diff --git a/docs/_source/package_overview.rst b/docs/_source/package_overview.rst
index 1ad55015c3109f59fb632cf75014bf8648df27d9..2fbe16c2bd4a398b40a1343cebbcf5947e549b99 100644
--- a/docs/_source/package_overview.rst
+++ b/docs/_source/package_overview.rst
@@ -24,10 +24,10 @@ Use the links below or in the side menu to see detailed descriptions of individu
:header: "Package", "Description"
:widths: 15, 30
- :ref:`Coordinator<coordinator_overview>`, "Coordinates the running of all pipeline modules"
- :ref:`Post processing<post_processing_overview>`, "Determines the business performed by the Coordinator pipeline ""post-processing"" step"
- :ref:`Job flagging<flagdir_overview>`, "Basic flag-file handling within a provided directory"
- :ref:`Plotting<plotting_overview>`, "Plots maps from the pipeline outputs"
+ :class:`coordinator`, "Coordinates the running of all pipeline modules"
+ :class:`ews_postprocessing`, "Determines the business performed by the Coordinator pipeline ""post-processing"" step"
+ :class:`flagdir`, "Basic flag-file handling within a provided directory"
+ :class:`plotting`, "Plots maps from the pipeline outputs"
**Deposition:**
@@ -35,7 +35,7 @@ Use the links below or in the side menu to see detailed descriptions of individu
:header: "Package", "Description"
:widths: 15, 30
- :ref:`Source calculation<source_calc_overview>`, "Calculates daily spore sources from a host map and surveillance points.
+ :class:`source_gen`, "Calculates daily spore sources from a host map and surveillance points.
Used by the MetOffice for the NAME dispersal calculations"
**Environmental suitability:**
@@ -44,8 +44,8 @@ Use the links below or in the side menu to see detailed descriptions of individu
:header: "Package", "Description"
:widths: 15, 30
- :ref:`Met processing<met_processing_overview>`, "Extracts incoming Met Data and runs :class:`~met_processing.post_processing.common.timepoint_processor_base.TimePointProcessorBase` implementations to calculate weather-and-time-based values"
- :ref:`Environmental suitability<env_suit_overview>`, ":class:`~met_processing.post_processing.common.timepoint_processor_base.TimePointProcessorBase` implementations to calculate the environmental conditions of wheat rust infection."
+ :class:`met_processing`, "Extracts incoming Met Data and runs :class:`~met_processing.post_processing.common.timepoint_processor_base.TimePointProcessorBase` implementations to calculate weather-and-time-based values"
+ :class:`environmental_suitability`, ":class:`~met_processing.post_processing.common.timepoint_processor_base.TimePointProcessorBase` implementations to calculate the environmental conditions of wheat rust infection."
**Epidemiology:**
@@ -53,7 +53,7 @@ Use the links below or in the side menu to see detailed descriptions of individu
:header: "Package", "Description"
:widths: 15, 30
- :ref:`Epidemiology<epidemiology_overview>`, "Simulates infected area of grid cells according to epidmiological formulations and various input data streams."
+ :class:`EpiModel`, "Simulates infected area of grid cells according to epidmiological formulations and various input data streams."
**Advisory builder:**
@@ -62,4 +62,4 @@ Use the links below or in the side menu to see detailed descriptions of individu
:header: "Package", "Description"
:widths: 15, 30
- :ref:`Advisory builder<advisory_overview>`, "Simulates infected area of grid cells according to epidmiological formulations and various input data streams."
+ :class:`AdvisoryBuilder`, "Simulates infected area of grid cells according to epidmiological formulations and various input data streams."
diff --git a/docs/_source/packages/advisory.rst b/docs/_source/packages/advisory.rst
deleted file mode 100644
index 8289ca264a887b8e2dc91cfcb5f3a96bb981d6e0..0000000000000000000000000000000000000000
--- a/docs/_source/packages/advisory.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _advisory_overview:
-
-Advisory builder
-================
-
-Overview
---------
-
-Full-depth advisory docs
-
-APIs
-----
-
-:class:`Advisory` API
diff --git a/docs/_source/packages/coordinator.rst b/docs/_source/packages/coordinator.rst
deleted file mode 100644
index f5759be3b753d0c649a5586ab6f71178ab4f8fc5..0000000000000000000000000000000000000000
--- a/docs/_source/packages/coordinator.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _coordinator_overview:
-
-Coordinator
-===========
-
-Overview
---------
-
-Full-depth coordinator docs
-
-APIs
-----
-
-:class:`coordinator` API
diff --git a/docs/_source/packages/env_suit.rst b/docs/_source/packages/env_suit.rst
deleted file mode 100644
index a0dabb67bcd932e909b5d1bd6c4dd74ace0e8bfd..0000000000000000000000000000000000000000
--- a/docs/_source/packages/env_suit.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _env_suit_overview:
-
-Environmental suitability
-=========================
-
-Overview
---------
-
-Full-depth coordinator docs
-
-APIs
-----
-
-:class:`environmental_suitability` API
diff --git a/docs/_source/packages/epidemiology.rst b/docs/_source/packages/epidemiology.rst
deleted file mode 100644
index 512369792e5d450b405b86fd4b415d3dd23f3839..0000000000000000000000000000000000000000
--- a/docs/_source/packages/epidemiology.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _epidemiology_overview:
-
-Epidemiology
-============
-
-Overview
---------
-
-Full-depth epi docs
-
-APIs
-----
-
-:class:`EpiModel` API
diff --git a/docs/_source/packages/job_flagging.rst b/docs/_source/packages/job_flagging.rst
deleted file mode 100644
index cbe07ec515c2bc8cb0f8ad5ee303ec42a8846c67..0000000000000000000000000000000000000000
--- a/docs/_source/packages/job_flagging.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _flagdir_overview:
-
-JOb flagging
-============
-
-Overview
---------
-
-Full-depth flagging docs
-
-APIs
-----
-
-:class:`flagdir` API
diff --git a/docs/_source/packages/media_scraping.rst b/docs/_source/packages/media_scraping.rst
deleted file mode 100644
index 0f446a3b4fe45dc0dbd576c4c1c576d10526e809..0000000000000000000000000000000000000000
--- a/docs/_source/packages/media_scraping.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-.. _media_scraper_overview:
-
-Media scraper
-=============
-
-Overview
---------
-
-Full-depth scraper docs
-
-APIs
-----
-
-:class:`` API
diff --git a/docs/_source/packages/met_processing.rst b/docs/_source/packages/met_processing.rst
deleted file mode 100644
index 00aa31852055dad708c9e275ad4f32a6077a98e4..0000000000000000000000000000000000000000
--- a/docs/_source/packages/met_processing.rst
+++ /dev/null
@@ -1,23 +0,0 @@
-.. _met_processing_overview:
-
-Met Processing
-==============
-
-Full-depth Met Processing docs
-
-Overview
---------
-
-The Met Processing package processes Met data supplied by the UK Met Office (UKMETO)
-
-.. autosummary::
- met_processing.common
- met_processing.met_extraction
- met_processing.post_processing
- met_processing.runner
-
-APIs
-----
-
-:class:`met_processing` API
-
diff --git a/docs/_source/packages/plotting.rst b/docs/_source/packages/plotting.rst
deleted file mode 100644
index 5db288f03d639392bffb3657f05b86a65e919210..0000000000000000000000000000000000000000
--- a/docs/_source/packages/plotting.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-.. _plotting_overview:
-
-Plotting
-========
-
-Full-depth Plotting docs
-
-Overview
---------
-
-The plotting produces the images. It receives input csvs produced by the :class:`met_processing` module.
-The :class:`plotting.common.plotting_coordinator` module uses the `disease plotting coordinators` to iterate over
-the known disease types and weekly/daily/hourly output files.
-The :class:`plotting.common.plot_images` module contains the matplotlib functions for producing the image components.
-
-.. image:: /_images/depo.png
- :scale: 25 %
- :alt: alternate text
-
-
-APIs
-----
-
-:class:`plotting` API
-
diff --git a/docs/_source/packages/post_processing.rst b/docs/_source/packages/post_processing.rst
deleted file mode 100644
index ea72b16ab5adce82c9ab5a730bb30cc49fd2b17d..0000000000000000000000000000000000000000
--- a/docs/_source/packages/post_processing.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-.. _post_processing_overview:
-
-Post-processing
-===============
-
-Full-depth post-processing docs
-
-Overview
---------
-
-The post-processing package contains lifecycle functions for the EWS coordinator pipelines. post-processing steps are
-called after the main work of the variout ews pipelines are complete. Post-processers generally deal with data wrangling
-and plotting.
-
-*table showing the different post processors and summary of function*
-
-
-APIs
-----
-
-:class:`ews_postprocessing` API
-
diff --git a/docs/_source/packages/source_calculation.rst b/docs/_source/packages/source_calculation.rst
deleted file mode 100644
index 1e5ccc13b4558f4c21fd0abc2b437fa7c27a2607..0000000000000000000000000000000000000000
--- a/docs/_source/packages/source_calculation.rst
+++ /dev/null
@@ -1,16 +0,0 @@
-.. _source_calc_overview:
-
-Source calculation
-==================
-
-Overview
---------
-
-Full-depth source calc docs
-
-**the module is still called `source_gen` despite renaming the gitlab project - should we rename source_gen to match?**
-
-APIs
-----
-
-:class:`source_gen` API
diff --git a/docs/api.rst b/docs/api.rst
index 3d57073301b307ffbeb4f08da253caf2ac081c6f..92c6af18c4618c7a5de60e983a8304f22acc9f17 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -6,7 +6,7 @@ API
:template: custom-module-template.rst
:recursive:
-.. coordinator
+ coordinator
plotting
ews_postprocessing
met_processing