Merge pull request #1160 from GeoscienceAustralia/develop

Prepare for deploying the new DEA Docs Site

.github/CODEOWNERS

@@ -2,4 +2,4 @@
 # for any pull requests in this repository.
 
 # Default reviewers for the entire repository
-*       @robbibt @BexDunn @erialC-P @uchchwhash @Matt-dea @Kooie-cate @geoscience-aman @JM-GA @treefern @margaretharrison @vnewey @Ariana-B @amanda2099 @supermarkion @erin-telfer
+*       @robbibt @BexDunn @erialC-P @uchchwhash @Kooie-cate @geoscience-aman @JM-GA @margaretharrison @vnewey @Ariana-B @amanda2099 @supermarkion @erin-telfer

.github/ISSUE_TEMPLATE/bug_report.md

@@ -21,4 +21,4 @@ Steps to reproduce the behaviour. For example:
 A clear and concise description of what you expected to happen.
 
 **Environment information**
-What datacube environment are you using? i.e. [DEA Sandbox](https://docs.dea.ga.gov.au/setup/sandbox.html) or the [NCI (Gadi or VDI)](https://docs.dea.ga.gov.au/setup/NCI/README.html)
+What datacube environment are you using? i.e. [DEA Sandbox](https://docs.dea.ga.gov.au/guides/setup/Sandbox/sandbox/) or the [NCI (Gadi or VDI)](https://docs.dea.ga.gov.au/guides/setup/NCI/README/)

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,7 +11,7 @@ Include a brief description of the changes being proposed, and why they are nece
 - [ ] Remove any unused/empty code cells
 - [ ] Remove any guidance cells (e.g. `General advice`)
 - [ ] Ensure that all code cells follow the [PEP8 standard](https://www.python.org/dev/peps/pep-0008/) for code. The `jupyterlab_code_formatter` tool can be used to format code cells to a consistent style: select each code cell, then click `Edit` and then one of the `Apply X Formatter` options (`YAPF` or `Black` are recommended).
-- [ ] Include relevant tags in the final notebook cell (refer to the [DEA Tags Index](https://docs.dea.ga.gov.au/genindex.html), and re-use tags if possible)
+- [ ] Include relevant tags in the final notebook cell (refer to the [DEA Tags Index](https://docs.dea.ga.gov.au/genindex/), and re-use tags if possible)
 - [ ] Clear all outputs, run notebook from start to finish, and save the notebook in the state where all cells have been sequentially evaluated
 - [ ] Test notebook on both the `NCI` and `DEA Sandbox` (flag if not working as part of PR and ask for help to solve if needed)
 - [ ] If applicable, update the `Notebook currently compatible with the NCI|DEA Sandbox environment only` line below the notebook title to reflect the environments the notebook is compatible with

.github/workflows/configs/spellcheck_wordlist.txt

@@ -193,6 +193,7 @@ Thiel
 Ticehurst
 timeseries
 toctree
+titlesonly
 toolchain
 Tsai
 Tseng
@@ -212,4 +213,4 @@ WR
 www
 xarray
 yaml
-yml
+yml

.gitignore

@@ -6,3 +6,4 @@
 *.xml
 __pycache__
 Transitory_notebooks/
+Tools/gen

Beginners_guide/01_Jupyter_notebooks.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Introduction to Jupyter notebooks <img align=\"right\" src=\"../Supplementary_data/dea_logo.jpg\">\n",
     "\n",
-    "* [**Sign up to the DEA Sandbox**](https://docs.dea.ga.gov.au/setup/sandbox.html) to run this notebook interactively from a browser\n",
+    "* **[Sign up to the DEA Sandbox](https://app.sandbox.dea.ga.gov.au/)** to run this notebook interactively from a browser\n",
     "* **Compatibility**: Notebook currently compatible with both the `NCI` and `DEA Sandbox` environments\n",
     "* **Prerequisites**: \n",
     "    * There is no prerequisite learning required, as this document is designed for a novice user of the Jupyter environment"
@@ -208,7 +208,7 @@
     "\n",
     "To rename this notebook to something more useful, right-click on it in the file browser and select \"Rename\".\n",
     "\n",
-    "> **Note:** The `dea-notebooks` repository provides a **template notebook** containing a consistent structure and style that is recommended for all DEA Jupyter notebooks. To use this template rather than start a notebook from scratch, click [this link to open the \"DEA_notebooks_template.ipynb\"](../DEA_notebooks_template.ipynb) notebook, then click \"File\" and \"Save Notebook As...\" to create a copy of the template in your desired location."
+    "> **Note:** The `dea-notebooks` repository provides a **template notebook** containing a consistent structure and style that is recommended for all DEA Jupyter notebooks. To use this template rather than start a notebook from scratch, click [this link to open the \"DEA_notebooks_template.ipynb\"](../../DEA_notebooks_template.ipynb) notebook, then click \"File\" and \"Save Notebook As...\" to create a copy of the template in your desired location."
    ]
   },
   {
@@ -251,15 +251,15 @@
     "**Contact:** If you need assistance, please post a question on the [Open Data Cube Slack channel](http://slack.opendatacube.org/) or on the [GIS Stack Exchange](https://gis.stackexchange.com/questions/ask?tags=open-data-cube) using the `open-data-cube` tag (you can view previously asked questions [here](https://gis.stackexchange.com/questions/tagged/open-data-cube)).\n",
     "If you would like to report an issue with this notebook, you can file one on [Github](https://github.com/GeoscienceAustralia/dea-notebooks).\n",
     "\n",
-    "**Last modified:** March 2021"
+    "**Last modified:** December 2023"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Tags\n",
-    "Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex.html)"
+    "<!-- Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex/) -->"
    ]
   },
   {

Beginners_guide/02_DEA.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Introduction to Digital Earth Australia <img align=\"right\" src=\"../Supplementary_data/dea_logo.jpg\">\n",
     "\n",
-    "* [**Sign up to the DEA Sandbox**](https://docs.dea.ga.gov.au/setup/sandbox.html) to run this notebook interactively from a browser\n",
+    "* **[Sign up to the DEA Sandbox](https://app.sandbox.dea.ga.gov.au/)** to run this notebook interactively from a browser\n",
     "* **Compatibility**: Notebook currently compatible with both the `NCI` and `DEA Sandbox` environments\n",
     "* **Prerequisites**:  Users of this notebook should have a basic understanding of:\n",
     "    * How to run a [Jupyter notebook](01_Jupyter_notebooks.ipynb)"
@@ -104,7 +104,7 @@
     "Figure 1 shows the spectral bands for recent Landsat and Sentinel-2 sensors, allowing a direct comparison of how each sensor samples the overall electromagnetic spectrum.\n",
     "Landsat 5 TM is not displayed in this image; for reference, it measured light in seven bands that covered the same regions as bands 1 to 7 on Landsat 7 ETM+.\n",
     "\n",
-    "![Image](https://www.eoportal.org/ftp/satellite-missions/l/Landsat9_180722/Landsat9_Auto2E.jpeg)\n",
+    "![Image](../Supplementary_data/02_DEA/Landsat9_Auto2E.jpeg)\n",
     "\n",
     "> **Figure 1:** The bands that are detected by each of the satellites are shown in the numbered boxes and the width of each box represents the spectral range that band detects.\n",
     "The bands are overlaid on the percentage transmission of each wavelength returned to the atmosphere from the Earth relative to the amount of incoming solar radiation. \n",
@@ -168,7 +168,8 @@
     "\n",
     "![Comparison between NBAR and NBART](../Supplementary_data/02_DEA/nbar_nbart_animation.gif)\n",
     "\n",
-    "> **Figure 2:** The animation above demonstrates how the NBART correction results in a significantly more two-dimensional looking image that is less affected by terrain illumination and shadow.\n",
+    "\n",
+    "**Figure 2:** The animation above demonstrates how the NBART correction results in a significantly more two-dimensional looking image that is less affected by terrain illumination and shadow.\n",
     "Black pixels in the NBART image represent areas of deep terrain shadow that can't be corrected as they're determined not to be viewable by either the sun or the satellite. \n",
     "These are represented by -999 `nodata` values in the data.\n"
    ]
@@ -247,7 +248,7 @@
     "\n",
     "By default, the spatial extent of the DEA data holdings is approximately the Australian coastal shelf. \n",
     "The actual extent varies based on the sensor and product. \n",
-    "The current extents of each DEA product can be viewed using the interactive [DEA Datacube Explorer](http://explorer.sandbox.dea.ga.gov.au/ga_ls8c_ard_3)."
+    "The current extents of each DEA product can be viewed using the interactive [DEA Datacube Explorer](https://explorer.dea.ga.gov.au)."
    ]
   },
   {
@@ -273,15 +274,15 @@
     "* **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_products\" 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://docs.dea.ga.gov.au/) (CMI) containing detailed product metadata, or the \"DEA_products\" notebooks in this repository."
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Recommended next steps\n",
-    "For more detailed information on the concepts introduced in this notebook, please see the [DEA User Guide](https://docs.dea.ga.gov.au/index.html#) and [Open Data Cube Manual](https://datacube-core.readthedocs.io/en/latest/).\n",
+    "For more detailed information on the concepts introduced in this notebook, please see the [DEA User Guide](https://docs.dea.ga.gov.au/) and [Open Data Cube Manual](https://datacube-core.readthedocs.io/en/latest/).\n",
     "For more information on the development of the DEA platform, please see [Dhu et al. 2017](https://doi.org/10.1080/20964471.2017.1402490).\n",
     "\n",
     "To continue with the beginner's guide, the following notebooks are designed to be worked through in the following order:\n",
@@ -318,15 +319,15 @@
     "**Contact:** If you need assistance, please post a question on the [Open Data Cube Slack channel](http://slack.opendatacube.org/) or on the [GIS Stack Exchange](https://gis.stackexchange.com/questions/ask?tags=open-data-cube) using the `open-data-cube` tag (you can view previously asked questions [here](https://gis.stackexchange.com/questions/tagged/open-data-cube)).\n",
     "If you would like to report an issue with this notebook, you can file one on [Github](https://github.com/GeoscienceAustralia/dea-notebooks).\n",
     "\n",
-    "**Last modified:** October 2020"
+    "**Last modified:** December 2023"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "## Tags\n",
-    "Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex.html)"
+    "<!-- Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex/) -->"
    ]
   },
   {

Beginners_guide/03_Products_and_measurements.ipynb

@@ -6,10 +6,10 @@
    "source": [
     "# Introduction to products and measurements <img align=\"right\" src=\"../Supplementary_data/dea_logo.jpg\">\n",
     "\n",
-    "* [**Sign up to the DEA Sandbox**](https://docs.dea.ga.gov.au/setup/sandbox.html) to run this notebook interactively from a browser\n",
+    "* **[Sign up to the DEA Sandbox](https://app.sandbox.dea.ga.gov.au/)** to run this notebook interactively from a browser\n",
     "* **Compatibility:** Notebook currently compatible with both the `NCI` and `DEA Sandbox` environments\n",
     "* **Products used:** \n",
-    "[ga_ls5t_ard_3](https://explorer.sandbox.dea.ga.gov.au/ga_ls5t_ard_3)\n",
+    "[ga_ls5t_ard_3](https://explorer.dea.ga.gov.au/products/ga_ls5t_ard_3)\n",
     "* **Prerequisites:** Users of this notebook should have a basic understanding of:\n",
     "    * How to run a [Jupyter notebook](01_Jupyter_notebooks.ipynb)\n",
     "    * The basic structure of the DEA [satellite datasets](02_DEA.ipynb)"
@@ -119,7 +119,7 @@
     "Products listed under **name** in the following table represent the product options available when querying the datacube. \n",
     "The table below provides some useful information about each product, including a brief product **description**, the data's **license**, and the product's default **crs** (coordinate reference system) and **resolution** if applicable.\n",
     "\n",
-    "> For a comprehensive product description and access to complete product metadata, users are directed to the Geoscience Australia [Content Management Interface](https://cmi.ga.gov.au)\n",
+    "> For a comprehensive product description and access to complete product metadata, users are directed to the Geoscience Australia [Content Management Interface]()\n",
     "\n"
    ]
   },
@@ -1631,8 +1631,8 @@
     "\n",
     "There is a different Datacube Explorer page for both the NCI and DEA Sandbox environments to account for the different datasets that are available in each of these datacubes:\n",
     "\n",
-    "* [NCI DEA Datacube Explorer](http://explorer.dea.ga.gov.au)\n",
-    "* [DEA Sandbox Datacube Explorer](http://explorer.sandbox.dea.ga.gov.au)\n",
+    "* [NCI DEA Datacube Explorer](https://explorer.nci.dea.ga.gov.au)\n",
+    "* [DEA Sandbox Datacube Explorer](http://explorer.dea.ga.gov.au)\n",
     "\n",
     "![DEA Explorer](../Supplementary_data/03_Products_and_measurements/DEAExplorer.JPG)"
    ]
@@ -1674,7 +1674,7 @@
     "**Contact:** If you need assistance, please post a question on the [Open Data Cube Slack channel](http://slack.opendatacube.org/) or on the [GIS Stack Exchange](https://gis.stackexchange.com/questions/ask?tags=open-data-cube) using the `open-data-cube` tag (you can view previously asked questions [here](https://gis.stackexchange.com/questions/tagged/open-data-cube)).\n",
     "If you would like to report an issue with this notebook, you can file one on [Github](https://github.com/GeoscienceAustralia/dea-notebooks).\n",
     "\n",
-    "**Last modified:** May 2022\n",
+    "**Last modified:** December 2023\n",
     "\n",
     "**Compatible datacube version:** "
    ]
@@ -1701,7 +1701,7 @@
    "metadata": {},
    "source": [
     "## Tags\n",
-    "Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex.html)"
+    "<!-- Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex/) -->"
    ]
   },
   {

Beginners_guide/04_Loading_data.ipynb

@@ -6,11 +6,11 @@
    "source": [
     "# Introduction to loading data <img align=\"right\" src=\"../Supplementary_data/dea_logo.jpg\">\n",
     "\n",
-    "* [**Sign up to the DEA Sandbox**](https://docs.dea.ga.gov.au/setup/sandbox.html) to run this notebook interactively from a browser\n",
+    "* **[Sign up to the DEA Sandbox](https://app.sandbox.dea.ga.gov.au/)** to run this notebook interactively from a browser\n",
     "* **Compatibility:** Notebook currently compatible with both the `NCI` and `DEA Sandbox` environments\n",
     "* **Products used:** \n",
-    "[ga_ls7e_nbart_gm_cyear_3](https://explorer.sandbox.dea.ga.gov.au/ga_ls7e_nbart_gm_cyear_3),\n",
-    "[ga_ls8c_nbart_gm_cyear_3](https://explorer.sandbox.dea.ga.gov.au/ga_ls8c_nbart_gm_cyear_3)\n",
+    "[ga_ls7e_nbart_gm_cyear_3](https://explorer.dea.ga.gov.au/ga_ls7e_nbart_gm_cyear_3),\n",
+    "[ga_ls8c_nbart_gm_cyear_3](https://explorer.dea.ga.gov.au/ga_ls8c_nbart_gm_cyear_3)\n",
     "* **Prerequisites:** Users of this notebook should have a basic understanding of:\n",
     "    * How to run a [Jupyter notebook](01_Jupyter_notebooks.ipynb)\n",
     "    * The basic structure of the DEA [satellite datasets](02_DEA.ipynb)\n",
@@ -114,7 +114,7 @@
     "* `y`: The spatial region in the *y* dimension. The dimensions ``longitude``/``latitude`` and ``x``/``y`` can be used interchangeably.\n",
     "* `time`: The temporal extent. The time dimension can be specified using a tuple of datetime objects or strings in the \"YYYY\", \"YYYY-MM\" or \"YYYY-MM-DD\" format. \n",
     "\n",
-    "For example, to load 2015 data from the [Landsat 8 NBAR-T annual geomedian product](https://explorer.sandbox.dea.ga.gov.au/ga_ls8c_nbart_gm_cyear_3) for Moreton Bay in southern Queensland, use the following parameters:\n",
+    "For example, to load 2015 data from the [Landsat 8 NBAR-T annual geomedian product](https://explorer.dea.ga.gov.au/ga_ls8c_nbart_gm_cyear_3) for Moreton Bay in southern Queensland, use the following parameters:\n",
     "\n",
     "* `product`: `ga_ls8c_nbart_gm_cyear_3`\n",
     "* `x`: `(153.3, 153.4)`\n",
@@ -6615,7 +6615,7 @@
     "**Contact:** If you need assistance, please post a question on the [Open Data Cube Slack channel](http://slack.opendatacube.org/) or on the [GIS Stack Exchange](https://gis.stackexchange.com/questions/ask?tags=open-data-cube) using the `open-data-cube` tag (you can view previously asked questions [here](https://gis.stackexchange.com/questions/tagged/open-data-cube)).\n",
     "If you would like to report an issue with this notebook, you can file one on [Github](https://github.com/GeoscienceAustralia/dea-notebooks).\n",
     "\n",
-    "**Last modified:** May 2023\n",
+    "**Last modified:** December 2023\n",
     "\n",
     "**Compatible datacube version:** "
    ]
@@ -6642,7 +6642,7 @@
    "metadata": {},
    "source": [
     "## Tags\n",
-    "Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex.html)"
+    "<!-- Browse all available tags on the DEA User Guide's [Tags Index](https://docs.dea.ga.gov.au/genindex/) -->"
    ]
   },
   {