Merge branch 'docs' into pawsey_testing

Author: cjproud

.gitignore

@@ -23,6 +23,7 @@ dist/*
 profiling.md
 *.swp
 /docs/_build
+/docs/build
 /docs/doctrees
 example_data/
 build/

docs/requirements.txt

@@ -1,3 +1,4 @@
 sphinx
 sphinx-rtd-theme
+sphinxcontrib-mermaid
 myst-parser

docs/source/conf.py

@@ -31,12 +31,17 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'myst_parser'
+    'myst_parser',
+    'sphinxcontrib.mermaid'
 ]
 # mappings for parsing files
 source_suffix = {'.rst':'restructuredtext',
                  '.md':'markdown'}
-                 
+
+# mermaid config
+mermaid_output_format = "raw"
+mermaid_version = "latest"
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

docs/source/index.rst

@@ -17,4 +17,5 @@ Robbie - A batch processing workflow for the detection of radio transients and v
 
    installation
    quickstart
-   visualisation
+   visualisation
+   workflow

docs/source/introduction.md

@@ -1,4 +1,4 @@
-## Description
+# Description
 
 Robbie automates the process of cataloguing sources, finding variables, and identifying transients.
 

docs/source/workflow.md

@@ -1,5 +1,5 @@
 (workflow)=
-## Workflow
+# Workflow
 The workflow was described initially in [Hancock et al. 2018](https://ui.adsabs.harvard.edu/abs/2019A%26C....27...23H/abstract) however the current workflow is shown below:
 - Preprocessing:
   - Convolve all images to a common psf (optional)
@@ -17,28 +17,28 @@ The workflow was described initially in [Hancock et al. 2018](https://ui.adsabs.
   - Concatenate transients into a single catalogue, identifying the epoch of each detection
 
 
-```mermaid
-flowchart TD
-  subgraph Preprocessing
-    direction LR
-    img[Raw images] --> psf["PSF correction (?)"]
-    psf --> bkg[Create background/noise maps]
-    bkg --> warp["Fits warping (?)"]
-    warp --> epim[Epoch images]
-  end
-  subgraph Persistent sources
-    epim --> mean[Mean image]
-    mean --> pscat[Persistent sources]
-    epim --> pscat
-    pscat --> vout[(Flux table, variability table, light curves, variabiltiy plot)]
-  end
-  subgraph Transients
-    mean --> mask[Masked epoch images]
-    epim --> mask
-    pscat --> mask
-    mask --> trans[Transient candidates]
-    trans --> tout[(Filtered candidates, transients plot)]
-  end
+```{mermaid}
+  flowchart TD
+    subgraph Preprocessing
+      direction LR
+      img[Raw images] --> psf["PSF correction (?)"]
+      psf --> bkg[Create background/noise maps]
+      bkg --> warp["Fits warping (?)"]
+      warp --> epim[Epoch images]
+    end
+    subgraph Persistent sources
+      epim --> mean[Mean image]
+      mean --> pscat[Persistent sources]
+      epim --> pscat
+      pscat --> vout[(Flux table, variability table, light curves, variabiltiy plot)]
+    end
+    subgraph Transients
+      mean --> mask[Masked epoch images]
+      epim --> mask
+      pscat --> mask
+      mask --> trans[Transient candidates]
+      trans --> tout[(Filtered candidates, transients plot)]
+    end
 ```
 
 Items with a (?) are optional processing steps that can be turned on/off.