pulling dev into matt's branch (#1046)

* Readme update (#1019)

* test this

* permalink to the template notebook

* trying to get the link working

* Update README.rst

* Update README.rst

---------

Co-authored-by: Nathan <95725385+treefern@users.noreply.github.com>

* upgrade docker-compose postgres image version to 13

* Update bandindices.py (#1022)

Added Normalised Difference Turbidity Index to the 'calculate_indices' tool.
NB. acronym 'NDTI' is already in use for Tillage Index. Acronym 'TI' used in lieu.

* Readme Update (#1025)

Updating to include link back to wiki for approving/reviewing pull requests.

* Tiny doc update to remote build trigger (#1026)

* Update trigger_docs.yaml

Add explanation of triggering build in other doc repo

* Formatting suggestions from review

* Fix `pixel_tides` issues when `ds` has no time dimension (#1028)

* Update pixel_tides func to cover edge cases

* Sync with develop branch

* Hard code dimension order instead of getting dims from ds

* Clean code

* Update USAGE.rst (#1029)

I've added a recently accepted manuscript where I used DEA to calulcate Geomedians and show landscape changes. And the relevant years where we've used DEA sandbox in our remote sensing topics at Flidners university.
Additionally added a conference presentation from AEO22 from Earth Observation Australia 2022 in Brisbane,

* Update spellcheck_wordlist.txt

* Update DEA Notebooks directory structure (#1027)

* New interactive apps folder, moved appropriate notebooks inside

* Deleted scientific_workflows

* rename DEA_datasets folder to DEA_products

* updated 17 notebook references from DEA_datasets to DEA_products

* Rename frequently used code

* Fix incorrect repo folders

* Revert to before dir rename

* Rename frequently used code

* Update readme for DEA_products and How_to_guides

* replace notebook references to Frequently_used_code with How_to_guides

* replace notebook references to frequently used code with How_to_guides

* replaced notebook references to DEA_datasets

* Add readme to interactive apps

* updated Real_world_examples readme

* Remove defunct tests (replaced by nbval --lax)

* Update readme to include interactive apps

* Use stable branch

* Update real world examples format

* Update guided tutorial link

* Update template to remove mention of scientific workflows and Scripts dir

* Fix formatting

* Fix formatting

* Last attempt to fix template notebook formatting

* Final final fix of formatting

---------

Co-authored-by: erialC-P <claire.phillips@ga.gov.au>

* Fix geocoding func to still work if geocoding service is down (#1030)

* Fix geocoding func to still work if geocoding service is down

* Fix format

* Extract coastline app from product notebook and move to Interctive_apps (#1032)

* Update spellcheck_wordlist.txt (#1037)

add:
Ai
Fanson
Fickas
Ronan

* Update USAGE.rst (#1036)

Added Wetlands paper!!

* Replace conference paper with Wetlands paper (#1034)

updated citation list with paper

* Update plotting.py

Added a tool named 'plot_variable_images' primarily for use in the "Burnt_area_mapping_near_real_time" notebook.

* Update plotting.py

* Update plotting.py

* small correction to new tool in plotting.py

Added extra check to handle error when the input xarray dataset has 0 images.

* Update plotting.py

Actioned suggestion to raise error.

* Add Sentinel-2 and Landsat option to animation notebook (#1043)

* Add Sentinel-2 and Landsat option to animation notebook

* Set default resolutions

* Fix bug where choosing combined product didn't trigger data reload

* Update functions to use `odc-geo` and add additional content to tests (#1039)

* Make geobox adding func more generic

* Remove deprecated map_shapefiles func and replace with .explore

* Use odc-geo geobox in xr_animation

* Add geomedian collection option to calculate_indices

* Update animation notebook to use geomedian so we can add it to tests

* Update tests to run on animation notebook

* Fix collection number in segmentation notebook

* Update rgb func to use odc-geo

* Fix attributes being dropped by xr.where, update deprecation version

* Remove assign_crs from rgb (not needed), and add error handling to xr_animation

* Use better error

* Re-run affected notebooks

* Update collection param in ML notebooks

* Add manual reload trigger to layer selection (#1044)

---------

Co-authored-by: Bex Dunn <BexDunn@users.noreply.github.com>
Co-authored-by: Nathan <95725385+treefern@users.noreply.github.com>
Co-authored-by: Pin Jin <pindge.j@gmail.com>
Co-authored-by: Pin Jin <pin.jin@ga.gov.au>
Co-authored-by: Matt-dea <129345253+Matt-dea@users.noreply.github.com>
Co-authored-by: LaurenSchenk1 <125851593+LaurenSchenk1@users.noreply.github.com>
Co-authored-by: Robbi Bishop-Taylor <Robbi.BishopTaylor@ga.gov.au>
Co-authored-by: mdasi00 <91014391+mdasi00@users.noreply.github.com>
Co-authored-by: erialC-P <claire.phillips@ga.gov.au>

.github/workflows/configs/spellcheck_wordlist.txt

@@ -1,184 +1,200 @@
+Ai
+AEO
+ANU
 Abhik
-actioncheckout
 Alam
-ANU
-apache
-ard
-autosummary
-bandindices
 Biogeosciences
-bom
 Brovey
-changefilmstrips
-Cherukuru
-Choo
-conda
-creativecommons
-crophealth
 CRSs
 CSVs
+Cherukuru
+Choo
 Customizable
+DEA's
+DOI
+DaSilva
 Dask
-dask
-datahandling
-dataset
-datasets
 De
-dea
-deacoastlines
-DEA's
-decadal
 Deckker
 Dieback
-DOI
-doi
+Downes
 Drosdowsky
 Drylands
-dx
-ecss
-El
-else's
+Dunefield
+EO
 ESA
+El
 Estuarine
-faq
+Fanson
+Fickas
+Flinders
+Freebairn
 Fäth
-fbf
 Förtsch
-Freebairn
+GIS
 Gb
+GeoTIFF
+GeoTIFFs
 Geoinformation
-geojson
-geomedian
 Geomorphic
 Geopython
 Geoscience
 GeoscienceAustralia
 Geospatial
-geospatial
-GeoTIFF
-GeoTIFFs
-GIS
-gis
 GitHub
-github
 Github's
 Grayson
-graysoncooke
-gridded
 Guerschman
 Hendon
+Hesp
+Hillman
 Hsin
-html
-http
-https
 Hutley
-hyperparameter
-Ierodiaconou
 IGARSS
-imageexport
-img
-intertidal
-io
-ipynb
-jpg
+Ierodiaconou
 Jupyter
 Karim
 Krause
 Kuo
-landcover
+Landforms
 Lehmann
 Lun
 Lymburner
 Marvanek
-maxdepth
 McPhail
-mdpi
 Metternicht
-miningrehab
 Mujahid
-Müller
 Multidecadal
-Nanson
+Müller
 NDVI
 NDWI
+NSW
+Nanson
 NetCDFs
 Newey
 Niño
-NSW
-numpy
 ODC
 Opdyke
-opendatacube
-opensource
 Otte
 Paget
-pansharpening
-parallelization
-pdf
 Penton
-phenology
+Photogrammetry
 Pillans
 Polygonise
-pre
 Preprint
 Pucino
 PyPI
-pypi
 PySpelling
-pyspelling
+README
+RG
+RGB
+RSGISLIB
 Ransley
-rasterising
 Rasterize
-rasters
-README
 Reflectance
 Renzullo
 Reprojecting
-RG
-RGB
+Ronan
+STAC
+Sagar
+Schuldt
+Sengupta
+Shendryk
+Sixsmith
+Streeton
+Subpixel
+Teng
+Thiel
+Ticehurst
+Tsai
+Tseng
+UAV
+USGS's
+Ullmann
+Usback
+Vaze
+WR
+Waterbodies
+actioncheckout
+apache
+ard
+autosummary
+bandindices
+bom
+changefilmstrips
+conda
+creativecommons
+crophealth
+da
+dask
+datahandling
+dataset
+datasets
+dea
+deacoastlines
+decadal
+doi
+dx
+ecss
+else's
+faq
+fbf
+geojson
+geomedian
+geospatial
+gis
+github
+graysoncooke
+gridded
+html
+http
+https
+hyperparameter
+imageexport
+img
+intertidal
+io
+ipynb
+jpg
+landcover
+maxdepth
+mdpi
+miningrehab
+numpy
+opendatacube
+opensource
+pansharpening
+parallelization
+pdf
+phenology
+postgrad
+pre
+pypi
+pyspelling
+rasterising
+rasters
 rgb
 rse
-RSGISLIB
 rst
-Sagar
 scalability
 scalable
-Schuldt
-Sengupta
 shapefile
 shapefiles
-Shendryk
-Sixsmith
-STAC
 stackexchange
-Streeton
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-Subpixel
 subpixel
 svg
 sys
 tandfonline
-Teng
-Thiel
-Ticehurst
 timeseries
 toctree
 toolchain
-Tsai
-Tseng
-UAV
 ubuntu
-Ullmann
-Usback
-USGS's
-Vaze
 vectorising
 vectorize
-Waterbodies
 waterbodies
 waterbody
 widgetconstructors
-WR
 www
 xarray
 yaml

.github/workflows/trigger_docs.yaml

@@ -1,5 +1,9 @@
 
 name: Trigger DEA Docs Build
+# Documentation in this repo is not built in this GitHub Action. Instead, it is built by a separate Action in the dea-docs repo.
+# See here: https://github.com/GeoscienceAustralia/dea-docs/blob/master/.github/workflows/main.yml
+
+# The below action triggers a build in dea-docs when changes are pushed to the 'stable' branch in the current repo
 
 on:
   push:
@@ -15,4 +19,5 @@ jobs:
         with:
           token: ${{ secrets.REPO_PAT }}
           repository: GeoscienceAustralia/dea-docs
-          event-type: republish-docs
+          event-type: republish-docs
+

Beginners_guide/01_Jupyter_notebooks.ipynb

@@ -233,9 +233,9 @@
     "\n",
     "Once you have worked through the beginner's guide, you can join advanced users by exploring:\n",
     "\n",
-    "* The \"DEA datasets\" directory in the repository, where you can explore DEA products in depth.\n",
-    "* The \"Frequently used code\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
-    "* The \"Real-world examples\" directory, which provides more complex workflows and analysis case studies."
+    "* The \"DEA_products\" directory in the repository, where you can explore DEA products in depth.\n",
+    "* The \"How_to_guides\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
+    "* The \"Real_world_examples\" directory, which provides more complex workflows and analysis case studies."
    ]
   },
   {

Beginners_guide/02_DEA.ipynb

@@ -184,7 +184,7 @@
     "The OA product allows users to exclude pixels that do not meet the quality criteria for their analysis.\n",
     "The capacity to automatically exclude such pixels is essential for analysing any change over time, since poor-quality pixels can significantly alter the percieved change over time.\n",
     "The most common use of OA is for cloud masking, where users can choose to remove images that have too much cloud, or ignore the clouds within each satellite image.\n",
-    "A demonstration of how to use cloud masking can be found in the [masking data](../Frequently_used_code/Masking_data.ipynb) notebook.\n",
+    "A demonstration of how to use cloud masking can be found in the [masking data](../How_to_guides/Masking_data.ipynb) notebook.\n",
     "\n",
     "The OA suite of measurements include the following observation pixel-based attributes:\n",
     "\n",
@@ -273,7 +273,7 @@
     "* **National Intertidal Digital Elevation Model (NIDEM):** The National Intertidal Digital Elevation Model (NIDEM) is a national dataset that maps the three-dimensional structure of Australia’s intertidal zone. NIDEM provides a first-of-its kind source of intertidal elevation data for Australia’s entire coastline. \n",
     "\n",
     "Each of the products above have dataset-specific naming conventions, measurements, resolutions, data types and coordinate reference systems.\n",
-    "For more information about DEA's derived products, refer to the [DEA website](http://www.ga.gov.au/dea/products), the [Content Management Interface](https://cmi.ga.gov.au/) (CMI) containing detailed product metadata, or the \"DEA datasets\" notebooks in this repository."
+    "For more information about DEA's derived products, refer to the [DEA website](http://www.ga.gov.au/dea/products), the [Content Management Interface](https://cmi.ga.gov.au/) (CMI) containing detailed product metadata, or the \"DEA_products\" notebooks in this repository."
    ]
   },
   {
@@ -298,10 +298,10 @@
     "\n",
     "Once you have worked through the beginner's guide, you can join advanced users by exploring:\n",
     "\n",
-    "* The demonstration of how to use cloud masking in the [masking data](../Frequently_used_code/Masking_data.ipynb) notebook.\n",
-    "* The \"DEA datasets\" directory in the repository, where you can explore DEA products in depth.\n",
-    "* The \"Frequently used code\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
-    "* The \"Real-world examples\" directory, which provides more complex workflows and analysis case studies."
+    "* The demonstration of how to use cloud masking in the [masking data](../How_to_guides/Masking_data.ipynb) notebook.\n",
+    "* The \"DEA_products\" directory in the repository, where you can explore DEA products in depth.\n",
+    "* The \"How_to_guides\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
+    "* The \"Real_world_examples\" directory, which provides more complex workflows and analysis case studies."
    ]
   },
   {

Beginners_guide/03_Products_and_measurements.ipynb

@@ -1657,9 +1657,9 @@
     "\n",
     "Once you have worked through the beginner's guide, you can join advanced users by exploring:\n",
     "\n",
-    "* The \"DEA datasets\" directory in the repository, where you can explore DEA products in depth.\n",
-    "* The \"Frequently used code\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
-    "* The \"Real-world examples\" directory, which provides more complex workflows and analysis case studies."
+    "* The \"DEA_products\" directory in the repository, where you can explore DEA products in depth.\n",
+    "* The \"How_to_guides\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
+    "* The \"Real_world_examples\" directory, which provides more complex workflows and analysis case studies."
    ]
   },
   {

Beginners_guide/04_Loading_data.ipynb

@@ -6593,10 +6593,10 @@
     "\n",
     "Once you have worked through the beginner's guide, you can join advanced users by exploring:\n",
     "\n",
-    "* A demonstration of how to load cloud-free observations in the [using load_ard](../Frequently_used_code/Using_load_ard.ipynb) notebook.\n",
-    "* The \"DEA datasets\" directory in the repository, where you can explore DEA products in depth.\n",
-    "* The \"Frequently used code\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
-    "* The \"Real-world examples\" directory, which provides more complex workflows and analysis case studies."
+    "* A demonstration of how to load cloud-free observations in the [using load_ard](../How_to_guides/Using_load_ard.ipynb) notebook.\n",
+    "* The \"DEA products\" directory in the repository, where you can explore DEA products in depth.\n",
+    "* The \"How_to_guides\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
+    "* The \"Real_world_examples\" directory, which provides more complex workflows and analysis case studies."
    ]
   },
   {

Beginners_guide/05_Plotting.ipynb

@@ -2767,9 +2767,9 @@
     "\n",
     "Once you have you have completed the beginner tutorials, join advanced users in exploring:\n",
     "\n",
-    "* The \"DEA datasets\" directory in the repository, where you can explore DEA products in depth.\n",
-    "* The \"Frequently used code\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
-    "* The \"Real-world examples\" directory, which provides more complex workflows and analysis case studies.\n",
+    "* The \"DEA products\" directory in the repository, where you can explore DEA products in depth.\n",
+    "* The \"How_to_guides\" directory, which contains a recipe book of common techniques and methods for analysing DEA data.\n",
+    "* The \"Real_world_examples\" directory, which provides more complex workflows and analysis case studies.\n",
     "\n",
     "\n"
    ]