fixing docs to work with new package structure

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
 
-   :class:`coordinator`, "Coordinates the running of all pipeline modules"
-   :class:`ews_postprocessing`, "Determines the business performed by the Coordinator pipeline ""post-processing"" step"
+   :class:`ews.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"
+   :class:`ews.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
 
-   :class:`source_gen`, "Calculates daily spore sources from a host map and surveillance points.
+   :class:`ews.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
 
-   :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."
+   :class:`ews.met_processing`, "Extracts incoming Met Data and runs :class:`~ews.met_processing.post_processing.common.timepoint_processor_base.TimePointProcessorBase` implementations to calculate weather-and-time-based values"
+   :class:`ews.environmental_suitability`, ":class:`~ews.met_processing.post_processing.common.timepoint_processor_base.TimePointProcessorBase` implementations to calculate the environmental conditions of wheat rust infection."
 
 **Epidemiology:**
 
@@ -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
 
-   :class:`AdvisoryBuilder`, "Simulates infected area of grid cells according to epidmiological formulations and various input data streams."
+   :class:`ews.advisory_builder`, "Simulates infected area of grid cells according to epidmiological formulations and various input data streams."

docs/index.rst

@@ -21,13 +21,13 @@ the pipeline currently running at the University of Cambridge.
    :hidden:
    :titlesonly:
 
-   coordinator API <_autosummary/coordinator>
-   plotting API <_autosummary/plotting>
-   post processing API <_autosummary/ews_postprocessing>
-   met processing API <_autosummary/met_processing>
-   env suit API <_autosummary/environmental_suitability>
-   source gen API <_autosummary/source_gen>
+   coordinator API <_autosummary/ews.coordinator>
+   plotting API <_autosummary/ews.plotting>
+   post processing API <_autosummary/ews.ews_postprocessing>
+   met processing API <_autosummary/ews.met_processing>
+   env suit API <_autosummary/ews.environmental_suitability>
+   source gen API <_autosummary/ews.source_gen>
    epimodel API <_autosummary/EpiModel>
-   advisory API <_autosummary/AdvisoryBuilder>
+   advisory API <_autosummary/ews.advisory_builder>