Merge pull request #1159 from GeoscienceAustralia/dea-docs-v2

Merging changes before publishing site live

.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/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."
    ]
   },
   {
@@ -259,7 +259,7 @@
    "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/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/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"
    ]
@@ -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",
@@ -326,7 +327,7 @@
    "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/03_Products_and_measurements.ipynb

@@ -6,7 +6,7 @@
    "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/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.dea.ga.gov.au/products/ga_ls5t_ard_3)\n",
@@ -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"
    ]
   },
@@ -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

@@ -6,7 +6,7 @@
    "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/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.dea.ga.gov.au/ga_ls7e_nbart_gm_cyear_3),\n",
@@ -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/) -->"
    ]
   },
   {

Beginners_guide/05_Plotting.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Introduction to plotting <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/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_ls8c_nbart_gm_cyear_3](https://explorer.dea.ga.gov.au/ga_ls8c_nbart_gm_cyear_3)\n",
@@ -33,7 +33,7 @@
    "source": [
     "## Description\n",
     "This introductory notebook demonstrates how to visualise DEA satellite data returned from running a datacube query.\n",
-    "The notebook demonstrates commonly used `xarray` plotting methods, as well as custom functions provided in the [dea_tools.plotting](../Tools/dea_tools/plotting.py) module.\n",
+    "The notebook demonstrates commonly used `xarray` plotting methods, as well as custom functions provided in the [dea_tools.plotting](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.plotting/) module.\n",
     "\n",
     "Topics covered in this notebook include:\n",
     "\n",
@@ -65,7 +65,7 @@
    "source": [
     "### Load packages\n",
     "The first step is to run `%matplotlib inline`, which ensures figures plot correctly in the Jupyter notebook.\n",
-    "Next, load the `datacube` package to enable loading data, and a selection of custom DEA functions from the [dea_tools.plotting](../Tools/dea_tools/plotting.py) module."
+    "Next, load the `datacube` package to enable loading data, and a selection of custom DEA functions from the [dea_tools.plotting](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.plotting/) module."
    ]
   },
   {
@@ -2763,7 +2763,7 @@
     "\n",
     "For advanced plotting and visualisation options, see:\n",
     "\n",
-    "* The [dea_tools.plotting](../Tools/dea_tools/plotting.py) module containing functions used for plotting and visualising DEA data.\n",
+    "* The [dea_tools.plotting](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.plotting/) module containing functions used for plotting and visualising DEA data.\n",
     "\n",
     "Once you have you have completed the beginner tutorials, join advanced users in exploring:\n",
     "\n",
@@ -2813,7 +2813,7 @@
    "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/06_Basic_analysis.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Performing a basic analysis <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/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_s2am_ard_3](https://explorer.dea.ga.gov.au/ga_s2am_ard_3)\n",
@@ -1216,7 +1216,7 @@
    "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/07_Intro_to_numpy.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Introduction to Numpy <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/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)"

Beginners_guide/08_Intro_to_xarray.ipynb

@@ -6,7 +6,7 @@
    "source": [
     "# Introduction to Xarray <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/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)\n",

Beginners_guide/09_Parallel_processing_with_Dask.ipynb

@@ -95,7 +95,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dc = datacube.Datacube(app=\"07_Parallel_processing_with_Dask\")"
+    "dc = datacube.Datacube(app=\"09_Parallel_processing_with_Dask\")"
    ]
   },
   {
@@ -6882,7 +6882,7 @@
    "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/Guided_tutorial.ipynb

@@ -47,7 +47,7 @@
     "Once signed in, the JupyterLab homepage should appear. \n",
     "The JupyterLab interface consists of the main work area (right-hand panel), the left sidebar (containing a file browser and other useful features), and a menu bar along the top:\n",
     "\n",
-    "![Sandbox work area](https://docs.dea.ga.gov.au/_images/sandbox-jupyterlab-startup.png)\n",
+    "![Sandbox work area](../Supplementary_data/Beginners_guide_Guided_tutorial/sandbox-jupyterlab-startup.png)\n",
     "\n",
     "---\n",
     "\n",
@@ -177,7 +177,7 @@
     "**Last modified:** April 2023\n",
     "\n",
     "## 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/README.rst

@@ -19,9 +19,9 @@ The Beginners Guide contains introductory notebooks aimed at introducing Jupyter
 
 Once you have you have completed the beginner tutorials, join advanced users in exploring:
 
-    - The "DEA_products" directory in the repository, where you can explore DEA products in depth.
-    - The "How_to_guides" directory, which contains a recipe book of common techniques and methods for analysing DEA data.
-    - 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.
+* The "How_to_guides" directory, which contains a recipe book of common techniques and methods for analysing DEA data.
+* The "Real_world_examples" directory, which provides more complex workflows and analysis case studies.  
 
 .. toctree::
    :maxdepth: 2