docs(updated-some-of-the-documentation-and-added-an-installation-section): updated some of the documentation and added an installation section

Author: acbuyan

_episodes/00-Installation.md

@@ -0,0 +1,86 @@
+---
+title: "Installation of the `galah-python` package"
+start: true
+teaching: 10
+exercises: 0
+questions:
+- "How do I install anaconda, galah-python and other packages for this workshop?"
+objectives:
+- "Install all packages necessary for the workshop."
+---
+
+# Installing anaconda
+
+Go to this website:
+
+https://www.anaconda.com/download/success
+
+and download the appropriate distribution for your OS (Mac, Windows, Linux etc.)
+
+# Setting up your environment
+
+## using anaconda-navigator
+
+First, open the navigator and go to `Environments`.
+
+![](../fig/anaconda-home.png)
+
+In `Environments`, go to the `Create` button.
+
+![](../fig/anaconda-environments.png)
+
+Name your environment what makes sense to you.  I used `galah-python-workshop` in this example.
+
+![](../fig/rename-environment.png)
+
+Click `Ok`, and then click on the environment. 
+
+## using the terminal
+
+When you open your terminal, create an environment using the following command (I've used `galah-python-workshop` as the name of the environment; however, feel free to name the environment whatever makes sense to you):
+
+```bash
+conda create -n galah-python-workshop python
+```
+
+To acivate your conda environment, run
+
+```bash
+conda activate galah-python-workshop
+```
+
+# Installing `galah-python` and other packages
+
+Unfortunately, I haven't gotten around to shipping `galah-python` to the `conda-forge` installer yet.  However, you can install other packages via `conda-forge` if you would like.
+
+## using Python Package Index (PIP)
+
+First, you need to open a terminal.  If this is your first time working with a terminal, awesome!  You can do it from the anaconda navigator:
+
+![](../fig/navigator-terminal.png)
+
+when the terminal is opened, type the following into the terminal:
+
+```bash
+pip install galah-python geopandas matplotlib jupyter
+```
+
+For those who are used to working with a terminal, ensure that you install these in your chosen `conda` environment
+
+## using anaconda-navigator
+
+This example is for `matplotlib`; however, it can be done for all packages except for `galah-python`.
+
+First, under your chosen environment, change the packages from `Installed` to `All`.
+
+![](../fig/installed.png)
+
+In the search button, search for `matplotlib`.  You will get something like this:
+
+![](../fig/matplotlib.png)
+
+Select `matplotlib` and then click `Apply` in the lower left-hand corner.  A pop-up window will come up looking like this:
+
+![](../fig/popup.png)
+
+Click `Apply`, and `matplotlib` will be installed, along with all its dependencies. 

_episodes/00-Intro-ALA-galah.md _episodes/01-Intro-ALA-galah.md

@@ -1,5 +1,5 @@
 ---
-title: "What is the ALA and the galah-python package?"
+title: "History of the `galah-python` package"
 start: true
 teaching: 10
 exercises: 0
@@ -69,49 +69,4 @@ To ensure that the R and Python packages are as similar as possible, we structur
 |                      | `select=`          | `galah.atlas_species()`     |
 |                      | `group_by=`        | `galah.atlas_media()`       |
 |                      | `polygon=`         |                             |
-|                      | `bbox=`            |                             |
-
-# Ok, now how do I install and use it?  Are there other packages I need to install?
-
-To install `galah-python`, ensure that you have the terminal open.  To do this via Anaconda, go to `Environments`.  Choose the environment you want, and then click the button that looks like a "Play" button.  Choose `Open Terminal`.
-
-In the terminal, type
-
-```bash
-pip install galah-python
-```
-
-You will need other packages in this workshop, namely `matplotlib` and `geopandas`.  To install them, run
-
-```bash
-pip install matplotlib geopandas
-```
-
-Then, in the terminal, type
-
-```bash
-python
-```
-
-and, when you see three `>>>`, type
-
-```python
->>> import galah
->>> import matplotlib
->>> import geopandas
-```
-
-If you get no errors, this has installed correctly.
-
-Now that you have installed `galah-python`, I will take you through these two examples: 
-
-- How to get occurrences of the species *Litoria peronii* and plot them on a map
-- How to get a list of all the species in the state of Victoria (or the ACT?)
-
-First, I will take you through how to build a query step by step.  Before this, we need to choose our Text Editor.  My preference is Jupyter Notebook.  You can open this in Anaconda by clicking the "Play" button, and choosing `Open with Jupyter Notebook`.  If you prefer working on the Terminal, type
-
-```bash
-jupyter notebook
-```
-
-and a new instance of jupyter will open in your browser.
+|                      | `bbox=`            |                             |

_episodes/02-Link-To-Intro-Python.md

@@ -0,0 +1,18 @@
+---
+title: "Lesson Link for Introduction To Python"
+start: true
+teaching: 10
+exercises: 0
+questions:
+objectives:
+- "Gain basic knowledge of the Python programming language and assigning variables before starting with galah-python"
+keypoints:
+---
+
+# What do you recommend as a starting point?
+
+I would recommend this lesson from the Programming with Python Software Carpentries workshop:
+
+https://swcarpentry.github.io/python-novice-inflammation/01-intro.html
+
+In it, it covers the basics of variables and in-built Python functions, which is what you will need for this workshop

_episodes/01-Query-Template.md _episodes/03-Query-Template.md

@@ -1,5 +1,5 @@
 ---
-title: "Creating Species lists"
+title: "Creating Species Lists and Filtering by Threatened Species"
 start: true
 teaching: 15
 exercises: 5

_episodes/02-Building-An-Example-Query.md _episodes/04-Building-An-Example-Query.md

@@ -68,31 +68,43 @@ <h3>Start</h3>
     <table class="table table-striped">
       <tr>               <!-- row 2   -->
         <td>09:30</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/00-Intro-ALA-galah/index.html">What is the ALA?</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/00-Installation/index.html">Installation</a></td>        <!-- content -->
       </tr>
       <tr>               <!-- row 2   -->
         <td>09:40</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/01-Query-Template/index.html">Guide and template to query building in galah-python</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/01-Intro-ALA-galah/index.html">A history of galah-python</a></td>        <!-- content -->
       </tr>
       <tr>               <!-- row 2   -->
         <td>09:50</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/02-Building-An-Example-Query/index.html">Building the query "Download record counts of Peron's tree frog since 2018 in New South Wales by FrogID"</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/02-Link-To-Intro-Python/index.html">Introduction to Python</a></td>        <!-- content -->
+      </tr>
+      <tr>               <!-- row 2   -->
+        <td>09:50</td>        <!-- time    -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/03-Query-Template/index.html">Guide and template to query building in galah-python</a></td>        <!-- content -->
       </tr>
       <tr>               <!-- row 2   -->
         <td>10:20</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/03-Break/index.html">Break</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/04-Taxonomy-Examples/index.html">Taxonomy Examples</a></td>        <!-- content -->
       </tr>
       <tr>               <!-- row 2   -->
         <td>10:25</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/04-Group-By-Example/index.html">Grouping your results by fields</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/05-Building-An-Example-Query/index.html">Building the query "Download record counts of Peron's tree frog since 2018 in New South Wales by FrogID"</a></td>        <!-- content -->
       </tr>
       <tr>               <!-- row 2   -->
         <td>10:45</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/05-Make-a-Map/index.html">Making a map using your query data</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/06-Break/index.html">Break</a></td>        <!-- content -->
+      </tr>
+      <tr>               <!-- row 2   -->
+        <td>11:05</td>        <!-- time    -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/07-Group-By-Example/index.html">Grouping your results by fields</a></td>        <!-- content -->
+      </tr>
+      <tr>               <!-- row 2   -->
+        <td>11:05</td>        <!-- time    -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/08-Make-a-Map/index.html">Making a map using your query data</a></td>        <!-- content -->
       </tr>
       <tr>               <!-- row 2   -->
         <td>11:05</td>        <!-- time    -->
-        <td><a href="{{ site.url }}{{ site.baseurl }}/06-Making-a-Species-List/index.html">How to make a species list</a></td>        <!-- content -->
+        <td><a href="{{ site.url }}{{ site.baseurl }}/09-Making-a-Species-List/index.html">How to make a species list</a></td>        <!-- content -->
       </tr>
         </table>
       <h3>END</h3>

_episodes/05-Taxonomy-Examples.md

@@ -49,7 +49,7 @@
 
 <p id="who">
   <strong>Who:</strong>
-  The course is aimed at graduate students and other researchers.
+  The course is aimed at those interested in getting biodiversity data through Python.
   <strong>
     You don't need to have any previous knowledge of the tools
     that will be presented at the workshop.

_episodes/03-Break.md _episodes/06-Break.md

@@ -3,18 +3,18 @@ layout: workshop      # DON'T CHANGE THIS.
 # More detailed instructions (including how to fill these variables for an
 # online workshop) are available at
 # https://carpentries.github.io/workshop-template/customization/index.html
-venue: "The University Club of Western Australia"        # brief name of the institution that hosts the workshop without address (e.g., "Euphoric State University")
-address: "Hacket Entrance #1, Hacket Drive, Crawley, WA 6009"      # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria"), videoconferencing URL, or 'online'
+venue: "Virtual"        # brief name of the institution that hosts the workshop without address (e.g., "Euphoric State University")
+address: "Virtual"      # full street address of workshop (e.g., "Room A, 123 Forth Street, Blimingen, Euphoria"), videoconferencing URL, or 'online'
 country: "au"      # lowercase two-letter ISO country code such as "fr" (see https://en.wikipedia.org/wiki/ISO_3166-1#Current_codes) for the institution that hosts the workshop
 language: "en"     # lowercase two-letter ISO language code such as "fr" (see https://en.wikipedia.org/wiki/List_of_ISO_639-1_codes) for the workshop
-latitude: "-31.975370"        # decimal latitude of workshop venue (use https://www.latlong.net/)
-longitude: "115.823140"       # decimal longitude of the workshop venue (use https://www.latlong.net)
-humandate: "Oct 9, 2023"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
-humantime: "9:30 am - 11:30 am AWST, 1:00 pm - 3:00 pm AWST"    # human-readable times for the workshop e.g., "9:00 am - 4:30 pm CEST (7:00 am - 2:30 pm UTC)"
-startdate: 2023-10-09      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
-enddate: 2023-10-09        # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
+latitude: ""        # decimal latitude of workshop venue (use https://www.latlong.net/)
+longitude: ""       # decimal longitude of the workshop venue (use https://www.latlong.net)
+humandate: "Mar 20, 2025"    # human-readable dates for the workshop (e.g., "Feb 17-18, 2020")
+humantime: "1:45 pm - 4:45 am AEST"    # human-readable times for the workshop e.g., "9:00 am - 4:30 pm CEST (7:00 am - 2:30 pm UTC)"
+startdate: 2025-03-20      # machine-readable start date for the workshop in YYYY-MM-DD format like 2015-01-01
+enddate: 2025-03-20        # machine-readable end date for the workshop in YYYY-MM-DD format like 2015-01-02
 instructor: ["Amanda Buyan"] # boxed, comma-separated list of instructors' names as strings, like ["Kay McNulty", "Betty Jennings", "Betty Snyder"]
-helper: []     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
+helper: ["Martin Westgate"]     # boxed, comma-separated list of helpers' names, like ["Marlyn Wescoff", "Fran Bilas", "Ruth Lichterman"]
 email: ["amanda.buyan@csiro.au","support@ala.org.au"]    # boxed, comma-separated list of contact email addresses for the host, lead instructor, or whoever else is handling questions, like ["marlyn.wescoff@example.org", "fran.bilas@example.org", "ruth.lichterman@example.org"]
 collaborative_notes:  # optional: URL for the workshop collaborative notes, e.g. an Etherpad or Google Docs document (e.g., https://pad.carpentries.org/2015-01-01-euphoria)
 eventbrite:           # optional: alphanumeric key for Eventbrite registration, e.g., "1234567890AB" (if Eventbrite is being used)
@@ -378,7 +378,7 @@ The lesson taught in this workshop is being piloted and a precise schedule is ye
 
 
 {% comment %}
-SETUP
+SETUP 
 
 Delete irrelevant sections from the setup instructions.  Each
 section is inside a 'div' without any classes to make the beginning
@@ -391,6 +391,9 @@ please preview your site before committing, and make sure to run
 
 <h2 id="setup">Setup</h2>
 
+<p>
+Installation instructions are found on the next page.
+</p>
 <p>
   To participate in a
   {% if site.carpentry == "swc" %}
@@ -439,4 +442,4 @@ during the workshop.
 Please check the "Setup" page of
 [the lesson site]({{ site.incubator_lesson_site }}) for instructions to follow
 to obtain the software and data you will need to follow the lesson.
-{% endif %}
+{% endif %}