top-sim · myxie · Aug 9, 2025 · Aug 10, 2025 · Aug 10, 2025 · Aug 10, 2025
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,25 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version, and other tools you might need
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/source/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
+   - requirements: requirements.txt
+
+
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1 @@
+sphinx_rtd_theme
diff --git a/docs/source/_static/css/custom.css b/docs/source/_static/css/custom.css
@@ -0,0 +1,30 @@
+@import "theme.css";
+
+.wy-side-nav-search {
+    background: #BEBEBE;
+}
+.wy-nav-side {
+    background: #F5F5F5;
+}
+
+.wy-menu-vertical p.caption{
+    color: #BEBEBE;
+}
+.wy-menu-vertical a{
+    color: black;
+}
+
+.wy-menu-vertical a:hover {
+    background-color: #BEBEBE;
+    color: black;
+}
+
+.wy-table-responsive table td,
+.wy-table-responsive table th {
+    white-space: normal !important; /* Allow text to wrap */
+    word-wrap: break-word !important;
+}
+
+.wy-nav-content {
+    max-width: 1000px
+}
diff --git a/docs/source/comparisons.rst b/docs/source/comparisons.rst
@@ -33,23 +33,12 @@ For comparative models, we use the following cumulative totals, subsequently der
     * Task transfer rates: These are described in the `graph` construction in the parametric model. These are used when determining the total offline workflow runtime.
 
 
-.. code-block::
-    :caption: A cool example
-
-        testing
-        testing
-
-
-The output of this line starts with four spaces.
-
-At :numref:`label` you can see
 
 Compute values
 ---------------
 
 Compute valuates
-
-
+----------------
 
 References
 -----------
@@ -58,4 +47,4 @@ References
 
 .. [2] https://github.com/ska-telescope/sdp-par-model/blob/master/notebooks/SKA1_Scheduling_New.ipynb
 
-.. [3] Nikolic, B. (2016). SDP Memo: Estimating the SDPComputational Efficiency (Memo SKA-TEL-SDP-0000086). http://ska-sdp.org/sites/default/files/attachments/ska-tel-sdp-0000086_c_rep_sdpmemoefficiencyprototyping_-_signed.pdf
+.. [3] Nikolic, B. (2016). SDP Memo: Estimating the SDPComputational Efficiency (Memo SKA-TEL-SDP-0000086) 
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -2,7 +2,7 @@
 #
 # This file only contains a selection of the most common options. For a full
 # list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
+# http://www.sphinx-doc.org/en/master/config
 
 # -- Path setup --------------------------------------------------------------
 
@@ -13,27 +13,28 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath('../../'))
+sys.path.insert(0, os.path.abspath('../../../'))
+
 import sphinx
 
 # -- Project information -----------------------------------------------------
 
-project = 'TopSim Pipelines'
-copyright = '2021, RW Bunney'
+project = 'SKAWorkflows'
+copyright = '2019-2025, RW Bunney'
 author = 'RW Bunney'
 
 master_doc = 'index'
-
 # -- General configuration ---------------------------------------------------
 
 # 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.ext.autodoc', 'sphinx.ext.napoleon',
-              'sphinx.ext.autosummary',
-              'sphinx.ext.viewcode']
+extensions = [
+    'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.autosummary',
+    'sphinx.ext.viewcode'
+]
 
-# Add any paths that contain templates here, relative to this directory.
+# Add any paths that contain templates here, relative to this sdirectory.
 templates_path = ['_templates']
 
 # List of patterns, relative to source directory, that match files and
@@ -44,15 +45,24 @@
 autodoc_member_order = 'bysource'
 autosummary_generate = True
 
-
-# -- Options for HTML output -------------------------------------------------
+# -- Options for HTML output ---------------------q----------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'pydata_sphinx_theme'
+html_theme = 'sphinx_rtd_theme'
 
+# html_theme_options = {"full_logo":"true"}
+html_theme_options = {
+    # "show_toc_level": True,
+    # "collapse_navigation": False,
+    # "navigation_depth": 2
+}
+html_logo = '' #'new_logo.svg'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
+html_css_files = ["css/custom.css"]
+html_style = "css/custom.css"
+html_title = 'SKAWorkflows'
diff --git a/docs/source/data/origins.rst b/docs/source/data/origins.rst
@@ -1,6 +1,6 @@
-========
+============
 Data origins
-========
+============
 
 System sizing
 --------------
@@ -10,18 +10,24 @@ work is spread throughout the SDP design documentation. The following is a
 list of where the information for certain values may be found.
 
 **Average FLOP-rate**:
+~~~~~~~~~~~~~~~~~~~~~~
 - SKA1 SDP System Sizing, 3.1 (Table 2).
+
 	- Weighted average FLOPs are put at 13.6 PFLOPs
+
 - SDP Memo 025; Updated SDP Cost basis of Estimate June 2016.
-	- Based on this document, which produces the system specification, this
-is reflecting a ~20% efficiency.
+
+	- Based on this document, which produces the system specification, this is reflecting a ~20% efficiency.
 	- This efficiency is reported in Broekma et al 2015
 	- This efficiency was updated in 2016 due to further analysis (~10%).
 	- However, the parametric model uses adjusted 9.623 (~13% efficiency).
+
 - SKA1 Scheduling and Archive Constraints, 3.3 pg. 13
+
 	- 10% efficiency estimations are used here.
 
-**Total buffer size**:
+Total buffer size
+~~~~~~~~~~~~~~~~~~~~~~
 - SKA SDP system sizing states 46PB for Low (Section 4)
 - SKA Memo 025 states ~67PB (and also 60.7)
 - Parametric model uses ~69PB

diff --git a/docs/source/generating_config.rst b/docs/source/generating_config.rst
@@ -14,11 +14,9 @@ required to produce a simulation configuration file and produces it, along
 with subdirectories containing each observations' workflow file.
 
 
-.. currentmodule:: pipelines.hpso_to_observation
+.. currentmodule:: skaworkflows.workflow.hpso_to_observation
 
-.. autofunction:: compile_observations_and_workflows
-
-.. autoclass:: pipelines.hpso_to_observation.Observation
+.. autoclass:: skaworkflows.workflow.hpso_to_observation.Observation
 	:members:
 
 --------------------
@@ -29,5 +27,4 @@ Where is everything?
 Recommended user 'flow'
 -------------------------
 
-There are two approaches one can use to generate configuration files for the
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -22,8 +22,12 @@ http://github/top-sim/ organisation.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :caption: Contents
 
+   quickstart
    data/origins
    telescope/telescope_overview
    generating_config
+   comparisons
+   observations/observations_overview
+   workflows/workflow_origins
diff --git a/docs/source/observations/generating_schedules.rst b/docs/source/observations/generating_schedules.rst
diff --git a/docs/source/observations/observations_overview.rst b/docs/source/observations/observations_overview.rst
@@ -10,19 +10,14 @@ In the simulation configuration, they are a sub-component of the `telescope`
 key, due to the Instrument actor needing to know its observation schedule.
 However, observations in the SKA workflows modules have a variety of
 components to themselves, and so it is necessary to create a separate series
-of pages for them.
+of pages for them::
 
 	"observations": [
-	{
-		"name": "hpso4a_0",
-		"start": 0,
-		"duration": 120,
-		"instrument_demand": 128,
-		"data_product_rate": 256
-	},
-
------
-Name
------
-
-The name of an observation
+		{
+			"name": "hpso4a_0",
+			"start": 0,
+			"duration": 120,
+			"instrument_demand": 128,
+			"data_product_rate": 256
+		},
+	]
diff --git a/docs/source/temporary.rst → docs/source/quickstart.rst b/docs/source/temporary.rst → docs/source/quickstart.rst
@@ -1,5 +1,7 @@
 
-## Features necessary to produce a TopSim configuration file
+Quickstart 
+##########
+
 
 In order to produce an observation workflow with appropriate node and edge costs (tasks and data transfer, respectively), the following is required:
 

diff --git a/docs/source/requirements.rst b/docs/source/requirements.rst
diff --git a/docs/source/system_sizing.rst b/docs/source/system_sizing.rst
diff --git a/docs/source/telescope/generating_telescope_config.rst b/docs/source/telescope/generating_telescope_config.rst
diff --git a/docs/source/telescope/telescope_overview.rst b/docs/source/telescope/telescope_overview.rst
@@ -10,19 +10,19 @@ focus on the workflows, and have the telescope act as a 'logical instrument'
 rather than a significant component of its own. The main details of the
 telescope in the characterisation of workflows, and in the configuration, is
 in the maximum number arrays that are available, and the maximum ingest rate
-expected from observations.
-
-"telescope": {
-	"total_arrays": 36,
-	max_ingest_resources
-	"pipelines:{
-		"hpso4a_0": {
-			"workflow": "test/data/config/workflow_config.json",
-			"ingest_demand": 64
-		},
-	...
-	}
-	...
+expected from observations::
+
+	"telescope": {
+		"total_arrays": 36,
+		max_ingest_resources
+		"pipelines:{
+			"hpso4a_0": {
+				"workflow": "test/data/config/workflow_config.json",
+				"ingest_demand": 64
+			},
+		...
+		}
+		...
 
 
 Arrays

diff --git a/docs/source/workflows/data.rst b/docs/source/workflows/data.rst