maxdepth: 2
    :caption: Contents

docs/roman_catalog_handler.rst

@@ -7,7 +7,7 @@ The ``roman_catalog_handler`` module provides functionality for handling catalog
 Module API
 ----------
 
-.. automodule:: roman_catalog_handler
+.. automodule:: roman_photoz.roman_catalog_handler
    :members:
    :undoc-members:
    :show-inheritance:
@@ -20,7 +20,7 @@ The following example demonstrates how to use the `RomanCatalogHandler` class to
 
      import os
      from pathlib import Path
-     from roman_catalog_handler import RomanCatalogHandler
+     from roman_photoz.roman_catalog_handler import RomanCatalogHandler
 
      # Ensure the TEST_BIGDATA environment variable is set
      test_bigdata = os.getenv("TEST_BIGDATA")

docs/roman_catalog_process.rst

@@ -7,7 +7,7 @@ This module provides functionality for processing catalog data related to the Ro
 Module API
 ----------
 
-.. automodule:: roman_catalog_process
+.. automodule:: roman_photoz.roman_catalog_process
    :members:
    :undoc-members:
    :show-inheritance:
@@ -17,7 +17,7 @@ Examples
 
 Basic usage::
 
-    from roman_catalog_process import process_catalog
+    from roman_photoz.roman_catalog_process import process_catalog
 
     process_catalog('input_catalog.fits', 'processed_catalog.fits')
 

docs/usage.rst

@@ -13,35 +13,20 @@ To use `roman_photoz`, follow these steps:
         import numpy as np
         from roman_photoz.roman_catalog_process import RomanCatalogProcess
 
-        argv = [
-            "--input_path",
-            "/path/to/input/file/",
-            "--input_filename",
-            "roman_simulated_catalog.asdf",
-            "--output_path",
-            "/path/to/output/file/",
-            "--output_filename",
-            "output_filename.asdf",
-            "--save_results",
-            "True",
-        ]
-
-        ####
-        # this approach will process the catalog
-        # and save the results to a file
-        # and will return an instance of RomanCatalogProcess
-        # that contains the results
-
-        # create a RomanCatalogProcess object
-        rcp = RomanCatalogProcess(config_filename=argv[1])
+        # create a RomanCatalogProcess object with default configuration
+        # and custom model filename
+        rcp = RomanCatalogProcess(
+            config_filename="",  # use default config
+            model_filename="custom_model.pkl"  # specify custom model filename
+        )
 
-        # and process the catalog
+        # process the catalog
         rcp.process(
-            input_path=argv[3],
-            input_filename=argv[5],
-            output_path=argv[7],
-            output_filename=argv[9],
-            save_results=argv[11],
+            input_path="/path/to/input/file/",
+            input_filename="roman_simulated_catalog.asdf",
+            output_path="/path/to/output/file/",
+            output_filename="output_filename.asdf",
+            save_results=True,
         )
 
         # examples of visualization
@@ -62,6 +47,8 @@ To use `roman_photoz`, follow these steps:
         from roman_photoz import roman_catalog_process
 
         argv = [
+            "--model_filename",
+            "custom_model.pkl",
             "--input_path",
             "/path/to/input/file/",
             "--input_filename",
@@ -80,4 +67,4 @@ To use `roman_photoz`, follow these steps:
 
     .. code-block:: bash
 
-        python -m roman_photoz --input_path=/path/to/input/file/ --input_filename=roman_simulated_catalog.asdf --output_path=/path/to/output/file/ --output_filename=output_filename.asdf --save_results=True
+        python -m roman_photoz --model_filename=custom_model.pkl --input_path=/path/to/input/file/ --input_filename=roman_simulated_catalog.asdf --output_path=/path/to/output/file/ --output_filename=output_filename.asdf --save_results=True

pyproject.toml

@@ -54,6 +54,7 @@ docs = [
     "stsci-rtd-theme",
     "sphinx-autobuild",
     "tomli; python_version <=\"3.11\"",
+    "sphinx-argparse",
 ]
 test = [
     "ci-watson >=0.5.0",