doc package build

.readthedocs.yaml

@@ -5,19 +5,20 @@
 version: 2
 
 # Set the OS, Python version, and other tools you might need
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Set the version of Python and other tools you might need
 build:
-  os: ubuntu-24.04
+  os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.10"
+  jobs:
+    post_create_environment:
+      - pip install poetry>=1.8.3
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
 
-# Build documentation in the "docs/" directory with Sphinx
+# Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
-
-# Optionally, but recommended,
-# declare the Python requirements required to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt
-
+  configuration: docs/source/conf.py

README.rst

@@ -0,0 +1,22 @@
+Contsub
+=======
+
+Image and uv-plane continuum subtraction tools for spectral line data.
+
+Installation
+------------
+
+PyPI (stable; recommended)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+    pip install contsub
+
+Latest (in development)
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: bash
+
+    pip install git+https://github.com/laduma-dev/contsub.git
+

contsub/parser/imcontsub.yaml

@@ -25,7 +25,7 @@ inputs:
     policies:
       repeat: "[]"
   fit-model:
-    info: Fit function to model the continuum. ** Only the spline is available in this version **.
+    info: "### NOT IMPLEMENTED ### Fit function to model the continuum."
     dtype: str
     choices:
       - spline

docs/source/conf.py

@@ -6,27 +6,52 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
+
+import contsub
+from datetime import date
+
 project = 'contsub'
-copyright = '2025, Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo'
 author = 'Amir Kazemi-Moridani, Sphesihle Makhathini, Mika Naidoo'
 release = '1.0.2'
+copyright = f'{date.today().year}, {author}'
+
+release = contsub.__version__
+version = contsub.__version__
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.napoleon",
-    "sphinx_rtd_theme",
-]
 
 templates_path = ['_templates']
 exclude_patterns = []
 
-language = 'Python'
+language = 'en'
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'alabaster'
-html_static_path = ['_static']
+html_theme = 'furo'
+#html_static_path = ['build/html/_static']
+
+
+needs_sphinx = "8.1"
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = [
+    "sphinx_copybutton",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.extlinks",
+    "sphinx_click.ext",
+]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"

docs/source/how-to/installation.rst

@@ -0,0 +1,16 @@
+.. _installation:
+
+
+Installation
+=============
+The stable version Simms 3.0 is available on `PyPI <https://pypi.org/project/contsub>`_ and can be installed using:
+
+.. code-block:: bash
+
+    pip install contsub
+
+The latest (in development) version can be installed directly from GitHub by using:
+
+.. code-block:: bash
+
+    pip install git+https://github.com/laduma-dev/contsub.git

docs/source/how-to/usage.rst

@@ -0,0 +1,40 @@
+.. _usage:
+
+.. role:: raw-math(raw)
+    :format: latex html
+
+Command-line Applications
+=================================
+
+:command:`imcontsub`
+---------------------
+The image-plane application :command:`imcontsub` is used to perform continuum subtraction on spectral line data cubes. It can handle large data cubes efficiently by processing them in chunks. The chunking is done along the RA-axis, i.e, the data cube is split into smaller sub-cubes that are processed in parallel.
+
+
+A key advantage of image-plane continuum subtraction is that it allows for robust on-the-fly thresholding due to the high signal-to-noise ratio compared to the uv-plane. This is particularly useful on for data cubes unknown line emission, which, if not accounted for, can lead to significant errors in the continuum subtraction process. This on-the-fly thresholding can be enabled by setting the ``--sigma-clip`` parameter.
+
+.. code-block:: bash
+
+    imcontsub --output-prefix output_prefix \
+                --sigma-clip 5 \
+                --order 3 \
+                --segments 250 \
+                --ra-chunks 64 \
+                --nworkers 8 \
+                input_fits_cube.fits
+
+However, if the line emission is known, a binary mask can be provided to the ``--mask-image`` option. In this case, the ``--sigma-clip`` parameter will be ignored (if set.)
+
+:command:`imcontsub` also allows the user to specify multiple ``--sigma-clip``, ``--order`` and ``--segments`` parameters. This allows the user to do the continuum subtraction in multiple iterations, each time using a different set of parameters. The advantage of this is that the user can start with a large ``--sigma-clip`` and wide ``--segments`` values to remove the most significant line emission, and then gradually decrease both to remove smaller line emission features. When using this mode, the ``--segments`` and ``--order`` must have the same length. Here's an example
+
+.. code-block:: bash
+
+    imcontsub --output-prefix output_prefix \
+                --sigma-clip 5 5 3 \
+                --order 3 2 2 \
+                --segments 400 300 250 \
+                --ra-chunks 64 \
+                --nworkers 8 \
+                input_fits_cube.fits
+
+

docs/source/index.rst

@@ -10,11 +10,12 @@ Welcome to contsub's documentation!
    :maxdepth: 2
    :caption: Contents:
 
+   how-to/installation
+   how-to/usage
+   reference/reference
+   tutorials/tutorials
 
 
-.. automodule:: your_module
-   :members:
-
 
 
 Indices and tables

docs/source/reference/reference.rst

@@ -0,0 +1,13 @@
+.. _reference:
+
+Reference
+###########
+.. role:: raw-math(raw)
+    :format: latex html
+
+
+.. click:: contsub.parser.imcontsub:runit
+    :prog: imcontsub
+    :nested: full
+
+

docs/source/tutorials/tutorials.rst

@@ -0,0 +1,5 @@
+.. highlight: yml
+.. _tutorials:
+
+Tutorials
+##############################